Tracking blaKPC Plasmid Dissemination within and between Enterobacterales across Michigan Over a Decade

Shankar, C.; Narayanan, D. B.; Miihlbach, A.; McNamara, S.; Brennan, B.; Miles-Jay, A.; Blankenship, H. M.; Bahr, A.; Snitkin, E. S.

doi:10.1101/2025.08.18.670900

bioRxiv · 10.1101/2025.08.18.670900

Tracking blaKPC Plasmid Dissemination within and between Enterobacterales across Michigan Over a Decade

Shankar, C.·Narayanan, D. B.·Miihlbach, A.·McNamara, S.·Brennan, B.·Miles-Jay, A.·Blankenship, H. M.·Bahr, A.·Snitkin, E. S.

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Abstract

AbstractblaKPC is endemic among Enterobacterales in the USA. While present on diverse plasmids, blaKPC burden is often associated with the clonal spread of multi-drug resistant (MDR) epidemic lineages. In this study we sought to determine the relative contributions of clonal spread and plasmid transfer to blaKPC burden across Michigan healthcare facilities over a decade. To this end we performed whole-genome sequencing of 1,058 KPC-producing isolates collected from 47 Michigan healthcare facilities between 2013 and 2022, including long-read sequencing for 527 isolates to enable precise plasmid tracking. Analysis with MOB-suite identified 64 distinct KPC plasmid types ("secondary clusters"), with the AK975 broad-host range plasmid being the most prevalent, found in 27% of isolates, spanning 20 species and 92 sequence types. Among genomes with AK975, 30% were from epidemic and 70% non-epidemic lineages, highlighting its broad role in regional blaKPC spread. Epidemic lineages of various species constituted 46% of the study population. Epidemic lineages differed in their primary plasmids, and even within epidemic lineages there were clonal expansions with distinct blaKPC plasmids, including in some cases AK975. These findings highlight two patterns of KPC spread: transmission of epidemic lineages harboring broad-range and lineage-specific KPC plasmids; and broader spread of AK975 among diverse species. Traditional surveillance studies often focus on common MDR lineages, potentially overlooking rare species and lineages that mediate the spread of plasmid-borne antimicrobial resistance (AMR) genes. Here we show how longitudinal studies tracking plasmids across species are essential to understand the pathways leading to AMR infections in hospitals. ImportanceThis decade-long longitudinal study highlights the persistence and spread of key KPC- carrying plasmid across multiple bacterial species in the region, including some uncommon ones. It also emphasizes the differences in KPC plasmids across lineages within the same species. While some lineages acquire multiple plasmids with resistance, they are unable to successfully maintain the plasmids. In contrast, clonal sub-populations of KPC-producing bacteria disseminate selected plasmids, establishing a stable host-plasmid combination. Comprehensive genomic surveillance that includes all pathogenic species and plasmids is crucial to understanding the regional transmission dynamics of plasmid-borne antimicrobial resistance (AMR). While outbreak studies define the blowup of a successful lineage and associated plasmids, longitudinal studies identify the reservoir-species and circulating plasmids in the context of plasmid- borne AMR.

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Shankar, C., Narayanan, D. B., Miihlbach, A., McNamara, S., Brennan, B., Miles-Jay, A., Blankenship, H. M., Bahr, A., Snitkin, E. S.. 2025-08-22. Tracking blaKPC Plasmid Dissemination within and between Enterobacterales across Michigan Over a Decade. https://doi.org/10.1101/2025.08.18.670900

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