Comparison of Environmental Microbiomes, Resistomes and Plasmidomes from a Human Tertiary Hospital and Companion Animal Veterinary Hospital in London, UK

Background: Human hospitals and veterinary centres are hotspots for resistant microbes and plasmids, and metagenomic sequencing offers an agnostic insight into microbiomes, resistomes, and mobilomes, informing strategies for reducing AMR spread. 

Methods: Environmental samples, including wastewater and surface swabs, were taken from a tertiary human hospital ward (36 samples) and a companion animal veterinary hospital (48 samples) in London. Whole DNA was extracted and metagenomic sequencing undertaken using Oxford Nanopore Technologies’ MinION. Data were analyzed for microbiomes, resistomes and mobilomes and compared. 

Results: Microbial diversity analyses highlight higher richness across human hospital (HH) environmental samples, but more evenness in veterinary hospital (VH) environmental samples. Diversity showed distinct microbial communities in the HH and VH samples. There were significantly more total antimicrobial resistance gene (ARG) types (p < 0.0001) in the environmental HH samples compared with the environmental VH samples. There was a significantly higher mean number of Enterobacteriales plasmid types (p ≤ 0.0001) in the HH samples. There were significantly more total Gram-Positive plasmid types (p ≤ 0.0001) in the VH samples. 

Discussion: This research highlights the presence of human and animal pathogens, ARGs and mobile genetic elements in clinical environments, underscoring the importance of multisectoral surveillance. Integrating taxonomic, resistome, and mobilome analyses provides a better understanding of the potential for AMR dissemination at the human–animal–environment interface. This provides insights relevant for the development of targeted surveillance and mitigation strategies within a OH framework.