Comprehensive analysis of horizontal gene transfer among multidrug-resistant bacterial pathogens in a single hospital

ABSTRACT Multidrug-resistant bacterial pathogens pose a serious public health threat, especially in hospital settings. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) contributes to this threat by facilitating the rapid spread of genes conferring antibiotic resistance, enhanced virulence, and environmental persistence between nosocomial pathogens. Despite recent advances in microbial genomics, studies of HGT in hospital settings remain limited in scope. The objective of this study was to identify and track the movement of MGEs within a single hospital system using unbiased methods. We screened the genomes of 2,173 bacterial isolates from healthcare-associated infections collected over an 18-month time period to identify nucleotide regions that were identical in the genomes of bacteria belonging to distinct genera. These putative MGEs were found in 196 isolates belonging to 11 different genera; they grouped into 51 clusters of related elements, and they were most often shared between related genera. To resolve the genomic locations of the most prevalent MGEs, we performed long-read sequencing on a subset of representative isolates and generated highly contiguous, hybrid-assembled genomes. Many of these genomes contained plasmids and chromosomal elements encoding one or more of the MGEs we identified, which were often arranged in a mosaic fashion. We then tracked the appearance of ten MGE-bearing plasmids in all 2,173 genomes, and found evidence supporting the transfer of plasmids between patients independent from bacterial transmission. Finally, we identified two instances of likely plasmid transfer across genera within individual patients. In one instance, the plasmid appeared to have subsequently transferred to a second patient. By surveying a large number of bacterial genomes sampled from infections at a single hospital in a systematic and unbiased manner, we were able to track the independent transfer of MGEs over time. This work expands our understanding of HGT in healthcare settings, and can inform efforts to limit the spread of drug-resistant pathogens in hospitals.