{"entity": "label", "iuid": "aa3bcd91b1dc43eabcdcbaa279dd25d4", "timestamp": "2026-07-20T03:43:57.534Z", "links": {"self": {"href": "https://publications.scilifelab.se/label/Clinical%20Genomics%20%C3%96rebro.json"}, "display": {"href": "https://publications.scilifelab.se/label/Clinical%20Genomics%20%C3%96rebro"}}, "value": "Clinical Genomics \u00d6rebro", "started": "2019", "ended": "", "created": "2020-01-20T13:36:51.614Z", "modified": "2021-03-15T14:17:01.022Z", "accounts": [{"entity": "account", "iuid": "32a436398938412b93e7ddcef018c708", "timestamp": "2026-07-20T03:43:57.534Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se"}}, "email": "christopher.erdmann@scilifelab.uu.se", "name": "Christopher Erdmann", "orcid": "", "role": "curator", "status": "enabled", "login": "2024-08-16T11:56:57.787Z", "created": "2024-08-16T10:01:32.844Z", "modified": "2025-10-17T13:05:06.782Z"}, {"entity": "account", "iuid": "5492dbd587dd44beb1c290872f165be2", "timestamp": "2026-07-20T03:43:57.534Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/bianca.stenmark%40regionorebrolan.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/bianca.stenmark%40regionorebrolan.se"}}, "email": "bianca.stenmark@regionorebrolan.se", "name": "Bianca Stenmark", "orcid": "", "role": "curator", "status": "enabled", "login": "2026-03-05T09:05:36.145Z", "created": "2020-01-24T12:13:29.512Z", "modified": "2026-03-05T09:05:36.145Z"}, {"entity": "account", "iuid": "6a38350bd21f4fb6aeeb1530037a99ae", "timestamp": "2026-07-20T03:43:57.534Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se"}}, "email": "sune.joubert@scilifelab.uu.se", "name": "Sun\u00e9 Joubert", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-10-31T11:15:37.113Z", "created": "2024-08-16T10:01:02.800Z", "modified": "2025-10-31T11:15:37.113Z"}], "publications_count": 66, "publications": [{"entity": "publication", "iuid": "dceda66778b243d48c35e4f210a2f93b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dceda66778b243d48c35e4f210a2f93b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dceda66778b243d48c35e4f210a2f93b"}}, "title": "Effects of incrementally increased plant-based protein intake on gut microbiota and inflammatory-metabolic biomarkers in healthy adults.", "authors": [{"family": "Prado", "given": "Samira", "initials": "S", "orcid": "0000-0003-4627-6291", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9912c2cd66d49a8a067770ef482c755.json"}}, {"family": "Kamm", "given": "Annalena", "initials": "A", "orcid": "0009-0002-9389-4172", "researcher": {"href": "https://publications.scilifelab.se/researcher/478d57e6063e4db89e513430f840207b.json"}}, {"family": "Dannenberg", "given": "Katharina", "initials": "K", "orcid": "0009-0008-1571-0044", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9525504fa7c427b8b19d361d38167c1.json"}}, {"family": "Keidel", "given": "Isabel", "initials": "I", "orcid": "0009-0000-9806-1087", "researcher": {"href": "https://publications.scilifelab.se/researcher/7276d82607474a99905643ac60082036.json"}}, {"family": "Castro-Alves", "given": "Victor", "initials": "V", "orcid": "0000-0002-9535-6821", "researcher": {"href": "https://publications.scilifelab.se/researcher/639528af2bd7482eaca6c998f2df3a94.json"}}, {"family": "Hy\u00f6tyl\u00e4inen", "given": "Tuulia", "initials": "T"}, {"family": "Lentjes", "given": "Marleen", "initials": "M", "orcid": "0000-0003-4713-907X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3579ded172f040698818c7f41ed60525.json"}}, {"family": "Repsilber", "given": "Dirk", "initials": "D"}, {"family": "Marques", "given": "Tatiana M", "initials": "TM"}, {"family": "Brummer", "given": "Robert J", "initials": "RJ"}], "type": "journal article", "published": "2026-01-26", "journal": {"title": "Food Funct", "issn": "2042-650X", "volume": "17", "issue": "2", "pages": "942-956", "issn-l": null}, "abstract": "Shifting to a plant-based diet naturally alters protein source choices. In many countries, protein from yellow pea is widely used as a main ingredient in meat alternatives. Still, its biological effects, especially regarding gastrointestinal health, remain incompletely understood. The aim of our study was to investigate how a weekly increase in the intake of a well-characterized pea protein isolate affects surrogate markers of health, fecal short-chain fatty acids and gut microbiota composition in healthy individuals. Male and female adults (N = 29) participated in this exploratory intervention study. A 4-week pre-intervention period for questionnaires and fecal samples collection was followed by a 4-week supplementation. Participants consumed isolated pea protein in weekly increasing amounts, starting from 0.25 g per kg body mass per day in week 5 to 1.00 g per kg body mass per day in week 8. Questionnaire data, fecal samples as well as fasting blood and 24 h urine samples were collected weekly. Data from biological samples and questionnaires confirmed a healthy study population and compliance. Fecal calprotectin levels significantly increased only in a subset of participants, which was accompanied by higher fecal water cytotoxicity in vitro. Short-chain fatty acids mainly rose in those subjects with stable calprotectin levels. Relative abundances of Limosilactobacillus frumenti, Odoribacter splanchnicus and Lactobacillus crispatus increased significantly in the total population during the intervention while the relative abundance of Bifidobacterium longum and Bifidobacterium catenulatum decreased. Our results indicate that an increased intake of pea protein isolate affects the growth of certain beneficial bacterial strains and differentially influences markers related to gut inflammation in healthy individuals.", "doi": "10.1039/d5fo02653a", "pmid": "41481420", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-03-05T09:09:35.428Z", "modified": "2026-03-05T09:09:35.867Z"}, {"entity": "publication", "iuid": "8f8dca39f51246e399479b7a8829b62d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f8dca39f51246e399479b7a8829b62d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f8dca39f51246e399479b7a8829b62d"}}, "title": "Plasma protein profiling predicts cancer in patients with non-specific symptoms.", "authors": [{"family": "Wannberg", "given": "Fredrika", "initials": "F", "orcid": "0009-0001-8505-3122", "researcher": {"href": "https://publications.scilifelab.se/researcher/15572474779e45a7a64e439cca882a73.json"}}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Qvick", "given": "Alvida", "initials": "A", "orcid": "0000-0001-6688-947X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4be159eaa724d22982b7b1e24e9ba79.json"}}, {"family": "Pongracz", "given": "Tamas", "initials": "T", "orcid": "0000-0002-8089-4352", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bdf2f1b85954a1b872b59339838fa57.json"}}, {"family": "Aguilera", "given": "Katherina", "initials": "K"}, {"family": "Adolfsson", "given": "Emma", "initials": "E", "orcid": "0000-0002-7954-0696", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c790fe832ec4bf68608578c0c9d4552.json"}}, {"family": "Essehorn", "given": "Louise", "initials": "L"}, {"family": "Gordon", "given": "Max", "initials": "M", "orcid": "0000-0002-8080-5815", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3f1f5ca4e2a4f17bf9454cd7b5a259d.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Helenius", "given": "Gisela", "initials": "G"}, {"family": "Hjalmar", "given": "Viktoria", "initials": "V"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Rosell", "given": "Axel", "initials": "A", "orcid": "0000-0001-6280-0562", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcddaba7a96a406b994756ab71427baf.json"}}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C", "orcid": "0009-0008-9471-3234", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a1c3368c5314543bb4b2204f2938159.json"}}], "type": "journal article", "published": "2025-12-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "pages": "151", "issn-l": "2041-1723"}, "abstract": "Cancer detection is challenging, especially in patients with diffuse symptoms that overlap with non-malignant conditions. Here we show that plasma protein profiling can identify cancer among patients with non-specific symptoms. Using proximity extension assay-based proteomics of 1463 plasma proteins from 456 patients presenting with non-specific symptoms sampled prior to cancer diagnostic work-up and diagnosis, we identify 29 proteins associated with new cancer diagnoses. We develop a model able to stratify 160 cancer cases and 296 non-cancer cases with an area under the curve of 0.80, maintaining performance (0.82) in an independent replication cohort of 238 patients. The model also distinguishes cancer from autoimmune, inflammatory and infectious diseases. Designed as a triage tool, our model based on a blood test could help prioritize patients at higher cancer risk for rapid and highly sensitive diagnostic modalities such as positron emission tomography-computed tomography. These findings emphasize the potential of blood proteome profiling to support timely diagnosis and transform clinical medicine.", "doi": "10.1038/s41467-025-67688-3", "pmid": "41457066", "labels": {"Affinity Proteomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12774938"}, {"db": "pii", "key": "10.1038/s41467-025-67688-3"}], "notes": [], "created": "2026-01-09T16:47:14.250Z", "modified": "2026-03-05T09:10:04.784Z"}, {"entity": "publication", "iuid": "d39af32e394d4cf1a1835ee46edffd2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d39af32e394d4cf1a1835ee46edffd2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d39af32e394d4cf1a1835ee46edffd2d"}}, "title": "Pan-Cancer Detection Through DNA Methylation Profiling Using Enzymatic Conversion Library Preparation with Targeted Sequencing.", "authors": [{"family": "Qvick", "given": "Alvida", "initials": "A", "orcid": "0000-0001-6688-947X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4be159eaa724d22982b7b1e24e9ba79.json"}}, {"family": "Adolfsson", "given": "Emma", "initials": "E", "orcid": "0000-0002-7954-0696", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c790fe832ec4bf68608578c0c9d4552.json"}}, {"family": "Torn\u00e9us", "given": "Lina", "initials": "L"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Carlsson", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8457-7592", "researcher": {"href": "https://publications.scilifelab.se/researcher/529469b7e1fa4bccadbea444d1e9fcd4.json"}}, {"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}, {"family": "Karlsson", "given": "Christina", "initials": "C", "orcid": "0000-0002-4669-1367", "researcher": {"href": "https://publications.scilifelab.se/researcher/166381bbbbc947cd8f5178f70df9602d.json"}}, {"family": "Helenius", "given": "Gisela", "initials": "G", "orcid": "0000-0003-2317-5738", "researcher": {"href": "https://publications.scilifelab.se/researcher/2994acfdacff45ceb9c6b29aae2148c7.json"}}], "type": "journal article", "published": "2025-10-19", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "20", "issn-l": null}, "abstract": "We investigated differences in circulating cell-free DNA (cfDNA) methylation between patients with cancer and those presenting with severe, nonspecific symptoms. Plasma cfDNA from 229 patients was analyzed, of whom 37 were diagnosed with a wide spectrum of cancer types within 12 months. Samples underwent enzymatic conversion, library preparation, and enrichment using the NEBNext workflow and Twist pan-cancer methylation panel, followed by sequencing. Methylation analysis was performed with nf-core/methylseq. Differentially methylated regions (DMRs) were identified with DMRichR. Machine learning with cross-validation was used to classify cancer and controls. The classifier was applied to an external validation set of 144 controls previously unseen by the model. Cancer samples showed higher overall CpG methylation than controls (1.82% vs. 1.34%, p < 0.001). A total of 162 DMRs were detected, 95.7% being hypermethylated in cancer. Machine learning identified 20 key DMRs for classification between cancer and controls. The final model achieved an AUC of 0.88 (83.8% sensitivity, 83.8% specificity), while mean cross-validation performance reached an AUC of 0.73 (57.1% sensitivity, 77.5% specificity). The specificity of the classifier on unseen control samples was 79.2%. Distinct methylation differences and DMR-based classification support cfDNA methylation as a robust biomarker for cancer detection in patients with confounding conditions.", "doi": "10.3390/ijms262010165", "pmid": "41155454", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12564489"}, {"db": "pii", "key": "ijms262010165"}], "notes": [], "created": "2025-11-19T15:16:19.361Z", "modified": "2025-11-19T15:16:19.949Z"}, {"entity": "publication", "iuid": "e081c532d4de40fea93e6cad64023850", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e081c532d4de40fea93e6cad64023850.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e081c532d4de40fea93e6cad64023850"}}, "title": "Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification.", "authors": [{"family": "Brunet", "given": "Sofia", "initials": "S"}, {"family": "Grankvist", "given": "Anna", "initials": "A"}, {"family": "Jaen-Luchoro", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5988-6227", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a821a703a144b5aa5a783e7f8043d86.json"}}, {"family": "Bergdahl", "given": "Maria", "initials": "M"}, {"family": "Tison", "given": "Jean-Luc", "initials": "JL"}, {"family": "Wester", "given": "Annica", "initials": "A"}, {"family": "Elfving", "given": "Karin", "initials": "K"}, {"family": "Brandenburg", "given": "Jule", "initials": "J"}, {"family": "Gullsby", "given": "Karolina", "initials": "K"}, {"family": "Lindsten", "given": "Christoffer", "initials": "C"}, {"family": "Arvidsson", "given": "Lars-Ola", "initials": "LO"}, {"family": "Larsson", "given": "Helena", "initials": "H", "orcid": "0000-0002-6851-3297", "researcher": {"href": "https://publications.scilifelab.se/researcher/21f2cca2f6b74c5393c0fc33bcf15ee6.json"}}, {"family": "Eilers", "given": "Hinnerk", "initials": "H"}, {"family": "Strand", "given": "Anna S\u00f6derlund", "initials": "AS"}, {"family": "Lannefors", "given": "Mimi", "initials": "M"}, {"family": "Keskitalo", "given": "Johanna", "initials": "J"}, {"family": "Rylander", "given": "Felicia", "initials": "F"}, {"family": "Welander", "given": "Jenny", "initials": "J"}, {"family": "Jungestrom", "given": "Malin Bergman", "initials": "MB"}, {"family": "Ge\u00f6rg", "given": "Miriam", "initials": "M"}, {"family": "Kaden", "given": "Rene", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications.scilifelab.se/researcher/018870b1d0034ee09552a3ae451d5504.json"}}, {"family": "Karlsson", "given": "Ida", "initials": "I"}, {"family": "Linde", "given": "Anna-Malin", "initials": "AM"}, {"family": "Mernelius", "given": "Sara", "initials": "S"}, {"family": "Berglind", "given": "Linda", "initials": "L"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Kerje", "given": "Susanne", "initials": "S", "orcid": "0000-0002-2944-9288", "researcher": {"href": "https://publications.scilifelab.se/researcher/078ca525f2cc4a68a430f2655e45efce.json"}}, {"family": "Karlsson", "given": "Linda", "initials": "L", "orcid": "0000-0003-2704-1788", "researcher": {"href": "https://publications.scilifelab.se/researcher/9942f9d57c094401a1bb9b965f300092.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Guerra-Blomqvist", "given": "Lina", "initials": "L"}, {"family": "Wallin", "given": "Frans", "initials": "F"}, {"family": "Fagerstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0002-6276-8811", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8dc177a668c4256be2893eb98abddd4.json"}}, {"family": "Vondracek", "given": "Martin", "initials": "M"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Hallb\u00e4ck", "given": "Erika T\u00e5ng", "initials": "ET"}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Eur. J. Clin. Microbiol. Infect. Dis.", "issn": "1435-4373", "volume": "44", "issue": "8", "pages": "1907-1916", "issn-l": "0934-9723"}, "abstract": "Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration coordinated by Genomic Medicine Sweden.\n\nThirteen mock samples comprised of various bacterial strains and an External Quality Assessment (EQA) panel from QCMD (Quality Control for Molecular Diagnostics) were analysed by 20 microbiological laboratories across Sweden, using the recent v14 chemistry. Most laboratories generated full-length 16S rRNA sequencing libraries using an optimized protocol for the 16S Barcoding Kit 24, while two laboratories employed in-house PCR coupled with the Ligation Sequencing Kit. The commercial 16S bioinformatic pipeline from 1928 Diagnostics (1928-16S) was evaluated and compared with the open-sourced gms_16S pipeline that is based on the EMU classification tool (GMS-16S).\n\nSeventeen out of 20 laboratories successfully sequenced and analysed the samples. Laboratories that used sodium acetate-containing elution buffers faced compatibility issues during library construction, resulting in reduced read count. High bacterial load samples were generally well-characterized, whereas hard-to-lyse bacteria such as Gram-positive strains were detected at lower abundance. The GMS-16S tool provided improved species-level identification compared to the 1928-16S pipeline, particularly for closely related taxa within the Streptococcus and Staphylococcus genera.\n\nNanopore sequencing demonstrated promising potential for bacterial identification in a clinical setting. The results prompt further optimization of the protocol to improve detection of a broader range of species. This multicentre study highlights the feasibility of implementing Nanopore sequencing into clinical microbiological laboratories, for improved national precision diagnostics.", "doi": "10.1007/s10096-025-05158-w", "pmid": "40348924", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics Uppsala": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12321653"}, {"db": "pii", "key": "10.1007/s10096-025-05158-w"}], "notes": [], "created": "2025-07-08T13:51:52.338Z", "modified": "2025-11-26T14:14:27.926Z"}, {"entity": "publication", "iuid": "3629fbdd20714549bab70ec73d783648", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3629fbdd20714549bab70ec73d783648.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3629fbdd20714549bab70ec73d783648"}}, "title": "Staphylococcus aureus From Prosthetic Joint Infections and Blood Cultures Display the Same Genetic Background.", "authors": [{"family": "S\u00f6derquist", "given": "Bo", "initials": "B", "orcid": "0000-0001-5939-2932", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc4111ee338c4c52a17efbd0cfbab766.json"}}, {"family": "Wildeman", "given": "Peter", "initials": "P"}, {"family": "Stegger", "given": "Marc", "initials": "M"}, {"family": "Stenmark", "given": "Bianca", "initials": "B"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "APMIS", "issn": "1600-0463", "volume": "133", "issue": "7", "pages": "e70038", "issn-l": "0903-4641"}, "abstract": "Hematogenous prosthetic joint infections (PJIs) are primarily associated with Staphylococcus aureus, and there is a 30%-40% risk of contracting a hematogenous PJI following an S. aureus bacteremia. The aim of this study was to investigate whether identical strains of S. aureus were present in each patient from a cohort with both bacteremia and PJI and to explore the genomic differences between paired isolates obtained from blood cultures and tissue biopsies. All patients with a PJI and a temporally concomitant bacteremia due to S. aureus from 2005 to 2020 were included. Paired isolates of S. aureus from tissue biopsies and blood cultures were subjected to whole-genome sequencing. Twenty-four episodes of PJI were identified in 23 patients. All pairwise isolates from individual patients belonged to the same multilocus sequence type, clonal complex, and core genome multilocus sequence typing (cgMLST) complex type. The median number of single nucleotide polymorphisms (SNPs) in the conserved core genomes between the pairwise isolates was 3. In conclusion, identical cgMLST complex types and low levels of SNP differences between paired isolates of S. aureus from blood cultures and tissue biopsies suggest hematogenous seeding in all cases of PJI in this cohort.", "doi": "10.1111/apm.70038", "pmid": "40611607", "labels": {"Clinical Genomics": "Service", "Clinical Genomics \u00d6rebro": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12232108"}], "notes": [], "created": "2025-11-19T15:14:27.699Z", "modified": "2025-11-19T15:18:10.169Z"}, {"entity": "publication", "iuid": "2be38ff9355144368c27f39655529af8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2be38ff9355144368c27f39655529af8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2be38ff9355144368c27f39655529af8"}}, "title": "Development of Langat virus infectious clones as a platform for live-attenuated tick-borne encephalitis vaccine.", "authors": [{"family": "Asghar", "given": "Naveed", "initials": "N"}, {"family": "Jaafar", "given": "Rita", "initials": "R"}, {"family": "Valko", "given": "Anna", "initials": "A"}, {"family": "Merinder", "given": "Olivia", "initials": "O"}, {"family": "Ljungberg", "given": "Karl", "initials": "K"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Johansson", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2025-05-23", "journal": {"title": "Npj Viruses", "issn": "2948-1767", "volume": "3", "issue": "1", "pages": "44", "issn-l": null}, "abstract": "Tick-borne encephalitis (TBE) is one of the most important tick-transmitted diseases in Europe and Asia. With no specific antiviral treatment available, vaccination remains the most effective protective strategy for TBE. Unlike currently available inactivated TBE vaccines that require repeated boosters, live-attenuated vaccines could offer lifelong immunity with a single dose. Langat virus (LGTV) is a naturally attenuated strain of TBE virus (TBEV). In this study, we engineered and rescued four infectious clones (ICs) of LGTV using RNA- and DNA-based reverse genetics methods. The ICs rescued by DNA-based method showed higher genetic stability in cell culture. One of the ICs rescued by DNA-based method was further evaluated in vitro and in vivo, which exhibited growth kinetics and immune profile comparable to the LGTV strain in our laboratory. This reverse genetics platform will be utilized to introduce targeted mutations within the LGTV genome to develop a live-attenuated TBE vaccine.", "doi": "10.1038/s44298-025-00129-6", "pmid": "40410304", "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12102213"}, {"db": "pii", "key": "10.1038/s44298-025-00129-6"}], "notes": [], "created": "2025-11-19T15:16:17.785Z", "modified": "2025-11-19T15:16:17.848Z"}, {"entity": "publication", "iuid": "bdd145617e0c401ea708379b0493f458", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdd145617e0c401ea708379b0493f458.