Genomic epidemiology of complex, multi-species, plasmid-borne blaKPC carbapenemase in Enterobacterales in the UK, 2009-2014

Journal article

Carbapenem resistance in Enterobacterales is a public health threat. Klebsiella pneumoniae carbapenemase (encoded by alleles of the blaKPC family) is one of the commonest transmissible carbapenem resistance mechanisms worldwide. The dissemination of blaKPC has historically been associated with distinct K. pneumoniae lineages (clonal group 258 [lsqb]CG258[rsqb]), a particular plasmid family (pKpQIL), and a composite transposon (Tn4401). In the UK, 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 poly-species, 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 characterisation. We observed the dissemination of blaKPC (predominantly blaKPC-2; 573/604 [lsqb]95%[rsqb] 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 [lsqb]77%[rsqb] isolates), blaKPC spread appears to have been supported by highly fluid, modular exchange of larger genetic segments amongst plasmid populations dominated by IncFIB (580/604 isolates), IncFII (545/604 isolates) and IncR replicons (252/604 isolates). The subset of reconstructed plasmid sequences (21 isolates, 77 plasmids) also highlighted modular exchange amongst 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.

Authors: Stoesser, N; Phan, HTT; Seale, A; Aiken, Z; Thomas, S

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: American Society for Microbiology
• Journal: Antimicrobial Agents and Chemotherapy
• Volume: 64
• Issue: 5
• Article number: e02244-19
• Publication date: 2020-02-24
• Acceptance date: 2020-02-21
• DOI: 10.1128/AAC.02244-19
• ISSN: 0066-4804
• Language: English
• Keywords: short-read sequencing; KPC; long-read sequencing; carbapenemase; whole genome sequencing; FFR; enterobacterales