Abstract

Carbapenem-resistant Klebsiella pneumoniae is currently a global threat to public health and, due to their worldwide distribution, the strains belonging to the clonal complex 258 have received special attention, in particular the sequence type (ST) 258. The ancestral ST258 emerged from a chromosomal recombination event between strains from STs 11 and 443. After this event, and before epidemic spreading, the ancestral ST258 acquired a genomic island (GI) named ICEKp258.2 which encodes a putative type-III restriction-modification (RM) system and putative type-IV pilus-related proteins, features that suggest a role of this GI in the high dissemination capacity of ST258 and the restriction of the plasmids residing in these bacteria. Previous work from our laboratory identified ICEKp258.2 as an excisable island and a member of the Enterobacteriaceae-associated ROD21-like (EARL) family of GIs. Here, we describe the genetic features of ICEKp258.2 and its distribution. Also, to gain insight about the evolution of this GI, we identified the most closely related GIs to perform comparative and phylogenetic analyses. ICEKp258.2 carries 28 ORFs including 10 with predicted function. We found this GI not only in ST258 strains, but also in the single locus variants ST512, ST3795, and double locus variant ST1519. Related GIs (overall identity >88%) were found in several members of Enterobacteriaceae, including strains of Escherichia coli, Serratia marcescens, and K. pneumoniae strains from diverse STs. These islands, except by two, were integrated in an Asn-tRNA gene and belonged to the EARL family. The comparative analysis revealed that these GIs varied in gene content because the acquisition/lost and replacement of gene regions, conserving those involved in excision/integration, conjugation, type-IV pilus and the type-III RM. There were no identical GI to ICEKp258.2 in other Klebsiella STs or genus. However, the most similar island was found in a ST111 strain, differing only in four small ORFs without predicted function. This GI is likely a descendant of ICEKp258.2 according to our phylogenetic analysis based in four concatenated genes. The phylogeny also evidenced the intra and intergenus transmission of these GIs, which encode a putative TIR-domain-containing protein likely involved in subversion of the immune response. We hypothesize that the type-III RM system plays roles important for the biology of these GIs, contributing to their dissemination, together with putative virulence factors, among different pathogens from Enterobacteriaceae.