TY - JOUR
T1 - Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
AU - MetaSUB Consortium
AU - Chng, Kern Rei
AU - Li, Chenhao
AU - Bertrand, Denis
AU - Ng, Amanda Hui Qi
AU - Kwah, Junmei Samantha
AU - Low, Hwee Meng
AU - Tong, Chengxuan
AU - Natrajan, Maanasa
AU - Zhang, Michael Hongjie
AU - Xu, Licheng
AU - Ko, Karrie Kwan Ki
AU - Ho, Eliza Xin Pei
AU - Av-Shalom, Tamar V.
AU - Teo, Jeanette Woon Pei
AU - Khor, Chiea Chuen
AU - Danko, David
AU - Bezdan, Daniela
AU - Afshinnekoo, Ebrahim
AU - Ahsanuddin, Sofia
AU - Bhattacharya, Chandrima
AU - Butler, Daniel J.
AU - Chng, Kern Rei
AU - De Filippis, Francesca
AU - Hecht, Jochen
AU - Kahles, Andre
AU - Karasikov, Mikhail
AU - Kyrpides, Nikos C.
AU - Leung, Marcus H.Y.
AU - Meleshko, Dmitry
AU - Mustafa, Harun
AU - Mutai, Beth
AU - Neches, Russell Y.
AU - Ng, Amanda
AU - Nieto-Caballero, Marina
AU - Nikolayeva, Olga
AU - Nikolayeva, Tatyana
AU - Png, Eileen
AU - Sanchez, Jorge L.
AU - Shaaban, Heba
AU - Sierra, Maria A.
AU - Tong, Xinzhao
AU - Young, Ben
AU - Alicea, Josue
AU - Bhattacharyya, Malay
AU - Blekhman, Ran
AU - Castro-Nallar, Eduardo
AU - Cañas, Ana M.
AU - Chatziefthimiou, Aspassia D.
AU - Crawford, Robert W.
AU - Kelly, Frank J.
PY - 2020/6
Y1 - 2020/6
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85086157299&partnerID=8YFLogxK
U2 - 10.1038/s41591-020-0894-4
DO - 10.1038/s41591-020-0894-4
M3 - Article
C2 - 32514171
AN - SCOPUS:85086157299
SN - 1078-8956
VL - 26
SP - 941
EP - 951
JO - Nature Medicine
JF - Nature Medicine
IS - 6
ER -