Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
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 system...
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2019 |
| País: | España |
| Institución: | Universitat Autònoma de Barcelona |
| Repositorio: | Dipòsit Digital de Documents de la UAB |
| Idioma: | inglés |
| OAI Identifier: | oai:ddd.uab.cat:222673 |
| Acceso en línea: | https://ddd.uab.cat/record/222673 https://dx.doi.org/urn:doi:10.1038/s41467-019-08853-3 |
| Access Level: | acceso abierto |
| Palabra clave: | Africa Asia Bacteria Drug Resistance Epidemiological Monitoring Europe Genes Humans Metagenome Metagenomics Microbial Consortia North America Oceania Population Health Sewage Socioeconomic Factors South America |
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Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage |
| title |
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage |
| spellingShingle |
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage Hendriksen, Rene S. Africa Asia Bacteria Drug Resistance Epidemiological Monitoring Europe Genes Humans Metagenome Metagenomics Microbial Consortia North America Oceania Population Health Sewage Socioeconomic Factors South America |
| title_short |
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage |
| title_full |
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage |
| title_fullStr |
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage |
| title_full_unstemmed |
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage |
| title_sort |
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage |
| dc.creator.none.fl_str_mv |
Hendriksen, Rene S. Munk, Patrick|||0000-0001-8813-4019 Njage, Patrick van Bunnik, Bram|||0000-0003-2177-7073 McNally, Luke Lukjancenko, Oksana Röder, Timo Nieuwenhuijse, David Pedersen, Susanne Karlsmose Kjeldgaard, Jette Kaas, Rolf S. Clausen, Philip Thomas Lanken Conradsen Vogt, Josef Korbinian Leekitcharoenphon, Pimlapas van de Schans, Milou G. M. Zuidema, Tina de Roda Husman, Ana Maria Rasmussen, Simon|||0000-0001-6323-9041 Petersen, Bent|||0000-0002-2472-8317 Bego, Artan Rees, Charlotte Cassar, Susan Coventry, Kris Collignon, Peter Allerberger, Franz Rahube, Teddie O. Oliveira, Guilherme Ivanov, Ivan Vuthy, Yith Sopheak, Thet Yost, Christopher K. Ke, Changwen Zheng, Huanying Baisheng, Li Jiao, Xiaoyang Donado-Godoy, Pilar|||0000-0001-9839-9264 Coulibaly, Kalpy Julien Jergović, Matijana Hrenovic, Jasna Karpíšková, Renáta Villacis, Jose Eduardo Legesse, Mengistu Eguale, Tadesse Heikinheimo, Annamari Malania, Lile Nitsche, Andreas Brinkmann, Annika Saba, Courage Kosi Setsoafia Kocsis, Bela Solymosi, Norbert Thorsteinsdottir, Thorunn R. Hatha, Abdulla Mohamed Alebouyeh, Masoud Morris, Dearbhaile Cormican, Martin O'Connor, Louise Moran-Gilad, Jacob Alba, Patricia Battisti, Antonio Shakenova, Zeinegul Kiiyukia, Ciira Ng'eno, Eric Raka, Lul Avsejenko, Jeļena Bērziņš, Aivars Bartkevics, Vadims Penny, Christian Rajandas, Heraa Parimannan, Sivachandran Haber, Malcolm Vella Pal, Pushkar Jeunen, Gert-Jan Gemmell, Neil Fashae, Kayode Holmstad, Rune Hasan, Rumina Shakoor, Sadia Rojas, Maria Luz Zamudio Wasyl, Dariusz Bosevska, Golubinka Kochubovski, Mihail Radu, Cojocaru Gassama, Amy Radosavljevic, Vladimir Wuertz, Stefan Zuniga-Montanez, Rogelio Tay, Moon Y. F. Gavačová, Dagmar Pastuchova, Katarina Truska, Peter Trkov, Marija Esterhuyse, Kerneels Keddy, Karen Cerdà-Cuéllar, Marta|||0000-0001-6842-1299 Pathirage, Sujatha Norrgren, Leif Örn, Stefan Larsson, D. G. Joakim Heijden, Tanja Van der