About: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
Creator	Hernandez, Mark Ercolini, Danilo Wu, Jun Desnues, Christelle Semmler, Torsten Green, David Mason, Christopher Paez-Espino, David Nagarajan, Niranjan Castro-Nallar, Eduardo Butler, Daniel Iraola, Gregorio Kyrpides, Nikos Lee, Patrick Mongodin, Emmanuel Oliveira, Manuela Song, Le Velavan, Thirumalaisamy Moraes, Milton Deng, Youping Leung, Marcus Tong, Xinzhao Danko, David Hajirasouliha, Iman Kahles, Andre Rätsch, Gunnar Tighe, Scott Abudayyeh, Omar Bezdan, Daniela Gootenberg, Jonathan Hecht, Jochen Meleshko, Dmitry Afshinnekoo, Ebrahim Dybwad, Marius Shi, Leming Elhaik, Eran Mason-Buck, Gabriella Meydan, Cem Schriml, Lynn Sanchez, Jorge Sezerman, Osman Ahsanuddin, Sofia Alicea, Josue Bhattacharya, Chandrima Bhattacharyya, Malay Blekhman, Ran Cañas, Ana Chatziefthimiou, Aspassia Chng, Court, Denise Crawford, Robert De Filippis, Francesca Dias-Neto, Emmanuel Donnellan, Daisy Frolova, Alina Gankin, Dennis Graf, Alexandra Jang, Soojin Karasikov, Mikhail Kelly, Frank Kern, Rei Knights, Kaymisha Kuchin, Katerina Lyons, Abigail Mak, Lauren Mcgrath, Ken Mustafa, Harun Mutai, Beth Neches, Russell Ng, Amanda Nieto-Caballero, Marina Nikolayeva, Olga Nikolayeva, Tatyana Noushmehr, Houtan Ossowski, Stephan Osuolale, Olayinka Png, Eileen Rascovan, Nicolas Richard, Hugues Ryon, Krista Shaaban, Heba Shi, Tieliu Sierra, Maria Suzuki, Haruo Thomas, Dominique Udekwu, Klas Ugalde, Juan Valentine, Brandon Vayndorf, Elena Young, Ben Zambrano, María Zhu, Jifeng Zhu, Sibo
Source	BioRxiv
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.

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