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.
| Original language | English |
|---|---|
| Article number | 7251 |
| Number of pages | 16 |
| Journal | Nature Communications |
| Volume | 13 |
| DOIs | |
| Publication status | Published - 1 Dec 2022 |
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In: Nature Communications, Vol. 13, 7251, 01.12.2022.
Research output: Contribution to journal › Journal article › peer-review
TY - JOUR
T1 - Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
AU - Munk, Patrick
AU - Brinch, Christian
AU - Møller, Frederik Duus
AU - Petersen, Thomas N.
AU - Hendriksen, Rene S.
AU - Seyfarth, Anne Mette
AU - Kjeldgaard, Jette S.
AU - Svendsen, Christina Aaby
AU - van Bunnik, Bram
AU - Berglund, Fanny
AU - Bego, Artan
AU - Power, Pablo
AU - Rees, Catherine
AU - Lambrinidis, Dionisia
AU - Neilson, Elizabeth Heather Jakobsen
AU - Gibb, Karen
AU - Coventry, Kris
AU - Collignon, Peter
AU - Cassar, Susan
AU - Allerberger, Franz
AU - Begum, Anowara
AU - Hossain, Zenat Zebin
AU - Worrell, Carlon
AU - Vandenberg, Olivier
AU - Pieters, Ilse
AU - Victorien, Dougnon Tamègnon
AU - Gutierrez, Angela Daniela Salazar
AU - Soria, Freddy
AU - Grujić, Vesna Rudić
AU - Mazalica, Nataša
AU - Rahube, Teddie O.
AU - Tagliati, Carlos Alberto
AU - Rodrigues, Dalia
AU - Oliveira, Guilherme
AU - de Souza, Larissa Camila Ribeiro
AU - Ivanov, Ivan
AU - Juste, Bonkoungou Isidore
AU - Oumar, Traoré
AU - Sopheak, Thet
AU - Vuthy, Yith
AU - Ngandijo, Antoinette
AU - Nzouankeu, Ariane
AU - Olivier, Ziem A.Abah Jacques
AU - Yost, Christopher K.
AU - Kumar, Pratik
AU - Brar, Satinder Kaur
AU - Tabo, Djim Adjim
AU - Adell, Aiko D.
AU - Paredes-Osses, Esteban
AU - Martinez, Maria Cristina
AU - Cuadros-Orellana, Sara
AU - Ke, Changwen
AU - Zheng, Huanying
AU - Baisheng, Li
AU - Lau, Lok Ting
AU - Chung, Teresa
AU - Jiao, Xiaoyang
AU - Yu, Yongjie
AU - JiaYong, Zhao
AU - Morales, Johan F.Bernal
AU - Valencia, Maria Fernanda
AU - Donado-Godoy, Pilar
AU - Coulibaly, Kalpy Julien
AU - Hrenovic, Jasna
AU - Jergović, Matijana
AU - Karpíšková, Renáta
AU - Deogratias, Zozo Nyarukweba
AU - Elsborg, Bodil
AU - Hansen, Lisbeth Truelstrup
AU - Jensen, Pernille Erland
AU - Abouelnaga, Mohamed
AU - Salem, Mohamed Fathy
AU - Koolmeister, Marliin
AU - Legesse, Mengistu
AU - Eguale, Tadesse
AU - Heikinheimo, Annamari
AU - Le Guyader, Soizick
AU - Schaeffer, Julien
AU - Villacis, Jose Eduardo
AU - Sanneh, Bakary
AU - Malania, Lile
AU - Nitsche, Andreas
AU - Brinkmann, Annika
AU - Schubert, Sara
AU - Hesse, Sina
AU - Berendonk, Thomas U.
AU - Saba, Courage Kosi Setsoafia
AU - Mohammed, Jibril
AU - Feglo, Patrick Kwame
AU - Banu, Regina Ama
AU - Kotzamanidis, Charalampos
AU - Lytras, Efthymios
AU - Lickes, Sergio A.
AU - Kocsis, Bela
AU - Solymosi, Norbert
AU - Thorsteinsdottir, Thorunn R.
AU - Hatha, Abdulla Mohamed
AU - Ballal, Mamatha
AU - Bangera, Sohan Rodney
AU - Fani, Fereshteh
AU - Alebouyeh, Masoud
AU - Morris, Dearbhaile
AU - O’Connor, Louise
AU - Cormican, Martin
AU - Moran-Gilad, Jacob
AU - Battisti, Antonio
AU - Diaconu, Elena Lavinia
AU - Corno, Gianluca
AU - Di Cesare, Andrea
AU - Alba, Patricia
AU - Hisatsune, Junzo
AU - Yu, Liansheng
AU - Kuroda, Makoto
AU - Sugai, Motoyuki
AU - Kayama, Shizuo
AU - Shakenova, Zeinegul
AU - Kiiyukia, Ciira
AU - Ng’eno, Eric
AU - Raka, Lul
AU - Jamil, Kazi
AU - Fakhraldeen, Saja Adel
AU - Alaati, Tareq
AU - Bērziņš, Aivars
AU - Avsejenko, Jeļena
AU - Kokina, Kristina
AU - Streikisa, Madara
AU - Bartkevics, Vadims
AU - Matar, Ghassan M.
AU - Daoud, Ziad
AU - Pereckienė, Asta
AU - Butrimaite-Ambrozeviciene, Ceslova
AU - Penny, Christian
AU - Bastaraud, Alexandra
AU - Rasolofoarison, Tiavina
AU - Collard, Jean Marc
AU - Samison, Luc Hervé
AU - Andrianarivelo, Mala Rakoto
AU - Banda, Daniel Lawadi
AU - Amin, Arshana
AU - Rajandas, Heraa
AU - Parimannan, Sivachandran
AU - Spiteri, David
AU - Haber, Malcolm Vella
AU - Santchurn, Sunita J.
