{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T21:34:45Z","timestamp":1775511285549,"version":"3.50.1"},"reference-count":37,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T00:00:00Z","timestamp":1760313600000},"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. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Objectives<\/jats:title><jats:p>The rapid dissemination of carbapenem-resistant <jats:italic>Enterobacteriaceae<\/jats:italic> (CRE) poses a severe global health threat due to limited treatment options. Polymyxin is currently considered a last-resort therapy for human infections caused by CRE. The increasing clinical use of polymyxin has resulted in alarming resistance rates. This study investigated the clinical characteristics, molecular epidemiological characteristics, and resistance mechanisms of polymyxin-resistant CRE (PR-CRE) in Chongqing, China.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Antimicrobial susceptibility and resistance genes were analyzed by PCR-based amplification and sequence analysis. Molecular epidemiological characteristics were analyzed using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR and multilocus sequence typing (MLST). The gene expression of <jats:italic>pmrC<\/jats:italic> and <jats:italic>pmrK<\/jats:italic> was analyzed using qRT-PCR. Conjugation experiments were performed to determine plasmid transferability. Whole-genome sequencing (WGS) was performed to analyze their genetic environment.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Thirty PR-CRE isolates, including 21 <jats:italic>Klebsiella pneumoniae<\/jats:italic> and 9 <jats:italic>Escherichia coli<\/jats:italic>, exhibited multidrug resistance, with three pan-resistant <jats:italic>K. pneumoniae<\/jats:italic> strains. The predominant lineage was ST11-K64 <jats:italic>K. pneumoniae<\/jats:italic> (n=14\/21), with four genetically identical isolates from ICUs, confirming clonal transmission. In contrast, all <jats:italic>E. coli<\/jats:italic> displayed high genetic diversity. Hypervirulence determinants were detected in 38.1% (n=8\/21) of <jats:italic>K. pneumoniae<\/jats:italic>. Two rare <jats:italic>K. pneumoniae<\/jats:italic> strains were identified: one hypervirulent ST3984-KL64 strain co-harboring <jats:italic>bla<\/jats:italic><jats:sub>KPC-2<\/jats:sub> and <jats:italic>bla<\/jats:italic><jats:sub>NDM-1<\/jats:sub>, and one ST2383-KL81 strain harboring <jats:italic>bla<\/jats:italic><jats:sub>OXA-48<\/jats:sub>. Species-specific resistance mechanisms emerged: <jats:italic>K. pneumoniae<\/jats:italic> relied on chromosomal mutations in <jats:italic>mgrB<\/jats:italic>, <jats:italic>phoPQ<\/jats:italic>, and <jats:italic>pmrAB<\/jats:italic>, especially <jats:italic>mgrB<\/jats:italic> inactivation (57.1%, n=12\/21) via IS<jats:italic>Kpn26<\/jats:italic>\/IS<jats:italic>903B<\/jats:italic>\/IS<jats:italic>Aeme19<\/jats:italic>\/IS<jats:italic>Kpn14<\/jats:italic> and <jats:italic>pmrK<\/jats:italic> upregulation (95.2%, n=20\/21), while <jats:italic>E. coli<\/jats:italic> exclusively used plasmid-borne <jats:italic>mcr-1<\/jats:italic> with 55.6% (n=5\/9) conjugation efficiency, conferring low-level resistance. Genomic sequencing revealed that four identical IS<jats:italic>Aeme19<\/jats:italic> copies were first identified in ST11-KL64 hypervirulent CRKP-5: two on the chromosome (<jats:italic>mgrB<\/jats:italic> and <jats:italic>kdsD<\/jats:italic>), and two on plasmids (IncFII\/IncR pkp2007-KPC and recombinant pkp2007-D). Transposition of IS<jats:italic>Aeme19<\/jats:italic> from pkp2007-KPC to <jats:italic>mgrB<\/jats:italic> was evidenced by the inverted orientation and matching flanking repeats. Crucially, a pan-resistant ST11-KL64 <jats:italic>K. pneumoniae<\/jats:italic> harbored a fusion plasmid with dual <jats:italic>bla<\/jats:italic><jats:sub>KPC-2<\/jats:sub> and <jats:italic>catA2<\/jats:italic> copies bracketed by IS<jats:italic>26<\/jats:italic>, a previously unreported configuration. Additionally, four novel deleterious mutations were detected: <jats:italic>mgrB<\/jats:italic>-Asn25Thr, <jats:italic>phoP<\/jats:italic>-Lys199Met, <jats:italic>phoQ<\/jats:italic>-Tyr89His, and <jats:italic>RamR<\/jats:italic>-Ala17Thr.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>These findings reveal species-divergent resistance mechanisms to polymyxin, necessitating enhanced surveillance of these high-risk clones, mobile elements, and emergent resistance mechanisms.