Genomic dissection of endemic carbapenem resistance: metallo-beta-lactamase gene dissemination through clonal, plasmid and integron transfer pathways

Abstract

Infections caused by metallo-beta-lactamase-producing organisms (MBLs) are a global health threat. Our understanding of transmission dynamics and how MBLs establish endemicity remains limited. We analysed two decades of blaIMP-4 evolution in a hospital using sequence data from 270 clinical and environmental isolates (including 169 completed genomes) and identified extreme gene promiscuity across 7 Gram-negative genera, 68 bacterial strains and 7 distinct plasmid types. An initial multi-species outbreak of conserved IncC plasmids (95 genomes across 37 strains) allowed endemicity to be established through the ability of blaIMP-4 to disseminate in successful strain-genetic setting pairs we termed propagators, in particular Serratia marcescens and Enterobacter hormaechei. From this reservoir, blaIMP-4 persisted through diversification of genetic settings that resulted from transfer of blaIMP-4 plasmids between bacterial hosts and of the integron carrying blaIMP-4 between plasmids. Our findings provide a framework for understanding endemicity and spread of MBLs and may have broader applicability to other carbapenemase-producing organisms.

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

“…One study reported that bla KPC-2 being associated with IncL/M replicons a multi-clonal K. pneumoniae outbreak in a region in Argentina, but the relatedness between plasmids was not investigated ( 40 ). IncL/M plasmids are typically associated with bla NDM , bla IMP , and bla OXA -type carbapenemases ( 3 , 12 , 13 , 41 – 43 ), although a select few cases have been reported in diverse hosts ( 19 , 44 – 47 ). The pNE1280 IncL/M plasmid, which was one of the first IncL/M plasmids described carrying bla KPC-2 ( 45 ), clustered in the AL001 secondary cluster, which was not well represented in the Canadian data set.…”

“…It is important to recognize that any reference-based method for plasmid reconstruction involving mapping to reference sequences to infer presence assumes that plasmid structures are relatively conserved, and this approach can produce misleading results if plasmid plasticity is high ( 66 , 67 ). Similar studies have used short-read mappers such as BWA/Bowtie2/SMALT ( 13 , 43 , 68 , 69 ) or k-mer-based tools ( 60 , 70 ) to determine plasmid prevalence in incomplete assemblies, typically using a select few plasmids as references. We use a homology-based clustering approach with MOB-recon ( 24 ) to reconstruct plasmids using a relatively large set of complete Canadian plasmids (1,856 plasmids).…”