16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife
pas de clef wos pour cet article International audience The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly p...
Published in: | mSystems |
---|---|
Main Authors: | , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2016
|
Subjects: | |
Online Access: | https://hal.science/hal-01595274 https://hal.science/hal-01595274/document https://hal.science/hal-01595274/file/Galan_etal_2016_16S_rRNA_amplicon_%7B52027B95-6F29-4771-8598-12C1B18923E5%7D.pdf https://doi.org/10.1128/mSystems.00032-16 |
id |
ftciradhal:oai:HAL:hal-01595274v1 |
---|---|
record_format |
openpolar |
institution |
Open Polar |
collection |
CIRAD: HAL (Agricultural Research for Development) |
op_collection_id |
ftciradhal |
language |
English |
topic |
bacteria emerging infectious diseases high-throughput sequencing metabarcoding molecular epidemiology rodents West Africa zoonoses [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
spellingShingle |
bacteria emerging infectious diseases high-throughput sequencing metabarcoding molecular epidemiology rodents West Africa zoonoses [SDE.BE]Environmental Sciences/Biodiversity and Ecology Galan, Maxime Razzauti, Maria Bard, Emilie Bernard, Maria Brouat, Carine Charbonnel, Nathalie Dehne-Garcia, Alexandre Loiseau, Anne Tatard, Caroline Tamisier, Lucie Vayssier-Taussat, Muriel Vignes, Hélène Cosson, Jean-François 16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife |
topic_facet |
bacteria emerging infectious diseases high-throughput sequencing metabarcoding molecular epidemiology rodents West Africa zoonoses [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
description |
pas de clef wos pour cet article International audience The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of theseparameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other olecular surveillance tools of dealingwith a large spectrum of bacterial ... |
author2 |
Centre de Biologie pour la Gestion des Populations (UMR CBGP) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) Unité de Recherche d'Épidémiologie Animale (UR EpiA) Institut National de la Recherche Agronomique (INRA) Génétique Animale et Biologie Intégrative (GABI) Institut National de la Recherche Agronomique (INRA)-AgroParisTech Institut de biologie et chimie des protéines Lyon (IBCP) Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS) Génétique et Amélioration des Fruits et Légumes (GAFL) Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR) École nationale vétérinaire d'Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12) Agence Nationale de la Recherche (ANR) (ENEMI ANR-11-JSV7-0006 Institut National de la Recherche Agronomique (INRA) (MEM Patho-ID). European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012) |
format |
Article in Journal/Newspaper |
author |
Galan, Maxime Razzauti, Maria Bard, Emilie Bernard, Maria Brouat, Carine Charbonnel, Nathalie Dehne-Garcia, Alexandre Loiseau, Anne Tatard, Caroline Tamisier, Lucie Vayssier-Taussat, Muriel Vignes, Hélène Cosson, Jean-François |
author_facet |
Galan, Maxime Razzauti, Maria Bard, Emilie Bernard, Maria Brouat, Carine Charbonnel, Nathalie Dehne-Garcia, Alexandre Loiseau, Anne Tatard, Caroline Tamisier, Lucie Vayssier-Taussat, Muriel Vignes, Hélène Cosson, Jean-François |
author_sort |
Galan, Maxime |
title |
16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife |
title_short |
16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife |
title_full |
16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife |
title_fullStr |
16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife |
title_full_unstemmed |
16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife |
title_sort |
16s rrna amplicon sequencing for épidémiologie surveys of bacteria in wildlife |
publisher |
HAL CCSD |
publishDate |
2016 |
url |
https://hal.science/hal-01595274 https://hal.science/hal-01595274/document https://hal.science/hal-01595274/file/Galan_etal_2016_16S_rRNA_amplicon_%7B52027B95-6F29-4771-8598-12C1B18923E5%7D.pdf https://doi.org/10.1128/mSystems.00032-16 |
