Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Authors: Munk Patrick , Brinch Christian , Møller Frederik Duus , Petersen Thomas N. , Hendriksen Rene S. , Seyfarth Anne Mette , Kjeldgaard Jette S. , Svendsen Christina Aaby , van Bunnik Bram , Berglund Fanny ,   Global Sewage Surveillance Consortium, Bego Artan , Power Pablo , Rees Catherine , Lambrinidis Dionisia , Neilson Elizabeth Heather Jakobsen , Gibb Karen , Coventry Kris , Collignon Peter , Cassar Susan , Allerberger Franz , Begum Anowara , Hossain Zenat Zebin , Worrell Carlon , Vandenberg Olivier , Pieters Ilse , Victorien Dougnon Tamègnon , Gutierrez Angela Daniela Salazar , Soria Freddy , Grujić Vesna Rudić , Mazalica Nataša , Rahube Teddie O. , Tagliati Carlos Alberto , Rodrigues Dalia , Oliveira Guilherme , de Souza Larissa Camila Ribeiro , Ivanov Ivan , Juste Bonkoungou Isidore , Oumar Traoré , Sopheak Thet , Vuthy Yith , Ngandjio Antoinette , Nzouankeu Ariane , Olivier Ziem A. Abah Jacques , Yost Christopher K. , Kumar Pratik , Brar Satinder Kaur , Tabo Djim-Adjim , Adell Aiko D. , Paredes-Osses Esteban , Martinez Maria Cristina , Cuadros-Orellana Sara , Ke Changwen , Zheng Huanying , Baisheng Li , Lau Lok Ting , Chung Teresa , Jiao Xiaoyang , Yu Yongjie , JiaYong Zhao , Morales Johan F. Bernal , Valencia Maria Fernanda , Donado-Godoy Pilar , Coulibaly Kalpy Julien , Hrenovic Jasna , Jergović Matijana , Karpíšková Renáta , Deogratias Zozo Nyarukweba , Elsborg Bodil , Hansen Lisbeth Truelstrup , Jensen Pernille Erland , Abouelnaga Mohamed , Salem Mohamed Fathy , Koolmeister Marliin , 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 , Bērziņš Aivars , Avsejenko Jeļena , Kokina Kristina , Streikisa Madara , Bartkevics Vadims , Matar Ghassan M. , Daoud Ziad , Pereckienė Asta , Butrimaite-Ambrozeviciene Ceslova , Penny Christian , Bastaraud Alexandra , Rasolofoarison Tiavina , Collard Jean-Marc , Samison Luc Hervé , Andrianarivelo Mala Rakoto , 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-Pιrez Jorge , Vilchez Samuel , Ahmed Akeem Olayiwola , Adisa Ibrahim Raufu , Odetokun Ismail Ayoade , Fashae Kayode , Sørgaard Anne-Marie , Wester Astrid Louise , Ryrfors Pia , Holmstad Rune , Mohsin Mashkoor , Hasan Rumina , Shakoor Sadia , Gustafson Natalie Weiler , Schill Claudia Huber , Rojas Maria Luz Zamudio , Velasquez Jorge Echevarria , Magtibay Bonifacio B. , Catangcatang Kris , Sibulo Ruby , Yauce Felipe Campos , Wasyl Dariusz , Manaia Celia , Rocha Jaqueline , Martins Jose , Álvaro Pedro , Di Yoong Wen Doris , 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 , Gavačová Dagmar , Pastuchová Katarína , Truska Peter , Trkov Marija , Keddy Karen , Esterhuyse Kerneels , Song Min Joon , Quintela-Baluja Marcos , Lopez Mariano Gomez , Cerdà-Cuéllar Marta , Perera R. R. D. P. , Bandara N. K. B. K. R. G. W. , Premasiri H. I. , Pathirage Sujatha , Charlemagne Kareem , 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 , Leonard Anne , Graham David W. , Bunce Joshua T. , Zhang Lihong , Gaze William H. , Lefor Brett , Capone Drew , Sozzi Emanuele , Brown Joe , Meschke John Scott , Sobsey Mark D. , Davis Michael , Beck Nicola Koren , Sukapanpatharam Pardi , Truong Phuong , Lilienthal Ronald , Kang Sanghoon , Wittum Thomas E. , Rigamonti Natalia , Baklayan Patricia , Van Chinh Dang , Tran Doan Minh Nguyen , Do Phuc Nguyen , Kwenda Geoffrey , Larsson D. G. Joakim , Koopmans Marion , Woolhouse Mark , Aarestrup Frank M. 
Published: December 2022

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.