{"entity": "researcher", "timestamp": "2026-08-11T14:45:33.165Z", "family": "Ja\u00e9n-Luchoro", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5988-6227", "affiliations": ["Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/1a821a703a144b5aa5a783e7f8043d86.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/1a821a703a144b5aa5a783e7f8043d86"}}, "publications": [{"entity": "publication", "iuid": "7b2118e734d34424950d390248954deb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b2118e734d34424950d390248954deb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b2118e734d34424950d390248954deb"}}, "title": "Insights into the Metabolic Adaptations of a Carbapenem-Resistant Klebsiella pneumoniae Strain on Exposure to Sublethal Concentrations of Ertapenem.", "authors": [{"family": "Ja\u00e9n-Luchoro", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5988-6227", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a821a703a144b5aa5a783e7f8043d86.json"}}, {"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F", "orcid": "0000-0003-0173-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d15be15c484e6a99f22b466bf99166.json"}}, {"family": "Pi\u00f1eiro-Iglesias", "given": "Beatriz", "initials": "B", "orcid": "0000-0003-3125-0822", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f4f8871d0ce48149f88b24b6fb42c6c.json"}}, {"family": "Marathe", "given": "Nachiket", "initials": "N", "orcid": "0000-0003-2955-3402", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b806ecb68c246beacbf04550e422714.json"}}, {"family": "Moore", "given": "Edward R B", "initials": "ERB", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1c68436094391bfefd7de22757aba.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R", "orcid": "0000-0002-5919-2639", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9b10fd0fa34dd9a3de96f3c4860e32.json"}}], "type": "journal article", "published": "2025-09-15", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "18", "issn-l": null}, "abstract": "Klebsiella pneumoniae strains that are resistant to carbapenems are of great concern. Exposure to low concentrations of antibiotics may influence tolerance to antibiotics. Novel antibiotics and treatment options are thus needed, and this need is exacerbated by the rapid and global spread of antibiotic resistance. In this study, we determined the global proteome changes in a K. pneumoniae strain (CCUG 70747) carrying carbapenem resistance genes when exposed to low concentrations of ertapenem. Quantitative proteomics was achieved by the tandem mass tag labeling of peptides generated by trypsin proteolysis and mass spectrometry analysis. Bioinformatics analyses were used to observe changes in protein abundance, as well as the gene ontology (GO) terms and pathways associated with the differentially expressed proteins. The number of proteins detected with significant differential abundance were 87 at the highest concentration applied and 61 in the lowest concentration, all compared with the strain cultured without any antibiotics present. Several of these proteins, as well as the GO terms and pathways associated with the proteins, were linked to mechanisms of antibiotic resistance. However, this strain encodes a carbapenemase and other beta-lactamases, and thus, as expected, presented a reasonably modest adaptation in the global proteome upon exposure to the low concentrations of ertapenem applied. Nevertheless, our study identifies pathways that may lead to adaptation under sublethal concentrations of antibiotics leading to strains with higher tolerance.", "doi": "10.3390/ijms26188988", "pmid": "41009554", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12470040"}, {"db": "pii", "key": "ijms26188988"}], "notes": [], "created": "2025-10-23T12:42:51.224Z", "modified": "2025-10-23T12:42:51.506Z"}, {"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": "897829798c8a4cce94f81bdbe56dd9b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/897829798c8a4cce94f81bdbe56dd9b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/897829798c8a4cce94f81bdbe56dd9b7"}}, "title": "Comparative Genomics of Clinical Isolates of the Emerging Tick-Borne Pathogen Neoehrlichia mikurensis.", "authors": [{"family": "Grankvist", "given": "Anna", "initials": "A"}, {"family": "Ja\u00e9n-Luchoro", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5988-6227", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a821a703a144b5aa5a783e7f8043d86.json"}}, {"family": "Wass", "given": "Linda", "initials": "L"}, {"family": "Sikora", "given": "Per", "initials": "P"}, {"family": "Wenner\u00e5s", "given": "Christine", "initials": "C"}], "type": "journal article", "published": "2021-07-13", "journal": {"title": "Microorganisms", "issn": "2076-2607", "volume": "9", "issue": "7", "issn-l": "2076-2607"}, "abstract": "Tick-borne 'Neoehrlichia (N.) mikurensis' is the cause of neoehrlichiosis, an infectious vasculitis of humans. This strict intracellular pathogen is a member of the family Anaplasmataceae and has been unculturable until recently. The only available genetic data on this new pathogen are six partially sequenced housekeeping genes. The aim of this study was to advance the knowledge regarding 'N. mikurensis' genomic relatedness with other Anaplasmataceae members, intra-species genotypic variability and potential virulence factors explaining its tropism for vascular endothelium. Here, we present the de novo whole-genome sequences of three 'N. mikurensis' strains derived from Swedish patients diagnosed with neoehrlichiosis. The genomes were obtained by extraction of DNA from patient plasma, library preparation using 10\u00d7 Chromium technology, and sequencing by Illumina Hiseq-4500. 'N. mikurensis' was found to have the next smallest genome of the Anaplasmataceae family (1.1 Mbp with 27% GC contents) consisting of 845 protein-coding genes, every third of which with unknown function. Comparative genomic analyses revealed that 'N. mikurensis' was more closely related to Ehrlichia chaffeensis than to Ehrlichia ruminantium, the opposite of what 16SrRNA sequence-based phylogenetic analyses determined. The genetic variability of the three whole-genome-sequenced 'N. mikurensis' strains was extremely low, between 0.14 and 0.22\u2030, a variation that was associated with geographic origin. No protein-coding genes exclusively shared by N. mikurensis and E. ruminantium were identified to explain their common tropism for vascular endothelium.", "doi": "10.3390/microorganisms9071488", "pmid": "34361922", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "microorganisms9071488"}, {"db": "pmc", "key": "PMC8303192"}], "notes": [], "created": "2022-03-29T13:42:02.270Z", "modified": "2022-03-29T13:42:02.322Z"}]}