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdd145617e0c401ea708379b0493f458"}}, "title": "Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden.", "authors": [{"family": "T\u00e5ng Hallb\u00e4ck", "given": "Erika", "initials": "E"}, {"family": "Bj\u00f6rkman", "given": "Jonas T", "initials": "JT"}, {"family": "Dyrkell", "given": "Fredrik", "initials": "F"}, {"family": "Welander", "given": "Jenny", "initials": "J"}, {"family": "Fang", "given": "Hong", "initials": "H"}, {"family": "Sylvin", "given": "Isak", "initials": "I"}, {"family": "Kaden", "given": "Ren", "initials": "R", "orcid": "0000-0002-2111-9751", "researcher": {"href": "https://publications.scilifelab.se/researcher/018870b1d0034ee09552a3ae451d5504.json"}}, {"family": "Eilers", "given": "Hinnerk", "initials": "H"}, {"family": "S\u00f6derlund Strand", "given": "Anna", "initials": "A"}, {"family": "Mernelius", "given": "Sara", "initials": "S"}, {"family": "Berglind", "given": "Linda", "initials": "L"}, {"family": "Campillay Lagos", "given": "Amaya", "initials": "A"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}, {"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "11", "issue": "1", "issn-l": null}, "abstract": "Background. National epidemiological investigations of microbial infections greatly benefit from the increased information gained by whole-genome sequencing (WGS) in combination with standardized approaches for data sharing and analysis.Aim. To evaluate the quality and accuracy of WGS data generated by different laboratories but analysed by joint pipelines to reach a national surveillance approach.Methods. A national methicillin-resistant Staphylococcus aureus (MRSA) collection of 20 strains was distributed to nine participating laboratories that performed in-house procedures for WGS. Raw data were shared and analysed by three pipelines: 1928 Diagnostics, JASEN (GMS pipeline) and CLC-Genomics Workbench. The outcomes were compared according to quality, correct strain identification and genetic distances.Results. One isolate contained intraspecies contamination and was excluded from further analysis. The mean sequencing depth varied between sites and technologies. However, all analysis methods identified 12 strains that belonged to one of five outbreak clusters. The cut-off definition was set to <10 allele differences for core genome multilocus sequence typing (cgMLST) and <20 genetic differences for SNP analysis in a pairwise comparison.Conclusions. MRSA isolates, which are whole genome sequenced by different laboratories and analysed using the same bioinformatic pipelines, yielded comparable results for outbreak clustering for both cgMLST and SNP, using the 1928 analysis pipeline. In this study, JASEN was best suited to analyse Illumina data and CLC to analyse within respective technology. In the future, real-time sharing of data and harmonized analysis within the Genomic Medicine Sweden consortium will further facilitate investigations of outbreaks and transmission routes.", "doi": "10.1099/mgen.0.001331", "pmid": "39869391", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative", "Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11893271"}], "notes": [], "created": "2025-03-19T04:58:38.247Z", "modified": "2025-11-19T15:18:20.002Z"}, {"entity": "publication", "iuid": "c6e3d237e68d44dc8a2c6d1a4da50c10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6e3d237e68d44dc8a2c6d1a4da50c10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6e3d237e68d44dc8a2c6d1a4da50c10"}}, "title": "Evolution of community-associated MRSA: a 20-year genomic and epidemiological study in Region \u00d6rebro County, Sweden.", "authors": [{"family": "Kekki", "given": "Jan", "initials": "J"}, {"family": "Thegel", "given": "Annethe", "initials": "A"}, {"family": "Stenmark", "given": "Bianca", "initials": "B"}, {"family": "S\u00f6derquist", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2024-12-23", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "15", "pages": "1504860", "issn-l": "1664-302X"}, "abstract": "Methicillin-resistant Staphylococcus aureus (MRSA) has been an issue in healthcare since the 1960s. It was initially found only in healthcare facilities, but in the late 1990s it began to be seen with no healthcare connexion. The mechanisms of intercontinental and national spread are not fully understood, as sometimes novel outbreaks occur without any identifiable source or connexion to locally dominant clonal clusters.\n\nThis study investigated the epidemiology and genomics of community-associated MRSA in Region \u00d6rebro County, Sweden, through 330 isolates collected between 2000 and 2019.\n\nA shift in the dominant sequence type (ST) from ST80 to ST22 occurred in 2011-2019, along with an increase in the prevalence of STs belonging to clonal complexes CC5 and CC22. Both ST8 and ST80 isolates seemed to give way to emerging ST22 isolates, also indicated by the declining presence of the USA300 clone. The staphylococcal chromosomal cassette mec (SCCmec) type IV Remained dominant.\n\nThe SCCmec type IV characteristic appears to be relatively geographically stable, possibly due to its low fitness cost and transductal capabilities. This warrants further studies of SCCmec type IV variant's survival mechanics as well as the effects of migratory flow on local epidemiology, in preparation for future possible outbreaks.", "doi": "10.3389/fmicb.2024.1504860", "pmid": "39764449", "labels": {"Clinical Genomics": "Service", "Clinical Genomics \u00d6rebro": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11701036"}], "notes": [], "created": "2025-11-19T15:16:21.568Z", "modified": "2025-11-19T15:18:57.116Z"}, {"entity": "publication", "iuid": "cf96293ac8914046b7fb35a938cbff0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf96293ac8914046b7fb35a938cbff0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf96293ac8914046b7fb35a938cbff0c"}}, "title": "Sensitive and Specific Droplet Digital PCR Assays for Circulating Tumor HPV DNA: Development, Validation, and Clinical Application in HPV-Associated Cancers.", "authors": [{"family": "Qvick", "given": "Alvida", "initials": "A", "orcid": "0000-0001-6688-947X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4be159eaa724d22982b7b1e24e9ba79.json"}}, {"family": "Andersson", "given": "Elin", "initials": "E"}, {"family": "Oldaeus Almer\u00e9n", "given": "Anna", "initials": "A"}, {"family": "Waenerlund", "given": "Max", "initials": "M"}, {"family": "Stenmark", "given": "Bianca", "initials": "B"}, {"family": "Karlsson", "given": "Christina", "initials": "C"}, {"family": "Karlsson", "given": "Mats G", "initials": "MG"}, {"family": "Helenius", "given": "Gisela", "initials": "G"}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Mol Diagn Ther", "issn": "1179-2000", "volume": "28", "issue": "6", "pages": "835-845", "issn-l": null}, "abstract": "Human papillomavirus (HPV) has emerged as a significant contributor to cancer incidence globally, particularly in the context of oropharyngeal squamous cell carcinoma (OPSCC) and cancer of unknown primary (HNCUP). This study aimed to develop and validate droplet digital PCR (ddPCR) assays for the detection of circulating tumor HPV DNA (ctHPV-DNA) in plasma, focusing on high-risk HPV genotypes associated with these cancers.\n\nddPCR assays for HPV16, 18, 33, 35, 56, and 59 were developed and tested using gBlocks, HPV cell-free DNA, fragmented tumor HPV+ DNA, and plasma samples from patients with HPV+ OPSCC (n = 110) and HNCUP (n = 9).\n\nAssays demonstrated robust technical sensitivity across all tested HPV genotypes. Clinical application of the assays on a cohort of patients with HPV+ OPSCC and HNCUP revealed high sensitivity (91.6%) and wide variability in ctHPV-DNA levels. Analyses revealed correlations between ctHPV-DNA levels and TNM stage and tumor viral load. The association between ctHPV-DNA and tumor viral load persisted even after adjusting for TNM stage. At posttreatment, 72.5% of samples had reached undetectable ctHPV-DNA levels. Having detectable ctHPV-DNA posttreatment was associated with a higher ctHPV-DNA level at diagnosis and higher viral load at diagnosis.\n\nThe findings underscore the potential of ctHPV-DNA as a biomarker for monitoring HPV+ cancers and offer insights into tumor dynamics. Implementation of these assays in clinical practice could enhance no-invasive treatment monitoring and recurrence detection in HPV-associated cancers.\n\nNCT05904327.", "doi": "10.1007/s40291-024-00743-9", "pmid": "39325260", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11512825"}, {"db": "pii", "key": "10.1007/s40291-024-00743-9"}, {"db": "ClinicalTrials.gov", "key": "NCT05904327"}], "notes": [], "created": "2024-11-20T15:03:09.115Z", "modified": "2024-11-20T15:09:05.040Z"}, {"entity": "publication", "iuid": "7ddd1cde570245949a214b8e2e9a929c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7ddd1cde570245949a214b8e2e9a929c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7ddd1cde570245949a214b8e2e9a929c"}}, "title": "The power of hybridization capture - Illustrated using an expanded gene panel on 100 post mortem samples, focusing on sudden unexplained death.", "authors": [{"family": "Kling", "given": "Daniel", "initials": "D"}, {"family": "Adolfsson", "given": "Emma", "initials": "E"}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}, {"family": "Gr\u00e9en", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2024-10-11", "journal": {"title": "Forensic Sci Int Genet", "issn": "1878-0326", "volume": "74", "pages": "103160", "issn-l": "1872-4973"}, "abstract": "Sudden unexpected death (SUD) is an unexpected event that in many cases are caused by diseases with an underlying genetic background. Forensic molecular autopsy is an approach that has gained wide-spread attention, in part explained by the rapid progress of DNA sequencing techniques. The approach leverages genetic data in combination with medical autopsy findings in post-mortem samples to explore a potential underlying genetic cause of death. Traditional forensic approaches to molecular autopsy focus on a small panel of genes, say <200 genes, with strong association to heart conditions whereas clinical genetics tend to capture entire exomes while subsequently selecting targeted panels bioinformatically. The drop in price and the increased throughput has promoted wider exome sequencing as a viable method to discover genetic variants. We explore a targeted gene panel consisting of 2422 genes, selected based on their broad association to sudden unexplained death. A hybridization capture approach from Twist Bioscience based on double stranded DNA probes was used to target exons of the included genes. We selected and sequenced a total of 98 post-mortem samples from historical forensic autopsy cases where the cause of death could not be unambiguously determined based on medical findings and that had a previous negative molecular autopsy. In the current study, we focus on the performance of the hybridization capture technology on a 2422 gene panel and explore metrics related to sequencing success using a mid-end NextSeq 550 as well as a MiSeq FGx platform. With the latter we demonstrate that our sequence data benefits from 2\u00d7300 bp sequencing increasing coverage, in particular, for difficult regions where shadow coverage, i.e. regions outside the probes, are utilized. The results further illustrate a highly uniform capture across the panel of genes (mean fold80=1.5), in turn minimizing excessive sequencing costs to reach sufficient coverage, i.e. 20X. We outline a stepwise procedure to select genes associated with SUD through virtual bioinformatical panels extracting tier of genes with increasing strength of association to SUD. We propose some prioritization strategies to filter variants with highest potential and show that the number of high priority genetic variant requiring manual inspections is few (0-3 for all tiers of genes) when all filters are applied.", "doi": "10.1016/j.fsigen.2024.103160", "pmid": "39437498", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1872-4973(24)00156-X"}], "notes": [], "created": "2024-11-20T14:59:13.699Z", "modified": "2024-11-20T14:59:13.707Z"}, {"entity": "publication", "iuid": "add50568818049119cb2b383bdb33ad0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/add50568818049119cb2b383bdb33ad0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/add50568818049119cb2b383bdb33ad0"}}, "title": "Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020.", "authors": [{"family": "Dyrdak", "given": "Robert", "initials": "R"}, {"family": "Hodcroft", "given": "Emma B", "initials": "EB"}, {"family": "Broddesson", "given": "Sandra", "initials": "S"}, {"family": "Grabbe", "given": "Malin", "initials": "M"}, {"family": "Franklin", "given": "Hildur", "initials": "H"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Holm", "given": "Maricris E", "initials": "ME"}, {"family": "Lindh", "given": "Magnus", "initials": "M"}, {"family": "Nederby-\u00d6hd", "given": "Joanna", "initials": "J"}, {"family": "Ringlander", "given": "Johan", "initials": "J"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "Neher", "given": "Richard A", "initials": "RA"}, {"family": "Albert", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Euro Surveill.", "issn": "1560-7917", "volume": "29", "issue": "41", "issn-l": "1025-496X"}, "abstract": "BackgroundDespite the unprecedented measures implemented globally in early 2020 to prevent the spread of SARS-CoV-2, Sweden, as many other countries, experienced a severe first wave during the COVID-19 pandemic.AimWe investigated the introduction and spread of SARS-CoV-2 into Sweden.MethodsWe analysed stored respiratory specimens (n = 1,979), sampled 7 February-2 April 2020, by PCR for SARS-CoV-2 and sequenced PCR-positive specimens. Sequences generated from newly detected cases and stored positive specimens February-June 2020 (n = 954) were combined with sequences (Sweden: n = 730; other countries: n = 129,913) retrieved from other sources for Nextstrain clade assignment and phylogenetic analyses.ResultsTwelve previously unrecognised SARS-CoV-2 cases were identified: the earliest was sampled on 3 March, 1 week before recognised community transmission. We showed an early influx of clades 20A and 20B from Italy (201/328, 61% of cases exposed abroad) and clades 19A and 20C from Austria (61/328, 19%). Clade 20C dominated the first wave (20C: 908/1,684, 54%; 20B: 438/1,684, 26%; 20A: 263/1,684, 16%), and 800 of 1,684 (48%) Swedish sequences formed a country-specific 20C cluster defined by a spike mutation (G24368T). At the regional level, the proportion of clade 20C sequences correlated with an earlier weighted mean date of COVID-19 deaths.ConclusionCommunity transmission in Sweden started when mitigation efforts still focused on preventing influx. This created a transmission advantage for clade 20C, likely introduced from ongoing cryptic spread in Austria. Therefore, pandemic preparedness should have a comprehensive approach, including capacity for large-scale diagnostics to allow early detection of travel-related cases and community transmission.", "doi": "10.2807/1560-7917.ES.2024.29.41.2400021", "pmid": "39392000", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11484920"}], "notes": [], "created": "2024-11-20T15:02:27.986Z", "modified": "2024-11-23T14:20:51.972Z"}, {"entity": "publication", "iuid": "2b1f93156c57480db87debbb7a3c5f02", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b1f93156c57480db87debbb7a3c5f02.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b1f93156c57480db87debbb7a3c5f02"}}, "title": "In silico gepotidacin target mining among 33 213 global Neisseria gonorrhoeae genomes from 1928 to 2023 combined with gepotidacin MIC testing of 22 gonococcal isolates with different GyrA and ParC substitutions.", "authors": [{"family": "David", "given": "Alexandra", "initials": "A"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Stratton", "given": "Caleb", "initials": "C"}, {"family": "Lan", "given": "Pham Thi", "initials": "PT"}, {"family": "Shimuta", "given": "Ken", "initials": "K"}, {"family": "Sonnenberg", "given": "Pam", "initials": "P"}, {"family": "Field", "given": "Nigel", "initials": "N"}, {"family": "Ohnishi", "given": "Makoto", "initials": "M"}, {"family": "Davies", "given": "Christopher", "initials": "C"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}], "type": "journal article", "published": "2024-09-03", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "volume": "79", "issue": "9", "pages": "2221-2226", "issn-l": "0305-7453"}, "abstract": "The novel dual-target triazaacenaphthylene, gepotidacin, recently showed promising results in its Phase III randomized controlled trial for the treatment of gonorrhoea. We investigated alterations in the gepotidacin GyrA and ParC targets in gonococci by in silico mining of publicly available global genomes (n = 33 213) and determined gepotidacin MICs in isolates with GyrA A92 alterations combined with other GyrA and/or ParC alterations.\n\nWe examined gonococcal gyrA and parC alleles available at the European Nucleotide Archive. MICs were determined using the agar dilution method (gepotidacin) or Etest (four antimicrobials). Models of DNA gyrase and topoisomerase IV were obtained from AlphaFold and used to model gepotidacin in the binding site.\n\nGyrA A92 alterations were identified in 0.24% of genomes: GyrA A92P/S/V + S91F + D95Y/A/N (0.208%), A92P + S91F (0.024%) and A92P (0.003%), but no A92T (previously associated with gepotidacin resistance) was found. ParC D86 alterations were found in 10.6% of genomes: ParC D86N/G (10.5%), D86N + S87I (0.051%), D86N + S88P (0.012%) and D86G + E91G (0.003%). One isolate had GyrA A92P + ParC D86N alterations, but remained susceptible to gepotidacin (MIC = 0.125 mg/L). No GyrA plus ParC alterations resulted in a gepotidacin MIC > 4 mg/L. Modelling of gepotidacin binding to GyrA A92/A92T/A92P suggested that gepotidacin resistance due to GyrA A92T might be linked to the formation of a new polar contact with DNA.\n\nIn silico mining of 33 213 global gonococcal genomes (isolates from 1928 to 2023) showed that A92 is highly conserved in GyrA, while alterations in D86 of ParC are common. No GyrA plus ParC alterations caused gepotidacin resistance. MIC determination and genomic surveillance of potential antimicrobial resistance determinants are imperative.", "doi": "10.1093/jac/dkae217", "pmid": "39004438", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11368423"}, {"db": "pii", "key": "7708821"}], "notes": [], "created": "2024-11-20T14:58:43.743Z", "modified": "2024-11-20T14:58:43.776Z"}, {"entity": "publication", "iuid": "61449e65b85c46de81f329569ca2b533", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61449e65b85c46de81f329569ca2b533.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61449e65b85c46de81f329569ca2b533"}}, "title": "Conference report: the first bacterial genome sequencing pan-European network conference.", "authors": [{"family": "Germuskova", "given": "Zoja", "initials": "Z"}, {"family": "Sosa", "given": "Elisa", "initials": "E"}, {"family": "Lagos", "given": "Amaya Campillay", "initials": "AC"}, {"family": "Aamot", "given": "Hege Vangstein", "initials": "HV"}, {"family": "Beale", "given": "Mathew A", "initials": "MA"}, {"family": "Bertelli", "given": "Claire", "initials": "C"}, {"family": "Bj\u00f6rkmann", "given": "Jonas", "initials": "J"}, {"family": "Couto", "given": "Natacha", "initials": "N"}, {"family": "Feige", "given": "Lena", "initials": "L"}, {"family": "Greub", "given": "Gilbert", "initials": "G"}, {"family": "Hallb\u00e4ck", "given": "Erika T\u00e5ng", "initials": "ET"}, {"family": "Hodcroft", "given": "Emma B", "initials": "EB"}, {"family": "Harmsen", "given": "Dag", "initials": "D"}, {"family": "Jacob", "given": "Laurent", "initials": "L"}, {"family": "Jolley", "given": "Keith A", "initials": "KA"}, {"family": "Kahles", "given": "Andre", "initials": "A"}, {"family": "Mather", "given": "Alison E", "initials": "AE"}, {"family": "Neher", "given": "Richard A", "initials": "RA"}, {"family": "Neves", "given": "Aitana", "initials": "A"}, {"family": "Niemann", "given": "Stefan", "initials": "S"}, {"family": "Nolte", "given": "Oliver", "initials": "O"}, {"family": "Peacock", "given": "Sharon J", "initials": "SJ"}, {"family": "Razavi", "given": "Mohammad", "initials": "M"}, {"family": "Roloff", "given": "Tim", "initials": "T"}, {"family": "Schrenzel", "given": "Jacques", "initials": "J"}, {"family": "Sikora", "given": "Per", "initials": "P"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Egli", "given": "Adrian", "initials": "A"}], "type": "journal article", "published": "2024-08-30", "journal": {"title": "Microbes Infect", "issn": "1769-714X", "pages": "105410", "issn-l": null}, "abstract": null, "doi": "10.1016/j.micinf.2024.105410", "pmid": "39218348", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1286-4579(24)00152-7"}], "notes": [], "created": "2024-11-20T15:00:02.380Z", "modified": "2024-11-20T15:00:02.412Z"}, {"entity": "publication", "iuid": "af08cdee7c4e4e6d89242e17aa19f267", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af08cdee7c4e4e6d89242e17aa19f267.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af08cdee7c4e4e6d89242e17aa19f267"}}, "title": "The novel 2024 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations and superseded WHO N. gonorrhoeae reference strains-phenotypic, genetic and reference genome characterization.", "authors": [{"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}, {"family": "S\u00e1nchez-Bus\u00f3", "given": "Leonor", "initials": "L"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Shimuta", "given": "Ken", "initials": "K"}, {"family": "Lan", "given": "Pham Thi", "initials": "PT"}, {"family": "Eyre", "given": "David W", "initials": "DW"}, {"family": "Cole", "given": "Michelle", "initials": "M"}, {"family": "Maatouk", "given": "Ismael", "initials": "I", "orcid": "0000-0003-1008-7413", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bdc82f7504e46ea91e3343b025b1dab.json"}}, {"family": "Wi", "given": "Teodora", "initials": "T"}, {"family": "Lahra", "given": "Monica M", "initials": "MM"}], "type": "journal article", "published": "2024-08-01", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "volume": "79", "issue": "8", "pages": "1885-1899", "issn-l": "0305-7453"}, "abstract": "MDR and XDR Neisseria gonorrhoeae strains remain major public health concerns internationally, and quality-assured global gonococcal antimicrobial resistance (AMR) surveillance is imperative. The WHO global Gonococcal Antimicrobial Surveillance Programme (GASP) and WHO Enhanced GASP (EGASP), including metadata and WGS, are expanding internationally. We present the phenotypic, genetic and reference genome characteristics of the 2024 WHO gonococcal reference strains (n = 15) for quality assurance worldwide. All superseded WHO gonococcal reference strains (n = 14) were identically characterized.\n\nThe 2024 WHO reference strains include 11 of the 2016 WHO reference strains, which were further characterized, and four novel strains. The superseded WHO reference strains include 11 WHO reference strains previously unpublished. All strains were characterized phenotypically and genomically (single-molecule PacBio or Oxford Nanopore and Illumina sequencing).\n\nThe 2024 WHO reference strains represent all available susceptible and resistant phenotypes and genotypes for antimicrobials currently and previously used (n = 22), or considered for future use (n = 3) in gonorrhoea treatment. The novel WHO strains include internationally spreading ceftriaxone resistance, ceftriaxone resistance due to new penA mutations, ceftriaxone plus high-level azithromycin resistance and azithromycin resistance due to mosaic MtrRCDE efflux pump. AMR, serogroup, prolyliminopeptidase, genetic AMR determinants, plasmid types, molecular epidemiological types and reference genome characteristics are presented for all strains.\n\nThe 2024 WHO gonococcal reference strains are recommended for internal and external quality assurance in laboratory examinations, especially in the WHO GASP, EGASP and other GASPs, but also in phenotypic and molecular diagnostics, AMR prediction, pharmacodynamics, epidemiology, research and as complete reference genomes in WGS analysis.", "doi": "10.1093/jac/dkae176", "pmid": "38889110", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11290888"}, {"db": "pii", "key": "7695846"}], "notes": [], "created": "2024-11-20T14:58:06.821Z", "modified": "2024-11-20T14:58:06.930Z"}, {"entity": "publication", "iuid": "76598235f1fd43b39691a19b4806be7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/76598235f1fd43b39691a19b4806be7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/76598235f1fd43b39691a19b4806be7b"}}, "title": "The WHO Enhanced Gonococcal Antimicrobial Surveillance Programme (EGASP) identifies high levels of ceftriaxone resistance across Vietnam, 2023.", "authors": [{"family": "Lan", "given": "Pham Thi", "initials": "PT"}, {"family": "Nguyen", "given": "Hao Trong", "initials": "HT"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Thuy Van", "given": "Nguyen Thi", "initials": "NT"}, {"family": "Maatouk", "given": "Ismael", "initials": "I"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "EGASP-Vietnam WGS study group", "given": "", "initials": ""}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Lancet Reg Health West Pac", "issn": "2666-6065", "volume": "48", "pages": "101125", "issn-l": null}, "abstract": null, "doi": "10.1016/j.lanwpc.2024.101125", "pmid": "39040039", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11260586"}, {"db": "pii", "key": "S2666-6065(24)00119-6"}], "notes": [], "created": "2024-11-20T15:07:11.016Z", "modified": "2024-11-20T15:07:11.047Z"}, {"entity": "publication", "iuid": "76e1763ddefa4d3c8a39dbe015fbe8e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/76e1763ddefa4d3c8a39dbe015fbe8e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/76e1763ddefa4d3c8a39dbe015fbe8e7"}}, "title": "Diagnosis of external ventricular drainage related infections with real-time 16S PCR and third-generation 16S sequencing.", "authors": [{"family": "Wid\u00e9n", "given": "Johan", "initials": "J"}, {"family": "Mor\u00e9n", "given": "Jakob", "initials": "J"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Fagerstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Enblad", "given": "Per", "initials": "P"}, {"family": "Eriksson", "given": "Britt-Marie", "initials": "BM"}, {"family": "Ronne-Engstr\u00f6m", "given": "Elisabeth", "initials": "E"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "Westman", "given": "Gabriel", "initials": "G"}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Infect Dis (Lond)", "issn": "2374-4243", "volume": "56", "issue": "7", "pages": "521-530", "issn-l": "2374-4235"}, "abstract": "Investigate the performance of real-time 16S PCR and third-generation 16S sequencing in the diagnosis of external ventricular drain related infections (EVDRI).