TY - JOUR T1 - Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance JF - bioRxiv DO - 10.1101/724526 SP - 724526 AU - David C. Danko AU - Daniela Bezdan AU - Ebrahim Afshinnekoo AU - Sofia Ahsanuddin AU - Josue Alicea AU - Chandrima Bhattacharya AU - Malay Bhattacharyya AU - Ran Blekhman AU - Daniel J Butler AU - Eduardo Castro-Nallar AU - Ana M Cañas AU - Aspassia D Chatziefthimiou AU - Kern Rei Chng AU - David A Coil AU - Denise Syndercombe Court AU - Robert W Crawford AU - Christelle Desnues AU - Emmanuel Dias-Neto AU - Daisy Donnellan AU - Marius Dybwad AU - Jonathan A Eisen AU - Eran Elhaik AU - Danilo Ercolini AU - Francesca De Filippis AU - Alina Frolova AU - Alexandra B Graf AU - David C Green AU - Patrick K H Lee AU - Jochen Hecht AU - Mark Hernandez AU - Soojin Jang AU - Andre Kahles AU - Mikhail Karasikov AU - Kaymisha Knights AU - Nikos C. Kyrpides AU - Per Ljungdahl AU - Abigail Lyons AU - Gabriella Mason-Buck AU - Ken McGrath AU - Emmanuel F Mongodin AU - Harun Mustafa AU - Beth Mutai AU - Niranjan Nagarajan AU - Russell Y. Neches AU - Amanda Ng AU - Marina Nieto-Caballero AU - Olga Nikolayeva AU - Tatyana Nikolayeva AU - Houtan Noushmehr AU - Manuela Oliveira AU - Stephan Ossowski AU - Olayinka O Osuolale AU - David Paez-Espino AU - Eileen Png AU - Nicolas Rascovan AU - Hugues Richard AU - Gunnar Rätsch AU - Jorge L Sanchez AU - Lynn M Schriml AU - Heba Shaaban AU - Leming Shi AU - Maria A Sierra AU - Le Huu Song AU - Haruo Suzuki AU - Dominique Thomas AU - Klas I Udekwu AU - Juan A Ugalde AU - Brandon Valentine AU - Dimitar I Vassilev AU - Elena Vayndorf AU - Marcus H Y Leung AU - Ben Young AU - María M Zambrano AU - Jifeng Zhu AU - Sibo Zhu AU - Paweł P Łabaj AU - Christopher Mason AU - The International MetaSUB Consortium Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/08/05/724526.abstract N2 - Although studies have shown that urban environments and mass-transit systems have geospa-tially distinct metagenomes, no study has ever systematically studied 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 three years. The map provides annotated, geospatial data 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 contain a consistent “core” of 61 species which are predominantly not human commensal species. These data also show that AMR density across cities varies by several orders of magnitude with many AMRs present on plasmids with cosmopolitan distributions. Conversely, samples may be accurately (91.4%) classified to their city-of-origin using a linear support vector machine over taxa. Together, these results constitute a high-resolution global metagenomic atlas, which enables the discovery of new genetic components of the built human environment, forensic application, and an essential first draft of the global AMR burden of the world’s cities. ER -