Genomic Shift in Population Dynamics of mcr-1-positive Escherichia coli in Human Carriage

• Published in: Genomics, proteomics & bioinformatics Vol. 20; no. 6; pp. 1168 - 1179
• Main Authors: Shen, Yingbo, Zhang, Rong, Shao, Dongyan, Yang, Lu, Lu, Jiayue, Liu, Congcong, Wang, Xueyang, Jiang, Junyao, Wang, Boxuan, Wu, Congming, Parkhill, Julian, Wang, Yang, Walsh, Timothy R., Gao, George F., Shen, Zhangqi
• Format: Journal Article
• Language: English
• Published: China Elsevier B.V 01.12.2022; CAS Key Laboratory of Pathogenic Microbiology and Immunology,Institute of Microbiology,Chinese Academy of Sciences,Beijing 100101,China%The Second Affiliated Hospital of Zhejiang University School of Medicine,Zhejiang University,Hangzhou 310009,China%College of Veterinary Medicine,China Agricultural University,Beijing 100193,China%College of Veterinary Medicine,China Agricultural University,Beijing 100193,China; Guangdong Laboratory for Lingnan Modern Agriculture,Guangzhou 510641,China%Department of Veterinary Medicine,University of Cambridge,Cambridge CB3 0ES,UK%Department of Biology,University of Oxford,Oxford OX1 3SZ,UK%CAS Key Laboratory of Pathogenic Microbiology and Immunology,Institute of Microbiology,Chinese Academy of Sciences,Beijing 100101,China; College of Veterinary Medicine,China Agricultural University,Beijing 100193,China; Guangdong Laboratory for Lingnan Modern Agriculture,Guangzhou 510641,China; Chinese Center for Disease Control and Prevention,Beijing 102206,China; Elsevier; Oxford University Press
• Subjects: Anti-Bacterial Agents - pharmacology; antibiotic resistance; bioinformatics; Colistin; Drug Resistance, Bacterial - genetics; Escherichia coli; Escherichia coli - genetics; Escherichia coli Proteins - genetics; extraintestinal pathogenic Escherichia coli; Genomics; Human; Humans; intestines; mcr-1; Original Research; Plasmids; Population Dynamics; proteomics; public health; resistance genes; transposons; virulence; Human; Colistin; Escherichia coli; Genomics; mcr-1
• ISSN: 1672-0229; 2210-3244
• DOI: 10.1016/j.gpb.2022.11.006

Emergence of the colistin resistance gene, mcr-1, has attracted worldwide attention. Despite the prevalence of mcr-1-positive Escherichia coli (MCRPEC) strains in human carriage showing a significant decrease between 2016 and 2019, genetic differences in MCRPEC strains remain largely unknown. We therefore conducted a comparative genomic study on MCRPEC strains from fecal samples of healthy human subjects in 2016 and 2019. We identified three major differences in MCRPEC strains between these two time points. First, the insertion sequence ISApl1 was often deleted and the percentage of mcr-1-carrying IncI2 plasmids was increased in MCRPEC strains in 2019. Second, the antibiotic resistance genes (ARGs), aac(3)-IVa and blaCTX-M-1, emerged and coexisted with mcr-1 in 2019. Third, MCRPEC strains in 2019 contained more virulence genes, resulting in an increased proportion of extraintestinal pathogenic E. coli (ExPEC) strains (36.1%) in MCRPEC strains in 2019 compared to that in 2016 (10.5%), implying that these strains could occupy intestinal ecological niches by competing with other commensal bacteria. Our results suggest that despite the significant reduction in the prevalence of MCRPEC strains in humans from 2016 to 2019, MCRPEC exhibits increased resistance to other clinically important ARGs and contains more virulence genes, which may pose a potential public health threat.