\n\nSubjects with suspected EVDRI were prospectively included at Uppsala University Hospital. Subjects were included into three groups: subjects with negative CSF culture with and without antibiotic treatment and subjects with positive CSF culture, respectively. CSF was analysed with real-time 16S PCR and third-generation 16S sequencing. Real-time 16S PCR positivity/negativity and number of 16S sequence reads were compared between groups. For culture positive subjects, species identification in third-generation sequencing and routine culture was compared.\n\n84 subjects were included. There were 18, 44 and 22 subjects in the three groups. Real-time PCR was positive in 17 of 22 subjects in the culture positive group and negative in 61 of the 62 subjects in the two culture negative groups. The sensitivity and specificity for real-time 16S PCR compared to culture was estimated to 77% and 98%, respectively. Species identification in 16S sequencing and culture was concordant in 20 of 22 subjects. The number of 16S sequence reads were significantly higher in the culture positive group than in both culture negative groups (p < 0.001). There was no significant difference in number of 16S sequences between the two culture negative groups.\n\nReal-time 16S PCR predict culture results with sufficient reliability. Third-generation 16S sequencing could enhance sensitivity and species identification in diagnostics of EVD-related infections. False negative culture results appear to be uncommon in patients with suspected EVDRI.", "doi": "10.1080/23744235.2024.2331260", "pmid": "38530119", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-11-20T14:59:47.621Z", "modified": "2024-11-20T14:59:47.630Z"}, {"entity": "publication", "iuid": "b6e1325498d643fa99e0877c9212dcdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6e1325498d643fa99e0877c9212dcdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6e1325498d643fa99e0877c9212dcdf"}}, "title": "A laboratory-based predictive pathway for the development of Neisseria gonorrhoeae high-level resistance to corallopyronin A, an inhibitor of bacterial RNA polymerase.", "authors": [{"family": "Balthazar", "given": "Jacqueline T", "initials": "JT"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "Read", "given": "Timothy D", "initials": "TD", "orcid": "0000-0001-8966-9680", "researcher": {"href": "https://publications.scilifelab.se/researcher/01013702fa3542079dcd168495fcc1a0.json"}}, {"family": "Grosse", "given": "Miriam", "initials": "M"}, {"family": "Stadler", "given": "Marc", "initials": "M"}, {"family": "Pfarr", "given": "Kenneth", "initials": "K", "orcid": "0000-0003-3096-2465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b979204a52614894a2a93bad8c9585a9.json"}}, {"family": "Schiefer", "given": "Andrea", "initials": "A"}, {"family": "Hoerauf", "given": "Achim", "initials": "A"}, {"family": "Edwards", "given": "Jennifer L", "initials": "JL", "orcid": "0000-0003-3568-0344", "researcher": {"href": "https://publications.scilifelab.se/researcher/4681ac67168046ae8b31abb48d353e71.json"}}, {"family": "Vassylyev", "given": "Dmitry G", "initials": "DG"}, {"family": "Shafer", "given": "William M", "initials": "WM", "orcid": "0000-0001-9303-8777", "researcher": {"href": "https://publications.scilifelab.se/researcher/3db4c22ff7c84470b256cf08845f0bc7.json"}}], "type": "journal article", "published": "2024-06-04", "journal": {"title": "Microbiol Spectr", "issn": "2165-0497", "volume": "12", "issue": "6", "pages": "e0056024", "issn-l": null}, "abstract": "The continued emergence of Neisseria gonorrhoeae strains that express resistance to multiple antibiotics, including the last drug for empiric monotherapy (ceftriaxone), necessitates the development of new treatment options to cure gonorrheal infections. Toward this goal, we recently reported that corallopyronin A (CorA), which targets the switch region of the \u03b2' subunit (RpoC) of bacterial DNA-dependent RNA polymerase (RNAP), has potent anti-gonococcal activity against a panel of multidrug-resistant clinical strains. Moreover, in that study, CorA could eliminate gonococcal infection of primary human epithelial cells and gonococci in a biofilm state. To determine if N. gonorrhoeae could develop high-level resistance to CorA in a single step, we sought to isolate spontaneous mutants expressing any CorA resistance phenotypes. However, no single-step mutants with high-level CorA resistance were isolated. High-level CorA resistance could only be achieved in this study through a multi-step pathway involving over-expression of the MtrCDE drug efflux pump and single amino acid changes in the \u03b2 and \u03b2' subunits (RpoB and RpoC, respectively) of RNAP. Molecular modeling of RpoB and RpoC interacting with CorA was used to deduce how the amino acid changes in RpoB and RpoC could influence gonococcal resistance to CorA. Bioinformatic analyses of whole genome sequences of clinical gonococcal isolates indicated that the CorA resistance determining mutations in RpoB/C, identified herein, are very rare (\u2264 0.0029%), suggesting that the proposed pathway for resistance is predictive of how this phenotype could potentially evolve if CorA is used therapeutically to treat gonorrhea in the future.\n\nThe continued emergence of multi-antibiotic-resistant strains of Neisseria gonorrhoeae necessitates the development of new antibiotics that are effective against this human pathogen. We previously described that the RNA polymerase-targeting antibiotic corallopyronin A (CorA) has potent activity against a large collection of clinical strains that express different antibiotic resistance phenotypes including when such gonococci are in a biofilm state. Herein, we tested whether a CorA-sensitive gonococcal strain could develop spontaneous resistance. Our finding that CorA resistance could only be achieved by a multi-step process involving over-expression of the MtrCDE efflux pump and single amino acid changes in RpoB and RpoC suggests that such resistance may be difficult for gonococci to evolve if this antibiotic is used in the future to treat gonorrheal infections that are refractory to cure by other antibiotics.", "doi": "10.1128/spectrum.00560-24", "pmid": "38647280", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11237373"}], "notes": [], "created": "2024-11-20T15:06:27.426Z", "modified": "2024-11-20T15:06:27.908Z"}, {"entity": "publication", "iuid": "230c73a25d9e44ad8a846e16f341182a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/230c73a25d9e44ad8a846e16f341182a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/230c73a25d9e44ad8a846e16f341182a"}}, "title": "Recent dynamics in Neisseria gonorrhoeae genomic epidemiology in Brazil: antimicrobial resistance and genomic lineages in 2017-20 compared to 2015-16.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Bazzo", "given": "Maria Luiza", "initials": "ML"}, {"family": "Ahlstrand", "given": "Josefine", "initials": "J"}, {"family": "Sch\u00f6rner", "given": "Marcos Andr\u00e9", "initials": "MA"}, {"family": "Gaspar", "given": "Pamela Cristina", "initials": "PC"}, {"family": "de Melo Machado", "given": "Hanalydia", "initials": "H"}, {"family": "Martins", "given": "J\u00e9ssica Motta", "initials": "JM"}, {"family": "Bigolin", "given": "Alisson", "initials": "A"}, {"family": "Ramos", "given": "Mauro Cunha", "initials": "MC"}, {"family": "Ferreira", "given": "William Antunes", "initials": "WA"}, {"family": "Pereira", "given": "Gerson Fernando Mendes", "initials": "GFM"}, {"family": "Miranda", "given": "Angelica Espinosa", "initials": "AE"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}, {"family": "Brazilian-GASP Network", "given": "", "initials": ""}], "type": "journal article", "published": "2024-05-02", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "volume": "79", "issue": "5", "pages": "1081-1092", "issn-l": "0305-7453"}, "abstract": "Regular quality-assured WGS with antimicrobial resistance (AMR) and epidemiological data of patients is imperative to elucidate the shifting gonorrhoea epidemiology, nationally and internationally. We describe the dynamics of the gonococcal population in 11 cities in Brazil between 2017 and 2020 and elucidate emerging and disappearing gonococcal lineages associated with AMR, compare to Brazilian WGS and AMR data from 2015 to 2016, and explain recent changes in gonococcal AMR and gonorrhoea epidemiology.\n\nWGS was performed using Illumina NextSeq 550 and genomes of 623 gonococcal isolates were used for downstream analysis. Molecular typing and AMR determinants were obtained and links between genomic lineages and AMR (determined by agar dilution/Etest) examined.\n\nAzithromycin resistance (15.6%, 97/623) had substantially increased and was mainly explained by clonal expansions of strains with 23S rRNA C2611T (mostly NG-STAR CC124) and mtr mosaics (mostly NG-STAR CC63, MLST ST9363). Resistance to ceftriaxone and cefixime remained at the same levels as in 2015-16, i.e. at 0% and 0.2% (1/623), respectively. Regarding novel gonorrhoea treatments, no known zoliflodacin-resistance gyrB mutations or gepotidacin-resistance gyrA mutations were found. Genomic lineages and sublineages showed a phylogenomic shift from sublineage A5 to sublineages A1-A4, while isolates within lineage B remained diverse in Brazil.\n\nAzithromycin resistance, mainly caused by 23S rRNA C2611T and mtrD mosaics/semi-mosaics, had substantially increased in Brazil. This mostly low-level azithromycin resistance may threaten the recommended ceftriaxone-azithromycin therapy, but the lack of ceftriaxone resistance is encouraging. Enhanced gonococcal AMR surveillance, including WGS, is imperative in Brazil and other Latin American and Caribbean countries.", "doi": "10.1093/jac/dkae075", "pmid": "38517452", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7633595"}], "notes": [], "created": "2024-11-20T14:56:51.940Z", "modified": "2024-11-20T14:56:51.951Z"}, {"entity": "publication", "iuid": "0fc05f7c131445c9996a87a8afeb9686", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fc05f7c131445c9996a87a8afeb9686.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fc05f7c131445c9996a87a8afeb9686"}}, "title": "Pharmacodynamic evaluation of ceftriaxone single-dose therapy (0.125-1 g) to eradicate ceftriaxone-susceptible and ceftriaxone-resistant Neisseria gonorrhoeae strains in a hollow fibre infection model for gonorrhoea.", "authors": [{"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Oxelbark", "given": "Joakim", "initials": "J"}, {"family": "Kong", "given": "Fabian Y S", "initials": "FYS", "orcid": "0000-0002-9349-3080", "researcher": {"href": "https://publications.scilifelab.se/researcher/592aa4c01f1f459bb37fd93377d3040e.json"}}, {"family": "Brown", "given": "David", "initials": "D"}, {"family": "Louie", "given": "Arnold", "initials": "A", "orcid": "0000-0001-6227-7580", "researcher": {"href": "https://publications.scilifelab.se/researcher/e361bfdb54dd49cba340a5733c6654a2.json"}}, {"family": "Drusano", "given": "George", "initials": "G", "orcid": "0000-0001-9162-7332", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c67e6f2c51d455da8c196529c719dd3.json"}}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}], "type": "journal article", "published": "2024-05-02", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "volume": "79", "issue": "5", "pages": "1006-1013", "issn-l": "0305-7453"}, "abstract": "Antimicrobial resistance in Neisseria gonorrhoeae is threatening the gonorrhoea treatment, and optimizations of the current ceftriaxone-treatment regimens are crucial. We evaluated the pharmacodynamics of ceftriaxone single-dose therapy (0.125-1 g) against ceftriaxone-susceptible and ceftriaxone-resistant gonococcal strains, based on EUCAST ceftriaxone-resistance breakpoint (MIC > 0.125 mg/L), in our hollow fibre infection model (HFIM) for gonorrhoea.\n\nGonococcal strains examined were WHO F (ceftriaxone-susceptible, MIC < 0.002 mg/L), R (ceftriaxone-resistant, MIC = 0.5 mg/L), Z (ceftriaxone-resistant, MIC = 0.5 mg/L) and X (ceftriaxone-resistant, MIC = 2 mg/L). Dose-range HFIM 7 day experiments simulating ceftriaxone 0.125-1 g single-dose intramuscular regimens were conducted.\n\nCeftriaxone 0.125-1 g single-dose treatments rapidly eradicated WHO F (wild-type ceftriaxone MIC). Ceftriaxone 0.5 and 1 g treatments, based on ceftriaxone human plasma pharmacokinetic parameters, eradicated most ceftriaxone-resistant gonococcal strains (WHO R and Z), but ceftriaxone 0.5 g failed to eradicate WHO X (high-level ceftriaxone resistance). When simulating oropharyngeal gonorrhoea, ceftriaxone 0.5 g failed to eradicate all the ceftriaxone-resistant strains, while ceftriaxone 1 g eradicated WHO R and Z (low-level ceftriaxone resistance) but failed to eradicate WHO X (high-level ceftriaxone resistance). No ceftriaxone-resistant mutants were selected using any ceftriaxone treatments.\n\nCeftriaxone 1 g single-dose intramuscularly cure most of the anogenital and oropharyngeal gonorrhoea cases caused by the currently internationally spreading ceftriaxone-resistant gonococcal strains, which should be further confirmed clinically. A ceftriaxone 1 g dose (\u00b1azithromycin 2 g) should be recommended for first-line empiric gonorrhoea treatment. This will buy countries some time until novel antimicrobials are licensed. Using ceftriaxone 1 g gonorrhoea treatment, the EUCAST ceftriaxone-resistance breakpoint is too low.", "doi": "10.1093/jac/dkae063", "pmid": "38497988", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7630705"}], "notes": [], "created": "2024-11-20T14:55:40.522Z", "modified": "2024-11-20T14:55:41.289Z"}, {"entity": "publication", "iuid": "ce1932e862df4ee98b86f4423285bc25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce1932e862df4ee98b86f4423285bc25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce1932e862df4ee98b86f4423285bc25"}}, "title": "Antimicrobial-resistant Neisseria gonorrhoeae in Europe in 2020 compared with in 2013 and 2018: a retrospective genomic surveillance study.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Cole", "given": "Michelle J", "initials": "MJ"}, {"family": "S\u00e1nchez-Bus\u00f3", "given": "Leonor", "initials": "L"}, {"family": "Day", "given": "Michaela", "initials": "M"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Uthayakumaran", "given": "Thinushaa", "initials": "T"}, {"family": "Abad", "given": "Raquel", "initials": "R"}, {"family": "Bercot", "given": "Beatrice", "initials": "B"}, {"family": "Caugant", "given": "Dominique A", "initials": "DA"}, {"family": "Heuer", "given": "Dagmar", "initials": "D"}, {"family": "Jansen", "given": "Klaus", "initials": "K"}, {"family": "Pleininger", "given": "Sonja", "initials": "S"}, {"family": "Stefanelli", "given": "Paola", "initials": "P"}, {"family": "Aanensen", "given": "David M", "initials": "DM"}, {"family": "Bluemel", "given": "Benjamin", "initials": "B"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "Euro-GASP study group", "given": "", "initials": ""}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "Lancet Microbe", "issn": "2666-5247", "volume": "5", "issue": "5", "pages": "e478-e488", "issn-l": null}, "abstract": "Regular quality-assured whole-genome sequencing linked to antimicrobial resistance (AMR) and patient metadata is imperative to elucidate the shifting gonorrhoea epidemiology, both nationally and internationally. We aimed to examine the gonococcal population in the European Economic Area (EEA) in 2020, elucidate emerging and disappearing gonococcal lineages associated with AMR and patient metadata, compare with 2013 and 2018 whole-genome sequencing data, and explain changes in gonococcal AMR and gonorrhoea epidemiology.\n\nIn this retrospective genomic surveillance study, we analysed consecutive gonococcal isolates that were collected in EEA countries through the European Gonococcal Antimicrobial Surveillance Programme (Euro-GASP) in 2020, and made comparisons with Euro-GASP data from 2013 and 2018. All isolates had linked AMR data (based on minimum inhibitory concentration determination) and patient metadata. We performed whole-genome sequencing and molecular typing and AMR determinants were derived from quality-checked whole-genome sequencing data. Links between genomic lineages, AMR, and patient metadata were examined.\n\n1932 gonococcal isolates collected in 2020 in 21 EEA countries were included. The majority (81\u00b72%, 147 of 181 isolates) of azithromycin resistance (present in 9\u00b74%, 181 of 1932) was explained by the continued expansion of the Neisseria gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) clonal complexes (CCs) 63, 168, and 213 (with mtrD/mtrR promoter mosaic 2) and the novel NG-STAR CC1031 (semi-mosaic mtrD variant 13), associated with men who have sex with men and anorectal or oropharyngeal infections. The declining cefixime resistance (0\u00b75%, nine of 1932) and negligible ceftriaxone resistance (0\u00b71%, one of 1932) was largely because of the progressive disappearance of NG-STAR CC90 (with mosaic penA allele), which was predominant in 2013. No known resistance determinants for novel antimicrobials (zoliflodacin, gepotidacin, and lefamulin) were found.\n\nAzithromycin-resistant clones, mainly with mtrD mosaic or semi-mosaic variants, appear to be stabilising at a relatively high level in the EEA. This mostly low-level azithromycin resistance might threaten the recommended ceftriaxone-azithromycin therapy, but the negligible ceftriaxone resistance is encouraging. The decreased genomic population diversity and increased clonality could be explained in part by the COVID-19 pandemic resulting in lower importation of novel strains into Europe.\n\nEuropean Centre for Disease Prevention and Control and \u00d6rebro University Hospital.", "doi": "10.1016/S2666-5247(23)00370-1", "pmid": "38614111", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2666-5247(23)00370-1"}], "notes": [], "created": "2024-11-20T14:57:28.518Z", "modified": "2024-11-20T14:57:28.630Z"}, {"entity": "publication", "iuid": "efcf93f6fd1f41edace4d1a4948a14f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efcf93f6fd1f41edace4d1a4948a14f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efcf93f6fd1f41edace4d1a4948a14f7"}}, "title": "Complete reference genomes of two ceftriaxone-resistant Neisseria gonorrhoeae strains identified in routine surveillance in Bangkok, Thailand, using Nanopore Q20+ chemistry, VolTRAX V2b, and Illumina sequencing.", "authors": [{"family": "Sangprasert", "given": "Pongsathorn", "initials": "P"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Paopang", "given": "Porntip", "initials": "P"}, {"family": "Girdthep", "given": "Natnaree", "initials": "N"}, {"family": "Lawung", "given": "Ratana", "initials": "R"}, {"family": "Gopinath", "given": "Deyer", "initials": "D"}, {"family": "Thammawijaya", "given": "Panithee", "initials": "P"}, {"family": "Kittiyaowanarn", "given": "Rossaphorn", "initials": "R"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}], "type": "journal article", "published": "2024-03-12", "journal": {"title": "Microbiol Resour Announc", "issn": "2576-098X", "volume": "13", "issue": "3", "pages": "e0123123", "issn-l": "2576-098X"}, "abstract": "Ceftriaxone-resistant Neisseria gonorrhoeae strains, mostly associated with Asia, threaten gonorrhea treatment. We report the reference genomes of two ceftriaxone-resistant isolates found in routine surveillance in Bangkok, Thailand. The genomes belonged to the more antimicrobial-susceptible genomic lineage B, illustrating that both ceftriaxone-resistant strains and the mosaic penA-60.001 ceftriaxone-resistance determinant are spreading.", "doi": "10.1128/mra.01231-23", "pmid": "38299807", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10927671"}], "notes": [], "created": "2024-11-20T14:55:00.961Z", "modified": "2024-11-20T14:55:01.126Z"}, {"entity": "publication", "iuid": "b9e43ba1b111444688f58fa7e5accd34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9e43ba1b111444688f58fa7e5accd34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9e43ba1b111444688f58fa7e5accd34"}}, "title": "The Effects of Fermentable Dietary Fibre Supplementation on Intestinal Barrier Function, Intestinal Microbiome, and Inflammation in Microscopic Colitis Patients\u2014A Randomised, Triple-Blinded, Placebo-Controlled Trial", "authors": [{"family": "Forsg\u00e5rd", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-1905-918X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ede91a29a3ac423abd2225772ca766e8.json"}}, {"family": "K\u00f6nig", "given": "Julia", "initials": "J", "orcid": "0000-0003-0466-1861", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3c5d9204d874be59b433e0baf650755.json"}}, {"family": "Dannenberg", "given": "Katharina", "initials": "K"}, {"family": "Tison", "given": "Jean Luc", "initials": "JL"}, {"family": "Marques", "given": "Tatiana M", "initials": "TM"}, {"family": "Wall", "given": "Rebecca", "initials": "R"}, {"family": "Brummer", "given": "Robert J", "initials": "RJ", "orcid": "0000-0002-0362-0008", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce104fba3d194ef1b762ca3e2488eec0.json"}}], "type": "proceedings-article", "published": "2024-02-04", "journal": {"pages": "233", "issn-l": null}, "abstract": null, "doi": "10.3390/proceedings2023091233", "pmid": null, "labels": {"Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-03-05T09:07:14.430Z", "modified": "2026-03-05T09:07:48.763Z"}, {"entity": "publication", "iuid": "51ce186df53f47eabfec4017dff0ed47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51ce186df53f47eabfec4017dff0ed47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51ce186df53f47eabfec4017dff0ed47"}}, "title": "pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections.", "authors": [{"family": "S\u00e1nchez-Bus\u00f3", "given": "Leonor", "initials": "L"}, {"family": "S\u00e1nchez-Serrano", "given": "Andrea", "initials": "A"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "10", "issue": "1", "issn-l": null}, "abstract": "Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), allow inter-laboratory and inter-study comparability and reproducibility and provide an approximation to the gonococcal population structure. With whole-genome sequencing (WGS), we obtain a substantially higher and more accurate discrimination between strains compared to previous molecular typing schemes. However, WGS remains unavailable or not affordable in many laboratories, and thus bioinformatic tools that allow the integration of data among laboratories with and without access to WGS are imperative for a joint effort to increase our understanding of global pathogen threats. Here, we present pyngoST, a command-line Python tool for fast, simultaneous and accurate sequence typing of N. gonorrhoeae from WGS assemblies. pyngoST integrates