A global metagenomic map of urban microbiomes and antimicrobial resistance
Vitenskapelig artikkel
2021
David Danko
Daniela Bezdan
Evan E. Afshin
Sofia Ahsanuddin
Chandrima Bhattacharya
Daniel J. Butler
Kern Rei Chng
Daisy Donnellan
Jochen Hecht
Katelyn Jackson
Katerina Kuchin
Mikhail Karasikov
Abigail Lyons
Lauren Mak
Dmitry Meleshko
Harun Mustafa
Beth Mutai
Russell Y. Neches
Amanda Ng
Olga Nikolayeva
Tatyana Nikolayeva
Eileen Png
Krista A. Ryon
Jorge L. Sanchez
Heba Shaaban
Maria A. Sierra
Dominique Thomas
Ben Young
Omar O. Abudayyeh
Josue Alicea
Malay Bhattacharyya
Ran Blekhman
Eduardo Castro-Nallar
Ana M. Cañas
Aspassia D. Chatziefthimiou
Robert W. Crawford
Francesca De Filippis
Youping Deng
Christelle Desnues
Emmanuel Dias-Neto
Marius Dybwad
Eran Elhaik
Danilo Ercolini
Alina Frolova
Dennis Gankin
Jonathan S. Gootenberg
Alexandra B. Graf
Caroline Green
Iman Hajirasouliha
Jaden J.A. Hastings
Mark Hernandez
Gregorio Iraola
Soojin Jang
Andre Kahles
Frank J. Kelly
Kaymisha Knights
Nikos Kyrpides
Paweł P. Łabaj
Patrick K.H. Lee
Marcus H.Y. Leung
Per O. Ljungdahl
Gabriella Mason-Buck
Ken McGrath
Cem Meydan
Emmanuel F. Mongodin
Milton Ozorio Moraes
Niranjan Nagarajan
Marina Nieto-Caballero
Houtan Noushmehr
Manuela Oliveira
Stephan Ossowski
Olayinka O. Osuolale
Orhan Özcan
David Paez-Espino
Nicolás Rascovan
Hugues Richard
Gunnar Rätsch
Lynn M. Schriml
Torsten Semmler
Osman U. Sezerman
Leming Shi
Tieliu Shi
Rania Siam
Le Huu Song
Haruo Suzuki
Denise Syndercombe Court
Scott W. Tighe
Xinzhao Tong
Klas I. Udekwu
Juan A. Ugalde
Brandon Valentine
Dimitar I. Vassilev
Elena M. Vayndorf
Thirumalaisamy P. Velavan
Jun Wu
María M. Zambrano
Jifeng Zhu
Sibo Zhu
Christopher E. Mason
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.
Utgiverinformasjon
Danko, David; Bezdan, Daniela; Afshin, Evan E.; Ahsanuddin, Sofia; Bhattacharya, Chandrima; Butler, Daniel J.; Chng, Kern Rei; Donnellan, Daisy; Hecht, Jochen; Jackson, Katelyn; Kuchin, Katerina; Karasikov, Mikhail; Lyons, Abigail; Mak, Lauren; Meleshko, Dmitry; Mustafa, Harun; Mutai, Beth; Neches, Russell Y.; Ng, Amanda; Nikolayeva, Olga; Nikolayeva, Tatyana; Png, Eileen; Ryon, Krista A.; Sanchez, Jorge L.; Shaaban, Heba; Sierra, Maria A.; Thomas, Dominique; Young, Ben; Abudayyeh, Omar O.; Alicea, Josue; Bhattacharyya, Malay; Blekhman, Ran; Castro-Nallar, Eduardo; Cañas, Ana M.; Chatziefthimiou, Aspassia D.; Crawford, Robert W.; De Filippis, Francesca; Deng, Youping; Desnues, Christelle; Dias-Neto, Emmanuel; Dybwad, Marius; Elhaik, Eran; Ercolini, Danilo; Frolova, Alina; Gankin, Dennis; Gootenberg, Jonathan S.; Graf, Alexandra B.; Green, Caroline; Hajirasouliha, Iman; Hastings, Jaden J.A.; Hernandez, Mark; Iraola, Gregorio; Jang, Soojin; Kahles, Andre; Kelly, Frank J.; Knights, Kaymisha; Kyrpides, Nikos; Łabaj, Paweł P.; Lee, Patrick K.H.; Leung, Marcus H.Y.; Ljungdahl, Per O.; Mason-Buck, Gabriella; McGrath, Ken; Meydan, Cem; Mongodin, Emmanuel F.; Moraes, Milton Ozorio; Nagarajan, Niranjan; Nieto-Caballero, Marina; Noushmehr, Houtan; Oliveira, Manuela; Ossowski, Stephan; Osuolale, Olayinka O.; Özcan, Orhan; Paez-Espino, David; Rascovan, Nicolás; Richard, Hugues; Rätsch, Gunnar; Schriml, Lynn M.; Semmler, Torsten; Sezerman, Osman U.; Shi, Leming; Shi, Tieliu; Siam, Rania; Song, Le Huu; Suzuki, Haruo; Court, Denise Syndercombe; Tighe, Scott W.; Tong, Xinzhao; Udekwu, Klas I.; Ugalde, Juan A.; Valentine, Brandon; Vassilev, Dimitar I.; Vayndorf, Elena M.; Velavan, Thirumalaisamy P.; Wu, Jun; Zambrano, María M.; Zhu, Jifeng; Zhu, Sibo; Mason, Christopher E..
A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021 ;Volum 184.(13) s. 3376-3393.e17
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