AU - Vujacic, Aleksandar
AU - Djurovic, Dijana
AU - Bouchrif, Brahim
AU - Karraouan, Bouchra
AU - Vubil, Delfino Carlos
AU - Pal, Pushkar
AU - Schmitt, Heike
AU - van Passel, Mark
AU - Jeunen, Gert Jan
AU - Gemmell, Neil
AU - Chambers, Stephen T.
AU - Mendoza, Fania Perez
AU - Huete-Pιrez, Jorge
AU - Vilchez, Samuel
AU - Ahmed, Akeem Olayiwola
AU - Adisa, Ibrahim Raufu
AU - Odetokun, Ismail Ayoade
AU - Fashae, Kayode
AU - Sørgaard, Anne Marie
AU - Wester, Astrid Louise
AU - Ryrfors, Pia
AU - Holmstad, Rune
AU - Mohsin, Mashkoor
AU - Hasan, Rumina
AU - Shakoor, Sadia
AU - Gustafson, Natalie Weiler
AU - Schill, Claudia Huber
AU - Rojas, Maria Luz Zamudio
AU - Velasquez, Jorge Echevarria
AU - Magtibay, Bonifacio B.
AU - Catangcatang, Kris
AU - Sibulo, Ruby
AU - Yauce, Felipe Campos
AU - Wasyl, Dariusz
AU - Manaia, Celia
AU - Rocha, Jaqueline
AU - Martins, Jose
AU - Álvaro, Pedro
AU - Di Yoong Wen, Doris
AU - Shin, Hanseob
AU - Hur, Hor Gil
AU - Yoon, Sukhwan
AU - Bosevska, Golubinka
AU - Kochubovski, Mihail
AU - Cojocaru, Radu
AU - Burduniuc, Olga
AU - Hong, Pei Ying
AU - Perry, Meghan Rose
AU - Gassama, Amy
AU - Radosavljevic, Vladimir
AU - Tay, Moon Y.F.
AU - Zuniga-Montanez, Rogelio
AU - Wuertz, Stefan
AU - Gavačová, Dagmar
AU - Pastuchová, Katarína
AU - Truska, Peter
AU - Trkov, Marija
AU - Keddy, Karen
AU - Esterhuyse, Kerneels
AU - Song, Min Joon
AU - Quintela-Baluja, Marcos
AU - Lopez, Mariano Gomez
AU - Cerdà-Cuéllar, Marta
AU - Perera, R. R.D.P.
AU - Bandara, N. K.B.K.R.G.W.
AU - Premasiri, H. I.
AU - Pathirage, Sujatha
AU - Charlemagne, Kareem
AU - Rutgersson, Carolin
AU - Norrgren, Leif
AU - Örn, Stefan
AU - Boss, Renate
AU - Van der Heijden, Tanja
AU - Hong, Yu Ping
AU - Kumburu, Happiness Houka
AU - Mdegela, Robinson Hammerthon
AU - Hounmanou, Yaovi Mahuton Gildas
AU - Chonsin, Kaknokrat
AU - Suthienkul, Orasa
AU - Thamlikitkul, Visanu
AU - de Roda Husman, Ana Maria
AU - Bidjada, Bawimodom
AU - Njanpop-Lafourcade, Berthe Marie
AU - Nikiema-Pessinaba, Somtinda Christelle
AU - Levent, Belkis
AU - Kurekci, Cemil
AU - Ejobi, Francis
AU - Kalule, John Bosco
AU - Thomsen, Jens
AU - Obaidi, Ouidiane
AU - Jassim, Laila Mohamed
AU - Moore, Andrew
AU - Leonard, Anne
AU - Graham, David W.
AU - Bunce, Joshua T.
AU - Zhang, Lihong
AU - Gaze, William H.
AU - Lefor, Brett
AU - Capone, Drew
AU - Sozzi, Emanuele
AU - Brown, Joe
AU - Meschke, John Scott
AU - Sobsey, Mark D.
AU - Davis, Michael
AU - Beck, Nicola Koren
AU - Sukapanpatharam, Pardi
AU - Truong, Phuong
AU - Lilienthal, Ronald
AU - Kang, Sanghoon
AU - Wittum, Thomas E.
AU - Rigamonti, Natalia
AU - Baklayan, Patricia
AU - Van, Chinh Dang
AU - Tran, Doan Minh Nguyen
AU - Do Phuc, Nguyen
AU - Kwenda, Geoffrey
AU - Larsson, D. G.Joakim
AU - Koopmans, Marion
AU - Woolhouse, Mark
AU - Aarestrup, Frank M.
AU - Global Sewage Surveillance Consortium
N1 - We would like to acknowledge the Novo Nordisk Foundation (Grant: NNF16OC0021856: Global Surveillance of Antimicrobial Resistance) and the European Union’s Horizon 2020 research and innovation programme (Grant: 874735) for funding the work. Publisher Copyright: © 2022, The Author(s).
PY - 2022/12/1
Y1 - 2022/12/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85143185703&partnerID=8YFLogxK
U2 - 10.1038/s41467-022-34312-7
DO - 10.1038/s41467-022-34312-7
M3 - Journal article
C2 - 36456547
AN - SCOPUS:85143185703
SN - 2041-1723
VL - 13
JO - Nature Communications
JF - Nature Communications
M1 - 7251
ER -