MLST, NG-MAST and NG-STAR, and can also designate NG-STAR clonal complexes, NG-MAST genogroups and penA mosaicism, facilitating multiple sequence typing from large WGS assembly collections. Exact and closest matches for existing alleles and sequence types are reported. The implementation of a fast multi-pattern searching algorithm allows pyngoST to be rapid and report results on 500 WGS assemblies in under 1 min. The mapping of typing results on a core genome tree of 2375 gonococcal genomes revealed that NG-STAR is the scheme that best represents the population structure of this pathogen, emphasizing the role of antimicrobial use and antimicrobial resistance as a driver of gonococcal evolution. This article contains data hosted by Microreact.", "doi": "10.1099/mgen.0.001189", "pmid": "38288762", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10868605"}], "notes": [], "created": "2024-11-20T14:53:37.991Z", "modified": "2024-11-20T14:53:38.117Z"}, {"entity": "publication", "iuid": "5e79ab647b394ed68d5db302bddd8bff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e79ab647b394ed68d5db302bddd8bff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e79ab647b394ed68d5db302bddd8bff"}}, "title": "Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium.", "authors": [{"family": "Shaw", "given": "David", "initials": "D"}, {"family": "Abad", "given": "Raquel", "initials": "R"}, {"family": "Amin-Chowdhury", "given": "Zahin", "initials": "Z"}, {"family": "Bautista", "given": "Adriana", "initials": "A"}, {"family": "Bennett", "given": "Desiree", "initials": "D"}, {"family": "Broughton", "given": "Karen", "initials": "K"}, {"family": "Cao", "given": "Bin", "initials": "B"}, {"family": "Casanova", "given": "Carlo", "initials": "C"}, {"family": "Choi", "given": "Eun Hwa", "initials": "EH"}, {"family": "Chu", "given": "Yiu-Wai", "initials": "YW"}, {"family": "Claus", "given": "Heike", "initials": "H"}, {"family": "Coelho", "given": "Juliana", "initials": "J"}, {"family": "Corcoran", "given": "Mary", "initials": "M"}, {"family": "Cottrell", "given": "Simon", "initials": "S"}, {"family": "Cunney", "given": "Robert", "initials": "R"}, {"family": "Cuypers", "given": "Lize", "initials": "L"}, {"family": "Dalby", "given": "Tine", "initials": "T"}, {"family": "Davies", "given": "Heather", "initials": "H"}, {"family": "de Gouveia", "given": "Linda", "initials": "L"}, {"family": "Deghmane", "given": "Ala-Eddine", "initials": "AE"}, {"family": "Demczuk", "given": "Walter", "initials": "W"}, {"family": "Desmet", "given": "Stefanie", "initials": "S"}, {"family": "Domenech", "given": "Mirian", "initials": "M"}, {"family": "Drew", "given": "Richard", "initials": "R"}, {"family": "du Plessis", "given": "Mignon", "initials": "M"}, {"family": "Duarte", "given": "Carolina", "initials": "C"}, {"family": "Erlendsd\u00f3ttir", "given": "Helga", "initials": "H"}, {"family": "Fry", "given": "Norman K", "initials": "NK"}, {"family": "Fuursted", "given": "Kurt", "initials": "K"}, {"family": "Hale", "given": "Thomas", "initials": "T"}, {"family": "Henares", "given": "Desiree", "initials": "D"}, {"family": "Henriques-Normark", "given": "Birgitta", "initials": "B"}, {"family": "Hilty", "given": "Markus", "initials": "M"}, {"family": "Hoffmann", "given": "Steen", "initials": "S"}, {"family": "Humphreys", "given": "Hilary", "initials": "H"}, {"family": "Ip", "given": "Margaret", "initials": "M"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Johnson", "given": "Christopher", "initials": "C"}, {"family": "Johnston", "given": "Jillian", "initials": "J"}, {"family": "Jolley", "given": "Keith A", "initials": "KA"}, {"family": "Kawabata", "given": "An\u00edbal", "initials": "A"}, {"family": "Kozakova", "given": "Jana", "initials": "J"}, {"family": "Kristinsson", "given": "Karl G", "initials": "KG"}, {"family": "Krizova", "given": "Pavla", "initials": "P"}, {"family": "Kuch", "given": "Alicja", "initials": "A"}, {"family": "Ladhani", "given": "Shamez", "initials": "S"}, {"family": "L\u00e2m", "given": "Thi\u00ean-Tr\u00ed", "initials": "TT"}, {"family": "Le\u00f3n", "given": "Mar\u00eda Eugenia", "initials": "ME"}, {"family": "Lindholm", "given": "Laura", "initials": "L"}, {"family": "Litt", "given": "David", "initials": "D"}, {"family": "Maiden", "given": "Martin C J", "initials": "MCJ"}, {"family": "Martin", "given": "Irene", "initials": "I"}, {"family": "Martiny", "given": "Delphine", "initials": "D"}, {"family": "Mattheus", "given": "Wesley", "initials": "W"}, {"family": "McCarthy", "given": "Noel D", "initials": "ND"}, {"family": "Meehan", "given": "Mary", "initials": "M"}, {"family": "Meiring", "given": "Susan", "initials": "S"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Morfeldt", "given": "Eva", "initials": "E"}, {"family": "Morgan", "given": "Julie", "initials": "J"}, {"family": "Mulhall", "given": "Robert", "initials": "R"}, {"family": "Mu\u00f1oz-Almagro", "given": "Carmen", "initials": "C"}, {"family": "Murdoch", "given": "David", "initials": "D"}, {"family": "Murphy", "given": "Joy", "initials": "J"}, {"family": "Musilek", "given": "Martin", "initials": "M"}, {"family": "Mzabi", "given": "Alexandre", "initials": "A"}, {"family": "Novakova", "given": "Ludmila", "initials": "L"}, {"family": "Oftadeh", "given": "Shahin", "initials": "S"}, {"family": "Perez-Arg\u00fcello", "given": "Amaresh", "initials": "A"}, {"family": "P\u00e9rez-V\u00e1zquez", "given": "Maria", "initials": "M"}, {"family": "Perrin", "given": "Monique", "initials": "M"}, {"family": "Perry", "given": "Malorie", "initials": "M"}, {"family": "Prevost", "given": "Benoit", "initials": "B"}, {"family": "Roberts", "given": "Maria", "initials": "M"}, {"family": "Rokney", "given": "Assaf", "initials": "A"}, {"family": "Ron", "given": "Merav", "initials": "M"}, {"family": "Sanabria", "given": "Olga Marina", "initials": "OM"}, {"family": "Scott", "given": "Kevin J", "initials": "KJ"}, {"family": "Sheppard", "given": "Carmen", "initials": "C"}, {"family": "Siira", "given": "Lotta", "initials": "L"}, {"family": "Sintchenko", "given": "Vitali", "initials": "V"}, {"family": "Skoczy\u0144ska", "given": "Anna", "initials": "A"}, {"family": "Sloan", "given": "Monica", "initials": "M"}, {"family": "Slotved", "given": "Hans-Christian", "initials": "HC"}, {"family": "Smith", "given": "Andrew J", "initials": "AJ"}, {"family": "Steens", "given": "Anneke", "initials": "A"}, {"family": "Taha", "given": "Muhamed-Kheir", "initials": "MK"}, {"family": "Toropainen", "given": "Maija", "initials": "M"}, {"family": "Tzanakaki", "given": "Georgina", "initials": "G"}, {"family": "Vainio", "given": "Anni", "initials": "A"}, {"family": "van der Linden", "given": "Mark P G", "initials": "MPG"}, {"family": "van Sorge", "given": "Nina M", "initials": "NM"}, {"family": "Varon", "given": "Emmanuelle", "initials": "E"}, {"family": "Vohrnova", "given": "Sandra", "initials": "S"}, {"family": "von Gottberg", "given": "Anne", "initials": "A"}, {"family": "Yuste", "given": "Jose", "initials": "J"}, {"family": "Zanella", "given": "Rosemeire", "initials": "R"}, {"family": "Zhou", "given": "Fei", "initials": "F"}, {"family": "Brueggemann", "given": "Angela B", "initials": "AB"}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Lancet Digit Health", "issn": "2589-7500", "volume": "5", "issue": "9", "pages": "e582-e593", "issn-l": null}, "abstract": "The Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae. We aimed to analyse the incidence and distribution of these diseases during the first 2 years of the COVID-19 pandemic compared to the 2 years preceding the pandemic.\n\nFor this prospective analysis, laboratories in 30 countries and territories representing five continents submitted surveillance data from Jan 1, 2018, to Jan 2, 2022, to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype or group were examined. Interrupted time-series analyses were done to quantify the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models were used to estimate effect sizes and forecast counterfactual trends by hemisphere.\n\nOverall, 116 841 cases were analysed: 76 481 in 2018-19, before the pandemic, and 40 360 in 2020-21, during the pandemic. During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio 0\u00b747; 95% CI 0\u00b740-0\u00b755), H influenzae (0\u00b751; 0\u00b740-0\u00b766) and N meningitidis (0\u00b726; 0\u00b721-0\u00b731), while no significant changes were observed for S agalactiae (1\u00b702; 0\u00b775-1\u00b740), which is not transmitted via the respiratory route. No major changes in the distribution of cases were observed when stratified by patient age or serotype or group. An estimated 36 289 (95% prediction interval 17 145-55 434) cases of invasive bacterial disease were averted during the first 2 years of the pandemic among IRIS-participating countries and territories.\n\nCOVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae, and N meningitidis during the first 2 years of the pandemic, but cases began to increase in some countries towards the end of 2021 as pandemic restrictions were lifted. These IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to health-care service planning and provision of policies.\n\nWellcome Trust, NIHR Oxford Biomedical Research Centre, Spanish Ministry of Science and Innovation, Korea Disease Control and Prevention Agency, Torsten S\u00f6derberg Foundation, Stockholm County Council, Swedish Research Council, German Federal Ministry of Health, Robert Koch Institute, Pfizer, Merck, and the Greek National Public Health Organization.", "doi": "10.1016/S2589-7500(23)00108-5", "pmid": "37516557", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2589-7500(23)00108-5"}], "notes": [], "created": "2023-09-25T13:40:55.238Z", "modified": "2023-09-25T13:40:55.267Z"}, {"entity": "publication", "iuid": "ac8d82fc6f794a1dafc9287b22f51b50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac8d82fc6f794a1dafc9287b22f51b50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac8d82fc6f794a1dafc9287b22f51b50"}}, "title": "Sustained Transmission of Neisseria gonorrhoeae Strains with High-Level Azithromycin Resistance (MIC \u2265 256 \u03bcg/mL) in Argentina, 2018 to 2022.", "authors": [{"family": "Gianecini", "given": "Ricardo Ariel", "initials": "RA", "orcid": "0000-0002-0663-4456", "researcher": {"href": "https://publications.scilifelab.se/researcher/3770d5b5f9a547d4926df32673f104e4.json"}}, {"family": "Poklepovich", "given": "Tomas", "initials": "T"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Cuenca", "given": "Noelia", "initials": "N"}, {"family": "Scocozza", "given": "Laura", "initials": "L"}, {"family": "Bergese", "given": "Silvina", "initials": "S"}, {"family": "Canigia", "given": "Liliana Fern\u00e1ndez", "initials": "LF"}, {"family": "Vilches", "given": "Viviana", "initials": "V"}, {"family": "Lazzarino Elgart", "given": "Mar\u00eda Julia", "initials": "MJ"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "Campos", "given": "Josefina", "initials": "J"}, {"family": "Galarza", "given": "Patricia", "initials": "P"}], "type": "journal article", "published": "2023-08-17", "journal": {"title": "Microbiol Spectr", "issn": "2165-0497", "volume": "11", "issue": "4", "pages": "e0097023", "issn-l": null}, "abstract": "Azithromycin combined with ceftriaxone is the recommended dual therapy for uncomplicated gonorrhea in many countries. Nevertheless, the increasing prevalence of azithromycin resistance compromises the effectiveness of this treatment strategy. From 2018 to 2022, we collected 13 gonococcal isolates with high-level azithromycin resistance (MIC \u2265 256 \u03bcg/mL) across Argentina. Whole-genome sequencing revealed that these isolates were mainly represented by the internationally spreading Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) genogroup G12302, containing the 23S rRNA A2059G mutation (in all four alleles) together with mosaic mtrD and mtrR promoter 2 loci. This information is important to develop targeted public health policies to control the spread of azithromycin-resistant N. gonorrhoeae in Argentina and internationally. IMPORTANCE Azithromycin resistance in Neisseria gonorrhoeae has been increasing in numerous populations worldwide, which is of concern, as azithromycin is part of the recommended dual treatment in many countries. Here, we report 13 N. gonorrhoeae isolates with high-level azithromycin resistance (MIC \u2265 256 \u03bcg/mL). This study observed that high-level azithromycin-resistant gonococcal strains have shown sustained transmission in Argentina and are related to the successful international clone NG-MAST G12302. Genomic surveillance together with real-time tracing and data-sharing networks will be crucial in controlling the spread of azithromycin resistance in gonococcus.", "doi": "10.1128/spectrum.00970-23", "pmid": "37338369", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10433793"}], "notes": [], "created": "2023-09-25T13:37:47.831Z", "modified": "2023-09-25T13:37:47.880Z"}, {"entity": "publication", "iuid": "b1baf91c64c04ba1a7e8409f28c55fa6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1baf91c64c04ba1a7e8409f28c55fa6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1baf91c64c04ba1a7e8409f28c55fa6"}}, "title": "Genomic surveillance and antimicrobial resistance determinants in Neisseria gonorrhoeae isolates from Uganda, Malawi and South Africa, 2015-20.", "authors": [{"family": "Kakooza", "given": "Francis", "initials": "F"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Matoga", "given": "Mitch", "initials": "M", "orcid": "0000-0002-6542-8193", "researcher": {"href": "https://publications.scilifelab.se/researcher/543841792b5e4b0292e5078e30956bac.json"}}, {"family": "Maseko", "given": "Venessa", "initials": "V"}, {"family": "Lamorde", "given": "Mohammed", "initials": "M"}, {"family": "Krysiak", "given": "Robert", "initials": "R"}, {"family": "Manabe", "given": "Yuka C", "initials": "YC"}, {"family": "Chen", "given": "Jane S", "initials": "JS"}, {"family": "Kularatne", "given": "Ranmini", "initials": "R"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Godreuil", "given": "Sylvain", "initials": "S"}, {"family": "Hoffman", "given": "Irving", "initials": "I"}, {"family": "Bercot", "given": "Beatrice", "initials": "B", "orcid": "0000-0003-1603-3635", "researcher": {"href": "https://publications.scilifelab.se/researcher/d24554fac15140dfa03cbe50b3291501.json"}}, {"family": "Wi", "given": "Teodora", "initials": "T"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}], "type": "journal article", "published": "2023-08-02", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "volume": "78", "issue": "8", "pages": "1982-1991", "issn-l": "0305-7453"}, "abstract": "Global antimicrobial resistance (AMR) surveillance in Neisseria gonorrhoeae is essential. In 2017-18, only five (10.6%) countries in the WHO African Region reported to the WHO Global Gonococcal Antimicrobial Surveillance Programme (WHO GASP). Genomics enhances our understanding of gonococcal populations nationally and internationally, including AMR strain transmission; however, genomic studies from Africa are extremely scarce. We describe the gonococcal genomic lineages/sublineages, including AMR determinants, and baseline genomic diversity among strains in Uganda, Malawi and South Africa, 2015-20, and compare with sequences from Kenya and Burkina Faso.\n\nGonococcal isolates cultured in Uganda (n = 433), Malawi (n = 154) and South Africa (n = 99) in 2015-20 were genome-sequenced. MICs were determined using ETEST. Sequences of isolates from Kenya (n = 159), Burkina Faso (n = 52) and the 2016 WHO reference strains (n = 14) were included in the analysis.\n\nResistance to ciprofloxacin was high in all countries (57.1%-100%). All isolates were susceptible to ceftriaxone, cefixime and spectinomycin, and 99.9% were susceptible to azithromycin. AMR determinants for ciprofloxacin, benzylpenicillin and tetracycline were common, but rare for cephalosporins and azithromycin. Most isolates belonged to the more antimicrobial-susceptible lineage B (n = 780) compared with the AMR lineage A (n = 141), and limited geographical phylogenomic signal was observed.\n\nWe report the first multi-country gonococcal genomic comparison from Africa, which will support the WHO GASP and WHO enhanced GASP (EGASP). The high prevalence of resistance to ciprofloxacin (and empirical use continues), tetracycline and benzylpenicillin, and the emerging resistance determinants for azithromycin show it is imperative to strengthen the gonococcal AMR surveillance, ideally including genomics, in African countries.", "doi": "10.1093/jac/dkad193", "pmid": "37352017", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7205832"}], "notes": [], "created": "2023-09-25T13:37:50.394Z", "modified": "2023-09-25T13:37:50.518Z"}, {"entity": "publication", "iuid": "1a8ae2ebc9314bf38487740c1fe1f64b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a8ae2ebc9314bf38487740c1fe1f64b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a8ae2ebc9314bf38487740c1fe1f64b"}}, "title": "High-level in vitro resistance to gentamicin acquired in a stepwise manner in Neisseria gonorrhoeae.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Holley", "given": "Concerta L", "initials": "CL"}, {"family": "Shafer", "given": "William M", "initials": "WM"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}], "type": "journal article", "published": "2023-07-05", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "volume": "78", "issue": "7", "pages": "1769-1778", "issn-l": "0305-7453"}, "abstract": "Gentamicin is used in several alternative treatments for gonorrhoea. Verified clinical Neisseria gonorrhoeae isolates with gentamicin resistance are mainly lacking and understanding the mechanisms for gonococcal gentamicin resistance is imperative. We selected gentamicin resistance in gonococci in vitro, identified the novel gentamicin-resistance mutations, and examined the biofitness of a high-level gentamicin-resistant mutant.\n\nLow- and high-level gentamicin resistance was selected in WHO X (gentamicin MIC = 4 mg/L) on gentamicin-gradient agar plates. Selected mutants were whole-genome sequenced. Potential gentamicin-resistance fusA mutations were transformed into WT strains to verify their impact on gentamicin MICs. The biofitness of high-level gentamicin-resistant mutants was examined using a competitive assay in a hollow-fibre infection model.\n\nWHO X mutants with gentamicin MICs of up to 128 mg/L were selected. Primarily selected fusA mutations were further investigated, and fusAR635L and fusAM520I + R635L were particularly interesting. Different mutations in fusA and ubiM were found in low-level gentamicin-resistant mutants, while fusAM520I was associated with high-level gentamicin resistance. Protein structure predictions showed that fusAM520I is located in domain IV of the elongation factor-G (EF-G). The high-level gentamicin-resistant WHO X mutant was outcompeted by the gentamicin-susceptible WHO X parental strain, suggesting lower biofitness.\n\nWe describe the first high-level gentamicin-resistant gonococcal isolate (MIC = 128 mg/L), which was selected in vitro through experimental evolution. The most substantial increases of the gentamicin MICs were caused by mutations in fusA (G1560A and G1904T encoding EF-G M520I and R635L, respectively) and ubiM (D186N). The high-level gentamicin-resistant N. gonorrhoeae mutant showed impaired biofitness.", "doi": "10.1093/jac/dkad168", "pmid": "37253051", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7186569"}, {"db": "pmc", "key": "PMC10517096"}], "notes": [], "created": "2023-09-25T13:38:18.708Z", "modified": "2023-09-25T13:38:18.719Z"}, {"entity": "publication", "iuid": "3bd69792bbd0442c9be9d2511bb8e03b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bd69792bbd0442c9be9d2511bb8e03b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bd69792bbd0442c9be9d2511bb8e03b"}}, "title": "Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies.", "authors": [{"family": "Adolfsson", "given": "Emma", "initials": "E"}, {"family": "Kling", "given": "Daniel", "initials": "D"}, {"family": "Gunnarsson", "given": "Cecilia", "initials": "C"}, {"family": "Jonasson", "given": "Jon", "initials": "J"}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}, {"family": "Gr\u00e9en", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Int J Legal Med", "issn": "1437-1596", "issn-l": null, "volume": "137", "issue": "4", "pages": "1215-1234"}, "abstract": "Forensic molecular autopsies have emerged as a tool for medical examiners to establish the cause of death. It is particularly useful in sudden unexplained deaths where the cause of death cannot be determined with a regular medical autopsy. We provide the first study of exome data from formalin-fixed paraffin-embedded samples (FFPE) paired with data from high-quality blood samples in forensic applications. The approach allows exploration of the potential to use FFPE samples for molecular autopsies and identify variants in extensive exome data. We leverage the high uniformity of the hybridization capture approach provided by Twist Bioscience to target the complete exome and sequence the libraries on a NextSeq 550. Our findings suggest that exome sequencing is feasible for 24 out of a total of 35 included FFPE samples. When successful, the coverage across the exome is comparatively high (> 90% covered to 20X) and uniform (fold80 below 1.5). Detailed variant comparisons for matched FFPE and blood samples show high concordance with few false variants (positive predictive value of 0.98 and a sensitivity of 0.97) with no distinct FFPE artefacts. Ultimately, we apply carefully constructed forensic gene panels in a stepwise manner to find genetic variants associated with the clinical phenotype and with relevance to the sudden unexplained death.", "doi": "10.1007/s00414-022-02906-x", "pmid": "36346469", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10247852"}, {"db": "pii", "key": "10.1007/s00414-022-02906-x"}], "notes": [], "created": "2022-11-24T15:29:32.662Z", "modified": "2023-09-25T13:39:37.987Z"}, {"entity": "publication", "iuid": "347f4e6919984e159aa13938756ba62c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/347f4e6919984e159aa13938756ba62c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/347f4e6919984e159aa13938756ba62c"}}, "title": "Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization.", "authors": [{"family": "Koskela von Sydow", "given": "Anita", "initials": "A"}, {"family": "Lindqvist", "given": "Carl M\u00e5rten", "initials": "CM"}, {"family": "Asghar", "given": "Naveed", "initials": "N"}, {"family": "Johansson", "given": "Magnus", "initials": "M"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Stenmark", "given": "Bianca", "initials": "B"}], "type": "journal article", "published": "2023-04-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "6461", "issn-l": "2045-2322"}, "abstract": "The severe acute respiratory syndrome coronavirus 2 (SARS\u2011CoV\u20112) pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14-30 were run using three different protocols: the Twist Bioscience SARS\u2011CoV\u20112 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS\u2011CoV\u20112 sequencing and guidance in selecting suitable methods for various purposes.", "doi": "10.1038/s41598-023-33168-1", "pmid": "37081087", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC10116481"}, {"db": "pii", "key": "10.1038/s41598-023-33168-1"}], "notes": [], "created": "2023-09-25T13:34:58.667Z", "modified": "2023-09-25T13:34:58.672Z"}, {"entity": "publication", "iuid": "d0953f14f20e43729090b5ac6bf8c495", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d0953f14f20e43729090b5ac6bf8c495.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d0953f14f20e43729090b5ac6bf8c495"}}, "title": "Complete Reference Genome Sequence of the Clinical Neisseria gonorrhoeae Strain H035, with Resistance to the Novel Antimicrobial Zoliflodacin, Identified in Japan in 2000.