{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T16:27:12Z","timestamp":1787934432044,"version":"build-2784847793"},"reference-count":45,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,1,29]],"date-time":"2025-01-29T00:00:00Z","timestamp":1738108800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Colistin is commonly used as a last-resort antibiotic for multidrug resistance (MDR) bacterial infections. The emergence of colistin-resistant (CL-R) <jats:italic>Salmonella<\/jats:italic> has become a significant public health concern. However, the prevalence of CL-R <jats:italic>Salmonella<\/jats:italic> in Guizhou province remains unknown. Therefore, it is necessary to monitor CL-R <jats:italic>Salmonella<\/jats:italic> in Guizhou and systematically elucidate their characteristics-related resistance, virulence, and molecular epidemiology to develop effective public health strategies against resistant pathogens.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>The CL-R <jats:italic>Salmonella<\/jats:italic> isolates were identified from 933 <jats:italic>Salmonella<\/jats:italic> isolates by antimicrobial resistance testing. To further evaluate the molecular epidemiology, the CL-R <jats:italic>Salmonella<\/jats:italic> isolates underwent whole-genome sequencing (WGS) analysis followed by bioinformatic analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A total of 43 CL-R isolates (4.6%) were identified from 933 <jats:italic>Salmonella<\/jats:italic> isolates, of which 39 isolates being MDR (resistance to three or more classes of antimicrobials). WGS analysis revealed 34 antibiotic resistance genes (ARGs), and point mutations in the <jats:italic>gyrA<\/jats:italic> gene (D87Y and D87G) were identified in all 43 CL-R isolates. Only one isolate carried the mcr-1.1 gene, a known colistin resistance. All CL-R isolates were found to carry multidrug efflux pumps. Furthermore, the most common resistance gene was <jats:italic>aac(6\u2032)-ly<\/jats:italic> (40 out of 43), followed by <jats:italic>bla<jats:sub>TEM-1<\/jats:sub><\/jats:italic> (39 out of 43). The majority of CL-R isolates contained the virulence factor <jats:italic>spvB<\/jats:italic> and a notable diversity in other virulence factors with varied functions. Core genome multilocus sequence typing (cgMLST) revealed that 43 CL-R <jats:italic>Salmonella<\/jats:italic> isolates were divided into 19 cgSTs, with cgST179151 (10 out of 43) being the most prevalent. Additionally, the CL-R <jats:italic>Salmonella<\/jats:italic> isolates exhibited genetic similarities with human <jats:italic>Salmonella<\/jats:italic> isolates from Poland, Canada, and Zhejiang province. Among the 42 CL-R isolates lacking markers for CL-R, 12 single-nucleotide variations (SNVs) were observed in 24 isolates using genome-wide association study (GWAS) analysis, which was possibly associated with colistin resistance.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>This study revealed that the majority of CL-R <jats:italic>Salmonella<\/jats:italic> isolates in Guizhou province exhibited MDR, with complex resistance mechanisms, representing a significant public health challenge. The genetic similarities between isolates from Guizhou and other regions suggested the possibility of international transmission or shared reservoirs of resistance. These results highlighted the urgent need for enhanced surveillance and effective public health strategies to address the risks posed by these pathogens in Guizhou.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2025.1498995","type":"journal-article","created":{"date-parts":[[2025,1,29]],"date-time":"2025-01-29T06:46:14Z","timestamp":1738133174000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Genome analysis of colistin-resistant Salmonella isolates from human sources in Guizhou of southwestern China, 2019\u20132023"],"prefix":"10.3389","volume":"16","author":[{"given":"Jingtong","family":"Wu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongxian","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lv","family":"You","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyu","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junhua","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ge","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shijun","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,1,29]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1089\/fpd.2011.1015","article-title":"Tentative colistin epidemiological cut-off value for Salmonella spp","volume":"9","author":"Agers\u00f8","year":"2012","journal-title":"Foodborne Pathog. Dis."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"965","DOI":"10.2147\/IDR.S199844","article-title":"Molecular mechanisms related to colistin resistance in Enterobacteriaceae","volume":"12","author":"Aghapour","year":"2019","journal-title":"Infect Drug Resist."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1135614","DOI":"10.3389\/fmicb.2023.1135614","article-title":"Editorial: emerging multidrug-resistant bacterial pathogens \u201csuperbugs\u201d: a rising public health threat","volume":"14","author":"Algammal","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/s12920-024-01795-w","article-title":"Whole genome sequencing in clinical practice","volume":"17","author":"Bagger","year":"2024","journal-title":"BMC Med. Genet."