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Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance

By David Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J Butler, Kern Rei Chng, Francesca De Filippis, Jochen Hecht, Andre Kahles, Mikhail Karasikov, Nikos C. Kyrpides, Marcus H Y Leung, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y Neches, Amanda Ng, Marina Nieto-Caballero, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Jorge L Sanchez, Heba Shaaban, Maria A Sierra, Xinzhao Tong, Ben Young, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar, Ana M Cañas, Aspassia D Chatziefthimiou, Robert W Crawford, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Daisy Donnellan, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Alexandra B Graf, David C Green, Iman Hajirasouliha, Mark Hernandez, Gregorio Iraola, Soojin Jang, Angela Jones, Frank J Kelly, Kaymisha Knights, Paweł P Łabaj, Patrick K. H. Lee, Levy Shawn, Per Ljungdahl, Abigail Lyons, Gabriella Mason-Buck, Ken McGrath, Emmanuel F Mongodin, Milton Ozorio Moraes, Niranjan Nagarajan, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O Osuolale, Orhan Özcan, David Paez-Espino, Nicolas Rascovan, Hugues Richard, Gunnar Rätsch, Lynn M. Schriml, Torsten Semmler, Osman U Sezerman, Leming Shi, Le Huu Song, Haruo Suzuki, Denise Syndercombe Court, Dominique Thomas, Scott W Tighe, Klas I Udekwu, Juan A. Ugalde, Brandon Valentine, Dimitar I Vassilev, Elena Vayndorf, Thirumalaisamy P. Velavan, María M Zambrano, Jifeng Zhu, Sibo Zhu, Christopher E. Mason, The International MetaSUB Consortium

Posted 05 Aug 2019
bioRxiv DOI: 10.1101/724526

Although studies have shown that urban environments and mass-transit systems have distinct genetic profiles, there are no systematic studies of these dense, human/microbial ecosystems around the world. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit systems from 58 cities, spanning 3,741 samples and 4,424 taxonomically-defined microorganisms collected for from 2015-2017. The map provides annotated, geospatial details about microbial strains, functional genetics, antimicrobial resistance, and novel genetic elements, including 10,928 novel predicted viral species. Urban microbiomes often resemble human commensal microbiomes from the skin and airways, but also contain a consistent “core” of 61 species which are predominantly not human commensal species. Conversely, samples may be accurately (91.4%) classified to their city-of-origin using a linear support vector machine over taxa. These data also show that AMR density across cities varies by several orders of magnitude, including many AMRs present on plasmids with specific 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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