genre |
Rattus rattus |
genre_facet |
Rattus rattus |
op_source |
ISSN: 2379-5077 mSystems https://hal.science/hal-01595274 mSystems, 2016, 1 (4), pp.1-22. ⟨10.1128/mSystems.00032-16⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1128/mSystems.00032-16 info:eu-repo/semantics/altIdentifier/pmid/27822541 info:eu-repo/grantAgreement/EC/FP7/267196/EU/International Mobility Programme to Strengthen Skills and Excellence in Research for Agriculture/AGREENSKILLS hal-01595274 https://hal.science/hal-01595274 https://hal.science/hal-01595274/document https://hal.science/hal-01595274/file/Galan_etal_2016_16S_rRNA_amplicon_%7B52027B95-6F29-4771-8598-12C1B18923E5%7D.pdf doi:10.1128/mSystems.00032-16 PRODINRA: 367226 PUBMED: 27822541 WOS: 000408191700002 |
op_rights |
http://hal.archives-ouvertes.fr/licences/copyright/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1128/mSystems.00032-16 |
container_title |
mSystems |
container_volume |
1 |
container_issue |
4 |
_version_ |
1790607266803613696 |
spelling |
ftciradhal:oai:HAL:hal-01595274v1 2024-02-11T10:08:14+01:00 16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife Galan, Maxime Razzauti, Maria Bard, Emilie Bernard, Maria Brouat, Carine Charbonnel, Nathalie Dehne-Garcia, Alexandre Loiseau, Anne Tatard, Caroline Tamisier, Lucie Vayssier-Taussat, Muriel Vignes, Hélène Cosson, Jean-François Centre de Biologie pour la Gestion des Populations (UMR CBGP) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) Unité de Recherche d'Épidémiologie Animale (UR EpiA) Institut National de la Recherche Agronomique (INRA) Génétique Animale et Biologie Intégrative (GABI) Institut National de la Recherche Agronomique (INRA)-AgroParisTech Institut de biologie et chimie des protéines Lyon (IBCP) Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS) Génétique et Amélioration des Fruits et Légumes (GAFL) Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR) École nationale vétérinaire d'Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12) Agence Nationale de la Recherche (ANR) (ENEMI ANR-11-JSV7-0006 Institut National de la Recherche Agronomique (INRA) (MEM Patho-ID). European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012) 2016 https://hal.science/hal-01595274 https://hal.science/hal-01595274/document https://hal.science/hal-01595274/file/Galan_etal_2016_16S_rRNA_amplicon_%7B52027B95-6F29-4771-8598-12C1B18923E5%7D.pdf https://doi.org/10.1128/mSystems.00032-16 en eng HAL CCSD info:eu-repo/semantics/altIdentifier/doi/10.1128/mSystems.00032-16 info:eu-repo/semantics/altIdentifier/pmid/27822541 info:eu-repo/grantAgreement/EC/FP7/267196/EU/International Mobility Programme to Strengthen Skills and Excellence in Research for Agriculture/AGREENSKILLS hal-01595274 https://hal.science/hal-01595274 https://hal.science/hal-01595274/document https://hal.science/hal-01595274/file/Galan_etal_2016_16S_rRNA_amplicon_%7B52027B95-6F29-4771-8598-12C1B18923E5%7D.pdf doi:10.1128/mSystems.00032-16 PRODINRA: 367226 PUBMED: 27822541 WOS: 000408191700002 http://hal.archives-ouvertes.fr/licences/copyright/ info:eu-repo/semantics/OpenAccess ISSN: 2379-5077 mSystems https://hal.science/hal-01595274 mSystems, 2016, 1 (4), pp.1-22. ⟨10.1128/mSystems.00032-16⟩ bacteria emerging infectious diseases high-throughput sequencing metabarcoding molecular epidemiology rodents West Africa zoonoses [SDE.BE]Environmental Sciences/Biodiversity and Ecology info:eu-repo/semantics/article Journal articles 2016 ftciradhal https://doi.org/10.1128/mSystems.00032-16 2024-01-17T17:27:38Z pas de clef wos pour cet article International audience The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of theseparameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other olecular surveillance tools of dealingwith a large spectrum of bacterial ... Article in Journal/Newspaper Rattus rattus CIRAD: HAL (Agricultural Research for Development) mSystems 1 4 |