Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
01 12 2022
01 12 2022
Historique:
received:
25
07
2022
accepted:
20
10
2022
entrez:
1
12
2022
pubmed:
2
12
2022
medline:
6
12
2022
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 36456547
doi: 10.1038/s41467-022-34312-7
pii: 10.1038/s41467-022-34312-7
pmc: PMC9715550
doi:
Substances chimiques
Sewage
0
Anti-Bacterial Agents
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7251Subventions
Organisme : Medical Research Council
ID : MR/P028195/1
Pays : United Kingdom
Investigateurs
Artan Bego
(A)
Pablo Power
(P)
Catherine Rees
(C)
Dionisia Lambrinidis
(D)
Elizabeth Heather Jakobsen Neilson
(EHJ)
Karen Gibb
(K)
Kris Coventry
(K)
Peter Collignon
(P)
Susan Cassar
(S)
Franz Allerberger
(F)
Anowara Begum
(A)
Zenat Zebin Hossain
(ZZ)
Carlon Worrell
(C)
Olivier Vandenberg
(O)
Ilse Pieters
(I)
Dougnon Tamègnon Victorien
(DT)
Angela Daniela Salazar Gutierrez
(ADS)
Freddy Soria
(F)
Vesna Rudić Grujić
(VR)
Nataša Mazalica
(N)
Teddie O Rahube
(TO)
Carlos Alberto Tagliati
(CA)
Dalia Rodrigues
(D)
Guilherme Oliveira
(G)
Larissa Camila Ribeiro de Souza
(LCR)
Ivan Ivanov
(I)
Bonkoungou Isidore Juste
(BI)
Traoré Oumar
(T)
Thet Sopheak
(T)
Yith Vuthy
(Y)
Antoinette Ngandjio
(A)
Ariane Nzouankeu
(A)
Ziem A Abah Jacques Olivier
(ZAAJ)
Christopher K Yost
(CK)
Pratik Kumar
(P)
Satinder Kaur Brar
(SK)
Djim-Adjim Tabo
(DA)
Aiko D Adell
(AD)
Esteban Paredes-Osses
(E)
Maria Cristina Martinez
(MC)
Sara Cuadros-Orellana
(S)
Changwen Ke
(C)
Huanying Zheng
(H)
Li Baisheng
(L)
Lok Ting Lau
(LT)
Teresa Chung
(T)
Xiaoyang Jiao
(X)
Yongjie Yu
(Y)
Zhao JiaYong
(Z)
Johan F Bernal Morales
(JFB)
Maria Fernanda Valencia
(MF)
Pilar Donado-Godoy
(P)
Kalpy Julien Coulibaly
(KJ)
Jasna Hrenovic
(J)
Matijana Jergović
(M)
Renáta Karpíšková
(R)
Zozo Nyarukweba Deogratias
(ZN)
Bodil Elsborg
(B)
Lisbeth Truelstrup Hansen
(LT)
Pernille Erland Jensen
(PE)
Mohamed Abouelnaga
(M)
Mohamed Fathy Salem
(MF)
Marliin Koolmeister
(M)
Mengistu Legesse
(M)
Tadesse Eguale
(T)
Annamari Heikinheimo
(A)
Soizick Le Guyader
(S)
Julien Schaeffer
(J)
Jose Eduardo Villacis
(JE)
Bakary Sanneh
(B)
Lile Malania
(L)
Andreas Nitsche
(A)
Annika Brinkmann
(A)
Sara Schubert
(S)
Sina Hesse
(S)
Thomas U Berendonk
(TU)
Courage Kosi Setsoafia Saba
(CKS)
Jibril Mohammed
(J)
Patrick Kwame Feglo
(PK)
Regina Ama Banu
(RA)
Charalampos Kotzamanidis
(C)
Efthymios Lytras
(E)
Sergio A Lickes
(SA)
Bela Kocsis
(B)
Norbert Solymosi
(N)
Thorunn R Thorsteinsdottir
(TR)
Abdulla Mohamed Hatha
(AM)
Mamatha Ballal
(M)
Sohan Rodney Bangera
(SR)
Fereshteh Fani
(F)
Masoud Alebouyeh
(M)
Dearbhaile Morris
(D)
Louise O'Connor
(L)
Martin Cormican
(M)
Jacob Moran-Gilad
(J)
Antonio Battisti
(A)
Elena Lavinia Diaconu
(EL)
Gianluca Corno
(G)
Andrea Di Cesare
(A)
Patricia Alba
(P)
Junzo Hisatsune
(J)
Liansheng Yu
(L)
Makoto Kuroda
(M)
Motoyuki Sugai
(M)
Shizuo Kayama
(S)
Zeinegul Shakenova
(Z)
Ciira Kiiyukia
(C)
Eric Ng'eno
(E)
Lul Raka
(L)
Kazi Jamil
(K)
Saja Adel Fakhraldeen
(SA)
Tareq Alaati
(T)
Aivars Bērziņš
(A)
Jeļena Avsejenko
(J)
