Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Patrick Munk, Christian Brinch, Frederik Duus Møller, Thomas Nordahl Petersen, René S. Hendriksen, Anne Mette Seyfarth, Jette Sejer Kjeldgaard, Christina Aaby Svendsen, Bram van Bunnik, Fanny Berglund, Artan Bego, P.P. Power, Catherine A. Rees, Dionisia Lambrinidis, Elizabeth Heather Jakobsen Neilson, Karen Gibb, Kris Coventry, Peter Collignon, Susan Cassar, Franz Allerberger, Anowara Begum, Zenat Zebin Hossain, Carlon Worrell, Olivier Vandenberg, Ilse Y. Pieters, Victorien Dougnon, Angela Daniela Salazar Gutierrez, Freddy Soria, Vesna Rudić Grujić, Nataša Mazalica, Teddie O. Rahube, Carlos Alberto Tagliati, Dália dos Prazeres Rodrigues, Guilherme Oliveira, Larissa Camila Ribeiro de Souza, Ivan Ivanov, Bonkoungou Isidore Juste, Traoré Soumana Oumar, Thet Sopheak, Yith Vuthy, Antoinette Ngandjio, Ariane Nzouankeu, Ziem A. Abah Jacques Olivier, Christopher K. Yost, Pratik Kumar, Satinder Kaur Brar, Djim-Adjim Tabo, Aiko D. Adell, Esteban Paredes-Osses, Maria Cristina Martinez, Sara Cuadros-Orellana, Changwen Ke, Huanying Zheng, Li Baisheng, Lok Ting Lau, Teresa Chung, Xiaoyang Jiao, Yongjie Yu, Zhao JiaYong, Johan F. Bernal Morales, María Fernanda Valencia, Pilar Donado-Godoy, Kalpy Julien Coulibaly, Jasna Hrenović, Matijana Jergović, Renáta Karpíšková, Zozo Nyarukweba Deogratias, Bodil Elsborg, Lisbeth Truelstrup Hansen, Pernille Erland Jensen, M. Abouelnaga, Mohamed A. Salem, Marliin Koolmeister, Mengistu Legesse, Tadesse Eguale, Annamari Heikinheimo, Soizick Le Guyader, Julien Schaeffer, José E. Villacís, Bakary Sanneh, Lile Malania, Andreas Nitsche, Annika Brinkmann, Sara Schubert, Sina Hesse, Thomas U. Berendonk, Courage Kosi Setsoafia Saba, Jibril Mohammed, Patrick Kwame Feglo, Regina Ama Banu, Charalampos Kotzamanidis, Efthymios Lytras, Sergio A. Lickes, Béla Kocsis, Norbert Solymosi, Thorunn R. Thorsteinsdottir, A. A. Mohamed Hatha, Mamatha Ballal, Sohan Rodney Bangera, Fereshteh Fani
Abstract
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.