Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
2022
Munk, Patrick | Lefo, Brett | Van, Chinh Dang | Davis, Michael | Li Baisheng, Edit First Name! | Wittum, Thomas E. | Sozzi, Emanuele | Sobsey, Mark D. | Leonard, Anne | Beck, Nicola Koren | Meschke, John Scott | Gaze, William H. | Rigamonti, Natalia | Sukapanpatharam, Pardi | Graham, David W. | Truong, Phuong | Capone, Drew | Kang, Sanghoon | Zhang, Lihong | Bunce, Joshua T. | Lilienthal, Ronald | Baklayan, Patricia | Brown, Joe | Tran, Doan Minh Nguyen | Phuc, Nguyen Do | Brinch, Christian | Moller, Frederik Duus | Petersen, Thomas N. | Hendriksen, Rene S. | Seyfarth, Anne Mette | Kjeldgaard, Jette S. | Svendsen, Christina Aaby | van Bunnik, Bram | Berglund, Fanny | Larsson, D. G. Joakim | Koopmans, Marion | Woolhouse, Mark | Aarestrup, Frank M. | Power, Pablo | Lambrinidis, Dionisia | Neilson, Elizabeth Heather Jakobsen | Gibb, Karen | Collignon, Peter | Begum, Anowara | Hossain, Zenat Zebin | Pieters, Ilse | Victorien, Dougnon Tamegnon | Tagliati, Carlos Alberto | Rodrigues, Dalia | Oliveira, Guilherme | Ribeiro de Souza, Larissa Camila | Ivanov, Ivan | Sopheak, Thet | Vuthy, Yith | Ngandjio, Antoinette | Nzouankeu, Ariane | Jacques Olivier, Ziem A. Abah | Yost, Christopher K. | Kumar, Pratik | Brar, Satinder Kaur | Adell, Aiko D. | Cuadros-Orellana, Sara | Ke, Changwen | Zheng, Huanying | Lau, Lok Ting | Chung, Teresa | Jiao, Xiaoyang | Yu, Yongjie | Morales, Johan F. Bernal | Valencia, Maria Fernanda | Donado-Godoy, Pilar | Hrenovic, Jasna | Jergovic, Matijana | Karpiskova, Renata | Hansen, Lisbeth Truelstrup | Jensen, Pernille Erland | Abouelnaga, Mohamed | Salem, Mohamed Fathy | Legesse, Mengistu | Eguale, Tadesse | Heikinheimo, Annamari | Le Guyader, Soizick | Schaeffer, Julien | Villacis, Jose Eduardo | Sanneh, Bakary | Malania, Lile | Nitsche, Andreas | Brinkmann, Annika | Schubert, Sara | Hesse, Sina | Berendonk, Thomas U. | Saba, Courage Kosi Setsoafia | Mohammed, Jibril | Feglo, Patrick Kwame | Banu, Regina Ama | Kotzamanidis, Charalampos | Lytras, Efthymios | Lickes, Sergio A. | Kocsis, Bela | Solymosi, Norbert | Thorsteinsdottir, Thorunn R. | Hatha, Abdulla Mohamed | Ballal, Mamatha | Bangera, Sohan Rodney | Fani, Fereshteh | Alebouyeh, Masoud | Morris, Dearbhaile | O'Connor, Louise | Cormican, Martin | Moran-Gilad, Jacob | Battisti, Antonio | Diaconu, Elena Lavinia | Corno, Gianluca | Di Cesare, Andrea | Alba, Patricia | Hisatsune, Junzo | Yu, Liansheng | Kuroda, Makoto | Sugai, Motoyuki | Kayama, Shizuo | Shakenova, Zeinegul | Kiiyukia, Ciira | Ng'eno, Eric | Raka, Lul | Jamil, Kazi | Fakhraldeen, Saja Adel | Alaati, Tareq | Berzins, Aivars | Avsejenko, Jelena | Kokina, Kristina | Streikisa, Madara | Bartkevics, Vadims | Matar, Ghassan M. | Daoud, Ziad | Pereckiene, Asta | Butrimaite-Ambrozeviciene, Ceslova | Penny, Christian | Banda, Daniel Lawadi | Amin, Arshana | Rajandas, Heraa | Parimannan, Sivachandran | Spiteri, David | Haber, Malcolm Vella | Santchurn, Sunita J. | Vujacic, Aleksandar | Djurovic, Dijana | Bouchrif, Brahim | Karraouan, Bouchra | Vubil, Delfino Carlos | Pal, Pushkar | Schmitt, Heike | van Passel, Mark | Jeunen, Gert-Jan | Gemmell, Neil | Chambers, Stephen T. | Mendoza, Fania Perez | Huete-Pirez, Jorge | Vilchez, Samuel | Ahmed, Akeem Olayiwola | Adisa, Ibrahim Raufu | Odetokun, Ismail Ayoade | Fashae, Kayode | Sorgaard, Anne-Marie | Wester, Astrid Louise | Ryrfors, Pia | Holmstad, Rune | Mohsin, Mashkoor | Hasan, Rumina | Shakoor, Sadia | Gustafson, Natalie Weiler | Schill, Claudia Huber | Zamudio Rojas, Maria Luz | Echevarria Velasquez, Jorge | Magtibay, Bonifacio B. | Catangcatang, Kris | Sibulo, Ruby | Yauce, Felipe Campos | Wasyl, Dariusz | Manaia, Celia | Rocha, Jaqueline | Martins, Jose | Alvaro, Pedro | Wen, Doris Di Yoong | Shin, Hanseob | Hur, Hor-Gil | Yoon, Sukhwan | Bosevska, Golubinka | Kochubovski, Mihail | Cojocaru, Radu | Burduniuc, Olga | Hong, Pei-Ying | Perry, Meghan Rose | Gassama, Amy | Radosavljevic, Vladimir | Tay, Moon Y. F. | Zuniga-Montanez, Rogelio | Wuertz, Stefan | Gavacova, Dagmar | Pastuchova, Katarina | Truska, Peter | Trkov, Marija | Esterhuyse, Kerneels | Song, Min Joon | Quintela-Baluja, Marcos | Gomez Lopez, Mariano | Cerda-Cuellar, Marta | Perera, R. R. D. P. | Bandara, N. K. B. K. R. G. W. | Premasiri, H. I. | Pathirage, Sujatha | Rutgersson, Carolin | Norrgren, Leif | Örn, Stefan | Boss, Renate | Van der Heijden, Tanja | Hong, Yu-Ping | Kumburu, Happiness Houka | Mdegela, Robinson Hammerthon | Hounmanou, Yaovi Mahuton Gildas | Chonsin, Kaknokrat | Suthienkul, Orasa | Thamlikitkul, Visanu | de Roda Husman, Ana Maria | Bidjada, Bawimodom | Njanpop-Lafourcade, Berthe-Marie | Nikiema-Pessinaba, Somtinda Christelle | Levent, Belkis | Kurekci, Cemil | Ejobi, Francis | Kalule, John Bosco | Thomsen, Jens | Obaidi, Ouidiane | Jassim, Laila Mohamed | Moore, Andrew | Kwenda, Geoffrey
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
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