Kristina Kokina
(K)
Madara Streikisa
(M)
Vadims Bartkevics
(V)
Ghassan M Matar
(GM)
Ziad Daoud
(Z)
Asta Pereckienė
(A)
Ceslova Butrimaite-Ambrozeviciene
(C)
Christian Penny
(C)
Alexandra Bastaraud
(A)
Tiavina Rasolofoarison
(T)
Jean-Marc Collard
(JM)
Luc Hervé Samison
(LH)
Mala Rakoto Andrianarivelo
(MR)
Daniel Lawadi Banda
(DL)
Arshana Amin
(A)
Heraa Rajandas
(H)
Sivachandran Parimannan
(S)
David Spiteri
(D)
Malcolm Vella Haber
(MV)
Sunita J Santchurn
(SJ)
Aleksandar Vujacic
(A)
Dijana Djurovic
(D)
Brahim Bouchrif
(B)
Bouchra Karraouan
(B)
Delfino Carlos Vubil
(DC)
Pushkar Pal
(P)
Heike Schmitt
(H)
Mark van Passel
(M)
Gert-Jan Jeunen
(GJ)
Neil Gemmell
(N)
Stephen T Chambers
(ST)
Fania Perez Mendoza
(FP)
Jorge Huete-Pιrez
(J)
Samuel Vilchez
(S)
Akeem Olayiwola Ahmed
(AO)
Ibrahim Raufu Adisa
(IR)
Ismail Ayoade Odetokun
(IA)
Kayode Fashae
(K)
Anne-Marie Sørgaard
(AM)
Astrid Louise Wester
(AL)
Pia Ryrfors
(P)
Rune Holmstad
(R)
Mashkoor Mohsin
(M)
Rumina Hasan
(R)
Sadia Shakoor
(S)
Natalie Weiler Gustafson
(NW)
Claudia Huber Schill
(CH)
Maria Luz Zamudio Rojas
(MLZ)
Jorge Echevarria Velasquez
(JE)
Bonifacio B Magtibay
(BB)
Kris Catangcatang
(K)
Ruby Sibulo
(R)
Felipe Campos Yauce
(FC)
Dariusz Wasyl
(D)
Celia Manaia
(C)
Jaqueline Rocha
(J)
Jose Martins
(J)
Pedro Álvaro
(P)
Doris Di Yoong Wen
(D)
Hanseob Shin
(H)
Hor-Gil Hur
(HG)
Sukhwan Yoon
(S)
Golubinka Bosevska
(G)
Mihail Kochubovski
(M)
Radu Cojocaru
(R)
Olga Burduniuc
(O)
Pei-Ying Hong
(PY)
Meghan Rose Perry
(MR)
Amy Gassama
(A)
Vladimir Radosavljevic
(V)
Moon Y F Tay
(MYF)
Rogelio Zuniga-Montanez
(R)
Stefan Wuertz
(S)
Dagmar Gavačová
(D)
Katarína Pastuchová
(K)
Peter Truska
(P)
Marija Trkov
(M)
Karen Keddy
(K)
Kerneels Esterhuyse
(K)
Min Joon Song
(MJ)
Marcos Quintela-Baluja
(M)
Mariano Gomez Lopez
(MG)
Marta Cerdà-Cuéllar
(M)
R R D P Perera
(RRDP)
N K B K R G W Bandara
(NKBKRGW)
H I Premasiri
(HI)
Sujatha Pathirage
(S)
Kareem Charlemagne
(K)
Carolin Rutgersson
(C)
Leif Norrgren
(L)
Stefan Örn
(S)
Renate Boss
(R)
Tanja Van der Heijden
(T)
Yu-Ping Hong
(YP)
Happiness Houka Kumburu
(HH)
Robinson Hammerthon Mdegela
(RH)
Yaovi Mahuton Gildas Hounmanou
(YMG)
Kaknokrat Chonsin
(K)
Orasa Suthienkul
(O)
Visanu Thamlikitkul
(V)
Ana Maria de Roda Husman
(AM)
Bawimodom Bidjada
(B)
Berthe-Marie Njanpop-Lafourcade
(BM)
Somtinda Christelle Nikiema-Pessinaba
(SC)
Belkis Levent
(B)
Cemil Kurekci
(C)
Francis Ejobi
(F)
John Bosco Kalule
(JB)
Jens Thomsen
(J)
Ouidiane Obaidi
(O)
Laila Mohamed Jassim
(LM)
Andrew Moore
(A)
Anne Leonard
(A)
David W Graham
(DW)
Joshua T Bunce
(JT)
Lihong Zhang
(L)
William H Gaze
(WH)
Brett Lefor
(B)
Drew Capone
(D)
Emanuele Sozzi
(E)
Joe Brown
(J)
John Scott Meschke
(JS)
Mark D Sobsey
(MD)
Michael Davis
(M)
Nicola Koren Beck
(NK)
Pardi Sukapanpatharam
(P)
Phuong Truong
(P)
Ronald Lilienthal
(R)
Sanghoon Kang
(S)
Thomas E Wittum
(TE)
Natalia Rigamonti
(N)
Patricia Baklayan
(P)
Chinh Dang Van
(CD)
Doan Minh Nguyen Tran
(DMN)
Nguyen Do Phuc
(N)
Geoffrey Kwenda
(G)
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© 2022. The Author(s).
