Draft genome sequence of an NDM-5, CTX-M-15 and OXA-1 co-producing Escherichia coli ST167 clinical strain isolated from a urine sample

Abstract

Objectives: Escherichia coli is the leading cause of urinary tract infections worldwide. Carbapenemase-producing clinical isolates leave few therapeutic options. Here we report the draft genome sequence of an NDM-5, CTX-M-15, and OXA-1 co-producing E. coli sequence type 167 (ST167) multidrug-resistant clinical strain (ECWJ1) isolated from a urine sample of a hospitalised male patient diagnosed with intracranial injury from a road traffic accident.

Methods: The genome of E. coli ECWJ1 was sequenced using an Illumina HiSeq™ 4000 platform. The generated sequence reads were assembled using CLC Genomics Workbench. The draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) server, and further bioinformatics analysis was performed.

Results: Escherichia coli ECWJ1 belongs to ST167. The total genome length of the isolate is 4992753bp, with 4890 protein-coding sequences. The presence of bla_NDM-5, bla_CTX-M-15 and bla_OXA-1 genes was detected in addition to other antimicrobial resistance genes conferring resistance to aminoglycosides, fluoroquinolones, sulphonamides, trimethoprim and tetracyclines. Antimicrobial susceptibility testing revealed, that besides tigecycline and colistin, this isolate is resistant to all antimicrobials tested.

Conclusions: To our knowledge, this is the first report of an E. coli ST167 strain co-producing NDM-5, CTX-M-15 and OXA-1 isolated from urine sample in China. It may help us to understand the genomic features, molecular characteristics and resistance gene diversity of this bacterial pathogen. The genome sequence of E. coli ECWJ1 can be used as a reference sequence for comparative analysis of NDM-5-producing E. coli, aiming to reveal the mechanism of NDM-5 dissemination in this pathogen.

Keywords: Carbapenemase; Escherichia coli; NDM-5; Urinary tract infection; Whole-genome sequencing.