Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

• DOI: 10.1038/s41467-022-34312-7
• Publication Date: 2022-12-01T13:02:14Z
• Authors: Patrick Munk; Christian Brinch; Frederik Duus Møller; Thomas N. Petersen; Rene S. Hendriksen; Anne Mette Seyfarth; Jette S. Kjeldgaard; Christina Aaby Sv...; Bram van Bunnik; Fanny Berglund; ; Artan Bego; Pablo Power; Catherine Rees; Dionisia Lambrinidis; Elizabeth Heather...; Karen Gibb; Kris Coventry; Peter Collignon; Susan Cassar; Franz Allerberger; Anowara Begum; Zenat Zebin Hossain; Carlon Worrell; Olivier Vandenberg; Ilse Pieters; Dougnon Tamègnon ...; Angela Daniela Sa...; Freddy Soria; Vesna Rudić Grujić; Nataša Mazalica; Teddie O. Rahube; Carlos Alberto Ta...; Dalia Rodrigues; Guilherme Oliveira; Larissa Camila Ri...; Ivan Ivanov; Bonkoungou Isidor...; Traoré Oumar; Thet Sopheak; Yith Vuthy; Antoinette Ngandjio; Ariane Nzouankeu; Ziem A. Abah Jacq...; Christopher K. Yost; Pratik Kumar; Satinder Kaur Brar; Djim-Adjim Tabo; Aiko D. Adell; Esteban Paredes-O...; Maria Cristina Ma...; Sara Cuadros-Orel...; Changwen Ke; Huanying Zheng; Li Baisheng; Lok Ting Lau; Teresa Chung; Xiaoyang Jiao; Yongjie Yu; Zhao JiaYong; Johan F. Bernal M...; Maria Fernanda Va...; Pilar Donado-Godoy; Kalpy Julien Coul...; Jasna Hrenovic; Matijana Jergović; Renáta Karpíšková; Zozo Nyarukweba D...; Bodil Elsborg; Lisbeth Truelstru...; Pernille Erland J...; Mohamed Abouelnaga; Mohamed Fathy Salem; Marliin Koolmeister; Mengistu Legesse; Tadesse Eguale; Annamari Heikinheimo; Soizick Le Guyader; Julien Schaeffer; Jose Eduardo Vill...; Bakary Sanneh; Lile Malania; Andreas Nitsche; Annika Brinkmann; Sara Schubert; Sina Hesse; Thomas U. Berendonk; Courage Kosi Sets...; Jibril Mohammed; Patrick Kwame Feglo; Regina Ama Banu; Charalampos Kotza...; Efthymios Lytras; Sergio A. Lickes; Bela Kocsis; Norbert Solymosi; Thorunn R. Thorst...; Abdulla Mohamed H...; Mamatha Ballal; Sohan Rodney Bangera; Fereshteh Fani; Masoud Alebouyeh; Dearbhaile Morris; Louise O’Connor; Martin Cormican; Jacob Moran-Gilad; Antonio Battisti; Elena Lavinia Dia...; Gianluca Corno; Andrea Di Cesare; Patricia Alba; Junzo Hisatsune; Liansheng Yu; Makoto Kuroda; Motoyuki Sugai; Shizuo Kayama; Zeinegul Shakenova; Ciira Kiiyukia; Eric Ng’eno; Lul Raka; Kazi Jamil; Saja Adel Fakhral...; Tareq Alaati; Aivars Bērziņš; Jeļena Avsejenko; Kristina Kokina; Madara Streikisa; Vadims Bartkevics; Ghassan M. Matar; Ziad Daoud; Asta Pereckienė; Ceslova Butrimait...; Christian Penny; Alexandra Bastaraud; Tiavina Rasolofoa...; Jean-Marc Collard; Luc Hervé Samison; Mala Rakoto Andri...; Daniel Lawadi Banda; Arshana Amin; Heraa Rajandas; Sivachandran Pari...; David Spiteri; Malcolm Vella Haber; Sunita J. Santchurn; Aleksandar Vujacic; Dijana Djurovic; Brahim Bouchrif; Bouchra Karraouan; Delfino Carlos