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

Kern, Rei Chng; Chenhao, Li; Bertrand, Denis; Ng, Amanda Hui Qi; Kwah, Junmei Samantha; Hwee, Meng Low; Chengxuan, Tong; Natrajan, Maanasa; Zhang, Michael Hongjie; Licheng, Xu; Karrie, Kwan Ki Ko; Ho, Eliza Xin Pei; Av-Shalom, Tamar V.; Teo, Jeanette Woon Pei; Khor, Chiea Chuen; Chen, Swaine L.; Mason, Christopher E.; Ng, Oon Tek; Marimuthu, Kalisvar; Ang, Brenda; Nagarajan, Niranjan; MetaSUB Consortium

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

Detalhes bibliográficos
Autor(a) principal:	Kern, Rei Chng
Data de Publicação:	2020
Outros Autores:	Chenhao, Li, Bertrand, Denis, Ng, Amanda Hui Qi, Kwah, Junmei Samantha, Hwee, Meng Low, Chengxuan, Tong, Natrajan, Maanasa, Zhang, Michael Hongjie, Licheng, Xu, Karrie, Kwan Ki Ko, Ho, Eliza Xin Pei, Av-Shalom, Tamar V., Teo, Jeanette Woon Pei, Khor, Chiea Chuen, Chen, Swaine L., Mason, Christopher E., Ng, Oon Tek, Marimuthu, Kalisvar, Ang, Brenda, Nagarajan, Niranjan, MetaSUB Consortium
Tipo de documento:	Artigo
Idioma:	eng
Título da fonte:	Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo:	https://www.arca.fiocruz.br/handle/icict/46582
Resumo:	Milton Osório Moraes - Fundação Oswaldo Cruz Laboratório de Hanseníase, Rio de Janeiro, RJ, Brasil. MetaSUB Consortium.

