Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
René S. Hendriksen(Technical University of Denmark), Patrick Munk(Technical University of Denmark), Patrick Murigu Kamau Njage(Technical University of Denmark), Bram van Bunnik(University of Edinburgh), Luke McNally(University of Edinburgh), Oksana Lukjančenko(Technical University of Denmark), Timo Röder(Technical University of Denmark), David F. Nieuwenhuijse(Erasmus University Rotterdam), Susanne Karlsmose Pedersen(Technical University of Denmark), Jette Sejer Kjeldgaard(Technical University of Denmark), Rolf Sommer Kaas(Technical University of Denmark), Philip T. L. C. Clausen(Technical University of Denmark), Josef Korbinian Vogt(Technical University of Denmark), Pimlapas Leekitcharoenphon(Technical University of Denmark), Milou G.M. van de Schans(Wageningen University & Research), T. Zuidema(Wageningen University & Research), Ana Maria de Roda Husman(National Institute for Public Health and the Environment), Simon Rasmussen(Technical University of Denmark), Bent Petersen(Technical University of Denmark), Artan Bego(Institute of Public Health), Catherine A. Rees(Melbourne Water), Susan Cassar(Melbourne Water), Kris Coventry(Melbourne Water), Peter Collignon(Canberra Hospital), Franz Allerberger(Austrian Agency for Health and Food Safety), Teddie O. Rahube(Botswana International University of Science and Technology), Guilherme Oliveira(Vale (Brazil)), Ivan Ivanov(National Center of Infectious and Parasitic Diseases), Yith Vuthy(Institut Pasteur du Cambodge), Thet Sopheak(Institut Pasteur du Cambodge), Christopher K. Yost(University of Regina), Changwen Ke(Guangdong Provincial Center for Disease Control and Prevention), Huanying Zheng(Guangdong Provincial Center for Disease Control and Prevention), Li Baisheng(Guangdong Provincial Center for Disease Control and Prevention), Xiaoyang Jiao(Shantou University), Pilar Donado-Godoy(Colombian Corporation for Agricultural Research - AGROSAVIA), Kalpy Julien Coulibaly(Institut Pasteur de Côte d'Ivoire), Matijana Jergović(Andrija Stampar Teaching Institute of Public Health), Jasna Hrenović(University of Zagreb), Renáta Karpíšková(Veterinary Research Institute), José E. Villacís(Instituto Nacional de Investigación en Salud Pública), Mengistu Legesse(Addis Ababa University), Tadesse Eguale(Addis Ababa University), Annamari Heikinheimo(University of Helsinki), Lile Malania(National Center for Disease Control and Public Health), Andreas Nitsche(Robert Koch Institute), Annika Brinkmann(Robert Koch Institute), Courage Kosi Setsoafia Saba(University for Development Studies), Béla Kocsis(Semmelweis University), Norbert Solymosi(University of Veterinary Medicine), Thorunn R. Thorsteinsdottir(University of Iceland), A. A. Mohamed Hatha(Cochin University of Science and Technology), Masoud Alebouyeh(Shahid Beheshti University of Medical Sciences), Dearbháile Morris(Ollscoil na Gaillimhe – University of Galway), Martin Cormican(Ollscoil na Gaillimhe – University of Galway), Louise O’Connor(Ollscoil na Gaillimhe – University of Galway), Jacob Moran‐Gilad(Ben-Gurion University of the Negev), Patricia Alba(Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana), Antonio Battisti(Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana), Zeinegul Shakenova, Ciira Kiiyukia(Mount Kenya University), Eric Ng’eno(Kenya Medical Research Institute), Lul Raka(University of Prishtina), Jeļena Avsejenko(Institute of Food Safety, Animal Health and Environment “BIOR”), Aivars Bērziņš(Institute of Food Safety, Animal Health and Environment “BIOR”), Vadims Bartkevičs(Institute of Food Safety, Animal Health and Environment “BIOR”), Christian Penny(Luxembourg Institute of Science and Technology), Heraa Rajandas(Ministry for Health), Sivachandran Parimannan(AIMST University), Malcolm Vella Haber(Agriculture and Forestry University), Pushkar Pal(University of Otago), Gert‐Jan Jeunen(University of Ibadan), Neil J. Gemmell(University of Ibadan), Kayode Fashae(Norwegian Veterinary Centre for Contract Research and Commercial Services), Rune Holmstad(Aga Khan University), Rumina Hasan(National Institute of Quality), Sadia Shakoor(National Institute of Quality), Maria Luz Zamudio Rojas(National Veterinary Research Institute), Dariusz Wasyl(Institute of public health of Republic of Macedonia), Golubinka Boševska(Pharmaceutical Formulations (United States)), Mihail Kochubovski(Pharmaceutical Formulations (United States)), Radu Cojocaru(Institut Pasteur de Dakar), Amy Gassama, Vladimir Radosavljević(Nanyang Technological University), Stefan Wuertz(Nanyang Technological University), Rogelio Zuniga-Montanez(Nanyang Technological University), Moon Y. F. Tay(Public Health Authority of the Slovak Republic), Dagmar Gavačová(National Laboratory of Health, Environment and Food), Katarína Pastuchová(National Laboratory of Health, Environment and Food), Peter Truska(National Laboratory of Health, Environment and Food), Marija Trkov, Kerneels Esterhuyse(University of the Witwatersrand), Karen H. Keddy(Centre de Recerca en Sanitat Animal), Marta Cerdà‐Cuéllar(Medical Research Institute), Sujatha Pathirage(Swedish University of Agricultural Sciences), Leif Norrgren(University of Gothenburg), Stefan Örn(University of Gothenburg), D. G. Joakim Larsson, Tanja Van der Heijden(Kilimanjaro Christian Medical Centre), Happiness Kumburu(Ministry of Health and Social Welfare), Bakary Sanneh, Pawou Bidjada, Berthe‐Marie Njanpop‐Lafourcade(Togolese Ministry of Health), Somtinda Christelle Nikiema-Pessinaba, Belkıs Levent(University of Washington), John Scott Meschke, Nicola K. Beck, Chinh Dang Van(University of Zambia), Nguyen Do Phuc(University of Zambia), Doan Minh Nguyen Tran(University of Zambia), Geoffrey Kwenda(University of N'Djamena), Djim-adjim Tabo(Norwegian Institute of Public Health), Astrid Louise Wester(Catholic University of the Maule), Sara Cuadros-Orellana(Catholic University of the Maule), Clara Amid(European Bioinformatics Institute), Guy Cochrane(European Bioinformatics Institute), Thomas Sicheritz‐Pontén(AIMST University), Heike Schmitt(National Institute for Public Health and the Environment), Jorge Raul Matheu Alvarez(World Health Organization), Awa Aïdara‐Kane(World Health Organization), Sünje Johanna Pamp(Technical University of Denmark), Ole Lund(Technical University of Denmark), Tine Hald(Technical University of Denmark), Mark Woolhouse(University of Edinburgh), Marion Koopmans(Erasmus University Rotterdam), Håkan Vigre(Technical University of Denmark), Thomas Nordahl Petersen(Technical University of Denmark), Frank M. Aarestrup(Technical University of Denmark)
Cited by 1,143Open Access
Abstract
Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
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