{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T15:55:05Z","timestamp":1785772505056,"version":"3.56.0"},"reference-count":103,"publisher":"Microbiology Society","issue":"8","license":[{"start":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T00:00:00Z","timestamp":1785715200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"International Foundation for Science, Sweden","award":["IFS B\/5793-2"],"award-info":[{"award-number":["IFS B\/5793-2"]}]},{"name":"Deutscher Akademischer Austauschdienst","award":["Funding Program Number: 57693453"],"award-info":[{"award-number":["Funding Program Number: 57693453"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,3]]},"abstract":"<jats:p>\n                    Plasmid-mediated colistin and tigecycline resistance threatens last-resort therapeutic options. We investigated the farm-to-fork dissemination of\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    encoding\n                    <jats:italic>mcr-1.1<\/jats:italic>\n                    and\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) in a vertically integrated broiler production system. A total of 200\u2009samples were collected in 2024, representing four sequential production stages: broiler breeders, day-old chicks, day-30 broilers and retail meat. All positive [\n                    <jats:italic>mcr-1.1<\/jats:italic>\n                    and\/or\n                    <jats:italic>tet(X4<\/jats:italic>\n                    )] isolates underwent Illumina short-read sequencing, with long-read sequencing of three representatives. The study was enriched and analysed with\n                    <jats:italic>mcr-1.1<\/jats:italic>\n                    and\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) encoding 213 publicly available\n                    <jats:italic>E. coli<\/jats:italic>\n                    genomes from Pakistan. Of 18 isolates,\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) was detected in 11 and\n                    <jats:italic>mcr-1.1<\/jats:italic>\n                    in 7 isolates with a single breeder isolate (ST-398) co-harbouring both on separate plasmids.\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) predominated breeders and day-30 broilers, whereas\n                    <jats:italic>mcr-1.1<\/jats:italic>\n                    was distributed across all four stages. ST-1011 exhibited a pattern of clonal farm-to-fork transmission of\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) via IncFIB(AP001918)-IncFII providing molecular evidence suggestive of clonal transmission. Analysis of 231 genomes across 87 sequence types (STs) revealed contrasting evolutionary trajectories:\n                    <jats:italic>mcr-1.1<\/jats:italic>\n                    with post-mobilization stabilization marked by complete absence of ISApl1 and highly conserved IncI2 plasmid (93%), whereas\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) retained active transposition within IS26-bounded elements.\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) carriage was also associated with elevated resistance gene burden, driven by the IncF megaplasmids. All 18 isolates exhibited adhesion to chicken intestinal epithelial cells (CHIC-8E11), with high adhesion capacity among\n                    <jats:italic>tet<\/jats:italic>\n                    (X4)-positive isolates. This study demonstrates that\n                    <jats:italic>mcr-1.1<\/jats:italic>\n                    and\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) disseminate through poultry production via distinct mechanisms. These findings highlight the need for integrated One Health surveillance of antimicrobial resistance dissemination.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001800","type":"journal-article","created":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T15:15:38Z","timestamp":1785770138000},"source":"Crossref","is-referenced-by-count":0,"title":["Integrated poultry production as a reservoir of tet(X4) and mcr-1.1 encoding Escherichia coli in Pakistan"],"prefix":"10.1099","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-6930-7960","authenticated-orcid":false,"given":"Muhammad Ahmed","family":"Mushtaq","sequence":"first","affiliation":[{"name":"Department of Multiparametric diagnostics, Brandenburg University of Technology, Cottbus-Senftenberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Schierack","sequence":"additional","affiliation":[{"name":"Department of Multiparametric diagnostics, Brandenburg University of Technology, Cottbus-Senftenberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6516-9398","authenticated-orcid":false,"given":"Muhammad","family":"Yousaf","sequence":"additional","affiliation":[{"name":"Institute of Animal and Dairy Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5929-7900","authenticated-orcid":false,"given":"Fariha","family":"Fatima","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tayyaba","family":"Qamar","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5460-5780","authenticated-orcid":false,"given":"Mashkoor","family":"Mohsin","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4493-1563","authenticated-orcid":false,"given":"Muhammad Moman","family":"Khan","sequence":"additional","affiliation":[{"name":"Department of Multiparametric diagnostics, Brandenburg University of Technology, Cottbus-Senftenberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms12091920"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1004264"},{"key":"R3","article-title":"Antibiotic resistance and emerging alternatives for controlling foodborne pathogens","volume":"45","author":"Alsayeqh","year":"2025","journal-title":"Pak Vet J"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1136\/bmjgh-2024-016249"},{"key":"R5","article-title":"Estimating the economic costs of antimicrobial resistance: Model and Results","author":"Taylor","year":"2014"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1186\/s44263-023-00003-8"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1007\/s00216-024-05301-0"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1016\/j.glmedi.2024.100081"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.14202\/IJOH.2024.161-171"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(22)00387-1"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1186\/s13756-020-0697-x"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-56825-7"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.14202\/vetworld.2022.743-749"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1186\/s12916-022-02677-7"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00362"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.2144\/fsoa-2020-0189"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1016\/j.psj.2025.105089"},{"key":"R18","article-title":"Poultry