Metadados do item

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spelling	Kern, Rei ChngChenhao, LiBertrand, DenisNg, Amanda Hui QiKwah, Junmei SamanthaHwee, Meng LowChengxuan, TongNatrajan, MaanasaZhang, Michael HongjieLicheng, XuKarrie, Kwan Ki KoHo, Eliza Xin PeiAv-Shalom, Tamar V.Teo, Jeanette Woon PeiKhor, Chiea ChuenChen, Swaine L.Mason, Christopher E.Ng, Oon TekMarimuthu, KalisvarAng, BrendaNagarajan, NiranjanMetaSUB Consortium2021-04-08T18:47:26Z2021-04-08T18:47:26Z2020CHNG, Kernr Rei et al. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nature Medicine, v. 26, p. 941-951, June 2020.1078-8956https://www.arca.fiocruz.br/handle/icict/4658210.1038/s41591-020-0894-4Milton Osório Moraes - Fundação Oswaldo Cruz Laboratório de Hanseníase, Rio de Janeiro, RJ, Brasil. MetaSUB Consortium.Afiliação: Autores: 1Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore. 2Information Systems Technology and Design, Singapore University of Technology and Design, Singapore, Singapore. 3Department of Microbiology, Singapore General Hospital, Singapore, Singapore. 4Department of Molecular Pathology, Singapore General Hospital, Singapore, Singapore. 5Duke-NUS Graduate Medical School, Singapore, Singapore. 6Department of Laboratory Medicine, National University Hospital, Singapore, Singapore. 7Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. 8National Centre for Infectious Diseases, Singapore, Singapore. 9Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore. 10Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore. 11Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. 60These authors contributed equally: Kern Rei Chng, Chenhao Li, Denis Bertrand. *A full list of authors and their affiliations appears at the end of the paper. ✉e-mail: nagarajann@gis.a-star.edu.sgAutores MetaSUB Consortium: David Danko12,13, Daniela Bezdan12,13, Ebrahim Afshinnekoo12,13, Sofia Ahsanuddin14, Chandrima Bhattacharya12,13, Daniel J. Butler12,13, Kern Rei Chng15, Francesca De Filippis16, Jochen Hecht17, Andre Kahles18, Mikhail Karasikov18, Nikos C. Kyrpides19, Marcus H. Y. Leung20, Dmitry Meleshko12,13, Harun Mustafa18, Beth Mutai17,21, Russell Y. Neches19, Amanda Ng15, Marina Nieto-Caballero22, Olga Nikolayeva18, Tatyana Nikolayeva18, Eileen Png15, Jorge L. Sanchez12, Heba Shaaban12,13, Maria A. Sierra12,13, Xinzhao Tong20, Ben Young12,13, Josue Alicea12,13, Malay Bhattacharyya23, Ran Blekhman24, Eduardo Castro-Nallar25, Ana M. Cañas12, Aspassia D. Chatziefthimiou26, Robert W. Crawford27, Youping Deng28, Christelle Desnues29, Emmanuel Dias-Neto30, Daisy Donnellan12, Marius Dybwad31, Eran Elhaik32, Danilo Ercolini16, Alina Frolova33, Alexandra B. Graf34, David C. Green35, Iman Hajirasouliha12,13, Mark Hernandez22, Gregorio Iraola36, Soojin Jang37, Angela Jones38, Frank J. Kelly35, Kaymisha Knights12, Paweł P. Łabaj39, Patrick K. H. Lee20, Levy Shawn40, Per Ljungdahl41, Abigail Lyons12, Gabriella Mason-Buck35, Ken McGrath42, Emmanuel F. Mongodin43, Milton Ozorio Moraes44, Niranjan Nagarajan15, Houtan Noushmehr45, Manuela Oliveira46, Stephan Ossowski47, Olayinka O. Osuolale48, Orhan Özcan49, David Paez-Espino19, Nicolas Rascovan29, Hugues Richard50, Gunnar Rätsch18, Lynn M. Schriml43, Torsten Semmler51, Osman U. Sezerman49, Leming Shi52, Le Huu Song53, Haruo Suzuki54, Denise Syndercombe Court35, Dominique Thomas12, Scott W. Tighe55, Klas I. Udekwu41, Juan A. Ugalde56, Brandon Valentine12, Dimitar I. Vassilev57, Elena Vayndorf58, Thirumalaisamy P. Velavan59, María M. Zambrano38, Jifeng Zhu12, Sibo Zhu52 and Christopher E. Mason12,13.Afiliação MetaSUB Consortium: 12Weill Cornell Medicine, New York, NY, USA. 13The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA. 14Icahn School of Medicine at Mount Sinai, New York, NY, USA. 15Genome Institute of Singapore, Singapore, Singapore. 16University of Naples Federico II, Naples, Italy. 17The Barcelona Institute of Science and Technology, Barcelona, Spain. 18ETH Zurich, Zurich, Switzerland. 19Joint Genome Institute, Walnut Creek, CA, USA. 20City University of Hong Kong, Hong Kong SAR, China. 21Kenya Medical Research Institute/Medical Research Directorate-Africa, Kisumu, Kenya. 22University of Colorado Boulder, Boulder, CO, USA. 23Indian Statistical Institute, Kolkata, India. 24University of Minnesota, Minneapolis, MN, USA. 25Universidad Andrés Bello, Santiago, Chile. 26Weill Cornell Medicine—Qatar, Doha, Qatar. 27California State University Sacramento, Sacramento, CA, USA. 28University of Hawaii, Honolulu, HI, USA. 29Aix-Marseille Université, Marseille, France. 30A.C.Camargo Cancer Center, São Paulo, Brazil. 31Norwegian Defence Research Establishment, Kjeller, Norway. 32University of Sheffield, Sheffield, UK. 33Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine. 34University of Applied Sciences FH-Campus Wien, Vienna, Austria. 35King’s College London, London, UK. 36Institut Pasteur de Montevideo, Montevideo, Uruguay. 37Institut Pasteur Korea, Seongnam, South Korea. 38Corporación Corpogen, Bogotá, Colombia. 39Jagiellonian University, Kraków, Poland. 40HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. 41Stockholm University, Stockholm, Sweden. 42Microba, Brisbane, Australia. 43University of Maryland School of Medicine, Baltimore, MD, USA. 44Fundação Oswaldo Cruz Laboratório de Hanseníase, Rio de Janeiro, Brazil. 45Ribeirão Preto Medical School University of São Paulo, São Paulo, Brazil. 46Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal. 47University of Tübingen, Tübingen, Germany. 48Elizade University, Ondo State, Nigeria. 49Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey. 50Sorbonne University, Paris, France. 