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

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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. / MetaSUB Consortium.

в: Nature Medicine, Том 26, № 6, 06.2020, стр. 941-951.

Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование

BibTeX

@article{f64961c934c44debbd18abc1a30966d6,

title = "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.",

keywords = "Beds/microbiology, Biofilms, Cross Infection/drug therapy, Disinfection, Drug Resistance, Bacterial/genetics, Drug Resistance, Multiple, Bacterial/genetics, Equipment Contamination, Equipment and Supplies, Hospital/microbiology, Geographic Mapping, Humans, Infection Control, Metagenomics, Microbiota/genetics, Opportunistic Infections/drug therapy, Patients' Rooms, Singapore, Spatio-Temporal Analysis, Tertiary Care Centers",

author = "{MetaSUB Consortium} and Chng, {Kern Rei} and Chenhao Li and Denis Bertrand and Ng, {Amanda Hui Qi} and Kwah, {Junmei Samantha} and Low, {Hwee Meng} and Chengxuan Tong and Maanasa Natrajan and Zhang, {Michael Hongjie} and Licheng Xu 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 David Danko and Daniela Bezdan and Ebrahim Afshinnekoo and Sofia Ahsanuddin and Chandrima Bhattacharya and Butler, {Daniel J.} and Chng, {Kern Rei} and {De Filippis}, Francesca and Jochen Hecht and Andre Kahles and Mikhail Karasikov and Kyrpides, {Nikos C.} and Leung, {Marcus H.Y.} and Dmitry Meleshko and Harun Mustafa and Beth Mutai and Neches, {Russell Y.} and Amanda Ng and Marina Nieto-Caballero and Olga Nikolayeva and Tatyana Nikolayeva and Eileen Png and Sanchez, {Jorge L.} and Heba Shaaban and Sierra, {Maria A.} and Xinzhao Tong and Ben Young and Josue Alicea and Malay Bhattacharyya and Ran Blekhman and Eduardo Castro-Nallar and Ca{\~n}as, {Ana M.} and Chatziefthimiou, {Aspassia D.} and Crawford, {Robert W.} and Youping Deng",

year = "2020",

month = jun,

doi = "10.1038/s41591-020-0894-4",

language = "English",

volume = "26",

pages = "941--951",

journal = "Nature Medicine",

issn = "1078-8956",

publisher = "Nature Publishing Group",

number = "6",

}

RIS

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 - Deng, Youping

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.

KW - Beds/microbiology

KW - Biofilms

KW - Cross Infection/drug therapy

KW - Disinfection

KW - Drug Resistance, Bacterial/genetics

KW - Drug Resistance, Multiple, Bacterial/genetics

KW - Equipment Contamination

KW - Equipment and Supplies, Hospital/microbiology

KW - Geographic Mapping

KW - Humans

KW - Infection Control

KW - Metagenomics

KW - Microbiota/genetics

KW - Opportunistic Infections/drug therapy

KW - Patients' Rooms

KW - Singapore

KW - Spatio-Temporal Analysis

KW - Tertiary Care Centers

UR - http://www.scopus.com/inward/record.url?scp=85086157299&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/6ac29e2c-e33a-385f-b13b-c9f6afa03321/

U2 - 10.1038/s41591-020-0894-4

DO - 10.1038/s41591-020-0894-4

M3 - Article

C2 - 32514171

AN - SCOPUS:85086157299

VL - 26

SP - 941

EP - 951

JO - Nature Medicine

JF - Nature Medicine

SN - 1078-8956

IS - 6

ER -

ID: 62371613