{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T06:59:22Z","timestamp":1790405962586,"version":"4.1.0"},"reference-count":61,"publisher":"Microbiology Society","issue":"4","license":[{"start":{"date-parts":[[2020,4,1]],"date-time":"2020-04-01T00:00:00Z","timestamp":1585699200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["110243\/Z\/15\/Z"],"award-info":[{"award-number":["110243\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["WT098600"],"award-info":[{"award-number":["WT098600"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001638","name":"Dublin City University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001638","id-type":"DOI","asserted-by":"crossref"}]},{"name":"ESPRC Vaccine Hub"},{"name":"Department of Health","award":["HICF-T5-342"],"award-info":[{"award-number":["HICF-T5-342"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:p>\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3093\" xlink:type=\"simple\">Escherichia coli<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of\n                    <jats:italic>\n                      <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3093\" xlink:type=\"simple\">E. coli<\/jats:ext-link>\n                      <\/jats:named-content>\n                    <\/jats:italic>\n                    ST131 producing extended spectrum \u03b2-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (\n                    <jats:italic>n<\/jats:italic>\n                    =69) with other Irish (\n                    <jats:italic>n<\/jats:italic>\n                    =35) and global (\n                    <jats:italic>n<\/jats:italic>\n                    =690) ST131 genomes to reconstruct the evolutionary history and understand changes in population structure and genome architecture over time. This required a combination of short- and long-read genome sequencing,\n                    <jats:italic>de novo<\/jats:italic>\n                    assembly, read mapping, ESBL gene screening, plasmid alignment and temporal phylogenetics. We found that Clade C was the most prevalent (686 out of 794 isolates, 86\u200a%) of the three major ST131 clades circulating worldwide (A with\n                    <jats:italic>fimH41<\/jats:italic>\n                    , B with\n                    <jats:italic>fimH22<\/jats:italic>\n                    , C with\n                    <jats:italic>fimH30<\/jats:italic>\n                    ), and was associated with the presence of different ESBL alleles, diverse plasmids and transposable elements. Clade C was estimated to have emerged in\n                    <jats:italic>c<\/jats:italic>\n                    . 1985\u2009and subsequently acquired different ESBL gene variants (\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>\n                      <jats:italic>CTX-M-14<\/jats:italic>\n                    <\/jats:sub>\n                    vs\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>\n                      <jats:italic>CTX-M-15<\/jats:italic>\n                    <\/jats:sub>\n                    ). An ISEcp\n                    <jats:italic>1-<\/jats:italic>\n                    mediated transposition of the\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>\n                      <jats:italic>CTX-M-15<\/jats:italic>\n                    <\/jats:sub>\n                    gene further increased the diversity within Clade C. We discovered a local clonal expansion of a rare C2 lineage (C2_8) with a chromosomal insertion of\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>\n                      <jats:italic>CTX-M-15<\/jats:italic>\n                    <\/jats:sub>\n                    at the\n                    <jats:italic>mppA<\/jats:italic>\n                    gene. This was acquired from an IncFIA plasmid. The C2_8 lineage clonally expanded in the Irish LTCF from 2006, displacing the existing C1 strain (C1_10), highlighting the potential for novel ESBL-producing ST131 with a distinct genetic profile to cause outbreaks strongly associated with specific healthcare environments.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.000352","type":"journal-article","created":{"date-parts":[[2020,3,26]],"date-time":"2020-03-26T14:16:06Z","timestamp":1585232166000},"source":"Crossref","is-referenced-by-count":37,"title":["Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones"],"prefix":"10.1099","volume":"6","author":[{"given":"Catherine","family":"Ludden","sequence":"first","affiliation":[{"name":"London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK"},{"name":"Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6058-6483","authenticated-orcid":false,"given":"Arun Gonzales","family":"Decano","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Dublin City University, Dublin 9, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dorota","family":"Jamrozy","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Derek","family":"Pickard","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Cambridge, Box 157 Addenbrooke\u2019s Hospital, Hills Road, Cambridge CB2 0QQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dearbhaile","family":"Morris","sequence":"additional","affiliation":[{"name":"Ryan Institute Centre for One Health, National University of Ireland Galway, Ireland"},{"name":"Discipline of Bacteriology, School of Medicine, National University of Ireland, Galway, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7069-5958","authenticated-orcid":false,"given":"Julian","family":"Parkhill","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1718-2782","authenticated-orcid":false,"given":"Sharon J.","family":"Peacock","sequence":"additional","affiliation":[{"name":"Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK"},{"name":"Department of Medicine, University of Cambridge, Box 157 Addenbrooke\u2019s Hospital, Hills Road, Cambridge CB2 0QQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Cormican","sequence":"additional","affiliation":[{"name":"Discipline of Bacteriology, School of Medicine, National University of Ireland, Galway, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8385-6730","authenticated-orcid":false,"given":"Tim","family":"Downing","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Dublin City University, Dublin 9, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00143-10"},{"key":"R2","article-title":"Point prevalence survey of hospital acquired infections & antimicrobial use in european acute care hospitals: May 2012 Republic of Ireland National Report. 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