Kumburu, Happiness Houka Sanneh, Bakary Bidjada, Pawou Njanpop-Lafourcade, Berthe-Marie Nikiema-Pessinaba, Somtinda Christelle Levent, Belkis Meschke, John Scott Beck, Nicola Koren Van, Chinh Dang Phuc, Nguyen Do Tran, Doan Minh Nguyen Kwenda, Geoffrey Tabo, Djim-adjim Wester, Astrid Louise Cuadros-Orellana, Sara Amid, Clara|||0000-0001-6534-7425 Cochrane, Guy|||0000-0001-7954-7057 Sicheritz-Ponten, Thomas|||0000-0001-6615-1141 Schmitt, Heike|||0000-0002-0139-1934 Alvarez, Jorge Raul Matheu Aidara-Kane, Awa Pamp, Sünje J. Lund, Ole Hald, Tine Woolhouse, Mark Koopmans, Marion P. Vigre, Håkan Petersen, Thomas Nordahl Aarestrup, Frank|||0000-0002-7116-2723 |
| author |
Hendriksen, Rene S. |
| author_facet |
Hendriksen, Rene S. Munk, Patrick|||0000-0001-8813-4019 Njage, Patrick van Bunnik, Bram|||0000-0003-2177-7073 McNally, Luke Lukjancenko, Oksana Röder, Timo Nieuwenhuijse, David Pedersen, Susanne Karlsmose Kjeldgaard, Jette Kaas, Rolf S. Clausen, Philip Thomas Lanken Conradsen Vogt, Josef Korbinian Leekitcharoenphon, Pimlapas van de Schans, Milou G. M. Zuidema, Tina de Roda Husman, Ana Maria Rasmussen, Simon|||0000-0001-6323-9041 Petersen, Bent|||0000-0002-2472-8317 Bego, Artan Rees, Charlotte Cassar, Susan Coventry, Kris Collignon, Peter Allerberger, Franz Rahube, Teddie O. Oliveira, Guilherme Ivanov, Ivan Vuthy, Yith Sopheak, Thet Yost, Christopher K. Ke, Changwen Zheng, Huanying Baisheng, Li Jiao, Xiaoyang Donado-Godoy, Pilar|||0000-0001-9839-9264 Coulibaly, Kalpy Julien Jergović, Matijana Hrenovic, Jasna Karpíšková, Renáta Villacis, Jose Eduardo Legesse, Mengistu Eguale, Tadesse Heikinheimo, Annamari Malania, Lile Nitsche, Andreas Brinkmann, Annika Saba, Courage Kosi Setsoafia Kocsis, Bela Solymosi, Norbert Thorsteinsdottir, Thorunn R. Hatha, Abdulla Mohamed Alebouyeh, Masoud Morris, Dearbhaile Cormican, Martin O'Connor, Louise Moran-Gilad, Jacob Alba, Patricia Battisti, Antonio Shakenova, Zeinegul Kiiyukia, Ciira Ng'eno, Eric Raka, Lul Avsejenko, Jeļena Bērziņš, Aivars Bartkevics, Vadims Penny, Christian Rajandas, Heraa Parimannan, Sivachandran Haber, Malcolm Vella Pal, Pushkar Jeunen, Gert-Jan Gemmell, Neil Fashae, Kayode Holmstad, Rune Hasan, Rumina Shakoor, Sadia Rojas, Maria Luz Zamudio Wasyl, Dariusz Bosevska, Golubinka Kochubovski, Mihail Radu, Cojocaru Gassama, Amy Radosavljevic, Vladimir Wuertz, Stefan Zuniga-Montanez, Rogelio Tay, Moon Y. F. Gavačová, Dagmar Pastuchova, Katarina Truska, Peter Trkov, Marija Esterhuyse, Kerneels Keddy, Karen Cerdà-Cuéllar, Marta|||0000-0001-6842-1299 Pathirage, Sujatha Norrgren, Leif Örn, Stefan Larsson, D. G. Joakim Heijden, Tanja Van der Kumburu, Happiness Houka Sanneh, Bakary Bidjada, Pawou Njanpop-Lafourcade, Berthe-Marie Nikiema-Pessinaba, Somtinda Christelle Levent, Belkis Meschke, John Scott Beck, Nicola Koren Van, Chinh Dang Phuc, Nguyen Do Tran, Doan Minh Nguyen Kwenda, Geoffrey Tabo, Djim-adjim Wester, Astrid Louise Cuadros-Orellana, Sara Amid, Clara|||0000-0001-6534-7425 Cochrane, Guy|||0000-0001-7954-7057 Sicheritz-Ponten, Thomas|||0000-0001-6615-1141 Schmitt, Heike|||0000-0002-0139-1934 Alvarez, Jorge Raul Matheu Aidara-Kane, Awa Pamp, Sünje J. Lund, Ole Hald, Tine Woolhouse, Mark Koopmans, Marion P. Vigre, Håkan Petersen, Thomas Nordahl Aarestrup, Frank|||0000-0002-7116-2723 |
| author_role |
author |
| author2 |