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"1002","DOI":"10.3389\/fmicb.2016.01002","article-title":"Adhesion, biofilm formation, and genomic features of Campylobacter jejuni bf, an atypical strain able to grow under aerobic conditions","volume":"7","author":"Bronnec","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"e1007261","DOI":"10.1371\/journal.pgen.1007261","article-title":"A genomic overview of the population structure of Salmonella","volume":"14","author":"Casades\u00fas","year":"2018","journal-title":"PLoS Genet."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"106498","DOI":"10.1016\/j.ijantimicag.2021.106498","article-title":"Unveiling the evolution routes of TEM-type extended-spectrum \u03b2-lactamases","volume":"59","author":"Cheng","year":"2022","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref8","volume-title":"Performance Standards for Antimicrobial Susceptibility Testing","year":"2023"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"431","DOI":"10.3855\/jidc.157","article-title":"Typhi genes expressed during infection or involved in pathogenesis","volume":"2","author":"Daigle","year":"2008","journal-title":"J. Infect. Developing Countries"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"461","DOI":"10.3390\/microorganisms7100461","article-title":"Global burden of colistin-resistant bacteria: mobilized colistin resistance genes study (1980\u20132018)","volume":"7","author":"Elbediwi","year":"2019","journal-title":"Microorganisms"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1080\/22221751.2020.1754133","article-title":"Colistin and its role in the era of antibiotic resistance: an extended review (2000\u20132019)","volume":"9","author":"El-sayed Ahmed","year":"2020","journal-title":"Emerg. Microbes Infect."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"e8583","DOI":"10.2903\/j.efsa.2024.8583","article-title":"The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021-2022","volume":"22","author":"European Food Safety Prevention Control","year":"2024","journal-title":"EFSA J."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1128\/CMR.00066-12","article-title":"Salmonella enterica Serovar typhimurium skills to succeed in the host: virulence and regulation","volume":"26","author":"F\u00e0brega","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1111\/omi.12160","article-title":"Inactivation of the spxA1 or spxA2 gene of Streptococcus mutans decreases virulence in the rat caries model","volume":"32","author":"Galv\u00e3o","year":"2016","journal-title":"Mol Oral Microbiol"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"2005","DOI":"10.3390\/microorganisms11082005","article-title":"High levels of antibiotic resistance in MDR-strong biofilm-forming Salmonella Typhimurium ST34 in southern China","volume":"11","author":"Gao","year":"2023","journal-title":"Microorganisms"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/nrg2575","article-title":"Mapping genes for complex traits in domestic animals and their use in breeding programmes","volume":"10","author":"Goddard","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"1133241","DOI":"10.3389\/fmicb.2023.1133241","article-title":"Comprehensive profiling of serotypes, antimicrobial resistance and virulence of Salmonella isolates from food animals in China, 2015\u20132021","volume":"14","author":"Guo","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1038\/s44259-024-00023-w","article-title":"Multidrug efflux in gram-negative bacteria: structural modifications in active compounds leading to efflux pump avoidance","volume":"2","author":"Gurvic","year":"2024","journal-title":"npj Antimicrobals Resistance"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1089\/107662903764736319","article-title":"Topoisomerase IV mutations in quinolone-resistant salmonellae selected in vitro","volume":"9","author":"Heisig","year":"2003","journal-title":"Microb. Drug Resist."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1016\/j.ijantimicag.2016.09.016","article-title":"Colistin use and colistin resistance in bacteria from animals","volume":"48","author":"Isabelle","year":"2016","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"504","DOI":"10.14202\/vetworld.2019.504-521","article-title":"A review of Salmonella enterica with particular focus on the pathogenicity and virulence factors, host specificity and antimicrobial resistance including multidrug resistance","volume":"12","author":"Jajere","year":"2019","journal-title":"Vet. World"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1089\/fpd.2018.2468","article-title":"Increase in ceftriaxone resistance and widespread extended-spectrum \u03b2-lactamases genes among Salmonella enterica from human and nonhuman sources","volume":"15","author":"Kuang","year":"2018","journal-title":"Foodborne Pathog. Dis."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"12797","DOI":"10.1038\/ncomms12797","article-title":"Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes","volume":"7","author":"Lees","year":"2016","journal-title":"Nat. Commun."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/S1473-3099(15)00424-7","article-title":"Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study","volume":"16","author":"Liu","year":"2016","journal-title":"Lancet Infect. Dis."