Empirical genomic methods for tracking plasmid spread among healthcare-associated bacteria

BackgroundHealthcare-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 track plasmids circulating in a single hospital, and to identify epidemiologic links that indicated likely horizontal plasmid transfer. MethodsWe 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. FindingsOur analyses determined that 95% of analyzed genomes maintained roughly 95% of their plasmid genetic content at a nucleotide identity at least 99{middle dot}985%. Applying these similarity thresholds to identify horizontal plasmid transfer identified 45 plasmids circulating among clinical isolates. Ten plasmids met criteria for geotemporal links associated with horizontal transfer. Several plasmids with shared backbones also encoded different additional mobile genetic element content, and these elements were variably present among the sampled clinical isolate genomes. InterpretationThe horizontal transfer of plasmids among nosocomial bacterial pathogens is frequent within hospitals and can be monitored with whole genome sequencing and comparative genomics approaches. These approaches should incorporate both nucleotide identity and reference sequence coverage to study the dynamics of plasmid transfer in the hospital. FundingThis research was supported by the US National Institute of Allergy and Infectious Disease (NIAID) and the University of Pittsburgh School of Medicine. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSA search of PubMed for research articles containing the search terms "plasmid", "transfer", "epidemiology", "hospital", and "patients" identified 115 peer-reviewed manuscripts published before 01 January 2022. Twenty-four manuscripts documented the dissemination of one or more plasmids by horizontal transfer in a hospital setting. Most of these prior studies focused on a single plasmid, outbreak, antibiotic resistance gene or pathogen species, and none established an a priori approach to identify plasmids circulating among non-clonal bacterial genomes. While prior studies have quantified plasmid preservation and nucleotide identity, similarity thresholds to infer horizontal transfer were neither uniform across studies nor systematically derived from empirical data. Added value of this studyThis study advances the field of genomic epidemiology by proposing and demonstrating the utility of empirically derived thresholds of plasmid sequence similarity for inferring horizontal transfer in healthcare settings. It also advances the field by tracking horizontal plasmid transfer within a single hospital at a hitherto unprecedented scale, examining the evidence of horizontal transfer of 89 plasmids among thousands of clinical bacterial isolates sampled from a single medical center. Our systematic review of patient healthcare data related to horizontal transfer also occurred at a breadth not previously undertaken in hospital epidemiology. Implications of all the available evidenceWhen successfully integrated into contemporary methods for surveillance of nosocomial pathogens, comparative genomics can be used to track and intervene directly against the dissemination of plasmids that exacerbate virulence and antimicrobial resistance in healthcare-associated bacterial infections. Standardized thresholds of plasmid identity benefit epidemiologic investigations of horizontal transfer similar to those offered by establishing uniform thresholds of genome identity for investigations of bacterial transmission.