Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

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-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 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 and 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 such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients.

These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.

Authors: Kern Rei Chng, Chenhao Li, Denis Bertrand, Amanda Hui Qi Ng, Junmei Samantha Kwah, Hwee Meng Low, Chengxuan Tong, Maanasa Natrajan, Michael Hongjie Zhang, Licheng Xu, Karrie Kwan Ki Ko, Eliza Xin Pei Ho, Tamar V. Av-Shalom, Jeanette Woon Pei Teo, Chiea Chuen Khor, MetaSUB Consortium, Swaine L. Chen, Christopher E. Mason, Oon Tek Ng, Kalisvar Marimuthu, Brenda Ang, Niranjan Nagarajan