{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:33:41Z","timestamp":1785429221964,"version":"3.56.0"},"reference-count":59,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T00:00:00Z","timestamp":1776729600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T00:00:00Z","timestamp":1776729600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["RS-2024-00443714"],"award-info":[{"award-number":["RS-2024-00443714"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["RS-2026-25470080"],"award-info":[{"award-number":["RS-2026-25470080"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2026,4,21]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      sequence type (ST) 405, a high-risk international clone, has emerged as a critical lineage for the dissemination of antibiotic resistance genes (ARGs), including the\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      gene. This study aims to elucidate the genomic landscape of ST405 through comparative genomic analysis of both publicly available ST405 genomes and three ST405 isolates from sewage and wild-bird fecal samples in Pakistan. A total of 1,778\n                      <jats:italic toggle=\"yes\">E. coli<\/jats:italic>\n                      ST405 genomes were investigated through phylogenomic and population-structure analyses, revealing distinct clusters and subgroup lineages within this ST. Among these, subgroup B was identified as a pivotal contributor to the dissemination of the\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      gene within ST405. Temporal analysis indicates that subgroup B is expanding over time, raising concerns regarding its potential contributions to increased antibiotic resistance within ST405 populations. Genetic-structure analyses of\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      -carrying plasmids of the sewage isolates uncovered the presence of nearly identical plasmids in other multidrug-resistant STs, ST156 and ST648, suggesting a genetic linkage among these STs. Additionally, a novel\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      genetic context was identified in the animal isolate, characterized by unique composite-transposon and inversion structures mediated by IS\n                      <jats:italic toggle=\"yes\">26<\/jats:italic>\n                      replicative transposition, highlighting the dynamic evolution of the ST405-associated plasmid. These findings underscore the intra-ST dissemination of the\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      gene and the ongoing diversification of its genetic context within ST405. This comprehensive analysis advances our understanding of ST405, providing insights into the genetic mechanisms underlying its enhanced antibiotic resistance and the emergence of a novel ARG-carrying plasmid within the One Health framework.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      This study provides a comprehensive genomic landscape of ST405, a high-risk international clone and a carrier of the\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      gene, revealing phylogenetically distinct patterns in the distribution of antibiotic resistance genes and virulence factors, and a critical phylogenetic lineage that serves as a primary reservoir of the\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      gene. Furthermore, the genetic linkage between ST405 and other STs (ST156 and ST648) through the sharing of identical\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      -carrying plasmids, and the emergence of a novel\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      genetic structure in an animal isolate, underscore the pivotal role of ST405 in the dissemination of the\n                      <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      gene. These findings highlight the public health significance of ST405 and its contribution to the global spread of carbapenem resistance.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.01685-25","type":"journal-article","created":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T13:01:39Z","timestamp":1773666099000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Comparative genomic analyses of\n                    <i>Escherichia coli<\/i>\n                    ST405 strains from Pakistan"],"prefix":"10.1128","volume":"11","author":[{"given":"Nam-Hoon","family":"Kim","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05q92br09","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Life Sciences, Jeonbuk National University","place":["Jeonju, South 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