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

Chng, Kern Rei (author)
Li, Chenhao (author)
Bertrand, Denis (author)
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Ng, Amanda Hui Qi (author)
Kwah, Junmei Samantha (author)
Low, Hwee Meng (author)
Tong, Chengxuan (author)
Natrajan, Maanasa (author)
Zhang, Michael Hongjie (author)
Xu, Licheng (author)
Ko, Karrie Kwan Ki (author)
Ho, Eliza Xin Pei (author)
Av-Shalom, Tamar (author)
Teo, Jeanette Woon Pei (author)
Khor, Chiea Chuen (author)
Chen, Swaine L. (author)
Mason, Christopher E. (author)
Ng, Oon Tek (author)
Marimuthu, Kalisvar (author)
Ang, Brenda (author)
Nagarajan, Niranjan (author)
Danko, David (author)
Bezdan, Daniela (author)
Afshinnekoo, Ebrahim (author)
Ahsanuddin, Sofia (author)
Bhattacharya, Chandrima (author)
Butler, Daniel J. (author)
De Filippis, Francesca (author)
Hecht, Jochen (author)
Kahles, Andre (author)
Karasikov, Mikhail (author)
Kyrpides, Nikos C. (author)
Leung, Marcus H. Y. (author)
Meleshko, Dmitry (author)
Mustafa, Harun (author)
Mutai, Beth (author)
Neches, Russell Y. (author)
Ng, Amanda (author)
Nieto-Caballero, Marina (author)
Nikolayeva, Olga (author)
Nikolayeva, Tatyana (author)
Png, Eileen (author)
Sanchez, Jorge L. (author)
Shaaban, Heba (author)
Sierra, Maria A. (author)
Tong, Xinzhao (author)
Young, Ben (author)
Alicea, Josue (author)
Bhattacharyya, Malay (author)
Blekhman, Ran (author)
Castro-Nallar, Eduardo (author)
Canas, Ana M. (author)
Chatziefthimiou, Aspassia D. (author)
Crawford, Robert W. (author)
Deng, Youping (author)
Desnues, Christelle (author)
Dias-Neto, Emmanuel (author)
Donnellan, Daisy (author)
Dybwad, Marius (author)
Elhaik, Eran (author)
Ercolini, Danilo (author)
Frolova, Alina (author)
Graf, Alexandra B. (author)
Green, David C. (author)
Hajirasouliha, Iman (author)
Hernandez, Mark (author)
Iraola, Gregorio (author)
Jang, Soojin (author)
Jones, Angela (author)
Kelly, Frank J. (author)
Knights, Kaymisha (author)
Labaj, Pawel P. (author)
Lee, Patrick K. H. (author)
Shawn, Levy (author)
Ljungdahl, Per (author)
Stockholms universitet,Institutionen för molekylär biovetenskap, Wenner-Grens institut
Lyons, Abigail (author)
Mason-Buck, Gabriella (author)
McGrath, Ken (author)
Mongodin, Emmanuel F. (author)
Moraes, Milton Ozorio (author)
Noushmehr, Houtan (author)
Oliveira, Manuela (author)
Ossowski, Stephan (author)
Osuolale, Olayinka O. (author)
Ozcan, Orhan (author)
Paez-Espino, David (author)
Rascovan, Nicolas (author)
Richard, Hugues (author)
Raetsch, Gunnar (author)
Schriml, Lynn M. (author)
Semmler, Torsten (author)
Sezerman, Osman U. (author)
Shi, Leming (author)
Song, Le Huu (author)
Suzuki, Haruo (author)
Court, Denise Syndercombe (author)
Thomas, Dominique (author)
Tighe, Scott W. (author)
Udekwu, Klas (author)
Stockholms universitet,Institutionen för molekylär biovetenskap, Wenner-Grens institut
Ugalde, Juan A. (author)
Valentine, Brandon (author)
Vassilev, Dimitar (author)
Vayndorf, Elena (author)
Velavan, Thirumalaisamy P. (author)
Zambrano, Maria M. (author)
Zhu, Jifeng (author)
Zhu, Sibo (author)
Mason, Christopher E. (author)
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 (creator_code:org_t)
2020-06-08
2020
English.
In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 26, s. 941-951
  • Journal article (peer-reviewed)
Abstract Subject headings
Close  
  • 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. 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.