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2025.1678719","type":"journal-article","created":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T05:28:19Z","timestamp":1760333299000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Clonal transmission and species-specific mechanisms of polymyxin resistance in carbapenem-resistant Enterobacteriaceae from Southwest China"],"prefix":"10.3389","volume":"15","author":[{"given":"Tingting","family":"Si","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peiwen","family":"Xia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Na","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shiyu","family":"Tang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuqiong","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Han","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanyuan","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yingyi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yun","family":"Xia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,10,13]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuab049","article-title":"Global colistin use: a review of the emergence of resistant Enterobacterales and the impact on their genetic basis","volume":"46","author":"Binsker","year":"2021","journal-title":"FEMS Microbiol. Rev."},{"key":"B2","doi-asserted-by":"publisher","first-page":"5696","DOI":"10.1128\/aac.03110-14","article-title":"MgrB inactivation is a common mechanism of colistin resistance in KPC-producing klebsiella pneumoniae of clinical origin","volume":"58","author":"Cannatelli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B3","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B4","doi-asserted-by":"publisher","first-page":"2909","DOI":"10.1128\/AAC.04763-14","article-title":"Colistin resistance mechanisms in klebsiella pneumoniae strains from Taiwan","volume":"59","author":"Cheng","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"B5","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","article-title":"Identifying bacterial genes and endosymbiont DNA with Glimmer","volume":"23","author":"Delcher","year":"2007","journal-title":"Bioinforma. Oxf. Engl."},{"key":"B6","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":"B7","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1016\/j.jgar.2018.11.017","article-title":"Coexistence of three blaKPC-2 genes on an IncF\/IncR plasmid in ST11 Klebsiella pneumoniae","volume":"17","author":"Feng","year":"2019","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"B8","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/j.ijantimicag.2017.10.011","article-title":"Expansion of KPC-producing Klebsiella pneumoniae with various mgrB mutations giving rise to colistin resistance: the role of ISL3 on plasmids","volume":"51","author":"Giordano","year":"2018","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B9","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1196\/annals.1409.006","article-title":"The structure and function of francisella lipopolysaccharide","volume":"1105","author":"Gunn","year":"2007","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"B10","doi-asserted-by":"publisher","first-page":"e00762","DOI":"10.1128\/mBio.00762-15","article-title":"Insertion sequence IS26 reorganizes plasmids in clinically isolated multidrug-resistant bacteria by replicative transposition","volume":"6","author":"He","year":"2015","journal-title":"mBio"},{"key":"B11","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1038\/s41564-024-01612-1","article-title":"Carbapenem-resistant Klebsiella pneumoniae capsular types, antibiotic resistance and virulence factors in China: a longitudinal, multi-centre study","volume":"9","author":"Hu","year":"2024","journal-title":"Nat. Microbiol."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00331-24","article-title":"Double blaKPC-2 copies quadrupled minimum inhibitory concentration of ceftazidime-avibactam in hospital-derived Klebsiella pneumoniae","volume":"12","author":"Hu","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"B13","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1080\/22221751.2020.1717380","article-title":"Colistin-resistance gene mcr in clinical carbapenem-resistant Enterobacteriaceae strains in China\u20132019","volume":"9","author":"Huang","year":"2020","journal-title":"Emerg. Microbes Infect."},{"key":"B14","doi-asserted-by":"publisher","first-page":"2780","DOI":"10.1128\/AAC.05055-14","article-title":"Heteroresistance to colistin in Klebsiella pneumoniae associated with alterations in the PhoPQ regulatory system","volume":"59","author":"Jayol","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"B15","doi-asserted-by":"publisher","first-page":"4762","DOI":"10.1128\/aac.00084-14","article-title":"Resistance to Colistin Associated with a Single Amino Acid Change in Protein PmrB among Klebsiella pneumoniae Isolates of Worldwide Origin","volume":"58","author":"Jayol","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"B16","doi-asserted-by":"publisher","first-page":"W229","DOI":"10.1093\/nar\/gky352","article-title":"oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements","volume":"46","author":"Li","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B17","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1016\/j.tim.2023.10.006","article-title":"Plasmid-mediated colistin-resistance genes: mcr","volume":"32","author":"Liu","year":"2024","journal-title":"Trends Microbiol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"3027","DOI":"10.1016\/j.scib.2023.10.038","article-title":"Chasing the landscape for intrahospital transmission and evolution of hypervirulent carbapenem-resistant Klebsiella pneumoniae","volume":"68","author":"Liu","year":"2023","journal-title":"Sci. Bull."