Munk, Patrick|||0000-0001-8813-4019 Njage, Patrick van Bunnik, Bram|||0000-0003-2177-7073 McNally, Luke Lukjancenko, Oksana Röder, Timo Nieuwenhuijse, David Pedersen, Susanne Karlsmose Kjeldgaard, Jette Kaas, Rolf S. Clausen, Philip Thomas Lanken Conradsen Vogt, Josef Korbinian Leekitcharoenphon, Pimlapas van de Schans, Milou G. M. Zuidema, Tina de Roda Husman, Ana Maria Rasmussen, Simon|||0000-0001-6323-9041 Petersen, Bent|||0000-0002-2472-8317 Bego, Artan Rees, Charlotte Cassar, Susan Coventry, Kris Collignon, Peter Allerberger, Franz Rahube, Teddie O. Oliveira, Guilherme Ivanov, Ivan Vuthy, Yith Sopheak, Thet Yost, Christopher K. Ke, Changwen Zheng, Huanying Baisheng, Li Jiao, Xiaoyang Donado-Godoy, Pilar|||0000-0001-9839-9264 Coulibaly, Kalpy Julien Jergović, Matijana Hrenovic, Jasna Karpíšková, Renáta Villacis, Jose Eduardo Legesse, Mengistu Eguale, Tadesse Heikinheimo, Annamari Malania, Lile Nitsche, Andreas Brinkmann, Annika Saba, Courage Kosi Setsoafia Kocsis, Bela Solymosi, Norbert Thorsteinsdottir, Thorunn R. Hatha, Abdulla Mohamed Alebouyeh, Masoud Morris, Dearbhaile Cormican, Martin O'Connor, Louise Moran-Gilad, Jacob Alba, Patricia Battisti, Antonio Shakenova, Zeinegul Kiiyukia, Ciira Ng'eno, Eric Raka, Lul Avsejenko, Jeļena Bērziņš, Aivars Bartkevics, Vadims Penny, Christian Rajandas, Heraa Parimannan, Sivachandran Haber, Malcolm Vella Pal, Pushkar Jeunen, Gert-Jan Gemmell, Neil Fashae, Kayode Holmstad, Rune Hasan, Rumina Shakoor, Sadia Rojas, Maria Luz Zamudio Wasyl, Dariusz Bosevska, Golubinka Kochubovski, Mihail Radu, Cojocaru Gassama, Amy Radosavljevic, Vladimir Wuertz, Stefan Zuniga-Montanez, Rogelio Tay, Moon Y. F. Gavačová, Dagmar Pastuchova, Katarina Truska, Peter Trkov, Marija Esterhuyse, Kerneels Keddy, Karen Cerdà-Cuéllar, Marta|||0000-0001-6842-1299 Pathirage, Sujatha Norrgren, Leif Örn, Stefan Larsson, D. G. Joakim Heijden, Tanja Van der Kumburu, Happiness Houka Sanneh, Bakary Bidjada, Pawou Njanpop-Lafourcade, Berthe-Marie Nikiema-Pessinaba, Somtinda Christelle Levent, Belkis Meschke, John Scott Beck, Nicola Koren Van, Chinh Dang Phuc, Nguyen Do Tran, Doan Minh Nguyen Kwenda, Geoffrey Tabo, Djim-adjim Wester, Astrid Louise Cuadros-Orellana, Sara Amid, Clara|||0000-0001-6534-7425 Cochrane, Guy|||0000-0001-7954-7057 Sicheritz-Ponten, Thomas|||0000-0001-6615-1141 Schmitt, Heike|||0000-0002-0139-1934 Alvarez, Jorge Raul Matheu Aidara-Kane, Awa Pamp, Sünje J. Lund, Ole Hald, Tine Woolhouse, Mark Koopmans, Marion P. Vigre, Håkan Petersen, Thomas Nordahl Aarestrup, Frank|||0000-0002-7116-2723 |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Africa Asia Bacteria Drug Resistance Epidemiological Monitoring Europe Genes Humans Metagenome Metagenomics Microbial Consortia North America Oceania Population Health Sewage Socioeconomic Factors South America |
| topic |
Africa Asia Bacteria Drug Resistance Epidemiological Monitoring Europe Genes Humans Metagenome Metagenomics Microbial Consortia North America Oceania Population Health Sewage Socioeconomic Factors South America |
| description |
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. |
| publishDate |
2019 |
| dc.date.none.fl_str_mv |
2 2019-01-01 2019 2019-01-01 |
| dc.type.none.fl_str_mv |
Article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://ddd.uab.cat/record/222673 https://dx.doi.org/urn:doi:10.1038/s41467-019-08853-3 |
| url |
https://ddd.uab.cat/record/222673 https://dx.doi.org/urn:doi:10.1038/s41467-019-08853-3 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.relation.none.fl_str_mv |
European Commission https://doi.org/10.13039/501100000780 643476 |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
| dc.rights.openaire.fl_str_mv |
info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/ |
| eu_rights_str_mv |
openAccess |
| dc.format.none.fl_str_mv |
