Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms

Abstract

BackgroundKlebsiella pneumoniae is an important opportunistic pathogen associated with nosocomial and community-acquired infections. A wide repertoire of virulence and antimicrobial resistance genes is present in K. pneumoniae genomes, which can constitute extra challenges in the treatment of infections caused by some strains. K. pneumoniae Kp13 is a multidrug-resistant strain responsible for causing a large nosocomial outbreak in a teaching hospital located in Southern Brazil. Kp13 produces K. pneumoniae carbapenemase (KPC-2) but is unrelated to isolates belonging to ST 258 and ST 11, the main clusters associated with the worldwide dissemination of KPC-producing K. pneumoniae. In this report, we perform a genomic comparison between Kp13 and each of the following three K. pneumoniae genomes: MGH 78578, NTUH-K2044 and 342.ResultsWe have completely determined the genome of K. pneumoniae Kp13, which comprises one chromosome (5.3 Mbp) and six plasmids (0.43 Mbp). Several virulence and resistance determinants were identified in strain Kp13. Specifically, we detected genes coding for six beta-lactamases (SHV-12, OXA-9, TEM-1, CTX-M-2, SHV-110 and KPC-2), eight adhesin-related gene clusters, including regions coding for types 1 (fim) and 3 (mrk) fimbrial adhesins. The rmtG plasmidial 16S rRNA methyltransferase gene was also detected, as well as efflux pumps belonging to five different families. Mutations upstream the OmpK35 porin-encoding gene were evidenced, possibly affecting its expression. SNPs analysis relative to the compared strains revealed 141 mutations falling within CDSs related to drug resistance which could also influence the Kp13 lifestyle. Finally, the genetic apparatus for synthesis of the yersiniabactin siderophore was identified within a plasticity region. Chromosomal architectural analysis allowed for the detection of 13 regions of difference in Kp13 relative to the compared strains.ConclusionsOur results indicate that the plasticity occurring at many hierarchical levels (from whole genomic segments to individual nucleotide bases) may play a role on the lifestyle of K. pneumoniae Kp13 and underlie the importance of whole-genome sequencing to study bacterial pathogens. The general chromosomal structure was somewhat conserved among the compared bacteria, and recombination events with consequent gain/loss of genomic segments appears to be driving the evolution of these strains.

Population Structure of KPC-Producing Klebsiella pneumoniae Isolates from Midwestern U.S. Hospitals

“…The cps locus in ST258b strains has one nucleotide difference from the wzi-81 allele in the typing scheme of Brisse et al (16) and bears rhamnoseutilizing genes. The cps locus in these strains was most similar to that in the bla KPC-2 -producing Kp13 strain from Brazil (17,18) and clade 2 strains in reference 8, cps in reference 19, and to the cps locus in the KPNIH strains, with more than 99.99% nucleotide identity throughout the 50-kb region. The cps locus in ST258a strains (wzi-29) was nearly identical to the cps locus in the ST258 clade 1 (8), in VA360 (ANGI00000000), a bla KPC-2 ST258 strain from Ohio, in KpMDU1 (AMWO00000000), a bla KPC-2 strain from Australia, and to cps 207-2 (19).…”

The Challenge of Efflux-Mediated Antibiotic Resistance in Gram-Negative Bacteria

“…The genome of K. pneumoniae shows the presence of a large number of drug efflux pumps similar to those observed in E. coli (290). The overexpression of efflux pumps, most probably that of AcrAB, is important in resistance to certain agents, such as chloramphenicol and tetracycline but especially fluoroquinolones (see references 291 and 292).…”

Aminoglycoside Resistance

“…60,61 rmtG is flanked downstream by IS Vsa3 , but this insertion sequence likely belongs to the site of insertion of the module carrying rmtG rather than the rmtG -containing module itself. 62 There are currently no data on the epidemiology of rmtG .…”