},{"key":"B19","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1080\/22221751.2022.2036078","article-title":"Emergence of colistin-resistant hypervirulent Klebsiella pneumoniae (CoR-HvKp) in China","volume":"11","author":"Liu","year":"2022","journal-title":"Emerg. Microbes Infect."},{"key":"B20","doi-asserted-by":"publisher","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: a general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.941358","article-title":"Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update","volume":"12","author":"Mmatli","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1124\/pharmrev.120.000020","article-title":"Rescuing the last-line polymyxins: achievements and challenges","volume":"73","author":"Nang","year":"2021","journal-title":"Pharmacol. Rev."},{"key":"B23","doi-asserted-by":"publisher","first-page":"mgen000519","DOI":"10.1099\/mgen.0.000519","article-title":"Emerging carbapenem-resistant Klebsiella pneumoniae sequence type 16 causing multiple outbreaks in a tertiary hospital in southern Vietnam","volume":"7","author":"Nguyen","year":"2021","journal-title":"Microb. Genomics"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1016\/j.envint.2024.108554","article-title":"Molecular epidemiology and mechanisms of carbapenem and colistin resistance in Klebsiella and other Enterobacterales from treated wastewater in Croatia","volume":"185","author":"Puljko","year":"2024","journal-title":"Environ. Int."},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2021.106426","article-title":"Polymyxin resistance in Enterobacterales: overview and epidemiology in the Americas","volume":"58","author":"Rodr\u00edguez-Santiago","year":"2021","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1016\/j.genrep.2022.101635","article-title":"Global distribution, genotypes and prevalent sequence types of colistin-resistant Klebsiella pneumoniae isolated from clinical samples; A systematic review","volume":"28","author":"Sameni","year":"2022","journal-title":"Gene Rep."},{"key":"B27","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B28","doi-asserted-by":"publisher","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: the reference centre for bacterial insertion sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"B29","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1016\/S1473-3099(18)30792-8","article-title":"Effect of carbapenem resistance on outcomes of bloodstream infection caused by Enterobacteriaceae in low-income and middle-income countries (PANORAMA): a multinational prospective cohort study","volume":"19","author":"Stewardson","year":"2019","journal-title":"Lancet Infect. Dis."},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanwpc.2024.101204","article-title":"Heterogeneity of colistin resistance mechanism in clonal populations of carbapenem-resistant Klebsiella pneumoniae in Vietnam","volume":"51","author":"Sy","year":"2024","journal-title":"Lancet Reg. Health West. Pac."},{"key":"B31","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1016\/S1473-3099(19)30755-8","article-title":"Molecular and clinical epidemiology of carbapenem-resistant Enterobacterales in the (CRACKLE-2): a prospective cohort study","volume":"20","author":"van Duin","year":"2020","journal-title":"Lancet Infect. Dis."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PloS One"},{"key":"B33","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1016\/j.ijantimicag.2017.05.009","article-title":"Molecular epidemiology of colistin-resistant Enterobacteriaceae in inpatient and avian isolates from China: high prevalence of mcr-negative Klebsiella pneumoniae","volume":"50","author":"Wang","year":"2017","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PloS Comput. Biol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1038\/s43856-025-00748-3","article-title":"Increasing polymyxin resistance in clinical carbapenem-resistant Klebsiella pneumoniae strains in China between 2000 and 2023","volume":"5","author":"Xie","year":"2025","journal-title":"Commun. Med."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02624-21","article-title":"Comparison of two distinct subpopulations of klebsiella pneumoniae ST16 co-occurring in a single patient","volume":"10","author":"Zhang","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1277320","article-title":"Role of the ISKpn element in mediating mgrB gene mutations in ST11 hypervirulent colistin-resistant Klebsiella pneumoniae","volume":"14","author":"Zhu","year":"2023","journal-title":"Front. Microbiol."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1678719\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T05:28:20Z","timestamp":1760333300000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1678719\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,13]]},"references-count":37,"alternative-id":["10.3389\/fcimb.2025.1678719"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2025.1678719","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,13]]},"article-number":"1678719"}}