Plasmid genomic epidemiology of bla NDM carbapenemase-producing Enterobacterales in Canada from 2010 to 2023

Carbapenems are broad-spectrum antibiotics that are losing effectiveness against infections caused by multidrug-resistant <i>Enterobacterales</i> that have acquired carbapenemase genes. The New Delhi metallo-<i>β</i>-lactamase (<i>bla</i> _NDM) is one of the most common carbapenemases in Canada and around the globe. These genes are frequently found on conjugative plasmids, which can disseminate through horizontal gene transfer. We applied whole-genome sequencing to characterize 1,032 <i>bla</i> _NDM carbapenemase-producing <i>Enterobacterales</i> isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2023. Using a combination of short-read and long-read sequencing, we obtained 226 complete and circular <i>bla</i> _NDM-encoding plasmids. Unlike other carbapenemases in Canada, we found that <i>bla</i> _NDM plasmids were very diverse; there was a lack of dominant clusters identified using MOB-suite, and clustering methods were not able to accurately predict plasmid clusters for short-read-only data. The majority of <i>bla</i> _NDM plasmids were IncF-type (69.0%, 156/226). Both <i>bla</i> _NDM and <i>bla</i> _OXA-48-type carbapenemase genes were found in 11.4% (118/1,032) of isolates, and we identified several instances of both carbapenemase genes co-harboured on the same plasmid replicon (<i>n</i>=9). Our findings highlight that plasmid transfer has not played a major role in <i>bla</i> _NDM transmission across Canada and that long-read sequencing is essential for resolving <i>bla</i> _NDM plasmid structure and cluster membership.