Unique genes identified in the epidemic extremely drug-resistant KPC-producing Klebsiella pneumoniae sequence type 258

A KPC-producing Klebsiella pneumoniae clone, sequence type (ST) 258, has emerged and spread worldwide. This study aimed to identify putative genes that may contribute to the extraordinary dissemination of the KPC-producing ST258 clone. A suppressive subtractive hybridization (SSH) library was constructed using two KPC-producing strains: an epidemic ST258 and a non-epidemic ST376. The fragments obtained were sequenced, analysed and their presence among 27 additional ST258 isolates and 21 isolates of non-epidemic STs was determined. The functions of the putative proteins were extracted from NCBI databases. Localization to plasmid/chromosome was determined by PCR after transformation and by Southern hybridization. In silico homologues for the subtractive fragments were searched among sequences available in the NCBI database. SSH yielded 42 fragments (50 proteins) specific to the ST258 isolate tested, 30 of them located on various plasmids. The ST258 strains examined could be divided into two groups, one in which all 50 genes were ubiquitous and another group that lost 11 fragments, all located on one of the plasmids. This group of 50 genes was absent among other STs tested. Nineteen genes were unique to ST258 strains and 17 to CC258 (where CC stands for clonal complex). Most of the deduced proteins belonged to two major functional groups: 15 to the cell motility and secretion group, and 14 to the DNA repair and modification group. This study identifies unique genes in ST258 bacteria that may contribute to its epidemiological success as compared with other KPC-producing STs. Conservation of plasmid-encoded genes among ST258 isolates, despite plasmid variation, supports their importance in the success of this clone.