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A global metagenomic map of urban microbiomes and antimicrobial resistance

Danko, David and Bezdan, Daniela and Afshin, Evan E. and Ahsanuddin, Sofia and Bhattacharya, Chandrima and Butler, Daniel J. and Chng, Kern Rei and Donnellan, Daisy and Hecht, Jochen and Jackson, Katelyn and Kuchin, Katerina and Karasikov, Mikhail and Lyons, Abigail and Mak, Lauren and Meleshko, Dmitry and Mustafa, Harun and Mutai, Beth and Neches, Russell Y. and Ng, Amanda and Nikolayeva, Olga and Nikolayeva, Tatyana and Png, Eileen and Ryon, Krista A. and Sanchez, Jorge L. and Shaaban, Heba and Sierra, Maria A. and Thomas, Dominique and Young, Ben and Abudayyeh, Omar O. and Alicea, Josue and Bhattacharyya, Malay and Blekhman, Ran and Castro-Nallar, Eduardo and Canas, Ana M. and Chatziefthimiou, Aspassia D. and Crawford, Robert W. and De Filippis, Francesca and Deng, Youping and Desnues, Christelle and Dias-Neto, Emmanuel and Dybwad, Marius and Elhaik, Eran and Ercolini, Danilo and Frolova, Alina and Gankin, Dennis and Gootenberg, Jonathan S. and Graf, Alexandra B. and Green, David C. and Hajirasouliha, Iman and Hastings, Jaden J. A. and Hernandez, Mark and Iraola, Gregorio and Kahles, Andre and Kelly, Frank J. and Knights, Kaymisha and Kyrpides, Nikos C. and Labaj, Pawel P. and Lee, Patrick K. H. and Leung, Marcus H. Y. and Ljungdahl, Per O. and Mason-Buck, Gabriella and McGrath, Ken and Meydan, Cem and Mongodin, Emmanuel F. and Moraes, Milton Ozorio and Nagarajan, Niranjan and Nieto-Caballero, Marina and Noushmehr, Houtan and Oliveira, Manuela and Ossowski, Stephan and Osuolale, Olayinka O. and Ozcan, Orhan and Paez-Espino, David and Rascovan, Nicolas and Richard, Hugues and Ratsch, Gunnar and Schriml, Lynn M. and Semmler, Torsten and Sezerman, Osman U. and Shi, Leming and Shi, Tieliu and Song, Le Huu and Suzuki, Haruo and Court, Denise Syndercombe and Tighe, Scott W. and Tong, Xinzhao and Udekwu, Klas and Ugalde, Juan A. and Valentine, Brandon and Vassilev, Dimitar and Vayndorf, Elena M. and Velavan, Thirumalaisamy P. and Wu, Jun and Zambrano, Maria M. and Zhu, Jifeng and Zhu, Sibo and Mason, Christopher E. and Jang, Soojin and Siam, Rania (2021). A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. 184 , 3376-+
[Research article]

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Abstract

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

Authors/Creators:Danko, David and Bezdan, Daniela and Afshin, Evan E. and Ahsanuddin, Sofia and Bhattacharya, Chandrima and Butler, Daniel J. and Chng, Kern Rei and Donnellan, Daisy and Hecht, Jochen and Jackson, Katelyn and Kuchin, Katerina and Karasikov, Mikhail and Lyons, Abigail and Mak, Lauren and Meleshko, Dmitry and Mustafa, Harun and Mutai, Beth and Neches, Russell Y. and Ng, Amanda and Nikolayeva, Olga and Nikolayeva, Tatyana and Png, Eileen and Ryon, Krista A. and Sanchez, Jorge L. and Shaaban, Heba and Sierra, Maria A. and Thomas, Dominique and Young, Ben and Abudayyeh, Omar O. and Alicea, Josue and Bhattacharyya, Malay and Blekhman, Ran and Castro-Nallar, Eduardo and Canas, Ana M. and Chatziefthimiou, Aspassia D. and Crawford, Robert W. and De Filippis, Francesca and Deng, Youping and Desnues, Christelle and Dias-Neto, Emmanuel and Dybwad, Marius and Elhaik, Eran and Ercolini, Danilo and Frolova, Alina and Gankin, Dennis and Gootenberg, Jonathan S. and Graf, Alexandra B. and Green, David C. and Hajirasouliha, Iman and Hastings, Jaden J. A. and Hernandez, Mark and Iraola, Gregorio and Kahles, Andre and Kelly, Frank J. and Knights, Kaymisha and Kyrpides, Nikos C. and Labaj, Pawel P. and Lee, Patrick K. H. and Leung, Marcus H. Y. and Ljungdahl, Per O. and Mason-Buck, Gabriella and McGrath, Ken and Meydan, Cem and Mongodin, Emmanuel F. and Moraes, Milton Ozorio and Nagarajan, Niranjan and Nieto-Caballero, Marina and Noushmehr, Houtan and Oliveira, Manuela and Ossowski, Stephan and Osuolale, Olayinka O. and Ozcan, Orhan and Paez-Espino, David and Rascovan, Nicolas and Richard, Hugues and Ratsch, Gunnar and Schriml, Lynn M. and Semmler, Torsten and Sezerman, Osman U. and Shi, Leming and Shi, Tieliu and Song, Le Huu and Suzuki, Haruo and Court, Denise Syndercombe and Tighe, Scott W. and Tong, Xinzhao and Udekwu, Klas and Ugalde, Juan A. and Valentine, Brandon and Vassilev, Dimitar and Vayndorf, Elena M. and Velavan, Thirumalaisamy P. and Wu, Jun and Zambrano, Maria M. and Zhu, Jifeng and Zhu, Sibo and Mason, Christopher E. and Jang, Soojin and Siam, Rania
Title:A global metagenomic map of urban microbiomes and antimicrobial resistance
Series Name/Journal:Cell
Year of publishing :2021
Volume:184
Page range:3376-+
Number of Pages:35
Publisher:CELL PRESS
ISSN:0092-8674
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
URN:NBN:urn:nbn:se:slu:epsilon-p-113028
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-113028
Additional ID:
Type of IDID
DOI10.1016/j.cell.2021.05.002
Web of Science (WoS)000665547300006
ID Code:25006
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Aquatic Sciences and Assessment
Deposited By: SLUpub Connector
Deposited On:24 Aug 2021 13:26
Metadata Last Modified:24 Aug 2021 13:31

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