Genomic insights into colistin-resistant Escherichia coli from clinical isolates in Thailand: Diversity of sequence types, plasmid-borne mcr variants, and One Health implications
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Abstract
Background: Colistin is a last-resort antimicrobial agent for treating multidrugresistant Enterobacterales. However, resistance has emerged globally through plasmid-mediated mcr genes and chromosomal mutations. Reports of wholegenome sequencing of colistin-resistant Escherichia coli from clinical settings in Thailand remain limited.
Objectives: To characterize the molecular and phenotypic features of colistinresistant E. coli isolated from a tertiary hospital in Thailand using wholegenome sequencing (WGS).
Materials and methods: Fourteen colistin-resistant E. coli isolates were collected from clinical specimens between 2021 and 2022. Antimicrobial susceptibility testing was performed using broth microdilution. WGS was applied to identify resistance determinants, plasmid replicons, virulence genes, phylogroups, and sequence types.
Results: The prevalence of colistin-resistant E. coli was 1.2% (14/1203 isolates). Most isolates exhibited an ESBL-like multidrug-resistant profile with preserved carbapenem susceptibility. WGS revealed diverse sequence types (including ST131, ST95, ST58, ST69) and phylogroups, indicating polyclonal dissemination. Two mcr variants (mcr-1.1 and mcr-3.5) were identified on mobile plasmids (IncX4, IncI2, IncFII, IncHI2), with some isolates carrying both variants. Several isolates without mcr carried chromosomal mutations in mgrB, phoPQ, or pmrAB. Virulence genes, particularly adhesins, siderophore systems, and capsule- related determinants, were widely distributed. The detection of mcr-3.5, previously reported in livestock, within clinical isolates highlights potential zoonotic or foodborne transmission.
Conclusion: Colistin-resistant E. coli in Thailand shows significant genetic diversity and frequent coexistence of mcr and ESBL genes, often on plasmids with high potential for horizontal transfer. These findings emphasize the importance of antimicrobial stewardship, stricter control of drug use in animals, and integrated genomic surveillance under a One Health framework to mitigate the dissemination of colistin resistance.
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