Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
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Date
2020-06
Journal Title
Journal ISSN
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Publisher
Nature Medicine
Abstract
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.
Description
Staff Publication
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Citation
Chng, K. R., Li, C., Bertrand, D., Ng, A. H. Q., Kwah, J. S., … Nagarajan, N. (2020). Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nature Medicine. doi:10.1038/s41591-020-0894-4