application/pdf |
| dc.source.none.fl_str_mv |
reponame:Dipòsit Digital de Documents de la UAB instname:Universitat Autònoma de Barcelona |
| instname_str |
Universitat Autònoma de Barcelona |
| reponame_str |
Dipòsit Digital de Documents de la UAB |
| collection |
Dipòsit Digital de Documents de la UAB |
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|
| _version_ |
1869415658538663936 |
| spelling |
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewageHendriksen, Rene S.Munk, Patrick|||0000-0001-8813-4019Njage, Patrickvan Bunnik, Bram|||0000-0003-2177-7073McNally, LukeLukjancenko, OksanaRöder, TimoNieuwenhuijse, DavidPedersen, Susanne KarlsmoseKjeldgaard, JetteKaas, Rolf S.Clausen, Philip Thomas Lanken ConradsenVogt, Josef KorbinianLeekitcharoenphon, Pimlapasvan de Schans, Milou G. M.Zuidema, Tinade Roda Husman, Ana MariaRasmussen, Simon|||0000-0001-6323-9041Petersen, Bent|||0000-0002-2472-8317Bego, ArtanRees, CharlotteCassar, SusanCoventry, KrisCollignon, PeterAllerberger, FranzRahube, Teddie O.Oliveira, GuilhermeIvanov, IvanVuthy, YithSopheak, ThetYost, Christopher K.Ke, ChangwenZheng, HuanyingBaisheng, LiJiao, XiaoyangDonado-Godoy, Pilar|||0000-0001-9839-9264Coulibaly, Kalpy JulienJergović, MatijanaHrenovic, JasnaKarpíšková, RenátaVillacis, Jose EduardoLegesse, MengistuEguale, TadesseHeikinheimo, AnnamariMalania, LileNitsche, AndreasBrinkmann, AnnikaSaba, Courage Kosi SetsoafiaKocsis, BelaSolymosi, NorbertThorsteinsdottir, Thorunn R.Hatha, Abdulla MohamedAlebouyeh, MasoudMorris, DearbhaileCormican, MartinO'Connor, LouiseMoran-Gilad, JacobAlba, PatriciaBattisti, AntonioShakenova, ZeinegulKiiyukia, CiiraNg'eno, EricRaka, LulAvsejenko, JeļenaBērziņš, AivarsBartkevics, VadimsPenny, ChristianRajandas, HeraaParimannan, SivachandranHaber, Malcolm VellaPal, PushkarJeunen, Gert-JanGemmell, NeilFashae, KayodeHolmstad, RuneHasan, RuminaShakoor, SadiaRojas, Maria Luz ZamudioWasyl, DariuszBosevska, GolubinkaKochubovski, MihailRadu, CojocaruGassama, AmyRadosavljevic, VladimirWuertz, StefanZuniga-Montanez, RogelioTay, Moon Y. F.Gavačová, DagmarPastuchova, KatarinaTruska, PeterTrkov, MarijaEsterhuyse, KerneelsKeddy, KarenCerdà-Cuéllar, Marta|||0000-0001-6842-1299Pathirage, SujathaNorrgren, LeifÖrn, StefanLarsson, D. G. JoakimHeijden, Tanja Van derKumburu, Happiness HoukaSanneh, BakaryBidjada, PawouNjanpop-Lafourcade, Berthe-MarieNikiema-Pessinaba, Somtinda ChristelleLevent, BelkisMeschke, John ScottBeck, Nicola KorenVan, Chinh DangPhuc, Nguyen DoTran, Doan Minh NguyenKwenda, GeoffreyTabo, Djim-adjimWester, Astrid LouiseCuadros-Orellana, SaraAmid, Clara|||0000-0001-6534-7425Cochrane, Guy|||0000-0001-7954-7057Sicheritz-Ponten, Thomas|||0000-0001-6615-1141Schmitt, Heike|||0000-0002-0139-1934Alvarez, Jorge Raul MatheuAidara-Kane, AwaPamp, Sünje J.Lund, OleHald, TineWoolhouse, MarkKoopmans, Marion P.Vigre, HåkanPetersen, Thomas NordahlAarestrup, Frank|||0000-0002-7116-2723AfricaAsiaBacteriaDrug ResistanceEpidemiological MonitoringEuropeGenesHumansMetagenomeMetagenomicsMicrobial ConsortiaNorth AmericaOceaniaPopulation HealthSewageSocioeconomic FactorsSouth AmericaAntimicrobial 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. 22019-01-0120192019-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/222673https://dx.doi.org/urn:doi:10.1038/s41467-019-08853-3reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengEuropean Commission https://doi.org/10.13039/501100000780 643476open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2226732026-06-06T12:50:31Z |
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15.300719 |