Genomic Epidemiology of Complex, Multispecies, Plasmid-Borne bla _KPC Carbapenemase in Enterobacterales in the United Kingdom from 2009 to 2014

Abstract

Carbapenem resistance in Enterobacterales is a public health threat. Klebsiella pneumoniae carbapenemase (encoded by alleles of the blaKPC family) is one of the most common transmissible carbapenem resistance mechanisms worldwide. The dissemination of blaKPC historically has been associated with distinct K. pneumoniae lineages (clonal group 258 [CG258]), a particular plasmid family (pKpQIL), and a composite transposon (Tn4401). In the United Kingdom, blaKPC has represented a large-scale, persistent management challenge for some hospitals, particularly in North West England. The dissemination of blaKPC has evolved to be polyclonal and polyspecies, but the genetic mechanisms underpinning this evolution have not been elucidated in detail; this study used short-read whole-genome sequencing of 604 blaKPC-positive isolates (Illumina) and long-read assembly (PacBio)/polishing (Illumina) of 21 isolates for characterization. We observed the dissemination of blaKPC (predominantly blaKPC-2; 573/604 [95%] isolates) across eight species and more than 100 known sequence types. Although there was some variation at the transposon level (mostly Tn4401a, 584/604 [97%] isolates; predominantly with ATTGA-ATTGA target site duplications, 465/604 [77%] isolates), blaKPC spread appears to have been supported by highly fluid, modular exchange of larger genetic segments among plasmid populations dominated by IncFIB (580/604 isolates), IncFII (545/604 isolates), and IncR (252/604 isolates) replicons. The subset of reconstructed plasmid sequences (21 isolates, 77 plasmids) also highlighted modular exchange among non-blaKPC and blaKPC plasmids and the common presence of multiple replicons within blaKPC plasmid structures (>60%). The substantial genomic plasticity observed has important implications for our understanding of the epidemiology of transmissible carbapenem resistance in Enterobacterales for the implementation of adequate surveillance approaches and for control.

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

“…We resolved this paradox by showing how bla KPC-2 can still be preserved in the host: the carrier transposon is first transferred to another plasmid before IncFIB(pQil) removal from the host. Such spread of KPC genes between plasmids over short time scales has been documented previously [80, 81].…”

Molecular Analysis of bla KPC-2 -Harboring Plasmids: Tn 4401a Interplasmid Transposition and Tn 4401a -Carrying ColRNAI Plasmid Mobilization from Klebsiella pneumoniae to Citrobacter europaeus and Morganella morganii in a Single Patient

“…To date, nine Tn 4401 isoforms have been reported ( 12 – 17 ). The IncF group pKpQIL-like plasmid carrying Tn 4401 has been analyzed in detail ( 18 – 21 ). Furthermore, bla KPC -carrying Inc plasmids, e.g., IncFIIK1, IncFIIK2, IncFIA, IncN, IncI2, IncX, IncA/C, IncR, and ColE1, have been detected in various ST258 clones ( 5 , 18 , 22 ).…”

Distinguishing bla KPC Gene-Containing IncF Plasmids from Epidemiologically Related and Unrelated Enterobacteriaceae Based on Short- and Long-Read Sequence Data

“…Despite this, a recent study has stated that even these OXA-48 containing plasmids from outbreak-related patients could not be distinguished from similar plasmids of non-outbreak-related patients based on SNPs (26). Interestingly, other studies found bla KPC -containing plasmids to be highly variable in their nucleotide sequence within the same outbreak and even within patients (18,28). This suggests that the plasmid content could also be highly unstable in vivo during hospital outbreaks.…”

“…A pangenome was constructed, and phylogenetic distance based on gene presence/absence between the different plasmids was determined using Roary v1.13.2 (34). All plasmids were pairwise aligned using dnadiff, and a similarity index was calculated between the different plasmids as described by Stoesser et al (28) (Stoesser similarity index). This similarity index can vary from 0 (completely unsimilar plasmids) to 1 (identical plasmids) and, contrary to both Roary phylogenetic distance and number of SNPs, penalizes size differences between plasmids.…”