Gijs Teunis (RIVM)

Summary of presentation:
Background
Carbapenemase-producing (CP) organisms are a growing public health concern. Genomic surveillance of carbapenemase-producing (CP) organisms focuses on clonal lineages, yet carbapenem resistance often spreads via plasmid-mediated horizontal gene transfer (HGT). Plasmids are modular, mobile elements that frequently carry antimicrobial resistance genes (ARGs). Therefore, we developed a multi-species plasmid clustering model to characterize plasmid dissemination in the Netherlands.

Methods
We characterized 4,596 plasmids of 1,315 isolates from the Dutch CPE surveillance (2012-2022), thereby identifying diverse plasmids with and without ARGs using ResFinder. We compared mge-cluster with COPLA, PlasmidFinder, and MOB-cluster using adjusted Rand index (ARI). Cluster homology was assessed using MASH and average nucleotide identity (ANI) with PyANI. We applied Moran’s I to detect spatial dissemination, LOESS regression for temporal trends, and spatio-temporal outbreaks through SaTScan.

Results
Our mge-cluster model shows moderate congruence with other tools (mean ARI 0.56) but offers lower numbers of unclustered plasmids (COPLA: 20%, mge-cluster: 5%), particularly resistance plasmids (COPLA: 13%, mge-cluster: <1%). Plasmid clusters often contain both plasmids with and without ARGs. Moreover, some non-mobilisable plasmid clusters with diverse ARGs span multiple genera, suggesting diverse mechanisms of dissemination. Spatial analysis revealed broad dissemination across the Netherlands, while temporal trends indicated an increasing diversity of plasmids, largely driven by expanded isolate sampling. Outbreak detection revealed multiple clusters of which the majority were carbapenemase-encoding plasmids associated with clonal outbreaks. The SaTScan detected plasmid outbreaks included isolates of multiple sequence types, species, or genera. This indicates a combination of vertical and horizontal transmission as a method of persistence.

Conclusions
These results demonstrate that plasmid-centric surveillance through our model can detect outbreaks across bacterial lineages. Additionally, it provides insights into the spread of carbapenem resistance through plasmids and highlights the utility of our plasmid model for epidemiological surveillance and infection control strategies.