{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T01:56:10Z","timestamp":1790214970804,"version":"4.1.0"},"reference-count":21,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2025,5,20]],"date-time":"2025-05-20T00:00:00Z","timestamp":1747699200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,5,20]],"date-time":"2025-05-20T00:00:00Z","timestamp":1747699200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100003243","name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["NU22-09-00645"],"award-info":[{"award-number":["NU22-09-00645"]}],"id":[{"id":"10.13039\/501100003243","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003243","name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["DRO 65269705"],"award-info":[{"award-number":["DRO 65269705"]}],"id":[{"id":"10.13039\/501100003243","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001824","name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["24-12527S"],"award-info":[{"award-number":["24-12527S"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Veterinarni Univerzita Brno","award":["206\/2024\/FVHE"],"award-info":[{"award-number":["206\/2024\/FVHE"]}]},{"DOI":"10.13039\/100007672","name":"Faculty of Medicine in Pilsen, Charles University","doi-asserted-by":"publisher","award":["LX22NPO5103"],"award-info":[{"award-number":["LX22NPO5103"]}],"id":[{"id":"10.13039\/100007672","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2025,5,20]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      IncF plasmids are mobile genetic elements found in bacteria from the\n                      <jats:italic toggle=\"yes\">Enterobacteriaceae<\/jats:italic>\n                      family and often carry critical antibiotic and virulence gene cargo. The classification of IncF plasmids using the plasmid Multi-Locus Sequence Typing (pMLST) tool from the Center for Genomic Epidemiology (CGE;\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.genomicepidemiology.org\/\" xlink:type=\"simple\">https:\/\/www.genomicepidemiology.org\/<\/jats:ext-link>\n                      ) compares the sequences of IncF alleles against a database to create a plasmid sequence type (ST). Accurate identification of plasmid STs is useful as it enables an assessment of IncF plasmid lineages associated with pandemic enterobacterial STs. Our initial observations showed discrepancies in IncF allele variants reported by pMLST in a collection of 898\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      ST131 genomes. To evaluate the limitations of the pMLST tool, we interrogated an in-house and public repository of 70,324\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      genomes of various STs and other\n                      <jats:italic toggle=\"yes\">Enterobacteriaceae<\/jats:italic>\n                      genomes (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 1247). All short-read assemblies and representatives selected for long-read sequencing were used to assess pMLST allele variants and to compare the output of pMLST tool versions. When multiple allele variants occurred in a single bacterial genome, the Python and web versions of the tool randomly selected one allele to report, leading to limited and inaccurate ST identification. Discrepancies were detected in 5,804 of 72,469 genomes (8.01%). Long-read sequencing of 27 genomes confirmed multiple IncF allele variants on one plasmid or two separate IncF plasmids in a single bacterial cell. The pMLST tool was unable to accurately distinguish allele variants and their location on replicons using short-read genome assemblies, or long-read genome assemblies if the same allele variant was present more than once.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>Plasmid sequence type is crucial for describing IncF plasmids due to their capacity to carry important antibiotic and virulence gene cargo and consequently due to their association with disease-causing enterobacterial lineages exhibiting resistance to clinically relevant antibiotics in humans and food-producing animals. As a result, precise reporting of IncF allele variants in IncF plasmids is necessary. Comparison of the FAB formulae generated by the pMLST tool with annotated long-read genome assemblies identified inconsistencies, including examples where multiple IncF allele variants were present on the same plasmid but missing in the FAB formula, or in cases where two IncF plasmids were detected in one bacterial cell, and the pMLST output provided information only about one plasmid. Such inconsistencies may cloud interpretation of IncF plasmid replicon type in specific bacterial lineages or inaccurate assumptions of host strain clonality.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.01010-24","type":"journal-article","created":{"date-parts":[[2025,4,8]],"date-time":"2025-04-08T09:01:08Z","timestamp":1744102868000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":8,"title":["The presence of multiple variants of IncF plasmid alleles in a single genome sequence can hinder accurate replicon sequence typing using\n                    <i>in silico<\/i>\n                    pMLST tools"],"prefix":"10.1128","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0769-1978","authenticated-orcid":false,"given":"Michaela","family":"Ruzickova","sequence":"first","affiliation":[{"name":"Central European Institute of Technology, University of Veterinary Sciences Brno","place":["Brno, Czechia"]},{"name":"Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno","place":["Brno, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine in Pilsen, Charles University","place":["Pilsen, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"Palkovicova","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology, University of Veterinary Sciences Brno","place":["Brno, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine in Pilsen, Charles University","place":["Pilsen, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo","family":"Papousek","sequence":"additional","affiliation":[{"name":"Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno","place":["Brno, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9333-7160","authenticated-orcid":true,"given":"Max L.","family":"Cummins","sequence":"additional","affiliation":[{"name":"Australian Institute for Microbiology and Infection, University of Technology Sydney","place":["Sydney, Australia"]},{"name":"The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney","place":["Sydney, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9301-5372","authenticated-orcid":true,"given":"Steven P.","family":"Djordjevic","sequence":"additional","affiliation":[{"name":"Australian Institute for Microbiology and Infection, University of Technology Sydney","place":["Sydney, Australia"]},{"name":"The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney","place":["Sydney, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7877-483X","authenticated-orcid":true,"given":"Monika","family":"Dolejska","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology, University of Veterinary Sciences Brno","place":["Brno, Czechia"]},{"name":"Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno","place":["Brno, Czechia"]},{"name":"Department of Microbiology, Faculty of Medicine in Pilsen, Charles University","place":["Pilsen, Czechia"]},{"name":"Division of Clinical Microbiology and Immunology, Department of Laboratory Medicine, The University Hospital Brno","place":["Brno, Czechia"]},{"name":"Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno","place":["Brno, 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