farming in Pakistan: challenges & opportunities. Agricultural economist","author":"Awais"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1111\/jam.13169"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1429200"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-023-01509-7"},{"key":"R22","article-title":"Exploring the diversity and dissemination dynamics of antimicrobial resistance genes in enterobacteriaceae plasmids across varied ecological niches","volume":"45","author":"Munir","year":"2025","journal-title":"Pak Vet J"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-020-01148-0"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1502528"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00695-21"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01673-24"},{"key":"R27","first-page":"1303","article-title":"Characteristics of the plasmid-mediate colistin-resistance gene mcr-1 in Escherichia coli isolated from pig farm in Jiangxi","volume":"44","author":"Wu","year":"2024","journal-title":"Pak Vet J"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0445-2"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2018.23.6.17-00672"},{"key":"R30","article-title":"Breakpoint tables for interpretation of mics and zone diameters","year":"2025"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1186\/s12917-023-03672-7"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01068-20"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9020372"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"R36","article-title":"Dorado","year":"2023"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0163962"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty149"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0072-8"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1101\/gr.214270.116"},{"key":"R42","article-title":"Medaka","year":"2023"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv351"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01940-w"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03198-7"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000685"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac920"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkaa345"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2019.10.022"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01953-y"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx433"},{"key":"R54","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj014"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000206"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02823-7"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-12-402"},{"key":"R58","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fnag014"},{"key":"R59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0345168"},{"key":"R60","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007732"},{"key":"R61","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa015"},{"key":"R62","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx281"},{"key":"R63","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae268"},{"key":"R64","doi-asserted-by":"publisher","DOI":"10.1099\/acmi.0.000143"},{"key":"R65","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000728"},{"key":"R66","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-024-10525-6"},{"key":"R67","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02413-23"},{"key":"R68","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.29032.3"},{"key":"R69","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab007"},{"key":"R70","author":"Wilkins","year":"2025"},{"key":"R71","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01945-16"},{"key":"R72","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2014.0083"},{"key":"R73","doi-asserted-by":"publisher","DOI":"10.1128\/Spectrum.00416-21"},{"key":"R74","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.941358"},{"key":"R75","first-page":"913","article-title":"Co-transfer of mcr-1 and mcr-3 variant in Escherichia coli ST1632 isolate in China: silence is not always golden","volume":"45","author":"Li","year":"2025","journal-title":"Pak Vet J"},{"key":"R76","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02421-09"},{"key":"R77","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2005.2.38"},{"key":"R78","doi-asserted-by":"publisher","DOI":"10.1128\/microbiolspec.UTI-0006-2012"},{"key":"R79","doi-asserted-by":"publisher","DOI":"10.4291\/wjgp.v5.i3.213"},{"key":"R80","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01457-16"},{"key":"R81","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02381-17"},{"key":"R82","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.01217"},{"key":"R83","doi-asserted-by":"publisher","DOI":"10.1111\/1348-0421.12549"},{"key":"R84","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-15539-7"},{"key":"R85","doi-asserted-by":"publisher","DOI":"10.1186\/s13756-017-0250-8"},{"key":"R86","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00015-09"},{"key":"R87","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-62455-w"},{"key":"R88","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2019.2680"},{"key":"R89","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0496-4"},{"key":"R90","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.969769"},{"key":"R91","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2022.154010"},{"key":"R92","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00762-15"},{"key":"R93","doi-asserted-by":"publisher","DOI":"10.29261\/pakvetj\/2018.052"},{"key":"R94","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01167-19"},{"key":"R95","doi-asserted-by":"publisher","DOI":"10.29261\/pakvetj\/2025.199"},{"key":"R96","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2001.02261.x"},{"key":"R97","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(16)00056-6"},{"key":"R98","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2021.147613"},{"key":"R99","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00196-22"},{"key":"R100","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2021.02.010"},{"key":"R101","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00584-23"},{"key":"R102","doi-asserted-by":"publisher","DOI":"10.2147\/IDR.S302687"},{"key":"R103","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.818548"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001800?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T15:15:41Z","timestamp":1785770141000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001800"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,3]]},"references-count":103,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8,3]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001800","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,3]]}}}