{"entity": "journal", "iuid": "285b12be14744991add78d23d3db58d0", "timestamp": "2026-07-20T12:46:16.666Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Eur.%20J.%20Clin.%20Microbiol.%20Infect.%20Dis..json"}, "display": {"href": "https://publications.scilifelab.se/journal/Eur.%20J.%20Clin.%20Microbiol.%20Infect.%20Dis."}}, "title": "Eur. J. Clin. Microbiol. Infect. Dis.", "issn": "1435-4373", "issn-l": "0934-9723", "publications_count": 4, "publications": [{"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": "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": "b50d96bb11744dd793d9494a64f6e8be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b50d96bb11744dd793d9494a64f6e8be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b50d96bb11744dd793d9494a64f6e8be"}}, "title": "In-hospital metabolite changes in infective endocarditis-a longitudinal 1H NMR-based study.", "authors": [{"family": "Klein", "given": "Christine Falk", "initials": "CF", "orcid": "0000-0001-9401-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/416a2b61715e444d9013247e002959db.json"}}, {"family": "Holle", "given": "Sarah Louise Kj\u00f8lhede", "initials": "SLK"}, {"family": "Andersen", "given": "Malene H\u00f8jgaard", "initials": "MH"}, {"family": "Pedersen", "given": "Anders", "initials": "A"}, {"family": "Bundgaard", "given": "Henning", "initials": "H"}, {"family": "Iversen", "given": "Kasper Karmark", "initials": "KK"}, {"family": "Malmendal", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2019-08-00", "journal": {"title": "Eur. J. Clin. Microbiol. Infect. Dis.", "issn": "1435-4373", "volume": "38", "issue": "8", "pages": "1553-1560", "issn-l": "0934-9723"}, "abstract": "Treatment of infective endocarditis (IE) is a 4-6-week provided course of intravenously administered antibiotics. The aim of this study was to investigate how serum metabolites as measured by proton nuclear magnetic resonance ( 1H NMR) spectroscopy are changing over time during the active phase of IE, and to see whether these metabolite changes might be used to monitor recovery in these patients. Patients hospitalized with first-time IE at Herlev Hospital, Denmark, from September 2015 to June 2017 were included. Longitudinal blood sampling was performed and serum was analyzed using 1H NMR. Orthogonal projection to latent structures discriminant analysis (OPLS-DA) was used to separate sample groups and analyze differences in metabolite profiles. Thirteen patients were included in the study (77% men, median age 62 years (IQR 53-77)). All patients were cured during the hospitalization without any relapse during 6 months of follow-up. We analyzed 61 serum samples (median 5 samples, range 2-8 per person) drawn in the treatment period after IE diagnosis. The main changes during the in-hospital period were decreased levels of glucose, mannose, leucine, isoleucine, phenylalanine, tyrosine, and signals from polyols and N-acetylated protein. The metabolomic changes could in contrast to the routinely used parameters CRP and leucocyte levels distinguish between the early and late stages of disease treatment. We present the first longitudinal study of 1H NMR metabolomics in patients with infective endocarditis. The metabolomic changes show a promising strength compared to routinely used clinical parameters.", "doi": "10.1007/s10096-019-03586-z", "pmid": "31119577", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s10096-019-03586-z"}], "notes": [], "created": "2020-01-07T11:43:00.353Z", "modified": "2025-10-17T13:03:57.723Z"}, {"entity": "publication", "iuid": "5c60d95ec1144a3f84f4f35dbac8f469", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c60d95ec1144a3f84f4f35dbac8f469.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c60d95ec1144a3f84f4f35dbac8f469"}}, "title": "Genomic analysis reveals the presence of a class D beta-lactamase with broad substrate specificity in animal bite associated Capnocytophaga species.", "authors": [{"family": "Zangenah", "given": "S", "initials": "S"}, {"family": "Andersson", "given": "A F", "initials": "AF"}, {"family": "\u00d6zenci", "given": "V", "initials": "V"}, {"family": "Bergman", "given": "P", "initials": "P"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "36", "issn": "1435-4373", "issue": "4", "pages": "657-662", "title": "Eur. J. Clin. Microbiol. Infect. Dis.", "issn-l": "0934-9723"}, "abstract": "Capnocytophga canimorsus and Capnocytophga cynodegmi can be transmitted from cats and dogs to humans, and can cause a wide range of infections including wound infections, sepsis, or endocarditis. We and others recently discovered two new Capnocytophaga species, C. canis and C. stomatis, mainly associated with wound infections. The first-line treatment of animal bite related infections is penicillin, and in case of allergy, doxycycline and trimethoprim/sulfamethoxazole. However, there is a lack of antibiotic susceptibility patterns for animal bite associated Capnocytophaga species. Thus, we \ufeffset out to study the antibiotic profiles against animal bite associated Capnocytophaga species isolated from wound and blood cultures after cat and dog bites and coupled the findings to whole genome sequencing data. A total of 24 strains were included in the study. Phenotypic analysis of antibiotic resistance was performed with E-tests. The web-based tool 'Resfinder' was used to identify resistance genes in the whole genome dataset. Two strains of C. cynodegmi and two strains of the recently discovered C. stomatis were resistant to penicillin (MIC\u2009> 24 mg\ufeff/L) and cephalosporins (MIC\u2009>\u200924 mg/\ufeffL), and three out of these strains also exhibited resistance to imipenem (MIC\u2009=\u200932 mg/\ufeffL). Genomic analysis revealed that these strains carried a class D beta-lactamase gene, which has not previously been found in Capnocytophaga spp. A class D beta lactamase with broad substrate specificity was found in animal bite associated Capnocytophaga species, which could have important implications when treating wound infections after cat and dog bites. It also suggests that pet animal bacteria can harbour resistance genes with relevance for human infections.", "doi": "10.1007/s10096-016-2842-2", "pmid": "27909820", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s10096-016-2842-2"}, {"db": "pmc", "key": "PMC5366173"}], "notes": [], "created": "2017-05-03T12:58:58.451Z", "modified": "2024-01-16T13:48:48.169Z"}], "created": "2017-05-09T09:12:30.929Z", "modified": "2020-11-27T13:14:02.705Z"}