First report and genomic characterization of an mcr-10.1-carrying Enterobacter kobei strain isolated from a domestic kitchen sink in China
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Background
The Enterobacter cloacae complex (ECC), a member of the genus Enterobacter within the family Enterobacteriaceae, is an important opportunistic pathogen associated with nosocomial infections. Colistin is considered a last-resort antimicrobial for multidrug-resistant Gram-negative infections; however, the emergence and dissemination of plasmid-mediated colistin resistance genes, particularly mcr variants, have raised significant public health concerns. Among these, mcr-10 has been increasingly detected in ECC isolates from diverse clinical and environmental sources, underscoring the importance of genomic surveillance to elucidate its genetic context and transmission potential.
Methods
Swab samples were collected from a kitchen sink and cultured for bacterial isolation, followed by species identification using MALDI-TOF MS. Antimicrobial susceptibility was determined by the broth microdilution method, with results interpreted according to EUCAST and CLSI guidelines. Whole-genome sequencing was performed using a hybrid approach combining Illumina short-read and Oxford Nanopore long-read sequencing. Genome annotation and antimicrobial resistance gene detection were conducted using RAST and ResFinder, respectively. Multilocus sequence typing and plasmid replicon typing were performed using the MLST and PlasmidFinder tools. Comparative plasmid analysis was carried out with EasyFig and BLAST Ring Image Generator, while phylogenetic relationships were inferred using a core-genome-based phylogenetic analysis, and the resulting tree was visualized with iTOL.
Results
Enterobacter kobei JX24083 was resistant to cefazolin, cefoxitin, and fosfomycin. Consistently, the isolate harbored the resistance genes bla ACT-9 and fosA on the chromosome. The colistin resistance gene mcr-10.1 was identified on an IncFIB plasmid in the isolate; however, the isolate remained susceptible to colistin (MIC = 1 mg/L). Exposure to subinhibitory concentrations of colistin upregulated mcr-10.1 expression in vitro. Comparative sequence analysis revealed a conserved xerC–mcr-10 genetic context among Enterobacter kobei isolates harboring plasmid-borne mcr-10. Phylogenetic analysis of JX24083 together with 46 mcr-10 -carrying ECC isolates from GenBank showed that several dominant sequence types, including ST681, ST125, and ST1, were distributed across different hosts and countries, indicating the potential for international dissemination.
Conclusion
The first report of an E. kobei isolate from a domestic kitchen sink in China carrying a conserved xerC–mcr-10 plasmid backbone, yet remaining susceptible to colistin, highlights the potential for silent dissemination of mcr-10 within the Enterobacter cloacae complex (ECC) and underscores the need for continuous One Health-oriented surveillance of environmental reservoirs.
