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

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dc.contributor.authorChng, Kern Rei
dc.contributor.authorLi, Chenhao
dc.contributor.authorBertrand, Denis
dc.contributor.authorNg, Amanda Hui Qi
dc.contributor.authorKwah, Junmei Samantha
dc.contributor.authorLow, Hwee Meng
dc.contributor.authorTong, Chengxuan
dc.contributor.authorNatrajan, Maanasa
dc.contributor.authorZhang, Michael Hongjie
dc.contributor.authorXu, Licheng
dc.contributor.authorKo, Karrie Kwan Ki
dc.contributor.authorHo, Eliza Xin Pei
dc.contributor.authorAv-Shalom V, Tamar
dc.contributor.authorTeo, Jeanette Woon Pei
dc.contributor.authorKhor, Chiea Chuen
dc.contributor.authorChen, Swaine L.
dc.contributor.authorMason, Christopher E.
dc.contributor.authorNg, Oon Tek
dc.contributor.authorMarimuthu, Kalisvar
dc.contributor.authorAng, Brenda
dc.contributor.authorNagarajan, Niranjan
dc.contributor.authorDanko, David
dc.contributor.authorBezdan, Daniela
dc.contributor.authorAfshinnekoo, Ebrahim
dc.contributor.authorAhsanuddin, Sofia
dc.contributor.authorBhattacharya, Chandrima
dc.contributor.authorButler, Daniel J.
dc.contributor.authorDe Filippis, Francesca
dc.contributor.authorHecht, Jochen
dc.contributor.authorKahles, Andre
dc.contributor.authorKarasikov, Mikhail
dc.contributor.authorKyrpides, Nikos C.
dc.contributor.authorLeung, Marcus H. Y.
dc.contributor.authorMeleshko, Dmitry
dc.contributor.authorMustafa, Harun
dc.contributor.authorMutai, Beth
dc.contributor.authorNeches, Russell Y.
dc.contributor.authorNg, Amanda
dc.contributor.authorNieto-Caballero, Marina
dc.contributor.authorNikolayeva, Olga
dc.contributor.authorNikolayeva, Tatyana
dc.contributor.authorPng, Eileen
dc.contributor.authorSanchez, Jorge L.
dc.contributor.authorShaaban, Heba
dc.contributor.authorSierra, Maria A.
dc.contributor.authorTong, Xinzhao
dc.contributor.authorYoung, Ben
dc.contributor.authorAlicea, Josue
dc.contributor.authorBhattacharyya, Malay
dc.contributor.authorBlekhman, Ran
dc.contributor.authorCastro-Nallar, Eduardo
dc.contributor.authorCanas, Ana M.
dc.contributor.authorChatziefthimiou, Aspassia D.
dc.contributor.authorCrawford, Robert W.
dc.contributor.authorDeng, Youping
dc.contributor.authorDesnues, Christelle
dc.contributor.authorDias-Neto, Emmanuel
dc.contributor.authorDonnellan, Daisy
dc.contributor.authorDybwad, Marius
dc.contributor.authorElhaik, Eran
dc.contributor.authorErcolini, Danilo
dc.contributor.authorFrolova, Alina
dc.contributor.authorGraf, Alexandra B.
dc.contributor.authorGreen, David C.
dc.contributor.authorHajirasouliha, Iman
dc.contributor.authorHernandez, Mark
dc.contributor.authorIraola, Gregorio
dc.contributor.authorJang, Soojin
dc.contributor.authorJones, Angela
dc.contributor.authorKelly, Frank J.
dc.contributor.authorKnights, Kaymisha
dc.contributor.authorLabaj, Pawel P.
dc.contributor.authorLee, Patrick K. H.
dc.contributor.authorShawn, Levy
dc.contributor.authorLjungdahl, Per
dc.contributor.authorLyons, Abigail
dc.contributor.authorMason-Buck, Gabriella
dc.contributor.authorMcGrath, Ken
dc.contributor.authorMongodin, Emmanuel F.
dc.contributor.authorMoraes, Milton Ozorio
dc.contributor.authorNoushmehr, Houtan
dc.contributor.authorOliveira, Manuela
dc.contributor.authorOssowski, Stephan
dc.contributor.authorOsuolale, Olayinka O.
dc.contributor.authorOzcan, Orhan
dc.contributor.authorPaez-Espino, David
dc.contributor.authorRascovan, Nicolas
dc.contributor.authorRichard, Hugues
dc.contributor.authorRaetsch, Gunnar
dc.contributor.authorSchriml, Lynn M.
dc.contributor.authorSemmler, Torsten
dc.contributor.authorSezerman, Osman U.
dc.contributor.authorShi, Leming
dc.contributor.authorSong, Le Huu
dc.contributor.authorSuzuki, Haruo
dc.contributor.authorCourt, Denise Syndercombe
dc.contributor.authorThomas, Dominique
dc.contributor.authorTighe, Scott W.
dc.contributor.authorUdekwu I, Klas
dc.contributor.authorUgalde, Juan A.
dc.contributor.authorValentine, Brandon
dc.contributor.authorVassilev I, Dimitar
dc.contributor.authorVayndorf, Elena
dc.contributor.authorVelavan, Thirumalaisamy P.
dc.contributor.authorZambrano, Maria M.
dc.contributor.authorZhu, Jifeng
dc.contributor.authorZhu, Sibo
dc.contributor.authorConsortium, MetaSU. B.
dc.date.accessioned2023-02-21T12:43:06Z
dc.date.available2023-02-21T12:43:06Z
dc.date.issued2020-01-01
dc.description.abstractAlthough 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. Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.
dc.description.issue6
dc.description.issueJUN
dc.description.pages941+
dc.description.volume26
dc.identifier.doi10.1038/s41591-020-0894-4
dc.identifier.urihttps://hdl.handle.net/11443/2877
dc.identifier.urihttp://dx.doi.org/10.1038/s41591-020-0894-4
dc.identifier.wosWOS:000538976400005
dc.publisherNATURE RESEARCH
dc.relation.ispartofNATURE MEDICINE
dc.titleCartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
dc.typeArticle
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