TY - JOUR T1 - Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance JF - bioRxiv DO - 10.1101/724526 SP - 724526 AU - David Danko AU - Daniela Bezdan AU - Ebrahim Afshinnekoo AU - Sofia Ahsanuddin AU - Chandrima Bhattacharya AU - Daniel J Butler AU - Kern Rei Chng AU - Francesca De Filippis AU - Jochen Hecht AU - Andre Kahles AU - Mikhail Karasikov AU - Nikos C Kyrpides AU - Marcus H Y Leung AU - Dmitry Meleshko AU - Harun Mustafa AU - Beth Mutai AU - Russell Y Neches AU - Amanda Ng AU - Marina Nieto-Caballero AU - Olga Nikolayeva AU - Tatyana Nikolayeva AU - Eileen Png AU - Jorge L Sanchez AU - Heba Shaaban AU - Maria A Sierra AU - Xinzhao Tong AU - Ben Young AU - Josue Alicea AU - Malay Bhattacharyya AU - Ran Blekhman AU - Eduardo Castro-Nallar AU - Ana M Cañas AU - Aspassia D Chatziefthimiou AU - Robert W Crawford AU - Youping Deng AU - Christelle Desnues AU - Emmanuel Dias-Neto AU - Daisy Donnellan AU - Marius Dybwad AU - Eran Elhaik AU - Danilo Ercolini AU - Alina Frolova AU - Alexandra B Graf AU - David C Green AU - Iman Hajirasouliha AU - Mark Hernandez AU - Gregorio Iraola AU - Soojin Jang AU - Angela Jones AU - Frank J Kelly AU - Kaymisha Knights AU - Paweł P Łabaj AU - Patrick K H Lee AU - Levy Shawn AU - Per Ljungdahl AU - Abigail Lyons AU - Gabriella Mason-Buck AU - Ken McGrath AU - Emmanuel F Mongodin AU - Milton Ozorio Moraes AU - Niranjan Nagarajan AU - Houtan Noushmehr AU - Manuela Oliveira AU - Stephan Ossowski AU - Olayinka O Osuolale AU - Orhan Özcan AU - David Paez-Espino AU - Nicolas Rascovan AU - Hugues Richard AU - Gunnar Rätsch AU - Lynn M Schriml AU - Torsten Semmler AU - Osman U Sezerman AU - Leming Shi AU - Le Huu Song AU - Haruo Suzuki AU - Denise Syndercombe Court AU - Dominique Thomas AU - Scott W Tighe AU - Klas I Udekwu AU - Juan A Ugalde AU - Brandon Valentine AU - Dimitar I Vassilev AU - Elena Vayndorf AU - Thirumalaisamy P Velavan AU - María M Zambrano AU - Jifeng Zhu AU - Sibo Zhu AU - Christopher E Mason AU - The International MetaSUB Consortium Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/10/04/724526.1.abstract N2 - 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. ER -