Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
(2020) In Nature Medicine 26. p.941-951- 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... (More)
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.
(Less)
- author
- author collaboration
- publishing date
- 2020-06-01
- type
- Contribution to journal
- publication status
- published
- in
- Nature Medicine
- volume
- 26
- pages
- 941 - 951
- publisher
- Nature Publishing Group
- external identifiers
-
- pmid:32514171
- scopus:85086157299
- ISSN
- 1078-8956
- DOI
- 10.1038/s41591-020-0894-4
- language
- English
- LU publication?
- no
- additional info
- Funding Information: Funding for this work was provided by A*STAR (N.N.), and we are grateful for support from NMRC (NMRC CGAug16C005: O.T.N. and K.M.). C.E.M. acknowledges support from the WorldQuant Foundation, the Bill and Melinda Gates Foundation (OPP1151054) and the Alfred P. Sloan Foundation (G-2015-13964). The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. We would like to thank J. Gilbert for insightful comments and feedback on this work. Publisher Copyright: © 2020, Nature Research. All rights reserved.
- id
- 6d6be10a-4ca7-4a7a-a4bf-aa7304407ca6
- date added to LUP
- 2022-03-28 12:10:28
- date last changed
- 2024-09-10 07:45:53
@article{6d6be10a-4ca7-4a7a-a4bf-aa7304407ca6, abstract = {{<p>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.</p>}}, author = {{Chng, Kern Rei and Li, Chenhao and Bertrand, Denis and Ng, Amanda Hui Qi and Kwah, Junmei Samantha and Low, Hwee Meng and Tong, Chengxuan and Natrajan, Maanasa and Zhang, Michael Hongjie and Xu, Licheng and Ko, Karrie Kwan Ki and Ho, Eliza Xin Pei and Av-Shalom, Tamar V. and Teo, Jeanette Woon Pei and Khor, Chiea Chuen and Chen, Swaine L. and Mason, Christopher E. and Ng, Oon Tek and Marimuthu, Kalisvar and Ang, Brenda and Nagarajan, Niranjan and Danko, David and Elhaik, Eran}}, issn = {{1078-8956}}, language = {{eng}}, month = {{06}}, pages = {{941--951}}, publisher = {{Nature Publishing Group}}, series = {{Nature Medicine}}, title = {{Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment}}, url = {{http://dx.doi.org/10.1038/s41591-020-0894-4}}, doi = {{10.1038/s41591-020-0894-4}}, volume = {{26}}, year = {{2020}}, }