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Ohnishi", "given": "Makoto", "initials": "M"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}], "type": "journal article", "published": "2023-03-16", "journal": {"title": "Microbiol Resour Announc", "issn": "2576-098X", "volume": "12", "issue": "3", "pages": "e0113022", "issn-l": "2576-098X"}, "abstract": "Zoliflodacin is a promising novel antimicrobial in clinical development for treatment of gonorrhea; currently, it is in a global phase 3 randomized controlled clinical trial. High activity against global Neisseria gonorrhoeae strains has been shown. We present the complete reference genome of the zoliflodacin-resistant strain H035, which was identified in Japan in 2000.", "doi": "10.1128/mra.01130-22", "pmid": "36853044", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10019152"}], "notes": [], "created": "2023-09-25T13:37:13.886Z", "modified": "2023-09-25T13:37:13.965Z"}, {"entity": "publication", "iuid": "bcaaf83321f84fa8936858f630cb8e32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bcaaf83321f84fa8936858f630cb8e32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bcaaf83321f84fa8936858f630cb8e32"}}, "title": "Multidrug-resistant Neisseria gonorrhoeae isolate SE690: mosaic penA-60.001 gene causing ceftriaxone resistance internationally has spread to the more antimicrobial-susceptible genomic lineage, Sweden, September 2022.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Vestberg", "given": "Nora", "initials": "N"}, {"family": "S\u00f6dersten", "given": "Wiktor", "initials": "W"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Ohnishi", "given": "Makoto", "initials": "M"}, {"family": "Fang", "given": "Hong", "initials": "H"}, {"family": "Bhattarai", "given": "Karin Haij", "initials": "KH"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "Euro Surveill.", "issn": "1560-7917", "volume": "28", "issue": "10", "issn-l": "1025-496X"}, "abstract": "We report a ceftriaxone-resistant, multidrug-resistant urogenital Neisseria gonorrhoeae in a female sex worker in Sweden, September 2022, who was treated with ceftriaxone 1 g, but did not return for test-of-cure. Whole genome sequencing of isolate SE690 identified MLST ST8130, NG-STAR CC1885 (new NG-STAR ST4859) and mosaic penA-60.001. The latter, causing ceftriaxone resistance in the internationally spreading FC428 clone, has now also spread to the more antimicrobial-susceptible genomic lineage B, showing that strains across the gonococcal phylogeny can develop ceftriaxone resistance.", "doi": "10.2807/1560-7917.ES.2023.28.10.2300125", "pmid": "36892469", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9999460"}], "notes": [], "created": "2023-09-25T13:37:16.399Z", "modified": "2023-09-25T13:37:16.403Z"}, {"entity": "publication", "iuid": "243985731a544d46a9037c1c55b1b648", "links": {"self": {"href": "https://publications.scilifelab.se/publication/243985731a544d46a9037c1c55b1b648.json"}, "display": {"href": "https://publications.scilifelab.se/publication/243985731a544d46a9037c1c55b1b648"}}, "title": "Prevalence and persistence of Neisseria meningitidis carriage in Swedish university students.", "authors": [{"family": "Olof", "given": "S\u00e4ll", "initials": "S", "orcid": "0000-0003-1999-3383", "researcher": {"href": "https://publications.scilifelab.se/researcher/736241f72af44c92b990ac5c8c880824.json"}}, {"family": "Lorraine", "given": "Eriksson", "initials": "E"}, {"family": "Berhane A", "given": "Idosa", "initials": "I"}, {"family": "Alexander", "given": "Persson", "initials": "P"}, {"family": "Anders", "given": "Magnuson", "initials": "M"}, {"family": "Sara", "given": "Thulin Hedberg", "initials": "TH"}, {"family": "Martin", "given": "Sundqvist", "initials": "S"}, {"family": "Per", "given": "Olc\u00e9n", "initials": "O"}, {"family": "Hans", "given": "Fredlund", "initials": "F"}, {"family": "Bianca", "given": "Stenmark", "initials": "S"}, {"family": "Eva", "given": "S\u00e4rndahl", "initials": "S"}, {"family": "Paula", "given": "M\u00f6lling", "initials": "M"}, {"family": "Susanne", "given": "Jacobsson", "initials": "J"}], "type": "journal article", "published": "2023-02-13", "journal": {"title": "Epidemiol. Infect.", "issn": "1469-4409", "volume": "151", "pages": "e25", "issn-l": "0950-2688"}, "abstract": "The bacterium Neisseria meningitidis causes life-threatening disease worldwide, typically with a clinical presentation of sepsis or meningitis, but can be carried asymptomatically as part of the normal human oropharyngeal microbiota. The aim of this study was to examine N. meningitidis carriage with regard to prevalence, risk factors for carriage, distribution of meningococcal lineages and persistence of meningococcal carriage. Throat samples and data from a self-reported questionnaire were obtained from 2744 university students (median age: 23 years) at a university in Sweden on four occasions during a 12-month period. Meningococcal isolates were characterised using whole-genome sequencing. The carriage rate among the students was 9.1% (319/3488; 95% CI 8.2-10.1). Factors associated with higher carriage rate were age \u226422 years, previous tonsillectomy, cigarette smoking, drinking alcohol and attending parties, pubs and clubs. Female gender and sharing a household with children aged 0-9 years were associated with lower carriage. The most frequent genogroups were capsule null locus (cnl), group B and group Y and the most commonly identified clonal complexes (cc) were cc198 and cc23. Persistent carriage with the same meningococcal strain for 12 months was observed in two students. Follow-up times exceeding 12 months are recommended for future studies investigating long-term carriage of N. meningitidis.", "doi": "10.1017/S0950268823000018", "pmid": "36775828", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9990396"}, {"db": "pii", "key": "S0950268823000018"}], "notes": [], "created": "2023-09-25T13:39:07.599Z", "modified": "2023-09-25T13:39:07.616Z"}, {"entity": "publication", "iuid": "610bae916a864515b21c96ba3f19f321", "links": {"self": {"href": "https://publications.scilifelab.se/publication/610bae916a864515b21c96ba3f19f321.json"}, "display": {"href": "https://publications.scilifelab.se/publication/610bae916a864515b21c96ba3f19f321"}}, "title": "GyrB in silico mining in 27 151 global gonococcal genomes from 1928-2021 combined with zoliflodacin in vitro testing of 71 international gonococcal isolates with different GyrB, ParC and ParE substitutions confirms high susceptibility.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "S\u00e1nchez-Bus\u00f3", "given": "Leonor", "initials": "L"}, {"family": "Bazzo", "given": "Maria Luiza", "initials": "ML"}, {"family": "Lan", "given": "Pham Thi", "initials": "PT"}, {"family": "Galarza", "given": "Patricia", "initials": "P"}, {"family": "Ohnishi", "given": "Makoto", "initials": "M"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}], "type": "journal article", "published": "2022-10-29", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "issn-l": "0305-7453"}, "abstract": "Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global threat and novel treatment alternatives are imperative. Herein, susceptibility to the novel antimicrobial zoliflodacin, currently in a global Phase 3 randomized controlled clinical trial for gonorrhoea treatment, was investigated by screening for zoliflodacin GyrB target mutations in publicly available gonococcal genomes and, where feasible, determination of the associated zoliflodacin MIC.\n\nThe European Nucleotide Archive was queried using the search term 'Taxon: 485'. DNA sequences from 27 151 gonococcal isolates were analysed and gyrB, gyrA, parC and parE alleles characterized.\n\nGyrB amino acid alterations were rare (97.0% of isolates had a wild-type GyrB sequence). GyrB V470L (2.7% of isolates) was the most prevalent alteration, followed by S467N (0.12%), N. meningitidis GyrB (0.092%), V470I (0.059%), Q468R/P (0.015%), A466T (0.0074%), L425I + L465I (0.0037%), L465I (0.0037%), G482S (0.0037%) and D429V (0.0037%). Only one isolate (0.0037%) carried a substitution in a resistance-associated GyrB codon (D429V), resulting in a zoliflodacin MIC of 8 mg/L. None of the other detected gyrB, gyrA, parC or parE mutations caused a zoliflodacin MIC outside the wild-type MIC distribution.\n\nThe zoliflodacin target GyrB was highly conserved among 27 151 global gonococcal isolates cultured in 1928-2021. The single zoliflodacin-resistant clinical isolate (0.0037%) was cultured from a male patient in Japan in 2000. Evidently, this strain has not clonally expanded nor has the gyrB zoliflodacin-resistance mutation disseminated through horizontal gene transfer to other strains. Phenotypic and genomic surveillance, including gyrB mutations, of zoliflodacin susceptibility are imperative.", "doi": "10.1093/jac/dkac366", "pmid": "36308328", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6779860"}], "notes": [], "created": "2022-11-08T08:00:26.029Z", "modified": "2022-11-08T08:00:26.053Z"}, {"entity": "publication", "iuid": "9f292637331b4d32979914e0da59f064", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f292637331b4d32979914e0da59f064.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f292637331b4d32979914e0da59f064"}}, "title": "Complete Reference Genome Sequence of the Extensively Drug-Resistant Strain Neisseria gonorrhoeae AT159, with Ceftriaxone Resistance and High-Level Azithromycin Resistance, Using Nanopore Q20+ Chemistry and Illumina Sequencing.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Pleininger", "given": "Sonja", "initials": "S"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Indra", "given": "Alexander", "initials": "A"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}], "type": "journal article", "published": "2022-09-15", "journal": {"title": "Microbiol Resour Announc", "issn": "2576-098X", "volume": "11", "issue": "9", "pages": "e0074422", "issn-l": "2576-098X"}, "abstract": "Extensively drug-resistant Neisseria gonorrhoeae (XDR-NG) strains with resistance to the last remaining first-line treatments (ceftriaxone monotherapy or combined with azithromycin) represent the emerging threat of untreatable gonorrhea. We present the complete reference genome sequence of the XDR-NG strain AT159, with ceftriaxone and high-level azithromycin resistance, from Austria.", "doi": "10.1128/mra.00744-22", "pmid": "36005764", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9476915"}], "notes": [], "created": "2022-11-08T08:00:06.914Z", "modified": "2022-11-08T08:00:06.938Z"}, {"entity": "publication", "iuid": "016fc8c9254a4755a39278991c90e838", "links": {"self": {"href": "https://publications.scilifelab.se/publication/016fc8c9254a4755a39278991c90e838.json"}, "display": {"href": "https://publications.scilifelab.se/publication/016fc8c9254a4755a39278991c90e838"}}, "title": "Genomic surveillance and antimicrobial resistance in Neisseria gonorrhoeae isolates in Bangkok, Thailand in 2018.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Kittiyaowamarn", "given": "Rossaphorn", "initials": "R"}, {"family": "Paopang", "given": "Porntip", "initials": "P"}, {"family": "Sangprasert", "given": "Pongsathorn", "initials": "P"}, {"family": "Sirivongrangson", "given": "Pachara", "initials": "P"}, {"family": "Franceschi", "given": "Francois", "initials": "F"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Wi", "given": "Teodora", "initials": "T"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}], "type": "journal article", "published": "2022-07-28", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "volume": "77", "issue": "8", "pages": "2171-2182", "issn-l": "0305-7453"}, "abstract": "Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a substantial global public health problem. Gonococcal infections acquired in or from Asia represent most verified ceftriaxone treatment failures, and several ceftriaxone-resistant strains have emerged in Asia and subsequently spread globally. Additionally, in Thailand the gonorrhoea incidence remains high. Herein, we investigate the genomic diversity, AMR and AMR determinants in gonococcal isolates cultured in 2018 in Bangkok, Thailand.\n\nGonococcal isolates from males (n = 37) and females (n = 62) were examined by Etest and WGS. AMR determinants and molecular epidemiological STs were characterized. For phylogenomic comparison, raw sequence data were included from China (432 isolates), Japan (n = 270), Vietnam (n = 229), Thailand (n = 3), a global dataset (n = 12 440) and the 2016 WHO reference strains plus WHO Q (n = 15).\n\nIn total, 88, 66 and 41 different NG-MAST, NG-STAR and MLST STs, respectively, and 31 different NG-STAR clonal complexes were found. A remarkably high frequency (88%) of \u03b2-lactamase TEM genes was detected and two novel TEM alleles were found. The phylogenomic analysis divided the isolates into the previously described lineages A and B, with a large proportion of Thai isolates belonging to the novel sublineage A3.\n\nWe describe the first molecular epidemiological study using WGS on gonococcal isolates from Thailand. The high prevalence of AMR and AMR determinants for ciprofloxacin, tetracycline and benzylpenicillin, and some strains belonging to clones/clades especially in sublineage A2 that are prone to develop resistance to extended-spectrum cephalosporins (ESCs) and azithromycin, should prompt continued and strengthened AMR surveillance, including WGS, of N. gonorrhoeae in Thailand.", "doi": "10.1093/jac/dkac158", "pmid": "35542983", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6583486"}], "notes": [], "created": "2022-11-08T07:59:31.161Z", "modified": "2022-11-08T07:59:31.167Z"}, {"entity": "publication", "iuid": "cc45a385a1484a509a44e7c6f527b9f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc45a385a1484a509a44e7c6f527b9f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc45a385a1484a509a44e7c6f527b9f6"}}, "title": "Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches.", "authors": [{"family": "Lagos", "given": "Amaya Campillay", "initials": "AC"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "Dyrkell", "given": "Fredrik", "initials": "F"}, {"family": "Stegger", "given": "Marc", "initials": "M"}, {"family": "S\u00f6derquist", "given": "Bo", "initials": "B"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2022-06-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "10541", "issn-l": "2045-2322"}, "abstract": "Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003-2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0-5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.", "doi": "10.1038/s41598-022-14640-w", "pmid": "35732699", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-022-14640-w"}, {"db": "pmc", "key": "PMC9214674"}], "notes": [], "created": "2022-11-08T07:52:20.067Z", "modified": "2022-11-08T07:55:59.793Z"}, {"entity": "publication", "iuid": "15722d5e7420402cafa53afd0f9b042c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15722d5e7420402cafa53afd0f9b042c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15722d5e7420402cafa53afd0f9b042c"}}, "title": "Extensively drug-resistant (XDR) Neisseria gonorrhoeae causing possible gonorrhoea treatment failure with ceftriaxone plus azithromycin in Austria, April 2022.", "authors": [{"family": "Pleininger", "given": "Sonja", "initials": "S"}, {"family": "Indra", "given": "Alexander", "initials": "A"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Heger", "given": "Florian", "initials": "F"}, {"family": "Schindler", "given": "Stefanie", "initials": "S"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Heidler", "given": "Stefan", "initials": "S"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "Euro Surveill.", "issn": "1560-7917", "volume": "27", "issue": "24", "issn-l": "1025-496X"}, "abstract": "We describe a gonorrhoea case with ceftriaxone plus high-level azithromycin resistance. In April 2022, an Austrian heterosexual male was diagnosed with gonorrhoea after sexual intercourse with a female sex worker in Cambodia. Recommended treatment with ceftriaxone (1 g) plus azithromycin (1.5 g) possibly failed. Worryingly, this is the second strain in an Asian Neisseria gonorrhoeae genomic sublineage including high-level azithromycin-resistant strains that developed ceftriaxone resistance by acquisition of mosaic penA-60.001. Enhanced resistance surveillance and actions are imperative to prevent spread.", "doi": "10.2807/1560-7917.ES.2022.27.24.2200455", "pmid": "35713023", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9205165"}], "notes": [], "created": "2022-11-08T07:59:50.908Z", "modified": "2022-11-08T07:59:50.910Z"}, {"entity": "publication", "iuid": "e695f1c7ca8c49188813b9b55b6ef9c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e695f1c7ca8c49188813b9b55b6ef9c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e695f1c7ca8c49188813b9b55b6ef9c8"}}, "title": "Pharmacodynamic Evaluation of Zoliflodacin Treatment of Neisseria gonorrhoeae Strains With Amino Acid Substitutions in the Zoliflodacin Target GyrB Using a Dynamic Hollow Fiber Infection Model.", "authors": [{"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Oxelbark", "given": "Joakim", "initials": "J"}, {"family": "Franceschi", "given": "Francois", "initials": "F"}, {"family": "Brown", "given": "David", "initials": "D"}, {"family": "Louie", "given": "Arnold", "initials": "A"}, {"family": "Drusano", "given": "George", "initials": "G"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2022-04-14", "journal": {"title": "Front Pharmacol", "issn": "1663-9812", "volume": "13", "pages": "874176", "issn-l": "1663-9812"}, "abstract": "Novel antimicrobials for effective treatment of uncomplicated gonorrhea are essential, and the first-in-class, oral spiropyrimidinetrione DNA gyrase B inhibitor zoliflodacin appears promising. Using our newly developed Hollow Fiber Infection Model (HFIM), the pharmacodynamics of zoliflodacin was examined. A clinical zoliflodacin-susceptible N. gonorrhoeae strain, SE600/18 (harbouring a GyrB S467N amino acid substitution; MIC = 0.25 mg/L), and SE600/18-D429N (zoliflodacin-resistant mutant with a second GyrB substitution, D429N, selected in the HFIM experiments; zoliflodacin MIC = 2 mg/L), were examined. Dose-range experiments, simulating zoliflodacin single oral dose regimens of 0.5, 1, 2, 3, and 4 g, were performed for SE600/18. For SE600/18-D429N, dose-range experiments, simulating zoliflodacin single oral 2, 3, 4, and 6 g doses, and zoliflodacin oral dose-fractionation experiments with 4, 6, and 8 g administered as q12 h were performed. Both strains grew well in the untreated HFIM growth control arms and mostly maintained growth at 1010-1011 CFU/ml for 7 days. Zoliflodacin 3 and 4 g single dose oral regimens successfully eradicated SE600/18 and no growth was recovered during the 7-days experiments. However, the single oral 0.5, 1, and 2 g doses failed to eradicate SE600/18, and zoliflodacin-resistant populations with a GyrB D429N substitution were selected with all these doses. The zoliflodacin-resistant SE600/18-D429N mutant was not eradicated with any examined treatment regimen. However, this in vitro-selected zoliflodacin-resistant mutant was substantially less fit compared to the zoliflodacin-susceptible SE600/18 parent strain. In conclusion, the rare clinical gonococcal strains with GyrB S467N substitution are predisposed to develop zoliflodacin resistance and may require treatment with zoliflodacin \u22653 g. Future development may need to consider the inclusion of diagnostics directed at identifying strains resistant or predisposed to resistance development at a population level and to strengthen surveillance (phenotypically and genetically), and possibly also at the patient level to guide treatment.", "doi": "10.3389/fphar.2022.874176", "pmid": "35496288", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "874176"}, {"db": "pmc", "key": "PMC9046595"}], "notes": [], "created": "2022-11-08T07:58:39.940Z", "modified": "2022-11-08T07:58:39.943Z"}, {"entity": "publication", "iuid": "8a03715623b44226aaab7c6134114480", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a03715623b44226aaab7c6134114480.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a03715623b44226aaab7c6134114480"}}, "title": "First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016.", "authors": [{"family": "Hadad", "given": "Ronza", "initials": "R"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Velicko", "given": "Inga", "initials": "I"}, {"family": "Ohlsson", "given": "Anna-Karin", "initials": "AK"}, {"family": "Lindroth", "given": "Ylva", "initials": "Y"}, {"family": "Ericson", "given": "Eva-Lena", "initials": "EL"}, {"family": "Fredlund", "given": "Hans", "initials": "H"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2022-01-13", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "820998", "issn-l": "1664-302X"}, "abstract": "The increasing transmission and antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health concern with worrying trends of decreasing susceptibility to also the last-line extended-spectrum cephalosporin (ESC) ceftriaxone. A dramatic increase of reported gonorrhea cases has been observed in Sweden from 2016 and onward. The aim of the present study was to comprehensively investigate the genomic epidemiology of all cultured N. gonorrhoeae isolates in Sweden during 2016, in conjunction with phenotypic AMR and clinical and epidemiological data of patients. In total, 1279 isolates were examined. Etest and whole-genome sequencing (WGS) were performed, and epidemiological data obtained from the Public Health Agency of Sweden. Overall, 51.1%, 1.7%, and 1.3% resistance to ciprofloxacin, cefixime, and azithromycin, respectively, was found. No isolates were resistant to ceftriaxone, however, 9.3% of isolates showed a decreased susceptibility to ceftriaxone and 10.5% to cefixime. In total, 44 penA alleles were found of which six were mosaic (n = 92). Using the typing schemes of MLST, NG-MAST, and NG-STAR; 133, 422, and 280 sequence types, respectively, and 93 NG-STAR clonal complexes were found. The phylogenomic analysis revealed two main lineages (A and B) with lineage A divided into two main sublineages (A1 and A2). Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were predominantly found in sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.", "doi": "10.3389/fmicb.2021.820998", "pmid": "35095823", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8794790"}], "notes": [], "created": "2022-11-08T07:53:28.355Z", "modified": "2024-01-16T13:48:37.731Z"}, {"entity": "publication", "iuid": "4340e269615042d6b11ad0cb879aa61c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4340e269615042d6b11ad0cb879aa61c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4340e269615042d6b11ad0cb879aa61c"}}, "title": "Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.", "authors": [{"family": "Beale", "given": "Mathew A", "initials": "MA", "orcid": "0000-0002-4740-3187", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4718563de5a457c8b68b01666a42032.json"}}, {"family": "Marks", "given": "Michael", "initials": "M", "orcid": "0000-0002-7585-4743", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bca83827645402fa72a583d9dde4405.json"}}, {"family": "Cole", "given": "Michelle J", "initials": "MJ"}, {"family": "Lee", "given": "Min-Kuang", "initials": "M"}, {"family": "Pitt", "given": "Rachel", "initials": "R"}, {"family": "Ruis", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0977-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/f34b9e4cd48949bc97daa8634c8b37ed.json"}}, {"family": "Balla", "given": "Eszter", "initials": "E", "orcid": "0000-0001-8519-9511", "researcher": {"href": "https://publications.scilifelab.se/researcher/a53748777c9f4c1eaf01aeca54cc0b63.json"}}, {"family": "Crucitti", "given": "Tania", "initials": "T"}, {"family": "Ewens", "given": "Michael", "initials": "M"}, {"family": "Fern\u00e1ndez-Naval", "given": "Candela", "initials": "C", "orcid": "0000-0002-5584-3537", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0c290084dc44e2c9a9f7fba6e5a5152.json"}}, {"family": "Grankvist", "given": "Anna", "initials": "A"}, {"family": "Guiver", "given": "Malcolm", "initials": "M"}, {"family": "Kenyon", "given": "Chris R", "initials": "CR"}, {"family": "Khairullin", "given": "Rafil", "initials": "R", "orcid": "0000-0001-9879-378X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ea33c6ce38e42a889c22bb24482e9ec.json"}}, {"family": "Kularatne", "given": "Ranmini", "initials": "R"}, {"family": "Arando", "given": "Maider", "initials": "M"}, {"family": "Molini", "given": "Barbara J", "initials": "BJ"}, {"family": "Obukhov", "given": "Andrey", "initials": "A", "orcid": "0000-0001-6320-9651", "researcher": {"href": "https://publications.scilifelab.se/researcher/4087639b65114b7fbac5a42c0f2cdf78.json"}}, {"family": "Page", "given": "Emma E", "initials": "EE"}, {"family": "Petrovay", "given": "Fruzsina", "initials": "F"}, {"family": "Rietmeijer", "given": "Cornelis", "initials": "C"}, {"family": "Rowley", "given": "Dominic", "initials": "D"}, {"family": "Shokoples", "given": "Sandy", "initials": "S"}, {"family": "Smit", "given": "Erasmus", "initials": "E", "orcid": "0000-0003-3286-798X", "researcher": {"href": "https://publications.scilifelab.se/researcher/139d006e299e4da7a3f126bcc267f960.json"}}, {"family": "Sweeney", "given": "Emma L", "initials": "EL"}, {"family": "Taiaroa", "given": "George", "initials": "G"}, {"family": "Vera", "given": "Jaime H", "initials": "JH", "orcid": "0000-0002-1165-0573", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aca5efcaa6e4491a5c46d4d391836dc.json"}}, {"family": "Wenner\u00e5s", "given": "Christine", "initials": "C"}, {"family": "Whiley", "given": "David M", "initials": "DM"}, {"family": "Williamson", "given": "Deborah A", "initials": "DA", "orcid": "0000-0001-7363-6665", "researcher": {"href": "https://publications.scilifelab.se/researcher/04a210096bb744e7b3ccf93d91f6fe5c.json"}}, {"family": "Hughes", "given": "Gwenda", "initials": "G"}, {"family": "Naidu", "given": "Prenilla", "initials": "P", "orcid": "0000-0002-7028-098X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d28ac2b12064e00a93aa799242d77b3.json"}}, {"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "Krajden", "given": "Mel", "initials": "M"}, {"family": "Lukehart", "given": "Sheila A", "initials": "SA", "orcid": "0000-0001-9778-3301", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3dd4beb73f040389b34ba7bc43fa2c9.json"}}, {"family": "Morshed", "given": "Muhammad G", "initials": "MG"}, {"family": "Fifer", "given": "Helen", "initials": "H"}, {"family": "Thomson", "given": "Nicholas R", "initials": "NR", "orcid": "0000-0002-4432-8505", "researcher": {"href": "https://publications.scilifelab.se/researcher/588f230c14f449099755e8540da91e4f.json"}}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Nat Microbiol", "issn": "2058-5276", "issn-l": "2058-5276", "volume": "6", "issue": "12", "pages": "1549-1560"}, "abstract": "Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides.", "doi": "10.1038/s41564-021-01000-z", "pmid": "34819643", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-021-01000-z"}, {"db": "pmc", "key": "PMC8612932"}, {"db": "mid", "key": "EMS137223"}], "notes": [], "created": "2021-12-08T10:02:12.372Z", "modified": "2021-12-08T12:25:29.171Z"}, {"entity": "publication", "iuid": "dc5ca47aafbe40018e69f95890ca6181", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc5ca47aafbe40018e69f95890ca6181.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc5ca47aafbe40018e69f95890ca6181"}}, "title": "Genomic Epidemiology of Azithromycin-Nonsusceptible Neisseria gonorrhoeae, Argentina, 2005-2019.", "authors": [{"family": "Gianecini", "given": "Ricardo Ariel", "initials": "RA"}, {"family": "Poklepovich", "given": "Tomas", "initials": "T"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Cuenca", "given": "Noelia", "initials": "N"}, {"family": "Tuduri", "given": "Ezequiel", "initials": "E"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "Campos", "given": "Josefina", "initials": "J"}, {"family": "Galarza", "given": "Patricia", "initials": "P"}, {"family": "Gonococcal Antimicrobial Susceptibility Surveillance Programme\u2014Argentina1", "given": "", "initials": ""}], "type": "journal article", "published": "2021-08-24", "journal": {"title": "Emerg. Infect. Dis.", "issn": "1080-6059", "issn-l": "1080-6040", "volume": "27", "issue": "9", "pages": "2369-2378"}, "abstract": "Azithromycin-nonsusceptible Neisseria gonorrhoeae strains are an emerging global public health threat. During 2015-2018, the prevalence of azithromycin-nonsusceptible gonococcal infection increased significantly in Argentina. To investigate the genomic epidemiology and resistance mechanisms of these strains, we sequenced 96 nonsusceptible isolates collected in Argentina during 2005-2019. Phylogenomic analysis revealed 2 main clades, which were characterized by a limited geographic distribution, circulating during January 2015-November 2019. These clades included the internationally spreading multilocus sequence types (STs) 1580 and 9363. The ST1580 isolates, which had MICs of 2-4 \u03bcg/mL, had mutations in the 23S rRNA. The ST9363 isolates, which had MICs of 2-4 or >256 \u03bcg/mL, had mutations in the 23S rRNA, a mosaic mtr locus, or both. Identifying the geographic dissemination and characteristics of these predominant clones will guide public health policies to control the spread of azithromycin-nonsusceptible N. gonorrhoeae in Argentina.", "doi": "10.3201/eid2709.204843", "pmid": "34424175", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8386799"}], "notes": [], "created": "2021-12-08T10:02:40.536Z", "modified": "2021-12-08T12:26:38.448Z"}, {"entity": "publication", "iuid": "68cd4d3d0cbf4b449e363e4101fbffbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68cd4d3d0cbf4b449e363e4101fbffbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68cd4d3d0cbf4b449e363e4101fbffbe"}}, "title": "Optimization of droplet digital PCR assays for the type-specific detection and quantification of five HPV genotypes, including additional data on viral loads of nine different HPV genotypes in cervical carcinomas.", "authors": [{"family": "Malin", "given": "Kaliff", "initials": "K"}, {"family": "Louise", "given": "Bohr Mordhorst", "initials": "BM"}, {"family": "Gisela", "given": "Helenius", "initials": "H"}, {"family": "Mats", "given": "Karlsson G", "initials": "KG"}, {"family": "Gabriella", "given": "Lillsunde-Larsson", "initials": "L"}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "J Virol Methods", "issn": "1879-0984", "issn-l": null, "volume": "294", "issue": null, "pages": "114193"}, "abstract": "The droplet digital PCR (ddPCR) system enables high-sensitivity detection of nucleic acids and direct absolute quantification of the targets. The aim of this research was to evaluate this system for viral load (VL) analysis of the human papillomavirus (HPV) genotypes HPV31, 35, 39, 51 and 56 measured in number of viral particles per cell. The sample types used for the optimization of the ddPCR assay were formalin-fixed paraffin-embedded (FFPE) tissues and cervical liquid cytology samples. The presently optimized ddPCR assays, together with assays optimized previously for HPV16, 18, 33 and 45, with the same ddPCR method, were used for the VL analysis of cervical tumor samples. Results published previously on the present study cohort showed that women with a cervical tumor containing multiple high-risk HPV genotypes had a worse prognosis compared to women with single-genotype-infected tumors. The VL was therefore analyzed in this study for the same cohort, as a possible explanatory factor to the prognostic differences. The results of the optimization part of the study, with analysis of VL using ddPCR in DNA from varying sample types (FFPE and liquid cytology samples), showed that each of the five assays demonstrated good inter- and intra-assay means with a coefficient of variation (CV) under 8% and 6% respectably. The cohort results showed no difference in VL between tumors with multiple and single HPV infections, and therefore did most likely not constitute a contributing factor for prognostic differences observed previously. However, tumors from women aged 60 years or older or containing certain HPV genotypes and genotype genera were associated with a higher VL.", "doi": "10.1016/j.jviromet.2021.114193", "pmid": "34022300", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0166-0934(21)00132-4"}], "notes": [], "created": "2021-12-08T10:03:45.212Z", "modified": "2021-12-08T12:27:26.291Z"}, {"entity": "publication", "iuid": "0b7436ca1dce4715b5530cdda02b0380", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b7436ca1dce4715b5530cdda02b0380.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b7436ca1dce4715b5530cdda02b0380"}}, "title": "Liquid biopsy as an option for predictive testing and prognosis in patients with lung cancer.", "authors": [{"family": "Qvick", "given": "Alvida", "initials": "A", "orcid": "0000-0001-6688-947X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4be159eaa724d22982b7b1e24e9ba79.json"}}, {"family": "Stenmark", "given": "Bianca", "initials": "B"}, {"family": "Carlsson", "given": "Jessica", "initials": "J"}, {"family": "Isaksson", "given": "Johan", "initials": "J"}, {"family": "Karlsson", "given": "Christina", "initials": "C"}, {"family": "Helenius", "given": "Gisela", "initials": "G"}], "type": "journal article", "published": "2021-07-03", "journal": {"title": "Mol. Med.", "issn": "1528-3658", "issn-l": "1076-1551", "volume": "27", "issue": "1", "pages": "68"}, "abstract": "The aim of this study was to investigate the clinical value of liquid biopsy as a primary source for variant analysis in lung cancer. In addition, we sought to characterize liquid biopsy variants and to correlate mutational load to clinical data.\r\n\r\nCirculating cell-free DNA was extracted from plasma from patients with lung cancer (n = 60) and controls with benign lung disease (n = 16). Variant analysis was performed using the AVENIO ctDNA Surveillance kit and the results were correlated to clinical and variant analysis data from tumor tissue or cytology retrieved from clinical routine diagnostics.\r\n\r\nThere were significantly more variants detected in lung cancer cases compared to controls (p = 0.011), but no difference between the histological subgroups of lung cancer was found (p = 0.465). Furthermore, significantly more variants were detected in patients with stage IIIb-IV disease compared to patients with stage I-IIIa (median 7 vs 4, p = 0.017). Plasma cfDNA mutational load was significantly associated with overall survival (p = 0.010). The association persisted when adjusted for stage and ECOG performance status (HR: 3.64, 95% CI 1.37-9.67, p = 0.009). Agreement between tumor and plasma samples significantly differed with stage; patients with stage IIIb-IV disease showed agreement in 88.2% of the cases with clinically relevant variants, compared to zero cases in stage I-IIIa (p = 0.004). Furthermore, one variant in EGFR, two in KRAS, and one in BRAF were detected in plasma but not in tumor samples.\r\n\r\nThis study concludes that in the vast majority of advanced NSCLC patients a reliable variant analysis can be performed using liquid biopsy from plasma. Furthermore, we found that the number of variants in plasma is associated with prognosis, possibly indicating a strategy for closer follow up on this crucial patient group.", "doi": "10.1186/s10020-021-00331-1", "pmid": "34217228", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1186/s10020-021-00331-1"}, {"db": "pmc", "key": "PMC8254966"}], "notes": [], "created": "2021-12-08T10:03:42.579Z", "modified": "2021-12-09T13:47:01.175Z"}, {"entity": "publication", "iuid": "d05f35a97a9b44f698145e4df041f8fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d05f35a97a9b44f698145e4df041f8fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d05f35a97a9b44f698145e4df041f8fd"}}, "title": "Technical in-depth comparison of two massive parallel DNA-sequencing methods for formalin-fixed paraffin-embedded tissue from victims of sudden cardiac death.", "authors": [{"family": "Adolfsson", "given": "Emma", "initials": "E"}, {"family": "Qvick", "given": "Alvida", "initials": "A"}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}, {"family": "Kling", "given": "Daniel", "initials": "D"}, {"family": "Gunnarsson", "given": "Cecilia", "initials": "C"}, {"family": "Jonasson", "given": "Jon", "initials": "J"}, {"family": "Gr\u00e9en", "given": "Anna", "initials": "A"}], "type": "comparative study", "published": "2021-07-00", "journal": {"title": "Forensic Sci Int Genet", "issn": "1878-0326", "issn-l": "1872-4973", "volume": "53", "issue": null, "pages": "102522"}, "abstract": "Sudden cardiac death (SCD) is a tragic and traumatic event. SCD is often associated with hereditary genetic disease and in such cases, sequencing of stored formalin fixed paraffin embedded (FFPE) tissue is often crucial in trying to find a causal genetic variant. This study was designed to compare two massive parallel sequencing assays for differences in sensitivity and precision regarding variants related to SCD in FFPE material. From eight cases of SCD where DNA from blood had been sequenced using HaloPlex, corresponding FFPE samples were collected six years later. DNA from FFPE samples were amplified using HaloPlex HS, sequenced on MiSeq, representing the first method, as well as amplified using modified Twist and sequenced on NextSeq, representing the second method. Molecular barcodes were included to distinguish artefacts from true variants. In both approaches, read coverage, uniformity and variant detection were compared using genomic DNA isolated from blood and corresponding FFPE tissue, respectively. In terms of coverage uniformity, Twist performed better than HaloPlex HS for FFPE samples. Despite higher overall coverage, amplicon-based HaloPlex technologies, both for blood and FFPE tissue, suffered from design and/or performance issues resulting in genes lacking complete coverage. Although Twist had considerably lower overall mean coverage, high uniformity resulted in equal or higher fraction of genes covered at \u2265 20X. By comparing variants found in the matched samples in a pre-defined cardiodiagnostic gene panel, HaloPlex HS for FFPE material resulted in high sensitivity, 98.0% (range 96.6-100%), and high precision, 99.9% (range 99.5-100%) for moderately fragmented samples, but suffered from reduced sensitivity (range 74.2-91.1%) in more severely fragmented samples due to lack of coverage. Twist had high sensitivity, 97.8% (range 96.8-98.7%) and high precision, 99.9% (range 99.3-100%) in all analyzed samples, including the severely fragmented samples.", "doi": "10.1016/j.fsigen.2021.102522", "pmid": "33945952", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1872-4973(21)00060-0"}], "notes": [], "created": "2021-12-08T10:03:54.798Z", "modified": "2021-12-08T12:28:03.886Z"}, {"entity": "publication", "iuid": "fec958a0ded040d0acf17e048362749c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fec958a0ded040d0acf17e048362749c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fec958a0ded040d0acf17e048362749c"}}, "title": "Lack of diagnostic-escape mutants of group B streptococcus in Slovenia.", "authors": [{"family": "Perme", "given": "Tina", "initials": "T"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "Jeverica", "given": "Samo", "initials": "S"}], "type": "letter", "published": "2021-07-00", "journal": {"title": "Clin. Microbiol. Infect.", "issn": "1469-0691", "issn-l": "1198-743X", "volume": "27", "issue": "7", "pages": "1054-1055"}, "abstract": null, "doi": "10.1016/j.cmi.2021.01.022", "pmid": "33540114", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1198-743X(21)00049-5"}], "notes": [], "created": "2021-12-08T09:56:29.635Z", "modified": "2021-12-08T12:28:16.478Z"}, {"entity": "publication", "iuid": "de2c4de3f4884b5292e1c5aaf4ff2fed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de2c4de3f4884b5292e1c5aaf4ff2fed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de2c4de3f4884b5292e1c5aaf4ff2fed"}}, "title": "Pharmacodynamic Evaluation of Dosing, Bacterial Kill, and Resistance Suppression for Zoliflodacin Against Neisseria gonorrhoeae in a Dynamic Hollow Fiber Infection Model.", "authors": [{"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Oxelbark", "given": "Joakim", "initials": "J"}, {"family": "Alirol", "given": "Emilie", "initials": "E"}, {"family": "Franceschi", "given": "Francois", "initials": "F"}, {"family": "Gustafsson", "given": "Tomas N", "initials": "TN"}, {"family": "Brown", "given": "David", "initials": "D"}, {"family": "Louie", "given": "Arnold", "initials": "A"}, {"family": "Drusano", "given": "George", "initials": "G"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2021-05-21", "journal": {"title": "Front Pharmacol", "issn": "1663-9812", "issn-l": "1663-9812", "volume": "12", "issue": null, "pages": "682135"}, "abstract": "Antimicrobial resistance in Neisseria gonorrhoeae is threatening the treatment and control of gonorrhea globally, and new treatment options are imperative. Utilizing our dynamic in vitro hollow fiber infection model (HFIM), we examined the pharmacodynamics of the first-in-class spiropyrimidinetrione (DNA gyrase B inhibitors), zoliflodacin, against the N. gonorrhoeae reference strains World Health Organization F (susceptible to all relevant antimicrobials) and WHO X (extensively drug resistant, including resistance to ceftriaxone) over 7 days. Dose-range experiments with both strains, simulating zoliflodacin single oral dose regimens of 0.5-8 g, and dose-fractionation experiments with WHO X, simulating zoliflodacin oral dose therapy with 1-4 g administered as q12 h and q8 h for 24 h, were performed. A kill-rate constant that reflected a rapid bacterial kill during the first 6.5 h for both strains and all zoliflodacin doses was identified. In the dose-range experiments, the zoliflodacin 2-8 g single-dose treatments successfully eradicated both WHO strains, and resistance to zoliflodacin was not observed. However, zoliflodacin as a single 0.5 g dose failed to eradicate both WHO strains, and a 1 g single dose failed to eradicate WHO X in one of two experiments. The zoliflodacin 1 g/day regimen also failed to eradicate WHO X when administered as two and three divided doses given at q12 h and q8 h in the dose-fractionation studies, respectively. All failed regimens selected for zoliflodacin-resistant mutants. In conclusion, these data demonstrate that zoliflodacin should be administered at >2 g as a single oral dose to provide effective killing and resistance suppression of N. gonorrhoeae. Future studies providing pharmacokinetic data for zoliflodacin (and other gonorrhea therapeutic antimicrobials) in urogenital and extragenital infection sites, particularly in the pharynx, and evaluation of gonococcal strains with different gyrB mutations would be important.", "doi": "10.3389/fphar.2021.682135", "pmid": "34093206", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "682135"}, {"db": "pmc", "key": "PMC8175963"}], "notes": [], "created": "2021-12-08T10:02:08.315Z", "modified": "2021-12-08T12:28:43.279Z"}, {"entity": "publication", "iuid": "8725a8ac290a47a4b94cd18445e274de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8725a8ac290a47a4b94cd18445e274de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8725a8ac290a47a4b94cd18445e274de"}}, "title": "Atypical presentation of Neisseria meningitidis serogroup W disease is associated with the introduction of the 2013 strain.", "authors": [{"family": "S\u00e4ll", "given": "Olof", "initials": "O", "orcid": "0000-0003-1999-3383", "researcher": {"href": "https://publications.scilifelab.se/researcher/736241f72af44c92b990ac5c8c880824.json"}}, {"family": "Stenmark", "given": "Bianca", "initials": "B"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Eriksson", "given": "Lorraine", "initials": "L"}, {"family": "Thulin Hedberg", "given": "Sara", "initials": "S"}, {"family": "Hertting", "given": "Olof", "initials": "O"}, {"family": "Fredlund", "given": "Hans", "initials": "H"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2021-04-29", "journal": {"title": "Epidemiol. Infect.", "issn": "1469-4409", "issn-l": "0950-2688", "volume": "149", "issue": null, "pages": "e126"}, "abstract": "Since 2015, the incidence of invasive meningococcal disease (IMD) caused by serogroup W (MenW) has increased in Sweden, due to the introduction of the 2013 strain belonging to clonal complex 11. The aim of this study was to describe the clinical presentation of MenW infections, in particular the 2013 strain, including genetic associations. Medical records of confirmed MenW IMD cases in Sweden during the years 1995-2019 (n = 113) were retrospectively reviewed and the clinical data analysed according to strain. Of all MenW patients, bacteraemia without the focus of infection was seen in 44%, bacteraemic pneumonia in 26%, meningitis in 13% and epiglottitis in 8%, gastrointestinal symptoms in 48% and 4% presented with petechiae. Phylogenetic analysis was used for possible links between genetic relationship and clinical picture. The 2013 strain infections, particularly in one cluster, were associated with more severe disease compared with other MenW infections. The patients with 2013 strain infections (n = 68) were older (52 years vs. 25 years for other strains), presented more often with diarrhoea as an atypical presentation (P = 0.045) and were more frequently admitted for intensive care (P = 0.032). There is a risk that the atypical clinical presentation of MenW infections, with predominantly gastrointestinal or respiratory symptoms rather than neck stiffness or petechiae, may lead to delay in life-saving treatment.", "doi": "10.1017/S0950268821001035", "pmid": "33910672", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0950268821001035"}, {"db": "pmc", "key": "PMC8161285"}], "notes": [], "created": "2021-12-08T10:03:14.690Z", "modified": "2021-12-08T12:29:09.277Z"}, {"entity": "publication", "iuid": "1a0289c420df4fc983dce95076ff7b8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a0289c420df4fc983dce95076ff7b8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a0289c420df4fc983dce95076ff7b8c"}}, "title": "A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch.", "authors": [{"family": "S\u00e1nchez-Bus\u00f3", "given": "Leonor", "initials": "L", "orcid": "0000-0002-4162-0228", "researcher": {"href": "https://publications.scilifelab.se/researcher/a13add576f1f464caa7ac0ceabadcbff.json"}}, {"family": "Yeats", "given": "Corin A", "initials": "CA"}, {"family": "Taylor", "given": "Benjamin", "initials": "B"}, {"family": "Goater", "given": "Richard J", "initials": "RJ"}, {"family": "Underwood", "given": "Anthony", "initials": "A"}, {"family": "Abudahab", "given": "Khalil", "initials": "K"}, {"family": "Argim\u00f3n", "given": "Silvia", "initials": "S"}, {"family": "Ma", "given": "Kevin C", "initials": "KC"}, {"family": "Mortimer", "given": "Tatum D", "initials": "TD"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Cole", "given": "Michelle J", "initials": "MJ"}, {"family": "Grad", "given": "Yonatan H", "initials": "YH"}, {"family": "Martin", "given": "Irene", "initials": "I"}, {"family": "Raphael", "given": "Brian H", "initials": "BH"}, {"family": "Shafer", "given": "William M", "initials": "WM"}, {"family": "Town", "given": "Katy", "initials": "K"}, {"family": "Wi", "given": "Teodora", "initials": "T"}, {"family": "Harris", "given": "Simon R", "initials": "SR"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "Aanensen", "given": "David M", "initials": "DM"}], "type": "journal article", "published": "2021-04-19", "journal": {"title": "Genome Med", "issn": "1756-994X", "issn-l": "1756-994X", "volume": "13", "issue": "1", "pages": "61"}, "abstract": "Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be used to identify new AMR clones and transmission networks and inform the development of point-of-care tests for antimicrobial susceptibility, novel antimicrobials and vaccines. Community-driven tools that provide an easy access to and analysis of genomic and epidemiological data is the way forward for public health surveillance.\r\n\r\nHere we present a public health-focussed scheme for genomic epidemiology of N. gonorrhoeae at Pathogenwatch ( https://pathogen.watch/ngonorrhoeae ). An international advisory group of experts in epidemiology, public health, genetics and genomics of N. gonorrhoeae was convened to inform on the utility of current and future analytics in the platform. We implement backwards compatibility with MLST, NG-MAST and NG-STAR typing schemes as well as an exhaustive library of genetic AMR determinants linked to a genotypic prediction of resistance to eight antibiotics. A collection of over 12,000 N. gonorrhoeae genome sequences from public archives has been quality-checked, assembled and made public together with available metadata for contextualization.