A global metagenomic map of urban microbiomes and antimicrobial resistance

David Danko (1) , Daniela Bezdan (1) , Evan Afshin (1) , Sofia Ahsanuddin (2) , Chandrima Bhattacharya (1) , Daniel Butler (1) , Kern Rei Chng (3) , Daisy Donnellan (1) , Jochen Hecht (4) , Katelyn Jackson (1) , Katerina Kuchin (1) , Mikhail Karasikov (5) , Abigail Lyons (1) , Lauren Mak (1) , Dmitry Meleshko (1) , Harun Mustafa (5) , Beth Mutai (4) , Russell Neches (6) , Amanda Ng (3) , Olga Nikolayeva (7) , Tatyana Nikolayeva (7) , Eileen Png (3) , Krista Ryon (1) , Jorge Sanchez (1) , Heba Shaaban (1) , Maria Sierra (1) , Dominique Thomas (1) , Ben Young (1) , Omar Abudayyeh (8) , Josue Alicea (1) , Malay Bhattacharyya (9) , Ran Blekhman (10) , Eduardo Castro-Nallar (11) , Ana Cañas (1) , Aspassia Chatziefthimiou (1) , Robert Crawford (12) , Francesca de Filippis (13) , Youping Deng (14) , Christelle Desnues (15) , Emmanuel Dias-Neto (16) , Marius Dybwad (17) , Eran Elhaik (18) , Danilo Ercolini (13) , Alina Frolova (19) , Dennis Gankin (8) , Jonathan Gootenberg (8) , Alexandra Graf (20) , David Green (21) , Iman Hajirasouliha (1) , Jaden J.A. Hastings (1) , Mark Hernandez (22) , Gregorio Iraola (23) , Soojin Jang (24) , Andre Kahles (5) , Frank Kelly (21) , Kaymisha Knights (1) , Nikos Kyrpides (6) , Paweł Łabaj (25) , Patrick K.H. Lee (26) , Marcus H.Y. Leung (26) , Per Ljungdahl (27) , Gabriella Mason-Buck (21) , Ken Mcgrath (7) , Cem Meydan (1) , Emmanuel Mongodin (28) , Milton Ozorio Moraes (29) , Niranjan Nagarajan (3) , Marina Nieto-Caballero (22) , Houtan Noushmehr (30) , Manuela Oliveira (31) , Stephan Ossowski (32) , Olayinka Osuolale (33) , Orhan Özcan (34) , David Paez-Espino (6) , Nicolás Rascovan (35) , Hugues Richard (36) , Gunnar Rätsch (5) , Lynn Schriml (28) , Torsten Semmler (37) , Osman Sezerman (34) , Leming Shi (25) , Tieliu Shi (38) , Rania Siam (39) , Le Huu Song (40) , Haruo Suzuki (41) , Denise Syndercombe Court (21) , Scott Tighe (42) , Xinzhao Tong (26) , Klas Udekwu (27) , Juan Ugalde (43) , Brandon Valentine (1) , Dimitar Vassilev (44) , Elena Vayndorf (45) , Thirumalaisamy Velavan (46) , Jun Wu (38) , María Zambrano (47) , Jifeng Zhu (1) , Sibo Zhu (25) , Christopher Mason (1) , Gabriela Albuquerque , Alex Alexiev , Kalyn Ali , Lucia Alvarado-Arnez , Sarh Aly , Jennifer Amachee , Maria Amorim , Majelia Ampadu , Muhammad Al-Fath Amran , Nala An , Watson Andrew , Harilanto Andrianjakarivony , Michael Angelov , Verónica Antelo , Catharine Aquino , Álvaro Aranguren , Luiza Araujo , Hitler Francois Vasquez Arevalo , Jenny Arevalo , Carme Arnan , Lucia Elena Alvarado Arnez , Fernanda Arredondo , Matthew Arthur , Freddy Asenjo , Thomas Saw Aung , Juliette Auvinet , Nuria Aventin , Sadaf Ayaz , Silva Baburyan , Abd-Manaaf Bakere , Katrin Bakhl , Thais Bartelli , Erdenetsetseg Batdelger , François Baudon , Kevin Becher , Carla Bello , Médine Benchouaia , Hannah Benisty , Anne-Sophie