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1093\/trstmh\/trw051","article-title":"Antimicrobial susceptibility pattern and sequence analysis of DNA gyrase and DNA topoisomerase IV in Salmonella entericaserovars typhi and paratyphi a isolates with decreased susceptibility to ciprofloxacin","volume":"110","author":"Misra","year":"2016","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1038\/s41429-021-00417-2","article-title":"Mutations in two component system (PhoPQ and PmrAB) in colistin resistant Klebsiella pneumoniae from North Indian tertiary care hospital","volume":"74","author":"Nirwan","year":"2021","journal-title":"J. Antibiot. (Tokyo)"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"643","DOI":"10.3389\/fmicb.2014.00643","article-title":"Mechanisms of polymyxin resistance: acquired and intrinsic resistance in bacteria","volume":"5","author":"Olaitan","year":"2014","journal-title":"Front. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1089\/fpd.2017.2403","article-title":"Health outcomes from multidrug-resistant Salmonella infections in high-income countries: a systematic review and meta-analysis","volume":"15","author":"Parisi","year":"2018","journal-title":"Foodborne Pathog. Dis."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analysis","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"ref001","year":"2023","journal-title":"R: A Language and Environment for Statistical Computing"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/mBio.02831-19","article-title":"The O-antigen epitope governs susceptibility to colistin in Salmonella enterica","volume":"11","author":"Ricci","year":"2020","journal-title":"MBio"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1574-6968.2010.01904.x","article-title":"So similar, yet so different: uncovering distinctive features in the genomes of Salmonella enterica serovars typhimurium and typhi","volume":"305","author":"Sabbagh","year":"2010","journal-title":"FEMS Microbiol. Lett."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1016\/j.tim.2018.02.006","article-title":"Towards understanding MCR-like colistin resistance","volume":"26","author":"Sun","year":"2018","journal-title":"Trends Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1186\/s12866-024-03306-4","article-title":"Genome analyses of colistin-resistant high-risk blaNDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings","volume":"24","author":"Talat","year":"2024","journal-title":"BMC Microbiol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1111\/j.1574-6976.2002.tb00606.x","article-title":"Antimicrobial drug resistance in Salmonella: problems and perspectives in food- and water-borne infections","volume":"26","author":"Threlfall","year":"2002","journal-title":"FEMS Microbiol. Rev."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"646","DOI":"10.3760\/cma.j.cn311365-20191220-00420","article-title":"Study on the serotype, drug sensitivity and virulence genes of clinical isolates of Salmonella in Zhejiang Province","volume":"38","author":"Wang","year":"2020","journal-title":"Chinese J. Infect. Dis."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"653","DOI":"10.16506\/j.1009-6639.2023.07.006","article-title":"Major serotypes and antibiotic resistance phenotype of Salmonella in patients with diarrhea in a district of Beijing, 2018-2021","volume":"24","author":"Wang","year":"2023","journal-title":"Chin. Prev. Med."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"e0282254","DOI":"10.1371\/journal.pone.0282254","article-title":"Serotype distribution, trend of multidrug resistance and prevalence of \u03b2-lactamase resistance genes in human Salmonella isolates from clinical specimens in Guizhou, China","volume":"18","author":"Wei","year":"2023","journal-title":"PLoS One"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"W587","DOI":"10.1093\/nar\/gkad359","article-title":"Tree visualization by one table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees","volume":"51","author":"Xie","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"3848","DOI":"10.20043\/j.cnki.MPM.202306546","article-title":"Analysis of epidemiological characteristics of other infectious diarrhea in Guizhou Province from 2018 to 2022","volume":"50","author":"Yang","year":"2023","journal-title":"Modern Prevent. Med."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"542","DOI":"10.13590\/j.cjfh.2021.05.004","article-title":"Analysis of molecular type and antimicrobial resistance of clinical strains of Salmonella in Shaoxing, 2017-2019","volume":"33","author":"Zhang","year":"2021","journal-title":"Chinese J. Food Hygiene"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"536","DOI":"10.13590\/j.cjfh.2021.05.003","article-title":"Serotypes and drug resistance characteristics of Salmonella isolated from diarrheal patients in Anhui Province, 2015-2020","volume":"33","author":"Zhang","year":"2021","journal-title":"Chinese J. Food Hygiene"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1292401","DOI":"10.3389\/fvets.2023.1292401","article-title":"Antimicrobial resistance and genomic characteristics of Salmonella from broilers in Shandong Province","volume":"10","author":"Zhao","year":"2023","journal-title":"Front. Vet. Sci."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1498995\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,29]],"date-time":"2025-01-29T06:46:23Z","timestamp":1738133183000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1498995\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,29]]},"references-count":45,"alternative-id":["10.3389\/fmicb.2025.1498995"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1498995","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,29]]},"article-number":"1498995"}}