\r\n\r\nAMR prediction from genome data revealed specificity values over 99% for azithromycin, ciprofloxacin and ceftriaxone and sensitivity values around 99% for benzylpenicillin and tetracycline. A case study using the Pathogenwatch collection of N. gonorrhoeae public genomes showed the global expansion of an azithromycin-resistant lineage carrying a mosaic mtr over at least the last 10 years, emphasising the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern.\r\n\r\nThe N. gonorrhoeae scheme in Pathogenwatch provides customised bioinformatic pipelines guided by expert opinion that can be adapted to public health agencies and departments with little expertise in bioinformatics and lower-resourced settings with internet connection but limited computational infrastructure. The advisory group will assess and identify ongoing public health needs in the field of gonorrhoea, particularly regarding gonococcal AMR, in order to further enhance utility with modified or new analytic methods.", "doi": "10.1186/s13073-021-00858-2", "pmid": "33875000", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s13073-021-00858-2"}, {"db": "pmc", "key": "PMC8054416"}], "notes": [], "created": "2021-12-08T10:01:03.147Z", "modified": "2021-12-08T12:29:21.543Z"}, {"entity": "publication", "iuid": "39b779b2142a463492160dd0c2f149da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39b779b2142a463492160dd0c2f149da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39b779b2142a463492160dd0c2f149da"}}, "title": "Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex.", "authors": [{"family": "Stenmark", "given": "Bianca", "initials": "B"}, {"family": "Eriksson", "given": "Lorraine", "initials": "L"}, {"family": "Thulin Hedberg", "given": "Sara", "initials": "S"}, {"family": "Anton", "given": "Brian P", "initials": "BP"}, {"family": "Fomenkov", "given": "Alexey", "initials": "A"}, {"family": "Roberts", "given": "Richard J", "initials": "RJ"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2021-03-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "11", "issue": "1", "pages": "6239"}, "abstract": "A rising incidence of meningococcal serogroup W disease has been evident in many countries worldwide. Serogroup W isolates belonging to the sequence type (ST)-11 clonal complex have been associated with atypical symptoms and increased case fatality rates. The continued expansion of this clonal complex in the later part of the 2010s has been largely due to a shift from the so-called original UK strain to the 2013 strain. Here we used single-molecule real-time (SMRT) sequencing to determine the methylomes of the two major serogroup W strains belonging to ST-11 clonal complex. Five methylated motifs were identified in this study, and three of the motifs, namely 5'-GATC-3', 5'-GAAGG-3', 5'-GCGCGC-3', were found in all 13 isolates investigated. The results showed no strain-specific motifs or difference in active restriction modification systems between the two strains. Two phase variable methylases were identified and the enrichment or depletion of the methylation motifs generated by these methylases varied between the two strains. Results from this work give further insight into the low diversity of methylomes in highly related strains and encourage further research to decipher the role of regions with under- or overrepresented methylation motifs.", "doi": "10.1038/s41598-021-85266-7", "pmid": "33737546", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-85266-7"}, {"db": "pmc", "key": "PMC7973814"}], "notes": [], "created": "2021-12-08T10:03:13.416Z", "modified": "2021-12-08T12:29:33.622Z"}, {"entity": "publication", "iuid": "ec32272b561945a2b138e0400fd4b204", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec32272b561945a2b138e0400fd4b204.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec32272b561945a2b138e0400fd4b204"}}, "title": "Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes are consistent with genomic phylogeny and provide simple nomenclature, rapid visualization and antimicrobial resistance (AMR) lineage predictions.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "S\u00e1nchez-Bus\u00f3", "given": "Leonor", "initials": "L"}, {"family": "Cole", "given": "Michelle", "initials": "M"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2021-03-12", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "issn-l": "0305-7453", "volume": "76", "issue": "4", "pages": "940-944"}, "abstract": "Surveillance of antimicrobial resistance (AMR) in Neisseria gonorrhoeae, supported by molecular typing, ideally through genome sequencing, is imperative. We defined N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes (CCs) and validated their usefulness in gonococcal AMR surveillance.\r\n\r\nAll NG-STAR alleles and STs available in the public database (https://ngstar.canada.ca/) were analysed using PHYLOViZ 2.0 to define CCs according to the closest founder ST with \u22655 identical alleles and founding ST with the highest number of links. The published 2013 European gonococcal dataset (n = 1054), the 2016 WHO reference strain panel (n = 14) and N. gonorrhoeae isolates with ceftriaxone resistance determinant penA-60.001 (n = 7) from several countries were used for validation.\r\n\r\nThe majority of the isolates (n = 1063) were designated to 71 CCs. The most common CC was CC90 (n = 194), followed by CC63 (n = 166), CC139 (n = 73), CC158 (n = 73) and CC127 (n = 62). CC90 included isolates belonging to the internationally spread MDR clone N. gonorrhoeae Multi-Antigen Sequence Typing (NG-MAST) G1407 (predominantly MLST ST1901). The ceftriaxone-resistant isolates with penA-60.001 (n = 7) belonged to CC73 or STs linking between CC90 and CC73 (ST233 and ST1133). Phylogenomic analysis revealed that NG-STAR CCs more appropriately correlated to phylogenomic AMR clusters compared with MLST STs, NG-MAST STs, NG-MAST genogroups and NG-STAR STs.\r\n\r\nNG-STAR CCs: are consistent with the gonococcal genome phylogeny; allow rapid visualizations with limited computational requirements; provide a simple, reproducible and portable nomenclature (for WGS and conventional Sanger sequencing data); and predict AMR lineages. Phenotypic AMR surveillance, supplemented with WGS, is imperative and NG-STAR CCs can effectively support this.", "doi": "10.1093/jac/dkaa552", "pmid": "33411920", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "6067623"}], "notes": [], "created": "2021-12-08T09:59:48.015Z", "modified": "2021-12-08T12:29:49.285Z"}, {"entity": "publication", "iuid": "b3a44e9303844b0e8fdb8f107fe28a22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b3a44e9303844b0e8fdb8f107fe28a22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b3a44e9303844b0e8fdb8f107fe28a22"}}, "title": "Genomic epidemiology of Neisseria gonorrhoeae elucidating the gonococcal antimicrobial resistance and lineages/sublineages across Brazil, 2015-16.", "authors": [{"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Bazzo", "given": "Maria Luiza", "initials": "ML"}, {"family": "Golfetto", "given": "Lisl\u00e9ia", "initials": "L"}, {"family": "Gaspar", "given": "Pamela Cristina", "initials": "PC"}, {"family": "Sch\u00f6rner", "given": "Marcos Andr\u00e9", "initials": "MA"}, {"family": "Schwartz Benzaken", "given": "Adele", "initials": "A"}, {"family": "Ramos", "given": "Mauro Cunha", "initials": "MC"}, {"family": "Ferreira", "given": "William Antunes", "initials": "WA"}, {"family": "Alonso Neto", "given": "Jos\u00e9 Boullosa", "initials": "JB"}, {"family": "Mendes Pereira", "given": "Gerson Fernando", "initials": "GF"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}, {"family": "Brazilian-GASP Network", "given": "", "initials": ""}], "type": "journal article", "published": "2020-11-01", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "issn-l": "0305-7453", "volume": "75", "issue": "11", "pages": "3163-3172"}, "abstract": "Neisseria gonorrhoeae antimicrobial resistance (AMR) surveillance is imperative internationally, but only eight (22.9%) countries in the WHO Region of the Americas reported complete AMR data to the WHO Global Gonococcal Antimicrobial Surveillance Program (WHO GASP) in 2016. Genomic studies are ideal for enhanced understanding of gonococcal populations, including the spread of AMR strains. To elucidate the circulating gonococcal lineages/sublineages, including their AMR determinants, and the baseline genomic diversity among gonococcal strains in Brazil, we conducted WGS on 548 isolates obtained in 2015-16 across all five macroregions in Brazil.\r\n\r\nA total of 548 gonococcal isolates cultured across Brazil in 2015-16 were genome sequenced. AMR was determined using agar dilution and/or Etest. Genome sequences of isolates from Argentina (n = 158) and the 2016 WHO reference strains (n = 14) were included in the analysis.\r\n\r\nWe found 302, 68 and 214 different NG-MAST, MLST and NG-STAR STs, respectively. The phylogenomic analysis identified one main antimicrobial-susceptible lineage and one AMR lineage, which was divided into two sublineages with different AMR profiles. Determination of NG-STAR networks of clonal complexes was shown as a new and valuable molecular epidemiological analysis. Several novel mosaic mtrD (and mtrR and mtrE) variants associated with azithromycin resistance were identified.\r\n\r\nWe describe the first genomic baseline data to support the Brazilian GASP. The high prevalence of resistance to ciprofloxacin, tetracycline and benzylpenicillin, and the high number of isolates with mosaic penA and azithromycin resistance mutations, should prompt continued and strengthened AMR surveillance, including WGS, of N. gonorrhoeae in Brazil.", "doi": "10.1093/jac/dkaa318", "pmid": "32785692", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "5891806"}], "notes": [], "created": "2020-11-27T14:02:26.079Z", "modified": "2021-12-08T12:30:15.933Z"}, {"entity": "publication", "iuid": "b8a2612630214776a9f44ac10c70474a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8a2612630214776a9f44ac10c70474a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8a2612630214776a9f44ac10c70474a"}}, "title": "Geographically widespread invasive meningococcal disease caused by a ciprofloxacin resistant non-groupable strain of the ST-175 clonal complex.", "authors": [{"family": "Willerton", "given": "Laura", "initials": "L"}, {"family": "Lucidarme", "given": "Jay", "initials": "J"}, {"family": "Campbell", "given": "Helen", "initials": "H"}, {"family": "Caugant", "given": "Dominique A", "initials": "DA"}, {"family": "Claus", "given": "Heike", "initials": "H"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Ladhani", "given": "Shamez N", "initials": "SN"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Neri", "given": "Arianna", "initials": "A"}, {"family": "Stefanelli", "given": "Paola", "initials": "P"}, {"family": "Taha", "given": "Muhamed-Kheir", "initials": "M"}, {"family": "Vogel", "given": "Ulrich", "initials": "U"}, {"family": "Borrow", "given": "Ray", "initials": "R"}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "J Infect", "issn": "1532-2742", "issn-l": null, "volume": "81", "issue": "4", "pages": "575-584"}, "abstract": "Invasive meningococcal disease (IMD) caused by non-serogroupable (NG) strains mainly affects immunocompromised individuals. Reduced susceptibility to penicillin in meningococci is increasing in Europe but ciprofloxacin resistance remains rare. In 2019, three travel-related meningococcal disease cases caused by a ciprofloxacin-resistant NG strain were identified in England, leading Germany to report four additional IMD cases (2016 to 2019). We describe these and newly identified cases and characterise the strain responsible.\r\n\r\nCases were identified as part of national surveillance and by analysing available genomes using PubMLST tools.\r\n\r\nOf the cases identified in England in 2019, two geographically distinct cases developed conjunctivitis after returning from Mecca (Kingdom of Saudi Arabia) and a third linked case presented with IMD. Of the four cases from Germany, three occurred in asylum seekers - two familial and a further geographically distinct case. Further IMD cases were identified in Italy (n = 2; 2017-2018), Sweden (n = 1; 2016) and England (n = 1; 2015). A single ST-175 clonal complex (cc175) strain with genosubtype P1.22-11,15-25 was responsible. Decreased susceptibility to penicillin was widespread with three ciprofloxacin resistant subclusters. Constituent isolates were potentially covered by subcapsular vaccines.\r\n\r\nThis disease associated NG cc175 strain exhibits resistance to antibiotics commonly used to prevent IMD but is potentially covered by subcapsular (meningococcal B) vaccines.", "doi": "10.1016/j.jinf.2020.08.030", "pmid": "32858070", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0163-4453(20)30570-3"}], "notes": [], "created": "2020-11-27T13:58:06.441Z", "modified": "2021-12-08T12:30:28.063Z"}, {"entity": "publication", "iuid": "f1ad03c52d0f4de4a17266b615dc643c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1ad03c52d0f4de4a17266b615dc643c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1ad03c52d0f4de4a17266b615dc643c"}}, "title": "Genomic epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates from Ukraine, 2013-2018.", "authors": [{"family": "Boiko", "given": "Iryna", "initials": "I"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Krynytska", "given": "Inna", "initials": "I"}, {"family": "Frankenberg", "given": "Arkadii", "initials": "A"}, {"family": "Shevchenko", "given": "Tetiana", "initials": "T"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "APMIS", "issn": "1600-0463", "issn-l": "0903-4641", "volume": "128", "issue": "7", "pages": "465-475"}, "abstract": "Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major health threat compromising the gonorrhoea treatment globally. AMR surveillance including whole genome sequencing (WGS)-based epidemiology provides ideal resolution to identify and describe AMR gonococcal clones, AMR determinants and populations, which can inform management guidelines and antimicrobial stewardship policies. Our aims were to, for the first time, elucidate the WGS-based epidemiology and characterize AMR determinants of gonococcal strains spreading in Ukraine, 2013-2018. Gonococcal isolates (n = 150) from Ternopil and Dnipro, Ukraine (2013-2018), were subjected to AMR testing (Etest) for eight antimicrobials and WGS. Overall, 11.3% of isolates were resistant to ciprofloxacin, 6.0% to tetracycline, and 0.7% to benzylpenicillin. No isolates were resistant to azithromycin, spectinomycin, ceftriaxone, or cefixime, but one isolate was bordering resistance to both cephalosporins. Twenty-five MLST STs, 50 NG-MAST STs, and 34 NG-STAR types were identified. The phylogenomic analysis revealed six main clusters, mostly associated with the internationally described multidrug-susceptible gonococcal lineage. Resistance to ciprofloxacin was associated with GyrA S91F and ParC S87R mutations; tetracyclines with rpsJ V57M and tetM; penicillins with mosaic penA-34.001 and \u03b2-lactamase; mtrR; PorB1b G101D, and PBP1 L421P mutations. One isolate of the multidrug-resistant NG-MAST ST1407, MLST ST1901 was found, which was bordering resistance to ceftriaxone and cefixime. The antimicrobial susceptibility of gonococcal strains spreading in Ternopil and Dnipro, Ukraine, in 2013-2018 was surprisingly high. Continued and expanded gonococcal AMR surveillance, ideally including WGS, in Ukraine is essential. This could inform action plans and public health policies to control the spread of AMR gonococcal strains in Ukraine.", "doi": "10.1111/apm.13060", "pmid": "32441045", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-11-27T14:03:21.732Z", "modified": "2021-12-08T12:30:39.145Z"}, {"entity": "publication", "iuid": "9818497461264e91949fb2485a056d4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9818497461264e91949fb2485a056d4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9818497461264e91949fb2485a056d4b"}}, "title": "High genomic-based predicted strain coverage among invasive meningococcal isolates when combining Bexsero and Trumenba vaccines.", "authors": [{"family": "S\u00e4ll", "given": "Olof", "initials": "O"}, {"family": "Olofsson", "given": "Emma", "initials": "E"}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}], "type": "journal article", "published": "2020-06-09", "journal": {"title": "Vaccine", "issn": "1873-2518", "volume": "38", "issue": "28", "pages": "4374-4378", "issn-l": null}, "abstract": "Two protein-based vaccines (Bexsero\u00ae and Trumenba\u00ae) are licensed for invasive meningococcal disease (IMD) caused by Neisseria meningitidis serogroup B (MenB). The aim of this study was to evaluate the possible protection of these vaccines, based on the genomic profiles of IMD isolates. All invasive meningococcal isolates in Sweden during 2014-2018 (n = 242) were analyzed with the vaccine coverage scheme available at the PubMLST database. The overall estimated genomic strain coverage among the Swedish invasive meningococcal isolates was 55% for Bexsero and 57% for Trumenba (p = 0.714). The estimated serogroup-specific coverage for Bexsero respectively Trumenba was: MenB; 67% and 90% (p < 0.05), MenW; 93% and 4% (p < 0.05), MenC; 87% and 30% (p < 0.05) and MenY; 1% and 96% (p < 0.05). With the combination of the two vaccines, the potential genomic-based strain coverage was 95%, indicating a possible additive effect of combining Bexsero and Trumenba, which, however, needs to be confirmed by analysis of phenotypic antigen expression.", "doi": "10.1016/j.vaccine.2020.04.074", "pmid": "32414653", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0264-410X(20)30591-0"}], "notes": [], "created": "2020-11-27T14:08:27.564Z", "modified": "2021-12-08T12:30:48.656Z"}, {"entity": "publication", "iuid": "d5a875da3329432092ef2545fdf51dfd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5a875da3329432092ef2545fdf51dfd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5a875da3329432092ef2545fdf51dfd"}}, "title": "Genomic analysis and antimicrobial resistance of Neisseria gonorrhoeae isolates from Vietnam in 2011 and 2015-16.", "authors": [{"family": "Lan", "given": "Pham Thi", "initials": "PT"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Ringlander", "given": "Johan", "initials": "J"}, {"family": "Van Hung", "given": "Le", "initials": "L"}, {"family": "Van Thuong", "given": "Nguyen", "initials": "N"}, {"family": "Unemo", "given": "Magnus", "initials": "M", "orcid": "0000-0003-1710-2081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f1494bae3b140a3a8761092e420a5de.json"}}], "type": "journal article", "published": "2020-06-01", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "issn-l": "0305-7453", "volume": "75", "issue": "6", "pages": "1432-1438"}, "abstract": "Antimicrobial resistance (AMR) in Neisseria gonorrhoeae, compromising gonorrhoea treatment, is a threat to reproductive health globally. South-East and East Asia have been major sources of emergence and subsequent international spread of AMR gonococcal strains during recent decades. We investigated gonococcal isolates from 2011 and 2015-16 in Vietnam using AMR testing, WGS and detection of AMR determinants.\r\n\r\nTwo hundred and twenty-nine gonococcal isolates cultured in 2015-16 (n = 121) and 2011 (n = 108) in Vietnam were examined. AMR testing was performed using Etest and WGS with Illumina MiSeq.\r\n\r\nResistance among the 2015-16 isolates was as follows: ciprofloxacin, 100%; tetracycline, 79%; benzylpenicillin, 50%; cefixime, 15%; ceftriaxone, 1%; spectinomycin, 0%; and 5% were non-WT to azithromycin. Eighteen (15%) isolates were MDR. The MIC range for gentamicin was 2-8 mg/L. Among the 2015-16 isolates, 27% (n = 33) contained a mosaic penA allele, while no isolates had a mosaic penA allele in 2011. Phylogenomic analysis revealed introduction after 2011 of two mosaic penA-containing clones (penA-10.001 and penA-34.001), which were related to cefixime-resistant strains spreading in Japan and Europe, and a minor clade (eight isolates) relatively similar to the XDR strain WHO Q.\r\n\r\nFrom 2011 to 2015-16, resistance in gonococci from Vietnam increased to all currently and previously used antimicrobials except ceftriaxone, spectinomycin and tetracycline. Two mosaic penA-containing clones were introduced after 2011, explaining the increased cefixime resistance. Significantly increased AMR surveillance, antimicrobial stewardship and use of WGS for molecular epidemiology and AMR prediction for gonococcal isolates in Vietnam and other Asian countries are crucial.", "doi": "10.1093/jac/dkaa040", "pmid": "32068837", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5740025"}, {"db": "pmc", "key": "PMC7382555"}], "notes": [], "created": "2020-11-27T14:03:55.802Z", "modified": "2021-12-08T12:31:02.326Z"}, {"entity": "publication", "iuid": "9f90d87b1407413a83ea24c025ed5e80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f90d87b1407413a83ea24c025ed5e80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f90d87b1407413a83ea24c025ed5e80"}}, "title": "Staphylococcus argenteus as an etiological agent of prosthetic hip joint infection: a case presentation.", "authors": [{"family": "S\u00f6derquist", "given": "Bo", "initials": "B"}, {"family": "Wildeman", "given": "Peter", "initials": "P"}, {"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}, {"family": "Stegger", "given": "Marc", "initials": "M"}], "type": "journal article", "published": "2020-05-25", "journal": {"title": "J Bone Jt Infect", "issn": "2206-3552", "issn-l": null, "volume": "5", "issue": "4", "pages": "172-175"}, "abstract": "This report presents a case of prosthetic hip infection caused by Staphylococcus argenteus, a potentially overlooked etiology of prosthetic joint infections (PJIs). Whole-genome sequencing showed that the S. argenteus isolate was an ST2250 and clustered within other CC2250 isolates, the largest clonal group of S. argenteus. This sequence type is prevalent and may be associated with invasive infections. The present isolate was phenotypically fully susceptible to all tested antimicrobial agents and genome analysis did not detect any resistance genes, nor were any staphylococcal cassette chromosome residues detected. Despite initial appropriate management with debridement and biofilm-active antibiotics, the outcome was unfavorable with recurrence and a persistent infection treated with suppressive antibiotics. Regarding the repertoire of genomic traits for virulence in S. argenteus, PJIs caused by this bacterium should be treated accordingly as Staphylococcus aureus PJIs.", "doi": "10.7150/jbji.44848", "pmid": "32670770", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "jbjiv05p0172"}, {"db": "pmc", "key": "PMC7358968"}], "notes": [], "created": "2020-11-27T13:57:12.857Z", "modified": "2021-12-08T12:31:15.365Z"}, {"entity": "publication", "iuid": "641969a706f64f77a960eb7a359de6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/641969a706f64f77a960eb7a359de6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/641969a706f64f77a960eb7a359de6c4"}}, "title": "Difference in virulence between Neisseria meningitidis serogroups W and Y in transgenic mice.", "authors": [{"family": "Eriksson", "given": "Lorraine", "initials": "L"}, {"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}, {"family": "Deghmane", "given": "Ala-Eddine", "initials": "A"}, {"family": "Thulin Hedberg", "given": "Sara", "initials": "S"}, {"family": "S\u00e4ll", "given": "Olof", "initials": "O"}, {"family": "Fredlund", "given": "Hans", "initials": "H"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Taha", "given": "Muhamed-Kheir", "initials": "M"}], "type": "comparative study", "published": "2020-04-15", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "issn-l": "1471-2180", "volume": "20", "issue": "1", "pages": "92"}, "abstract": "Neisseria meningitidis serogroups W and Y are the most common serogroups causing invasive meningococcal disease in Sweden. The majority of cases are caused by the serogroup W UK 2013 strain of clonal complex (cc) 11, and subtype 1 of the serogroup Y, YI strain of cc23. In this study, virulence factors of several lineages within cc11 and cc23 were investigated in transgenic BALB/c mice expressing human transferrin. Transgenic mice were infected intraperitoneally with serogroup W and Y isolates. Levels of bacteria and the proinflammatory cytokine CXCL1 were determined in blood collected 3 h and 24 h post-infection. Apoptosis was investigated in immune cells from peritoneal washes of infected mice. Adhesion and induction of apoptosis in human epithelial cells were also scored.