ITS 14 - Empirical Methods in Genomic Epidemiology Improve the Surveillance of Plasmids Exchanged Among Healthcare-associated Bacteria

Background: Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of plasmids in healthcare settings has been previously documented, but genomic and epidemiologic methods to study this phenomenon remain underdeveloped. The objectives of this study were to develop a method to systematically resolve and analyze plasmids circulating in a single hospital, and to identify epidemiologic links that indicated likely horizontal plasmid transfer.

Methods: We derived empirical thresholds of plasmid sequence similarity from comparisons of plasmids carried by bacterial isolates infecting individual patients over time or involved in hospital outbreaks. We then applied those metrics to perform a systematic screen of 3,074 genomes of nosocomial bacterial isolates from a single hospital for the presence of 89 plasmids. We also collected and reviewed data from electronic health records for evidence of geotemporal associations between patients infected with bacteria encoding plasmids of interest.

Results: Our analyses determined that 95% of analyzed genomes maintained roughly 95% of their plasmid genetic content at a nucleotide identity at least 99.985%. Applying these similarity thresholds to identify horizontal plasmid transfer identified 45 plasmids circulating among clinical isolates. Our approach yielded superior resolution and discrimination of plasmid sequences compared to previous methods. Ten plasmids met criteria for geotemporal links associated with horizontal transfer. Several plasmids with shared backbones also encoded different additional mobile genetic element content, which were variably present among the sampled clinical isolate genomes.

Conclusions: The horizontal transfer of plasmids among nosocomial bacterial pathogens is frequent within hospitals and can be monitored more effectively with whole genome sequencing and comparative genomics approaches. These approaches should incorporate both nucleotide identity and gene content preservation to study the dynamics of plasmid transfer in the hospital.