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

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.

Does Mycobacterium tuberculosis var. bovis Survival in the Environment Confound Bovine Tuberculosis Control and Eradication? A Literature Review

“…A recent biomedical example [ 151 ] used deep shotgun metagenomics on systematic samples taken from a hospital environment. They included quasi-metagenomics protocols using the nanopore long-range genome sequencing platform (MinION, Oxford Nanopore) to index thousands of genomes, phages, and plasmids from such samples in a relatively unbiased way; >60% were novel.…”

Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview

“…Notably, studying the taxonomic assignments of resistome elements using high-throughput sequencing goes beyond identifying ARGs in host-pathogen relations and can be used to study resistomes in environmental samples, such as those from water reservoirs ( Ekwanzala et al, 2020 ; Yu et al, 2020 ), hospitals ( MetaSUB Consortium et al, 2020 ), livestock wastewater and feces ( Jia S. et al, 2017 ), human feces ( Karkman et al, 2019 ), soil ( Chen et al, 2017 ), air ( Yang et al, 2018 ; Li et al, 2021 ), and biogeographical and biogeochemical processes ( Quinn et al, 2014 ; Kuang et al, 2016 ; Roose-Amsaleg and Laverman, 2016 ; Liu et al, 2018 ).…”

Leapfrogging laboratories: the promise and pitfalls of high-tech solutions for antimicrobial resistance surveillance in low-income settings

“…An international sewage study recently mapped geographical distribution of AMR genes garnered from sewage system metagenomes and another metagenomic study is surveilling resistance via public transportation systems. 56 57 Community surveillance disconnects surveillance from clinical practice (with the possible exception of those that surveil health facilities 58 ) and, in low-income countries, privileges better resourced communities, which have sewerage, public transport networks and concentrate resistance genes at tertiary care referral health centres. It also does not deconvolute human and animal resistance reservoirs, which may not be the same.…”