Whole genome sequence of an MCR-1-carrying, extended-spectrum β-lactamase (ESBL)-producing Escherichia coli ST746 isolate recovered from a community-acquired urinary tract infection

Abstract

Objectives: Colistin is regarded as one of the last-resort antimicrobials for severe infections. Isolates carrying the plasmid-borne mobile colistin resistance gene mcr-1 were rarely reported in community-acquired infections. Here we report the draft genome sequence of an MCR-1-carrying, extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolate from community-acquired urinary tract infection.

Methods: Antimicrobial susceptibility testing (AST) was performed by the broth microdilution method. Transferability of the mcr-bearing plasmid was determined by filter mating using E. coli EC600 as recipient strain. Multilocus sequence typing (MLST) was undertaken using the E. coli MLST database. The draft genome sequence of isolate LX13 was obtained using an Illumina HiSeq X-Ten platform. The genome was assembled using SOAPdenovo. Acquired antimicrobial resistance genes were identified using ResFinder 2.1.

Results: AST showed that LX13 was resistant to ampicillin, amoxicillin/clavulanic acid, piperacillin/tazobactam, cefazolin, cefepime and polymyxins. MLST showed that isolate LX13 belongs to ST746. The MCR-1-producing plasmid was conjugative and conferred increased resistance to colistin the transconjugant. The draft genome of E. coli LX13 was 4914035bp in size. In silico analysis revealed the presence of eight putative acquired resistance genes, including bla_CTX-M-14, bla_TEM-1B, aadA5, mcr-1, dfrA17, sul2, tet34 and tetA. plasmidSPAdes revealed that the mcr-1 gene was harboured by a plasmid of replicon type IncI2.

Conclusions: This study highlights the potential risk of spread of MCR-1-carrying, ESBL-producing E. coli in the community. The genome sequence of E. coli LX13 will facilitate the understanding of colistin resistance mechanisms and genomic features of clinically isolated colistin-resistant E. coli.

Keywords: Escherichia coli; ST746; Urinary tract infection; bla(CTX-M-14); mcr-1.