Subject headings

NATURVETENSKAP  -- Biologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences (hsv//eng)
MEDICIN OCH HÄLSOVETENSKAP  -- Klinisk medicin -- Infektionsmedicin (hsv//swe)
MEDICAL AND HEALTH SCIENCES  -- Clinical Medicine -- Infectious Medicine (hsv//eng)

Publication and Content Type

ref (subject category)
art (subject category)

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By the author/editor
Chng, Kern Rei
Li, Chenhao
Bertrand, Denis
Ng, Amanda Hui Q ...
Kwah, Junmei Sam ...
Low, Hwee Meng
show more...
Tong, Chengxuan
Natrajan, Maanas ...
Zhang, Michael H ...
Xu, Licheng
Ko, Karrie Kwan ...
Ho, Eliza Xin Pe ...
Av-Shalom, Tamar
Teo, Jeanette Wo ...
Khor, Chiea Chue ...
Chen, Swaine L.
Mason, Christoph ...
Ng, Oon Tek
Marimuthu, Kalis ...
Ang, Brenda
Nagarajan, Niran ...
Danko, David
Bezdan, Daniela
Afshinnekoo, Ebr ...
Ahsanuddin, Sofi ...
Bhattacharya, Ch ...
Butler, Daniel J ...
De Filippis, Fra ...
Hecht, Jochen
Kahles, Andre
Karasikov, Mikha ...
Kyrpides, Nikos ...
Leung, Marcus H. ...
Meleshko, Dmitry
Mustafa, Harun
Mutai, Beth
Neches, Russell ...
Ng, Amanda
Nieto-Caballero, ...
Nikolayeva, Olga
Nikolayeva, Taty ...
Png, Eileen
Sanchez, Jorge L ...
Shaaban, Heba
Sierra, Maria A.
Tong, Xinzhao
Young, Ben
Alicea, Josue
Bhattacharyya, M ...
Blekhman, Ran
Castro-Nallar, E ...
Canas, Ana M.
Chatziefthimiou, ...
Crawford, Robert ...
Deng, Youping
Desnues, Christe ...
Dias-Neto, Emman ...
Donnellan, Daisy
Dybwad, Marius
Elhaik, Eran
Ercolini, Danilo
Frolova, Alina
Graf, Alexandra ...
Green, David C.
Hajirasouliha, I ...
Hernandez, Mark
Iraola, Gregorio
Jang, Soojin
Jones, Angela
Kelly, Frank J.
Knights, Kaymish ...
Labaj, Pawel P.
Lee, Patrick K. ...
Shawn, Levy
Ljungdahl, Per
Lyons, Abigail
Mason-Buck, Gabr ...
McGrath, Ken
Mongodin, Emmanu ...
Moraes, Milton O ...
Noushmehr, Houta ...
Oliveira, Manuel ...
Ossowski, Stepha ...
Osuolale, Olayin ...
Ozcan, Orhan
Paez-Espino, Dav ...
Rascovan, Nicola ...
Richard, Hugues
Raetsch, Gunnar
Schriml, Lynn M.
Semmler, Torsten
Sezerman, Osman ...
Shi, Leming
Song, Le Huu
Suzuki, Haruo
Court, Denise Sy ...
Thomas, Dominiqu ...
Tighe, Scott W.
Udekwu, Klas
Ugalde, Juan A.
Valentine, Brand ...
Vassilev, Dimita ...
Vayndorf, Elena
Velavan, Thiruma ...
Zambrano, Maria ...
Zhu, Jifeng
Zhu, Sibo
show less...
About the subject
NATURAL SCIENCES
NATURAL SCIENCES
and Biological Scien ...
MEDICAL AND HEALTH SCIENCES
MEDICAL AND HEAL ...
and Clinical Medicin ...
and Infectious Medic ...
Articles in the publication
Nature Medicine
By the university
Stockholm University

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