Hospital Microbiome

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic-resistance cassettes in a tertiary hospital from repeated sampling (up to 1.5 years apart) of 179 sites from 45 beds. Deep shotgun-metagenomics unveiled distinct ecological niches of microbes and antibiotic-resistance genes characterized by biofilm-forming and human-microbiome influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome/mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely-distributed and stably-colonizing across sites. Comparisons with clinical isolates indicated that they persist in hospitals for extended periods (>8 years), opportunistically infecting patients. These findings highlight the importance of characterizing antibiotic-resistance reservoirs in hospitals and establishes feasibility of systematic surveys to target resources for preventing infections.