\r\n\r\nThe levels of bacteraemia, CXCL1, and apoptosis were higher in serogroup W infected mice than in serogroup Y infected mice. Serogroup W isolates also induced higher levels of apoptosis and adhesion in human epithelial cells. No significant differences were observed between different lineages within cc11 and cc23.\r\n\r\nN. meningitidis Serogroup W displayed a higher virulence in vivo in transgenic mice, compared to serogroup Y. This was reflected by higher bacteremia, proinflammatory activity, and ability to induce apoptosis in mouse immune cells and human epithelial cells.", "doi": "10.1186/s12866-020-01760-4", "pmid": "32295520", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-020-01760-4"}, {"db": "pmc", "key": "PMC7160935"}], "notes": [], "created": "2020-11-27T13:57:27.487Z", "modified": "2021-12-08T12:31:42.333Z"}, {"entity": "publication", "iuid": "f96a5077385748b2a9baf3c7ce7dc352", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f96a5077385748b2a9baf3c7ce7dc352.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f96a5077385748b2a9baf3c7ce7dc352"}}, "title": "Genomic characterization and outcome of prosthetic joint infections caused by Staphylococcus aureus.", "authors": [{"family": "Wildeman", "given": "Peter", "initials": "P"}, {"family": "Tevell", "given": "Staffan", "initials": "S"}, {"family": "Eriksson", "given": "Carl", "initials": "C"}, {"family": "Lagos", "given": "Amaya Campillay", "initials": "AC"}, {"family": "S\u00f6derquist", "given": "Bo", "initials": "B"}, {"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}], "type": "journal article", "published": "2020-04-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "5938"}, "abstract": "Staphylococcus aureus is a commensal colonizing the skin and mucous membranes. It can also act as a pathogen, and is the most common microorganism isolated from prosthetic joint infections (PJIs). The aim of this study was to explore the genomic relatedness between commensal and PJI S. aureus strains as well as microbial traits and host-related risk factors for treatment failure. Whole-genome sequencing (WGS) was performed on S. aureus isolates obtained from PJIs (n = 100) and control isolates from nares (n = 101). Corresponding clinical data for the PJI patients were extracted from medical records. No PJI-specific clusters were found in the WGS phylogeny, and the distribution of the various clonal complexes and prevalence of virulence genes among isolates from PJIs and nares was almost equal. Isolates from patients with treatment success and failure were genetically very similar, while the presence of an antibiotic-resistant phenotype and the use of non-biofilm-active antimicrobial treatment were both associated with failure.In conclusion, commensal and PJI isolates of S. aureus in arthroplasty patients were genetically indistinguishable, suggesting that commensal S. aureus clones are capable of causing PJIs. Furthermore, no association between genetic traits and outcome could be demonstrated, stressing the importance of patient-related factors in the treatment of S. aureus PJIs.", "doi": "10.1038/s41598-020-62751-z", "pmid": "32246045", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-62751-z"}, {"db": "pmc", "key": "PMC7125104"}], "notes": [], "created": "2020-11-27T13:56:08.647Z", "modified": "2021-12-08T12:31:56.319Z"}, {"entity": "publication", "iuid": "6cb7046ed9eb44dfbf9eb8ac97264bef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cb7046ed9eb44dfbf9eb8ac97264bef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cb7046ed9eb44dfbf9eb8ac97264bef"}}, "title": "Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease.", "authors": [{"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}, {"family": "Harrison", "given": "Odile B", "initials": "OB"}, {"family": "Eriksson", "given": "Lorraine", "initials": "L"}, {"family": "Anton", "given": "Brian P", "initials": "BP"}, {"family": "Fomenkov", "given": "Alexey", "initials": "A"}, {"family": "Roberts", "given": "Richard J", "initials": "RJ"}, {"family": "Tooming-Klunderud", "given": "Ave", "initials": "A"}, {"family": "Bratcher", "given": "Holly B", "initials": "HB"}, {"family": "Bray", "given": "James E", "initials": "JE"}, {"family": "Thulin-Hedberg", "given": "Sara", "initials": "S"}, {"family": "Maiden", "given": "Martin C J", "initials": "MCJ"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}], "type": "journal article", "published": "2020-02-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "3644"}, "abstract": "Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis emerged in Europe during the 2000s. Draft genomes of serogroup Y isolates in Sweden revealed that although the population structure of these isolates was similar to other serogroup Y isolates internationally, a distinct strain (YI) and more specifically a sublineage (1) of this strain was responsible for the increase of serogroup Y IMD in Sweden. We performed single molecule real-time (SMRT) sequencing on eight serogroup Y isolates from different sublineages to unravel the genetic and epigenetic factors delineating them, in order to understand the serogroup Y emergence. Extensive comparisons between the serogroup Y sublineages of all coding sequences, complex genomic regions, intergenic regions, and methylation motifs revealed small point mutations in genes mainly encoding hypothetical and metabolic proteins, and non-synonymous variants in genes involved in adhesion, iron acquisition, and endotoxin production. The methylation motif CACNNNNNTAC was only found in isolates of sublineage 2. Only seven genes were putatively differentially expressed, and another two genes encoding hypothetical proteins were only present in sublineage 2. These data suggest that the serogroup Y IMD increase in Sweden was most probably due to small changes in genes important for colonization and transmission.", "doi": "10.1038/s41598-020-59509-y", "pmid": "32108139", "labels": {"Clinical Genomics \u00d6rebro": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-59509-y"}, {"db": "pmc", "key": "PMC7046676"}], "notes": [], "created": "2020-11-27T13:55:39.557Z", "modified": "2021-12-08T12:32:12.168Z"}, {"entity": "publication", "iuid": "ce7f83d0c1e745a3bae613b39a81b281", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce7f83d0c1e745a3bae613b39a81b281.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce7f83d0c1e745a3bae613b39a81b281"}}, "title": "Comparative distribution of extended-spectrum beta-lactamase-producing Escherichia coli from urine infections and environmental waters.", "authors": [{"family": "Fagerstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0002-6276-8811", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8dc177a668c4256be2893eb98abddd4.json"}}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Khan", "given": "Faisal Ahmad", "initials": "FA"}, {"family": "Sundqvist", "given": "Martin", "initials": "M"}, {"family": "Jass", "given": "Jana", "initials": "J"}, {"family": "S\u00f6derquist", "given": "Bo", "initials": "B"}], "type": "comparative study", "published": "2019-11-07", "journal": {"volume": "14", "issn": "1932-6203", "issue": "11", "pages": "e0224861", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli have been reported in natural environments, and may be released through wastewater. In this study, the genetic relationship between ESBL-producing E. coli collected from patient urine samples (n = 45, both hospitalized patients and out-patients) and from environmental water (n = 82, from five locations), during the same time period, was investigated. Three independent water samples were collected from the municipal wastewater treatment plant, both incoming water and treated effluent water; the receiving river and lake; and a bird sanctuary near the lake, on two different occasions. The water was filtered and cultured on selective chromID ESBL agar plates in order to detect and isolate ESBL-producing E. coli. Illumina whole genome sequencing was performed on all bacterial isolates (n = 127). Phylogenetic group B2 was more common among the clinical isolates than the environmental isolates (44.4% vs. 17.1%, p < 0.01) due to a significantly higher prevalence of sequence type (ST) 131 (33.3% vs. 13.4%, p < 0.01). ST131 was, however, one of the most prevalent STs among the environmental isolates. There was no significant difference in diversity between the clinical isolates (DI 0.872 (0.790-0.953)) and the environmental isolates (DI 0.947 (0.920-0.969)). The distribution of ESBL genes was similar: blaCTX-M-15 dominated, followed by blaCTX-M-14 and blaCTX-M-27 in both the clinical (60.0%, 8.9%, and 6.7%) and the environmental isolates (62.2%, 12.2%, and 8.5%). Core genome multi-locus sequence typing showed that five environmental isolates, from incoming wastewater, treated wastewater, Svart\u00e5n river and Hj\u00e4lmaren lake, were indistinguishable or closely related (\u226410 allele differences) to clinical isolates. Isolates of ST131, serotype O25:H4 and fimtype H30, from the environment were as closely related to the clinical isolates as the isolates from different patients were. This study confirms that ESBL-producing E. coli are common in the aquatic environment even in low-endemic regions and suggests that wastewater discharge is an important route for the release of ESBL-producing E. coli into the aquatic environment.", "doi": "10.1371/journal.pone.0224861", "pmid": "31697734", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-19-22153"}, {"db": "pmc", "key": "PMC6837386"}], "notes": [], "created": "2020-02-18T14:44:33.415Z", "modified": "2021-06-16T16:19:59.874Z"}, {"entity": "publication", "iuid": "386b2c4079104522ae2b024959ecc507", "links": {"self": {"href": "https://publications.scilifelab.se/publication/386b2c4079104522ae2b024959ecc507.json"}, "display": {"href": "https://publications.scilifelab.se/publication/386b2c4079104522ae2b024959ecc507"}}, "title": "Genomic analysis of Staphylococcus capitis isolated from blood cultures in neonates at a neonatal intensive care unit in Sweden.", "authors": [{"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}, {"family": "Hellmark", "given": "Bengt", "initials": "B"}, {"family": "S\u00f6derquist", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2019-11-00", "journal": {"volume": "38", "issn": "1435-4373", "issue": "11", "pages": "2069-2075", "title": "Eur. J. Clin. Microbiol. Infect. Dis.", "issn-l": "0934-9723"}, "abstract": "Emergence of a genetically distinct, multidrug-resistant Staphylococcus capitis clone (NRCS-A) present in neonatal intensive care units has recently been extensively reported. The aims of the present study were to investigate which clones of S. capitis isolated from blood in a Swedish neonatal intensive care unit (NICU) have been present since 1987 and to investigate whether the NRCS-A clone has disseminated in Sweden. All S. capitis isolates from blood cultures of neonates (\u2264 28 days of age) between 1987 and 2017 (n = 46) were whole-genome sequenced, and core genome multilocus sequence typing (cgMLST) was performed. Single-nucleotide polymorphism (SNP)-based phylogenetic relationships between the S. capitis isolates and in silico predictions of presence of genetic traits specific to the NRCS-A clone were identified. Furthermore, antibiotic susceptibility testing, including screening for heterogeneous glycopeptide-intermediate resistance, was performed. Thirty-five isolates clustered closely to the isolates previously determined as belonging to the NRCS-A clone and had fewer than 81 core genome loci differences out of 1063. Twenty-one of these isolates were multidrug resistant. The NRCS-A clone was found in 2001. Six pairs of isolates had differences of fewer than two SNPs. Genetic traits associated with the NRCS-A clone such as nsr, ebh, tarJ, and CRISPR were found in all 35 isolates. The increasing incidence of S. capitis blood cultures of neonates is predominantly represented by the NRSC-A clone at our NICU in Sweden. Furthermore, there were indications of transmission between cases; adherence to basic hygiene procedures and surveillance measures are thus warranted.", "doi": "10.1007/s10096-019-03647-3", "pmid": "31396832", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s10096-019-03647-3"}, {"db": "pmc", "key": "PMC6800862"}], "notes": [], "created": "2020-02-18T14:47:11.352Z", "modified": "2021-06-18T13:53:17.024Z"}, {"entity": "publication", "iuid": "26f9d7ded5d54c578f9fc13b60b5692a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26f9d7ded5d54c578f9fc13b60b5692a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26f9d7ded5d54c578f9fc13b60b5692a"}}, "title": "Genome-based epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates with decreased susceptibility and resistance to extended-spectrum cephalosporins in Argentina in 2011-16.", "authors": [{"family": "Gianecini", "given": "Ricardo A", "initials": "RA"}, {"family": "Golparian", "given": "Daniel", "initials": "D"}, {"family": "Zittermann", "given": "Sandra", "initials": "S"}, {"family": "Litvik", "given": "Ana", "initials": "A"}, {"family": "Gonzalez", "given": "Silvia", "initials": "S"}, {"family": "Oviedo", "given": "Claudia", "initials": "C"}, {"family": "Melano", "given": "Roberto G", "initials": "RG"}, {"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "Galarza", "given": "Patricia", "initials": "P"}, {"family": "Gonococcal Antimicrobial Susceptibility Surveillance Programme-Argentina (GASSP-AR) Working Group", "given": "", "initials": ""}], "type": "journal article", "published": "2019-06-01", "journal": {"title": "J. Antimicrob. Chemother.", "issn": "1460-2091", "issn-l": "0305-7453", "volume": "74", "issue": "6", "pages": "1551-1559"}, "abstract": "Our aim was to describe the molecular epidemiology and antimicrobial resistance determinants of isolates of Neisseria gonorrhoeae with decreased susceptibility and resistance to extended-spectrum cephalosporins (ESCs) in Argentina in 2011-16.\r\n\r\nGonococcal isolates (n=158) with decreased susceptibility and resistance to ESCs collected in 2011-16 across Argentina were subjected to WGS and antimicrobial susceptibility testing for six antimicrobials.\r\n\r\nIn total, 50% of the isolates were resistant to cefixime, 1.9% were resistant to ceftriaxone, 37.3% were resistant to azithromycin and 63.9% of the isolates showed an MDR phenotype. Resistance and decreased susceptibility to ESCs was mainly associated with isolates possessing the mosaic penA-34.001, in combination with an mtrR promoter A deletion, and PorB1b amino acid substitutions G120K/A121N. Phylogenetic analysis revealed two main clades of circulating strains, which were associated with the N. gonorrhoeae multiantigen sequence typing (NG-MAST) ST1407 and closely related STs, and characterized by a high prevalence rate, wide geographical distribution and temporal persistence.\r\n\r\nN. gonorrhoeae isolates with decreased susceptibility and resistance to ESCs in Argentina have emerged and rapidly spread mainly due to two clonal expansions after importation of one or two strains, which are associated with the international MDR NG-MAST ST1407 clone. The identification of the geographical dissemination and characteristics of these predominant clones may help to focus action plans and public health policies to control the spread of ESC resistance in Argentina. Dual antimicrobial therapy (ceftriaxone plus azithromycin) for gonorrhoea needs to be considered in Argentina.", "doi": "10.1093/jac/dkz054", "pmid": "30820563", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5366949"}], "notes": [], "created": "2020-02-18T15:01:04.216Z", "modified": "2021-12-08T12:30:02.200Z"}, {"entity": "publication", "iuid": "7870bbb69dba4976877bef5a0bba8f2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7870bbb69dba4976877bef5a0bba8f2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7870bbb69dba4976877bef5a0bba8f2e"}}, "title": "Staphylococcus aureus isolates from nares of orthopaedic patients in Sweden are mupirocin susceptible.", "authors": [{"family": "Magnusson", "given": "Charlotta", "initials": "C"}, {"family": "Stegger", "given": "Marc", "initials": "M"}, {"family": "Hellmark", "given": "Bengt", "initials": "B"}, {"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}, {"family": "S\u00f6derquist", "given": "Bo", "initials": "B"}], "type": "letter", "published": "2019-06-00", "journal": {"volume": "51", "issn": "2374-4243", "issue": "6", "pages": "475-478", "title": "Infect Dis (Lond)", "issn-l": "2374-4235"}, "abstract": null, "doi": "10.1080/23744235.2019.1593500", "pmid": "30985251", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-02-18T14:46:36.269Z", "modified": "2021-07-06T16:32:58.855Z"}, {"entity": "publication", "iuid": "3ce51a658b344b678114eb92eeb3e55d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ce51a658b344b678114eb92eeb3e55d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ce51a658b344b678114eb92eeb3e55d"}}, "title": "Increase of invasive meningococcal serogroup W disease in Europe, 2013 to 2017.", "authors": [{"family": "Krone", "given": "Manuel", "initials": "M", "orcid": "0000-0002-1020-6454", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccff9c5df9944a5982a8de013944ece5.json"}}, {"family": "Gray", "given": "Steve", "initials": "S", "orcid": "0000-0002-8926-2802", "researcher": {"href": "https://publications.scilifelab.se/researcher/c20d2409ed0f4fe09a644b22d310ec23.json"}}, {"family": "Abad", "given": "Raquel", "initials": "R", "orcid": "0000-0002-8339-0950", "researcher": {"href": "https://publications.scilifelab.se/researcher/89c869a6979b4d4f816b898a6924fb8e.json"}}, {"family": "Skoczy\u0144ska", "given": "Anna", "initials": "A", "orcid": "0000-0002-2247-830X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7cef2432a554aad955d6739be6f53a6.json"}}, {"family": "Stefanelli", "given": "Paola", "initials": "P"}, {"family": "van der Ende", "given": "Arie", "initials": "A"}, {"family": "Tzanakaki", "given": "Georgina", "initials": "G", "orcid": "0000-0003-1773-2833", "researcher": {"href": "https://publications.scilifelab.se/researcher/18696502e2ac46b18616ee65bacb7537.json"}}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Jo\u00e3o Sim\u00f5es", "given": "Maria", "initials": "M", "orcid": "0000-0001-7514-5923", "researcher": {"href": "https://publications.scilifelab.se/researcher/5770f190c63f46b5880d3b0ffa21d352.json"}}, {"family": "K\u0159\u00ed\u017eov\u00e1", "given": "Pavla", "initials": "P"}, {"family": "Emonet", "given": "St\u00e9phane", "initials": "S"}, {"family": "Caugant", "given": "Dominique A", "initials": "DA", "orcid": "0000-0003-2765-9844", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d42fbae3fd5463fb359996f32716fde.json"}}, {"family": "Toropainen", "given": "Maija", "initials": "M"}, {"family": "Vazquez", "given": "Julio", "initials": "J"}, {"family": "Wa\u015bko", "given": "Izabela", "initials": "I", "orcid": "0000-0001-5494-3635", "researcher": {"href": "https://publications.scilifelab.se/researcher/497471b5e31d4c2f8b5f64944021f2d6.json"}}, {"family": "Knol", "given": "Mirjam J", "initials": "MJ", "orcid": "0000-0003-0645-5754", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f43a331b2a4a29b8e23e00c3aa6e82.json"}}, {"family": "Jacobsson", "given": "Susanne", "initials": "S"}, {"family": "Rodrigues Bettencourt", "given": "C\u00e9lia", "initials": "C"}, {"family": "Musilek", "given": "Martin", "initials": "M", "orcid": "0000-0003-2238-1599", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea8454d9ba3a4776beddcca7d6f93dee.json"}}, {"family": "Born", "given": "Rita", "initials": "R"}, {"family": "Vogel", "given": "Ulrich", "initials": "U"}, {"family": "Borrow", "given": "Ray", "initials": "R", "orcid": "0000-0002-0691-6568", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9e3e60eeef44a68612aaf6ab3ae9a2.json"}}], "type": "journal article", "published": "2019-04-00", "journal": {"volume": "24", "issn": "1560-7917", "issue": "14", "pages": null, "title": "Euro Surveill.", "issn-l": "1025-496X"}, "abstract": "BackgroundThe total incidence of invasive meningococcal disease (IMD) in Europe has been declining in recent years; however, a rising incidence due to serogroup W (MenW), predominantly sequence type 11 (ST-11), clonal complex 11 (cc11), was reported in some European countries.AimThe aim of this study was to compile the most recent laboratory surveillance data on MenW IMD from several European countries to assess recent trends in Europe.MethodsIn this observational, retrospective study, IMD surveillance data collected from 2013-17 by national reference laboratories and surveillance units from 13 European countries were analysed using descriptive statistics.ResultsThe overall incidence of IMD has been stable during the study period. Incidence of MenW IMD per 100,000 population (2013: 0.03; 2014: 0.05; 2015: 0.08; 2016: 0.11; 2017: 0.11) and the proportion of this serogroup among all invasive cases (2013: 5% (116/2,216); 2014: 9% (161/1,761); 2015: 13% (271/2,074); 2016: 17% (388/2,222); 2017: 19% (393/2,112)) continuously increased. The most affected countries were England, the Netherlands, Switzerland and Sweden. MenW was more frequent in older age groups (\u2265 45 years), while the proportion in children (< 15 years) was lower than in other age groups. Of the culture-confirmed MenW IMD cases, 80% (615/767) were caused by hypervirulent cc11.ConclusionDuring the years 2013-17, an increase in MenW IMD, mainly caused by MenW cc11, was observed in the majority of European countries. Given the unpredictable nature of meningococcal spread and the epidemiological potential of cc11, European countries may consider preventive strategies adapted to their contexts.", "doi": "10.2807/1560-7917.ES.2019.24.14.1800245", "pmid": "30968827", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6462787"}], "notes": [], "created": "2020-02-18T14:41:38.090Z", "modified": "2021-06-21T12:05:45.334Z"}, {"entity": "publication", "iuid": "cf3147fb7dd441a683f167b38270fb8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf3147fb7dd441a683f167b38270fb8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf3147fb7dd441a683f167b38270fb8d"}}, "title": "A suggestion to the medical librarians. 1920.", "authors": [{"family": "Smith", "given": "Laura E", "initials": "LE"}], "type": "biography", "published": "2012-10-00", "journal": {"title": "J Med Libr Assoc", "issn": "1558-9439", "volume": "100", "issue": "4 Suppl", "pages": "B", "issn-l": null}, "abstract": null, "doi": null, "pmid": "23509424", "labels": {"Clinical Genomics": "Service", "Clinical Genomics \u00d6rebro": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC3571666"}, {"db": "sici", "key": "i1536-5050-100-4s-30"}], "notes": [], "created": "2025-11-19T15:13:42.127Z", "modified": "2025-11-19T15:14:49.894Z"}, {"entity": "publication", "iuid": "ec231f679d2344bc904a45195515ba8b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec231f679d2344bc904a45195515ba8b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec231f679d2344bc904a45195515ba8b"}}, "title": "[Effect of combined use of steroid preparations with pyrroxane on the gonadotropic function of the hypophysis].", "authors": [{"family": "Veshohilova", "given": "T P", "initials": "TP"}], "type": "journal article", "published": "1975-10-00", "journal": {"title": "Akush Ginekol (Mosk)", "issn": "0300-9092", "issue": "10", "pages": "10-12", "issn-l": null}, "abstract": null, "doi": null, "pmid": "2025", "labels": {"Clinical Genomics": "Service", "Clinical Genomics \u00d6rebro": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-19T15:14:23.375Z", "modified": "2025-11-19T15:15:20.341Z"}]}