Benoiston , Joseph Benson , Diego Benítez , Juliana Bernardes , Denis Bertrand , Silvia Beurmann , Tristan Bitard-Feildel , Lucie Bittner , Christina Black , Guillaume Blanc , Brittany Blyther , Toni Bode , Julia Boeri , Bazartseren Boldgiv , Kevin Bolzli , Alexia Bordigoni , Ciro Borrelli , Sonia Bouchard , Jean-Pierre Bouly , Alicia Boyd , Gabriela Branco , Alessandra Breschi , Björn Brindefalk , Christian Brion , Alan Briones , Paulina Buczansla , Catherine Burke , Aszia Burrell , Alina Butova , Irvind Buttar , Jalia Bynoe , Sven Bönigk , Kari Bøifot , Hiram Caballero , Xiao Wen Cai , Dayana Calderon , Angela Cantillo , Miguel Carbajo , Alessandra Carbone , Anais Cardenas , Katerine Carrillo , Laurie Casalot , Sofia Castro , Ana Castro , Astred Castro , Ana Valeria B. Castro , Simone Cawthorne , Jonathan Cedillo , Salama Chaker , Jasna Chalangal , Allison Chan , Anastasia Chasapi , Starr Chatziefthimiou , Sreya Ray Chaudhuri , Akash Keluth Chavan , Francisco Chavez , Gregory Chem , Xiaoqing Chen , Michelle Chen , Jenn-Wei Chen , Ariel Chernomoretz , Allaeddine Chettouh , Daisy Cheung , Diana Chicas , Shirley Chiu , Hira Choudhry , Carl Chrispin , Kianna Ciaramella , Erika Cifuentes , Jake Cohen , David Coil , Sylvie Collin , Colleen Conger , Romain Conte , Flavia Corsi , Cecilia Cossio , Ana Costa , Delisia Cuebas , Bruno D’alessandro , Katherine Dahlhausen , Aaron Darling , Pujita Das , Lucinda Davenport , Laurent David , Natalie Davidson , Gargi Dayama , Stéphane Delmas , Chris Deng , Chloé Dequeker , Alexandre Desert , Monika Devi , Felipe Dezem , Clara Dias , Timothy Ryan Donahoe , Sonia Dorado , Lashonda Dorsey , Valeriia Dotsenko , Steven Du , Alexandra Dutan , Naya Eady , Jonathan Eisen , Miar Elaskandrany , Lennard Epping , Juan Escalera-Antezana , Cassie Ettinger , Iqra Faiz , Luice Fan , Nadine Farhat , Emile Faure , Fazlina Fauzi , Charlie Feigin , Skye Felice , Laís Pereira Ferreira , Gabriel Figueroa , Aubin Fleiss , Denisse Flores , Jhovana Velasco Flores , Marcos A.S. Fonseca , Jonathan Foox , Juan Carlos Forero , Aaishah Francis , Kelly French , Pablo Fresia , Jacob Friedman , Jaime Fuentes , Josephine Galipon , Mathilde Garcia , Laura Garcia , Catalina García , Annie Geiger , Samuel Gerner , Sonia Ghose , Dao Phuong Giang , Matías Giménez , Donato Giovannelli , Dedan Githae , Spyridon Gkotzis , Liliana Godoy , Samantha Goldman , Gaston Gonnet , Juana Gonzalez , Andrea Gonzalez , Camila Gonzalez-Poblete , Andrew Gray , Tranette Gregory , Charlotte Greselle , Sophie Guasco , Juan Guerra , Nika Gurianova , Wolfgang Haehr , Sebastien Halary , Felix Hartkopf , Arya Hawkins-Zafarnia , Nur Hazlin Hazrin-Chong , Eric Helfrich , Eva Hell , Tamera Henry , Samuel Hernandez , Pilar Lopez Hernandez , David Hess-Homeier , Lauren Hittle , Nghiem Xuan Hoan , Aliaksei Holik , Chiaki Homma , Irene Hoxie , Michael Huber , Elizabeth Humphries , Stephanie Hyland , Andrea Hässig , Roland Häusler , Nathalie Hüsser , Robert Petit , Badamnyambuu Iderzorig , Mizuki Igarashi , Shaikh Iqbal , Shino Ishikawa , Sakura Ishizuka , Sharah Islam , Riham Islam , Kohei Ito , Sota Ito , Takayuki Ito , Tomislav Ivankovic , Tomoki Iwashiro , Sarah Jackson , Joann Jacobs , Marisano James , Marianne Jaubert , Marie-Laure Jerier , Esmeralda Jiminez , Ayantu Jinfessa , Ymke de Jong , Hyun Woo Joo , Guilllaume Jospin , Takema Kajita , Affifah Saadah Ahmad Kassim , Nao Kato , Amrit Kaur , Inderjit Kaur , Fernanda de Souza Gomes Kehdy , Vedbar Khadka , Shaira Khan , Mahshid Khavari , Michelle Ki , Gina Kim , Hyung Jun Kim , Sangwan Kim , Ryan King , Giuseppe Kolomonaco , Ellen Koag , Nadezhda Kobko-Litskevitch , Maryna Korshevniuk , Michael Kozhar , Jonas Krebs , Nanami Kubota , Andrii Kuklin , Sheelta Kumar , Rachel Kwong , Lawrence Kwong , Ingrid Lafontaine , Juliana Lago , Tsoi Ying Lai , Elodie Laine , Manolo Laiola , Olha Lakhneko , Isha Lamba , Gerardo de Lamotte , Romain Lannes , Eleonora de Lazzari , Madeline Leahy , Hyunjung Lee , Yunmi Lee , Lucy Lee , Vincent Lemaire , Emily Leong , Dagmara Lewandowska , Chenhao Li , Weijun Liang , Moses Lin , Priscilla Lisboa , Anna Litskevitch , Eric Minwei Liu , Tracy Liu , Mayra Arauco Livia , Yui Him Lo , Sonia Losim , Manon Loubens , Jennifer Lu , Olexandr Lykhenko , Simona Lysakova , Salah Mahmoud , Sara Abdul Majid , Natalka Makogon , Denisse Maldonado , Krizzy Mallari , Tathiane Malta , Maliha Mamun , Dimitri Manoir , German Marchandon , Natalia Marciniak , Sonia Marinovic , Brunna Marques , Nicole Mathews , Yuri Matsuzaki , Vincent Matthys , Madelyn May , Elias Mccomb , Annabelle Meagher , Adiell Melamed , Wayne Menary , Katterinne Mendez , Ambar Mendez , Irène Mauricette Mendy , Irene Meng , Ajay Menon , Mark Menor , Roy Meoded , Nancy Merino , Karishma Miah , Mathilde Mignotte , Tanja Miketic , Wilson Miranda , Athena Mitsios , Ryusei Miura , Kunihiko Miyake , Maria Moccia , Natasha Mohan , Mohammed Mohsin , Karobi Moitra , Mauricio Moldes , Laura Molina , Jennifer Molinet , Orgil-Erdene Molomjamts , Eftar Moniruzzaman , Sookwon Moon , Isabelle de Oliveira Moraes , Mario Moreno , Maritza Mosella , Josef Moser , Christopher Mozsary , Amanda Muehlbauer , Oasima Muner , Muntaha Munia , Naimah Munim , Maureen Muscat , Tatjana Mustac , Cristina Muñoz , Francesca Nadalin , Areeg Naeem , Dorottya Nagy-Szakal , Mayuko Nakagawa , Ashanti Narce , Masaki Nasu , Irene González Navarrete , Hiba Naveed , Bryan Nazario , Narasimha Rao Nedunuri , Thomas Neff , Aida Nesimi , Wan Chiew Ng , Synti Ng , Gloria Nguyen , Elsy Ngwa , Agier Nicolas , Pierre Nicolas , Abdollahi Nika , Hosna Noorzi , Avigdor Nosrati , Diana Nunes , Kathryn O’brien , Niamh O’hara , Gabriella Oken , Rantimi Olawoyin , Javier Quilez Oliete , Kiara Olmeda , Tolulope Oluwadare , Itunu Oluwadare , Nils Ordioni , Jenessa Orpilla , Jacqueline Orrego , Melissa Ortega , Princess