Vubil; Pushkar Pal; Heike Schmitt; Mark van Passel; Gert-Jan Jeunen; Neil Gemmell; Stephen T. Chambers; Fania Perez Mendoza; Jorge Huete-Pιrez; Samuel Vilchez; Akeem Olayiwola A...; Ibrahim Raufu Adisa; Ismail Ayoade Ode...; Kayode Fashae; Anne-Marie Sørgaard; Astrid Louise Wester; Pia Ryrfors; Rune Holmstad; Mashkoor Mohsin; Rumina Hasan; Sadia Shakoor; Natalie Weiler Gu...; Claudia Huber Schill; Maria Luz Zamudio...; Jorge Echevarria ...; Bonifacio B. Magt...; Kris Catangcatang; Ruby Sibulo; Felipe Campos Yauce; Dariusz Wasyl; Celia Manaia; Jaqueline Rocha; Jose Martins; Pedro Álvaro; Doris Di Yoong Wen; Hanseob Shin; Hor-Gil Hur; Sukhwan Yoon; Golubinka Bosevska; Mihail Kochubovski; Radu Cojocaru; Olga Burduniuc; Pei-Ying Hong; Meghan Rose Perry; Amy Gassama; Vladimir Radosavl...; Moon Y. F. Tay; Rogelio Zuniga-Mo...; Stefan Wuertz; Dagmar Gavačová; Katarína Pastuchová; Peter Truska; Marija Trkov; Karen Keddy; Kerneels Esterhuyse; Min Joon Song; Marcos Quintela-B...; Mariano Gomez Lopez; Marta Cerdà-Cuéllar; R. R. D. P. Perera; N. K. B. K. R. G....; H. I. Premasiri; Sujatha Pathirage; Kareem Charlemagne; Carolin Rutgersson; Leif Norrgren; Stefan Örn; Renate Boss; Tanja Van der Hei...; Yu-Ping Hong; Happiness Houka K...; Robinson Hammerth...; Yaovi Mahuton Gil...; Kaknokrat Chonsin; Orasa Suthienkul; Visanu Thamlikitkul; Ana Maria de Roda...; Bawimodom Bidjada; Berthe-Marie Njan...; Somtinda Christel...; Belkis Levent; Cemil Kurekci; Francis Ejobi; John Bosco Kalule; Jens Thomsen; Ouidiane Obaidi; Laila Mohamed Jassim; Andrew Moore; Anne Leonard; David W. Graham; Joshua T. Bunce; Lihong Zhang; William H. Gaze; Brett Lefor; Drew Capone; Emanuele Sozzi; Joe Brown; John Scott Meschke; Mark D. Sobsey; Michael Davis; Nicola Koren Beck; Pardi Sukapanpath...; Phuong Truong; Ronald Lilienthal; Sanghoon Kang; Thomas E. Wittum; Natalia Rigamonti; Patricia Baklayan; Chinh Dang Van; Doan Minh Nguyen ...; Nguyen Do Phuc; Geoffrey Kwenda; D. G. Joakim Larsson; Marion Koopmans; Mark Woolhouse; Frank M. Aarestrup
• Keywords: 570; 550; Science; global health; Social Medicine and Epidemiology; Global Health; microbial ecology; Policy and public health in microbiology; Article; Anti-Bacterial Agents/pharmacology; Microbial Ecology; 619; 03 medical and health sciences; Drug Resistance, Bacterial; sewage; antimicrobial resistance; genomic analysis, sewage, antimicrobial resistance; metagenomics; Evolutionary Biology; 0303 health sciences; Sewage; Q; Drug Resistance, Bacterial/genetics; Public Health, Global Health, Social Medicine and Epidemiology; Genomics; policy and public health in microbiology; Anti-Bacterial Agents; genomic analysis; Metagenome; Public Health; Antimicrobial Resistance; Metagenomics

AbstractAntimicrobial 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.