First genome sequence of a blaKPC-2-carrying Citrobacter koseri isolate collected from a patient with diarrhoea.

Abstract

The blaKPC gene is rarely reported in Citrobacter koseri. Here we report the first draft genome sequence of a blaKPC-2-carrying C. koseri isolate from a patient with diarrhoea. Transferability of the blaKPC-2-bearing plasmid was determined by the filter mating method. The whole genome sequence of C. koseri L168 was determined using an Illumina HiSeq platform. The genome was de novo assembled using Velvet 1.2.10. Acquired antimicrobial resistance genes and plasmid replicons were identified using ResFinder 2.1 and PlasmidFinder 1.3, respectively. Antimicrobial susceptibility testing (AST) showed that C. koseri L168 was resistant to multiple antibiotics but was susceptible to ciprofloxacin, gentamicin, tobramycin, amikacin, tigecycline and colistin. A KPC-2-harbouring plasmid was conjugative and the transconjugants conferred increased resistance to carbapenems confirmed by conjugation experiments and AST. In silico analysis revealed the presence of the β-lactam resistance genes blaKPC-2 and blaMAL-1. Additionally, plasmids of incompatibility groups IncFII and IncX4 were identified in the genome by PlasmidFinder. BLAST analysis revealed that blaKPC-2 was located on a Tn3 transposon element in C. koseri L168 with the conserved linear structure ISKpn27-blaKPC-2-ΔISKpn6-korC-klcA. To our knowledge, this is only the second report of C. koseri producing KPC-2, and we report the first draft genome sequence of a blaKPC-2-carrying C. koseri isolate from a patient with diarrhoea in China. This work may facilitate our understanding of the pathogenesis, multidrug resistance mechanisms and genomic features of this species. Further monitoring of bacteria carrying carbapenemase genes in patients' gut microbiota is warranted.