Osma , Israel Osuolale , Oluwatosin Osuolale , Mitsuki Ota , Francesco Oteri , Yuya Oto , Rachid Ounit , Christos Ouzounis , Subhamitra Pakrashi , Rachel Paras , Coral Pardo-Este , Young-Ja Park , Paulina Pastuszek , Suraj Patel , Jananan Pathmanathan , Andrea Patrignani , Manuel Perez , Ante Peros , Sabrina Persaud , Anisia Peters , Adam Phillips , Lisbeth Pineda , Melissa Pizzi , Alma Plaku , Alketa Plaku , Brianna Pompa-Hogan , María Gabriela Portilla , Leonardo Posada , Max Priestman , Bharath Prithiviraj , Sambhawa Priya , Phanthira Pugdeethosal , Catherine Pugh , Benjamin Pulatov , Angelika Pupiec , Kyrylo Pyrshev , Tao Qing , Saher Rahiel , Savlatjon Rahmatulloev , Kannan Rajendran , Aneisa Ramcharan , Adan Ramirez-Rojas , Shahryar Rana , Prashanthi Ratnanandan , Timothy Read , Hubert Rehrauer , Renee Richer , Alexis Rivera , Michelle Rivera , Alessandro Robertiello , Courtney Robinson , Paula Rodríguez , Nayra Aguilar Rojas , Paul Roldán , Anyelic Rosario , Sandra Roth , Maria Ruiz , Stephen Eduard Boja Ruiz , Kaitlan Russell , Mariia Rybak , Thais Sabedot , Mahfuza Sabina , Ikuto Saito , Yoshitaka Saito , Gustavo Adolfo Malca Salas , Cecilia Salazar , Kaung Myat San , Khaliun Sanchir , Ryan Sankar , Paulo Thiago de Souza Santos , Zulena Saravi , Kai Sasaki , Yuma Sato , Masaki Sato , Seisuke Sato , Ryo Sato , Kaisei Sato , Nowshin Sayara , Steffen Schaaf , Oli Schacher , Anna-Lena Schinke , Ralph Schlapbach , Christian Schori , Jason Schriml , Felipe Segato , Felipe Sepulveda , Marianna Serpa , Paola de Sessions , Juan Severyn , Maheen Shakil , Sarah Shalaby , Aliyah Shari , Hyenah Shim , Hikaru Shirahata , Yuh Shiwa , Ophélie da Silva , Jordana Silva , Gwenola Simon , Shaleni Singh , Kasia Sluzek , Rebecca Smith , Eunice So , Núria Andreu Somavilla , Yuya Sonohara , Nuno Rufino de Sousa , Camila Souza , Jason Sperry , Nicolas Sprinsky , Stefan Stark , Antonietta La Storia , Kiyoshi Suganuma , Hamood Suliman , Jill Sullivan , Arif Asyraf Md Supie , Chisato Suzuki , Sora Takagi , Fumie Takahara , Naoya Takahashi , Kou Takahashi , Tomoki Takeda , Isabella Takenaka , Soma Tanaka , Anyi Tang , Yuk Man Tang , Emilio Tarcitano , Andrea Tassinari , Mahdi Taye , Alexis Terrero , Eunice Thambiraja , Antonin Thiébaut , Sade Thomas , Andrew Thomas , Yuto Togashi , Takumi Togashi , Anna Tomaselli , Masaru Tomita , Itsuki Tomita , Oliver Toth , Nora Toussaint , Jennifer Tran , Catalina Truong , Stefan Tsonev , Kazutoshi Tsuda , Takafumi Tsurumaki , Michelle Tuz , Yelyzaveta Tymoshenko , Carmen Urgiles , Mariko Usui , Sophie Vacant , Laura Vann , Fabienne Velter , Valeria Ventorino , Patricia Vera-Wolf , Riccardo Vicedomini , Michael Suarez-Villamil , Sierra Vincent , Renee Vivancos-Koopman , Andrew Wan , Cindy Wang , Tomoro Warashina , Ayuki Watanabe , Samuel Weekes , Johannes Werner , David Westfall , Lothar Wieler , Michelle Williams , Silver Wolf , Brian Wong , Yan Ling Wong , Tyler Wong , Rasheena Wright , Tina Wunderlin , Ryota Yamanaka , Jingcheng Yang , Hirokazu Yano , George Yeh , Olena Yemets , Tetiana Yeskova , Shusei Yoshikawa , Laraib Zafar , Yang Zhang , Shu Zhang , Amy Zhang , Yuanting Zheng , Stas Zubenko , Natasha Abdullah , Marcos Abraao , Adel Ait-Hamlat (48) , Muhammad Afaq , Faisal Al-Quaddoomi , Ireen Alam