Références
APMIS. 1998 Aug;106(8):745-70
pubmed: 9744762
mSystems. 2020 Oct 20;5(5):
pubmed: 33082278
Bioinformatics. 2015 Nov 15;31(22):3718-20
pubmed: 26209431
Ecol Evol. 2020 Jan 24;10(4):2007-2020
pubmed: 32128133
Lancet Planet Health. 2018 Sep;2(9):e398-e405
pubmed: 30177008
Nat Genet. 2015 Jun;47(6):632-9
pubmed: 25961941
Bull Math Biol. 2020 Apr 8;82(4):52
pubmed: 32270376
Clin Infect Dis. 1997 Jan;24 Suppl 1:S74-9
pubmed: 8994782
Nature. 2016 May 11;533(7602):212-6
pubmed: 27172044
Lancet Infect Dis. 2010 Sep;10(9):597-602
pubmed: 20705517
Nature. 2011 Oct 30;480(7376):241-4
pubmed: 22037308
BMC Biol. 2019 May 30;17(1):45
pubmed: 31146755
Microbiome. 2017 Dec 11;5(1):159
pubmed: 29228991
Curr Opin Microbiol. 2006 Oct;9(5):466-75
pubmed: 16942899
Lancet. 2022 Feb 12;399(10325):629-655
pubmed: 35065702
Science. 2020 Feb 7;367(6478):630-632
pubmed: 32029617
Emerg Infect Dis. 2021 May;27(5):1405-1415
pubmed: 33900177
J Antimicrob Chemother. 2014 Apr;69(4):964-8
pubmed: 24335515
Nat Commun. 2022 Mar 23;13(1):1553
pubmed: 35322038
Nat Commun. 2020 Sep 1;11(1):4379
pubmed: 32873785
Lancet Infect Dis. 2020 Jun;20(6):731-741
pubmed: 32151332
Front Microbiol. 2017 Nov 15;8:2224
pubmed: 29187837
J Antimicrob Chemother. 2012 Nov;67(11):2640-4
pubmed: 22782487
Bioinformatics. 2010 Oct 1;26(19):2460-1
pubmed: 20709691
mSystems. 2021 Jun 29;6(3):e0028321
pubmed: 34061588
Nature. 2013 Jul 11;499(7457):219-22
pubmed: 23748443
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
Science. 2003 Aug 15;301(5635):976-8
pubmed: 12881573
mSystems. 2016 Oct 18;1(5):
pubmed: 27822556
Microbiome. 2019 Jun 7;7(1):88
pubmed: 31174603
J Antimicrob Chemother. 2008 Feb;61(2):273-81
pubmed: 18077311
Antimicrob Agents Chemother. 1994 Jul;38(7):1447-51
pubmed: 7979269
Microbiol Spectr. 2021 Oct 31;9(2):e0138721
pubmed: 34612701
Int J Appl Basic Med Res. 2017 Jan-Mar;7(1):32-39
pubmed: 28251105
Genome Res. 2017 May;27(5):824-834
pubmed: 28298430
Nat Commun. 2019 Mar 8;10(1):1124
pubmed: 30850636
Nature. 2018 Aug;560(7717):233-237
pubmed: 30069051
Nat Rev Microbiol. 2010 Jul;8(7):523-9
pubmed: 20531276
Cell Host Microbe. 2021 Jun 9;29(6):975-987.e4
pubmed: 33887206
Nucleic Acids Res. 2021 Jan 8;49(D1):D29-D37
pubmed: 33245775
Sci Rep. 2020 Feb 20;10(1):3033
pubmed: 32080241
Nat Commun. 2019 Sep 27;10(1):4406
pubmed: 31562300
Nat Biotechnol. 2017 Jul;35(7):640-646
pubmed: 28553940
Gigascience. 2019 Jun 1;8(6):
pubmed: 31220250
Sci Rep. 2020 Aug 13;10(1):13748
pubmed: 32792677
Cell. 2021 Jun 24;184(13):3376-3393.e17
pubmed: 34043940
BMC Bioinformatics. 2018 Aug 29;19(1):307
pubmed: 30157759
Front Microbiol. 2021 May 13;12:657954
pubmed: 34054755
Science. 2015 May 22;348(6237):1261359
pubmed: 25999513
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
Nucleic Acids Res. 2019 Jan 8;47(D1):D195-D202
pubmed: 30380090
Nature. 2021 May;593(7858):266-269
pubmed: 33767447
Lancet Infect Dis. 2016 Feb;16(2):161-8
pubmed: 26603172