Hospital Resistome

Compared to other built environments, hospitals have stricter microbial control. The more stringent cleaning and confinement measures in hospitals lead to a decrease in microbial diversity but an increase in resistance genes. Given the rise of antimicrobial resistances and healthcare-associated infections, understanding the hospital microbiome and its resistome is crucial. This study compared the microbiome and resistome at different levels of confinement (CL) within a single hospital. Using amplicon sequencing, shotgun metagenomics, and genome/ plasmid reconstruction, we demonstrate that microbial composition stably differs between the CLs and that the most restrictive confinement level CL1 had the lowest microbial but the highest functional diversity. This CL also exhibited a greater abundance of functions related to virulence, disease, defense, and stress response. Comparison of antibiotic resistance also showed differences among CLs in terms of the selection process and specific mechanisms for antimicrobial/antibiotic resistance. The resistances found in the samples of CL1 were mostly mediated via antibiotic efflux pumps, but were mainly located on chromosomes, whereas in the other, less restrictive CL antibiotic resistances were mostly present on plasmids. Our results show that there are differences in the microbiome and resistome even within a single hospital, reflecting room utilization and confinement. Although restrictive confinement is indeed positively selective for resistant microorganisms, the spread of the resistance genes might be hindered by being rather chromosome bound.