1 Weill Cornell Medicine [Cornell University]
2 MSSM - Icahn School of Medicine at Mount Sinai [New York]
3 GIS - Genome Institute of Singapore
4 CRG - Centre for Genomic Regulation - Centre de Regulació Genòmica [Barcelona]
5 ETH Zürich - Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich]
6 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
7 AUTRES
8 MIT - Massachusetts Institute of Technology
9 Indian Statistical Institute [Kolkata]
10 UMN - University of Minnesota System
11 UNAB - Universidad Andrés Bello [Santiago]
12 California State University [Sacramento]
13 University of Naples Federico II = Università degli studi di Napoli Federico II
14 University of Hawaii
15 MIO - Institut méditerranéen d'océanologie
16 Medical Genomics Group
17 FFI - Norwegian Defence Research Establishment
18 Skane University Hospital [Lund]
19 Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine
20 University of Vienna [Vienna]
21 King‘s College London
22 University of Colorado [Boulder]
23 Institut Pasteur de Montevideo
24 Institut Pasteur Korea - Institut Pasteur de Corée
25 Fudan University [Shanghai]
26 CUHK - City University of Hong Kong [Hong Kong]
27 Stockholm University
28 University of Maryland School of Medicine
29 FIOCRUZ - Fundação Oswaldo Cruz / Oswaldo Cruz Foundation
30 USP - Universidade de São Paulo = University of São Paulo
31 IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto
32 BIST - Barcelona Institute of Science and Technology
33 Elizade University
34 Acibadem Mehmet Ali Aydınlar University
35 Paléogénomique microbienne - Microbial paleogenomics
36 SU - Sorbonne Université
37 RKI - Robert Koch Institute [Berlin]
38 ECNU - East China Normal University [Shangaï]
39 Cairo University
40 Vietnamese-German Center for Medical Research
41 Keio University [Tokyo]
42 Université du Vermont
43 Universidad del Desarrollo
44 Софийски университет = Sofia University
45 UAF - University of Alaska [Fairbanks]
46 Universitätsklinikum Tübingen - University Hospital of Tübingen
47 Corporación Corpogen-Research Center
48 LCQB - Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology

Mots clés: built Environment; metagenome; global health; antimicrobial resistance; microbiome; NGS; shotgun sequencing; de novo assembly; BGC; AMR

Domaines: Biodiversité et Ecologie; Microbiologie et Parasitologie; Biodiversité

David Danko, Daniela Bezdan, Evan Afshin, Sofia Ahsanuddin, Chandrima Bhattacharya, et al.. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell, 2021, 184 (13), pp.3376-3393.e17. ⟨10.1016/j.cell.2021.05.002⟩. ⟨hal-03357730⟩