1. Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
- Author
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Danilo Ercolini, David C. Green, Mikhail Karasikov, Soojin Jang, Olga Nikolayeva, Elena M. Vayndorf, Kern Rei Chng, Per O. Ljungdahl, Gabriella Mason-Buck, Aspassia D. Chatziefthimiou, Heba Shaaban, Alina Frolova, Eduardo Castro-Nallar, Houtan Noushmehr, Nicolás Rascovan, Chandrima Bhattacharya, Christopher E. Mason, Valentine B, Haruo Suzuki, Niranjan Nagarajan, Ken McGrath, Iman Hajirasouliha, David Danko, Emmanuel F. Mongodin, André Kahles, Abigail Lyons, Dimitar Vassilev, Ran Blekhman, Maria A. Sierra, Harun Mustafa, Malay Bhattacharyya, Deng Y, Nikolayeva T, Daniela Bezdan, Jonathan S. Gootenberg, O. Osuolale, Jun Wu, Klas I. Udekwu, Russell Y. Neches, Shanfeng Zhu, Juan A. Ugalde, David Paez-Espino, Christelle Desnues, Özcan O, Jochen Hecht, Omar O. Abudayyeh, Xinzhao Tong, Le Huu Song, Jackson K, Beth Mutai, Denise Syndercombe Court, Ebrahim Afshinnekoo, Tieliu Shi, Gregorio Iraola, Gankin D, Thirumalaisamy P. Velavan, Leung Mhy, De Filippis F, Png E, Emmanuel Dias-Neto, Marius Dybwad, Robert W. Crawford, Amanda Hui Qi Ng, María Mercedes Zambrano, Hugues Richard, Alicea J, Sofia Ahsanuddin, Cañas Am, Osman Ugur Sezerman, Mark Hernandez, Daniel Butler, Paweł P. Łabaj, Sanchez Jl, Katerina Kuchin, Cem Meydan, Frank J. Kelly, Eran Elhaik, Donnellan D, Alexandra B. Graf, Lynn M. Schriml, Knights K, Domonique Thomas, Jun Zhu, Nikos C. Kyrpides, Scott Tighe, Krista Ryon, Manuela Oliveira, Ben Young, Lee Pkh, Marina Nieto-Caballero, Torsten Semmler, Gunnar Rätsch, Lauren Mak, Leming Shi, Milton Ozório Moraes, Dmitry Meleshko, Stephan Ossowski, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
- Subjects
0303 health sciences ,education.field_of_study ,Resistance (ecology) ,biology ,030306 microbiology ,Transit system ,Population ,15. Life on land ,biology.organism_classification ,[SDE.ES]Environmental Sciences/Environmental and Society ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,03 medical and health sciences ,Geography ,13. Climate action ,Evolutionary biology ,Metagenomics ,Ecosystem ,Microbiome ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,education ,Built environment ,030304 developmental biology ,Archaea - Abstract
Although studies have shown that urban environments and mass-transit systems have distinct genetic profiles, there are no systematic worldwide studies of these dense, human microbial ecosystems. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit systems from 60 cities, spanning 4,728 samples and 4,424 taxonomically-defined microorganisms collected for three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance markers, and novel genetic elements, including 10,928 novel predicted viral species, 1302 novel bacteria, and 2 novel archaea. Urban microbiomes often resemble human commensal microbiomes from the skin and airways, but also contain a consistent “core” of 31 species which are predominantly not human commensal species. Samples show distinct microbial signatures which may be used to accurately predict properties of their city of origin including population, proximity to the coast, and taxonomic profile. These data also show that AMR density across cities varies by several orders of magnitude, including many AMRs present on plasmids with cosmopolitan distributions. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components of the built human environment, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world’s cities.
- Published
- 2020