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Global Genetic Cartography of Urban Metagenomes andAnti-Microbial Resistance

By David C Danko, Daniela Bezdan, Ebrahim Afshinnekoo, 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 Ryon, Jorge L Sanchez, Heba Shaaban, Maria A Sierra, Dominique Thomas, Ben Young, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar, Ana M Canas, Aspassia D Chatziefthimiou, Robert W Crawford, Christelle Desnues, Francesca De Filippis, Emmanuel Dias-Neto, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Alexandra B Graf, David C Green, Iman Hajirasouliha, Mark Hernandez, Gregorio Iraola, Soojin Jang, Andre Kahles, Kaymisha Knights, Nikos C Kyrpides, Pawel P Labaj, Patrick K. H. Lee, Marcus H Y Leung, Gabriella Mason-Buck, Ken McGrath, Cem Meydan, Emmanuel F Mongodin, Niranjan Nagarajan, Marina Nieto-Caballero, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O Osuolale, David Paez-Espino, Nicolas Rascovan, Hugues Richard, Gunnar Ratsch, Lynn M. Schriml, Leming Shi, Teliu Shi, Le Huu Song, Haruo Suzuki, Denise Syndercombe Court, Scott Tighe, Klas I Udekwu, Juan A. Ugalde, Brandon Valentine, Dimitar I Vassilev, Elena Vayndorf, Maria M. Zambrano, Jifeng Zhu, Sibo Zhu, Christopher Mason

Posted 05 Aug 2019
bioRxiv DOI: 10.1101/724526

We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging the urban microbial ecosystem. We identify taxonomically-defined microorganisms collected across three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1,302 bacteria, and 2 archaea novel species. We identify 4,4204 species of urban microorganisms and a consistent "core" of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Profiles of AMR genes show geographic variation in type and density. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world's cities.

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