{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T10:27:59Z","timestamp":1788776879715,"version":"build-2803163510"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T00:00:00Z","timestamp":1658793600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32121004"],"award-info":[{"award-number":["32121004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Innovation Team Project of Guangdong University","award":["2019KCXTD001"],"award-info":[{"award-number":["2019KCXTD001"]}]},{"name":"Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program","award":["2019BT02N054"],"award-info":[{"award-number":["2019BT02N054"]}]},{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"crossref","award":["2020A1515010310"],"award-info":[{"award-number":["2020A1515010310"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>To reconstruct the genomic epidemiology and evolution of MDR Salmonella Indiana in China.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>A total of 108 Salmonella Indiana strains were collected from humans and livestock in China. All isolates were subjected to WGS and antimicrobial susceptibility testing. Phylogenetic relationships and evolutionary analyses were conducted using WGS data from this study and the NCBI database.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Almost all 108 Salmonella Indiana strains displayed the MDR phenotype. Importantly, 84 isolates possessed concurrent resistance to ciprofloxacin and cefotaxime. WGS analysis revealed that class 1 integrons on the chromosome and IncHI2 plasmids were the key vectors responsible for multiple antibiotic resistance gene (ARG) [including ESBL and plasmid-mediated quinolone resistance (PMQR) genes] transmission among Salmonella Indiana. The 108 Salmonella Indiana dataset displayed a relatively large core genome and ST17 was the predominant ST. Moreover, the global ST17 Salmonella Indiana strains could be divided into five distinct lineages, each of which was significantly associated with a geographical distribution. Genomic analysis revealed multiple antimicrobial resistance determinants and QRDR mutations in Chinese lineages, which almost did not occur in other global lineages. Using molecular clock analysis, we hypothesized that ST17 isolates have existed since 1956 and underwent a major population expansion from the 1980s to the 2000s and the genetic diversity started to decrease around 2011, probably due to geographical barriers, antimicrobial selective pressure and MDR, favouring the establishment of this prevalent multiple antibiotic-resistant lineage and local epidemics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>This study revealed that adaptation to antimicrobial pressure was possibly pivotal in the recent evolutionary trajectory for the clonal spread of ST17 Salmonella Indiana in China.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jac\/dkac243","type":"journal-article","created":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T11:59:16Z","timestamp":1658836756000},"page":"2937-2945","source":"Crossref","is-referenced-by-count":20,"title":["Phylogenomic analysis of <i>Salmonella<\/i> Indiana ST17, an emerging MDR clonal group in China"],"prefix":"10.1093","volume":"77","author":[{"given":"Ruan-Yang","family":"Sun","sequence":"first","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen-Ying","family":"Guo","sequence":"additional","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji-Xing","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min-Ge","family":"Wang","sequence":"additional","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin-Lin","family":"Wang","sequence":"additional","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin-Lei","family":"Lian","sequence":"additional","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bi-Xia","family":"Ke","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Center for Disease Control and Prevention , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Sun","sequence":"additional","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chang-Wen","family":"Ke","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Center for Disease Control and Prevention , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya-Hong","family":"Liu","sequence":"additional","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou, Jiangsu, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Ping","family":"Liao","sequence":"additional","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang-Xing","family":"Fang","sequence":"additional","affiliation":[{"name":"National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University , Guangzhou, Guangdong, P. R. China"},{"name":"Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University , Guangzhou, Guangdong, P. R. 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by Salmonella indiana","volume":"82","author":"Price","year":"1967","journal-title":"Public Health Rep (1896)"},{"key":"2022102819184916100_dkac243-B4","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1111\/zph.12328","article-title":"Prevalence and antimicrobial resistance of Salmonella enterica serovar Indiana in China (1984-2016)","volume":"64","author":"Gong","year":"2017","journal-title":"Zoonoses Public Health"},{"key":"2022102819184916100_dkac243-B5","doi-asserted-by":"crossref","DOI":"10.1016\/j.foodcont.2021.108427","article-title":"Antimicrobial susceptibility and molecular characterization of Salmonella enterica serovar Indiana from foods, patients, and environments in China during 2007\u20132016","volume":"131","author":"Zhang","year":"2022","journal-title":"Food Control"},{"key":"2022102819184916100_dkac243-B6","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.ijfoodmicro.2017.09.012","article-title":"Emergence of Salmonella enterica serovar Indiana 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