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Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance

David Danko Daniela Bezdan Ebrahim Afshinnekoo Sofia Ahsanuddin Chandrima Bhattacharya Daniel Butler Kern Rei Chng Daisy Donnellan Jochen Hecht Katerina Kuchin Mikhail Karasikov Abigail Lyons Lauren Mak Dmitry Meleshko Harun Mustafa Beth Mutai Russell Neches Amanda Ng Olga Nikolayeva Tatyana Nikolayeva Eileen Png Krista Ryon Jorge Sanchez Heba Shaaban Maria Sierra Dominique Thomas Ben Young Omar Abudayyeh Josue Alicea Malay Bhattacharyya Ran Blekhman Eduardo Castro-Nallar Ana Cañas Aspassia Chatziefthimiou Robert Crawford Francesca de Filippis Youping Deng Christelle Desnues 1, 2 Emmanuel Dias-Neto Marius Dybwad Eran Elhaik Danilo Ercolini Alina Frolova Dennis Gankin Jonathan Gootenberg Alexandra Graf David Green Iman Hajirasouliha Mark Hernandez Gregorio Iraola Soojin Jang Andre Kahles Frank Kelly Kaymisha Knights Nikos Kyrpides Paweł Łabaj Patrick Lee Marcus Leung Per Ljungdahl Gabriella Mason-Buck Ken Mcgrath Cem Meydan Emmanuel Mongodin Milton Ozorio Moraes Niranjan Nagarajan Marina Nieto-Caballero Houtan Noushmehr Manuela Oliveira Stephan Ossowski Olayinka Osuolale Orhan Özcan David Paez-Espino Nicolas Rascovan Hugues Richard Gunnar Rätsch Lynn Schriml Torsten Semmler Osman Sezerman Leming Shi Tieliu Shi Le Huu Song Haruo Suzuki Scott Tighe Xinzhao Tong Klas Udekwu Juan Ugalde Brandon Valentine Dimitar Vassilev Elena Vayndorf Thirumalaisamy Velavan Jun Wu María Zambrano Jifeng Zhu Sibo Zhu Christopher Mason
Résumé : 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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https://hal-amu.archives-ouvertes.fr/hal-02962785
Contributor : Christelle Desnues <>
Submitted on : Friday, October 9, 2020 - 2:46:15 PM
Last modification on : Sunday, October 11, 2020 - 3:02:24 AM

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David Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Chandrima Bhattacharya, et al.. Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance. 2020. ⟨hal-02962785⟩

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