A global metagenomic map of urban microbiomes and antimicrobial resistance

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; Canas, 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, David C.; Hajirasouliha, Iman; Hastings, Jaden J. A.; Hernandez, Mark; Iraola, Gregorio; Jang, Soojin; Kahles, Andre; Kelly, Frank J.; Knights, Kaymisha; Kyrpides, Nikos C.; Labaj, Pawel 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.; Ozcan, Orhan; Paez-Espino, David; Rascovan, Nicolas; Richard, Hugues; Ratsch, 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, Maria M.; Zhu, Jifeng; Zhu, Sibo; Mason, Christopher E.

doi:10.1016/j.cell.2021.05.002

Research article2021Peer reviewedOpen access

A global metagenomic map of urban microbiomes and antimicrobial resistance

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;
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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.

Published in

Cell
2021, volume: 184, number: 13, pages: 3376-+
Publisher: CELL PRESS

SLU Authors

Udekwu, Klas
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
- Stockholm University

Associated SLU-program

AMR: Bacteria

Global goals (SDG)

SDG3 Good health and well-being

UKÄ Subject classification

Bioinformatics and Computational Biology (Methods development to be 10203)

Publication identifier

DOI: https://doi.org/10.1016/j.cell.2021.05.002

Permanent link to this page (URI)

https://res.slu.se/id/publ/113028