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

Chng, Kern Rei ; Li, Chenhao ; Bertrand, Denis ; Ng, Amanda Hui Qi ; Kwah, Junmei Samantha ; Low, Hwee Meng ; Tong, Chengxuan ; Natrajan, Maanasa ; Zhang, Michael Hongjie and Xu, Licheng , et al. (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.

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publishing date
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 (&gt;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 (&gt;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}},
}