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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 showed a significantly decrease between 2016 and 2019, genetic differences in MCRPEC strains remain largely unknown. We therefore conducted a comparative genomics study on MCRPEC strains from fecal samples from healthy human subjects in 2016 and 2019. We identified three major differences in MCRPEC between these two time points. (i) The insertion sequence ISApl1 was often deleted and the percentage of mcr-1-carrying IncI2 plasmids was increased. (ii) The antimicrobial resistance genes, aac(3)-IVa and blaCTX-M-1, emerged and coexisted with mcr-1 in 2019. (iii) MCRPEC strains in 2019 contain more virulence genes, resulting in an increase in the proportion of mcr-1 in extraintestinal pathogenic E. coli (ExPEC) strains (36.1%) compared to commensal E. coli strains (10.5%), implying that these strains could occupy intestinal ecological niches by competing with other commensal bacteria. Our data suggest that despite the significant reduction in the prevalence of MCRPEC strains in human subjects, mcr-1 is now associated with more stable genetic structures and widespread IncI2 plasmid. Furthermore, mcr-1 has an increased coexistence with other clinically important antibiotic resistance genes, and is increasingly associated with ExPEC strains, thus posing a potential public health threat.

Original publication




Journal article


Genomics Proteomics Bioinformatics

Publication Date



Colistin, Escherichia coli, Genomics, Human, mcr-1