Plasmid genomic epidemiology of bla _KPC carbapenemase-producing Enterobacterales in Canada, 2010–2021

Abstract

Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales , but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase ( bla KPC ) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn 4401 transposon. This means that alongside clonal expansion, bla KPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 bla KPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular bla KPC -encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian bla KPC -encoding plasmids. We further estimated the genomic location of incomplete bla KPC -encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of bla KPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to bla KPC spread and persistence in Canada.

Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies

“…Antimicrobial resistance genes carried on plasmids can have complicated patterns of transmission involving horizontal transfer between different bacterial species and lineages, transfer between different plasmid backbones, and integration into and excision from the bacterial chromosome [65][66][67]. Accurate plasmid assemblies are crucial in genomic epidemiology studies investigating transmission of antimicrobial-resistant bacteria within outbreak settings, as well as in a broader One Health context, where hundreds or even thousands of assemblies may be analysed [68][69][70][71]. Hybracter will facilitate the expansion of such studies, allowing for faster and more accurate automated complete genome assemblies than existing tools.…”

Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010−2021

“…The majority of OXA-48-type carbapenemase occurrences in Canada during this time period were predominantly from E. coli and K. pneumoniae species, which agrees with other countries [ 15,68 70 ]. This contrasts with bla KPC , which was found in more diverse genera in Canada during the same time period [ 71 ], and with bla NDM , which also was found in diverse genera around the world [ 72 ].…”

“…For IncX3/rep_cluster_1195 plasmids carrying bla OXA-181 (AA836), we found remarkably high conservation among plasmid sequences wherein many were 100 % identical to the reference sequence, agreeing with previous studies [ 8 15 69 73 74 ]. Although we found 1–3 SNVs in some plasmid sequences, these were scattered across the genome and did not appear to be linked to any epidemiological information which limits the usefulness of creating a Tn 2013 transposon typing scheme, as done for bla KPC genes with Tn 4401 [ 71 75 ]. Similarly for the 6.1 kb rep_cluster_1195 plasmids (AB484) plasmids, we observed 0–2 SNVs between plasmids isolated from organisms that have no epidemiological links.…”

“…These findings agree with Hendrickx et al [ 15 ], who also observed a lack of antimicrobial resistance genes on bla OXA-48-type plasmids in the Netherlands, and with a recent analysis of IncL/M plasmids in NCBI RefSeq which found 82.7 % (162/196) of IncL/M plasmids encoded bla OXA-48 as the only resistance gene [ 82 ]. The lack of antimicrobial resistance genes on OXA-48-type plasmids contrasts with other types of carbapenemase plasmids that frequently have multiple other types of antimicrobial resistance genes, such as bla KPC [ 71 ] and bla NDM genes [ 72 83 ].…”