Genomic analysis of two bacterial strains co-isolated from a urinary tract infection: NDM-1-producing Enterobacter cloacae accompanied by extended-spectrum β-lactamase-producing Escherichia coli.

Abstract

Escherichia coli and Enterobacter cloacae are two major pathogens causing urinary tract infection (UTI). Here we characterised the genome of an NDM-1-producing E. cloacae strain and an extended-spectrum β-lactamase (ESBL)-producing E. coli strain that were co-isolated from a UTI. The genomes of E. cloacae strain EC32 and E. coli strain EC33 were sequenced using an Illumina HiSeqTM platform. The whole genome sequences were assembled using CLC Genomics Workbench and were annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) server. Genomic analysis was further performed. The draft genome sequences of E. cloacae EC32 (ST66) and E. coli EC33 (ST1139) consisted of 89 contigs comprising 5 178 393 bp and 62 contigs comprising 5 057 666 bp, respectively. Including the blaNDM-1 gene, in total 13 resistance genes were identified in E. cloacae EC32 conferring resistance to β-lactams, rifampicin, phenicols, fosfomycin, macrolides, quinolones, sulfonamides and tetracycline. Nine resistance genes were identified in E. coli EC33 including the ESBL-encoding gene blaCTX-M-27. To our knowledge, this is the first report of genomic characterisation of NDM-1-producing E. cloacae and ESBL-producing E. coli co-isolated from a UTI in China. The two strains inhabiting in the same environment may allow the possibility of horizontal transfer of blaNDM-1 and blaCTX-M-27, making clinical treatment even difficult. This report also sheds light on geographically distinct Enterobacteriaceae strains from China enabling a comparative analysis of NDM-1- or ESBL-producing strains.