51Robert Koch Institute, Berlin, Germany. 52Fudan University, Shanghai, China. 53Vietnamese-German Center of Excellence, Hanoi, Vietnam. 54Keio University, Fujisawa, Japan. 55University of Vermont, Burlington, VT, USA. 56Millennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile. 57Sofia University, Sofia, Bulgaria. 58University of Alaska Fairbanks, Fairbanks, AK, USA. 59Univeristätsklinikum Tübingen, Tübingen, Germany.Múltipla autoria - ver em Notas.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.engNaturePatógenos oportunistascartografiaResistência a antibióticosGenesAmbiente hospitalar terciárioCartographyOpportunistic pathogensAntibiotic resistanceGenesTertiary hospital environmentCartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environmentinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; 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dc.title.pt_BR.fl_str_mv	Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
title	Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
spellingShingle	Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment Kern, Rei Chng Patógenos oportunistas cartografia Resistência a antibióticos Genes Ambiente hospitalar terciário Cartography Opportunistic pathogens Antibiotic resistance Genes Tertiary hospital environment
title_short	Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
title_full	Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
title_fullStr	Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
title_full_unstemmed	Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
title_sort	Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
author	Kern, Rei Chng
author_facet	Kern, Rei Chng Chenhao, Li Bertrand, Denis Ng, Amanda Hui Qi Kwah, Junmei Samantha Hwee, Meng Low Chengxuan, Tong Natrajan, Maanasa Zhang, Michael Hongjie Licheng, Xu Karrie, Kwan Ki Ko Ho, Eliza Xin Pei Av-Shalom, Tamar V. Teo, Jeanette Woon Pei Khor, Chiea Chuen Chen, Swaine L. Mason, Christopher E. Ng, Oon Tek Marimuthu, Kalisvar Ang, Brenda Nagarajan, Niranjan MetaSUB Consortium
author_role	author
author2	Chenhao, Li Bertrand, Denis Ng, Amanda Hui Qi Kwah, Junmei Samantha Hwee, Meng Low Chengxuan, Tong Natrajan, Maanasa Zhang, Michael Hongjie Licheng, Xu Karrie, Kwan Ki Ko Ho, Eliza Xin Pei Av-Shalom, Tamar V. Teo, Jeanette Woon Pei Khor, Chiea Chuen Chen, Swaine L. Mason, Christopher E. Ng, Oon Tek Marimuthu, Kalisvar Ang, Brenda Nagarajan, Niranjan MetaSUB Consortium
author2_role	author author author author author author author author author author author author author author author author author author author author author
dc.contributor.author.fl_str_mv	Kern, Rei Chng Chenhao, Li Bertrand, Denis Ng, Amanda Hui Qi Kwah, Junmei Samantha Hwee, Meng Low Chengxuan, Tong Natrajan, Maanasa Zhang, Michael Hongjie Licheng, Xu Karrie, Kwan Ki Ko Ho, Eliza Xin Pei Av-Shalom, Tamar V. Teo, Jeanette Woon Pei Khor, Chiea Chuen Chen, Swaine L. Mason, Christopher E. Ng, Oon Tek Marimuthu, Kalisvar Ang, Brenda Nagarajan, Niranjan MetaSUB Consortium
dc.subject.other.pt_BR.fl_str_mv	Patógenos oportunistas cartografia Resistência a antibióticos Genes Ambiente hospitalar terciário
topic	Patógenos oportunistas cartografia Resistência a antibióticos Genes Ambiente hospitalar terciário Cartography Opportunistic pathogens Antibiotic resistance Genes Tertiary hospital environment
dc.subject.en.pt_BR.fl_str_mv	Cartography Opportunistic pathogens Antibiotic resistance Genes Tertiary hospital environment
description	Milton Osório Moraes - Fundação Oswaldo Cruz Laboratório de Hanseníase, Rio de Janeiro, RJ, Brasil. MetaSUB Consortium.
publishDate	2020
dc.date.issued.fl_str_mv	2020
dc.date.accessioned.fl_str_mv	2021-04-08T18:47:26Z
dc.date.available.fl_str_mv	2021-04-08T18:47:26Z
dc.type.status.fl_str_mv	info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv	info:eu-repo/semantics/article
format	article
status_str	publishedVersion
dc.identifier.citation.fl_str_mv	CHNG, Kernr Rei et al. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nature Medicine, v. 26, p. 941-951, June 2020.
dc.identifier.uri.fl_str_mv	https://www.arca.fiocruz.br/handle/icict/46582
dc.identifier.issn.pt_BR.fl_str_mv	1078-8956
dc.identifier.doi.none.fl_str_mv	10.1038/s41591-020-0894-4
identifier_str_mv	CHNG, Kernr Rei et al. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nature Medicine, v. 26, p. 941-951, June 2020. 1078-8956 10.1038/s41591-020-0894-4
url	https://www.arca.fiocruz.br/handle/icict/46582
dc.language.iso.fl_str_mv	eng
language	eng
dc.rights.driver.fl_str_mv	info:eu-repo/semantics/openAccess
eu_rights_str_mv	openAccess
dc.publisher.none.fl_str_mv	Nature
publisher.none.fl_str_mv	Nature
dc.source.none.fl_str_mv	reponame:Repositório Institucional da FIOCRUZ (ARCA) instname:Fundação Oswaldo Cruz (FIOCRUZ) instacron:FIOCRUZ
instname_str	Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str	FIOCRUZ
institution	FIOCRUZ
reponame_str	Repositório Institucional da FIOCRUZ (ARCA)
collection	Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv	https://www.arca.fiocruz.br/bitstream/icict/46582/1/license.txt https://www.arca.fiocruz.br/bitstream/icict/46582/2/MiltonOzorio_MOraes_Consrtium_etal_IOC_2020.pdf https://www.arca.fiocruz.br/bitstream/icict/46582/3/MiltonOzorio_MOraes_Consrtium_etal_IOC_2020.pdf.txt
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bitstream.checksumAlgorithm.fl_str_mv	MD5 MD5 MD5
repository.name.fl_str_mv	Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv	repositorio.arca@fiocruz.br
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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

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