16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife

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 zoono...

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Published in:mSystems
Main Authors: razzauti sanfeliu, maria, Bard, Emilie, Bernard, Maria, Brouat, Carine, Charbonnel, Nathalie, Dehne Garcia, Alexandre, Loiseau, Anne, Tatard, Caroline, Tamisier, Lucie, Taussat, Muriel, Vignes, Hélène
Other Authors: Galan, Maxime, Cosson, Jean-Francois, Bik, Holly
Format: Article in Journal/Newspaper
Language:English
Published: 2016
Subjects:
Online Access:http://prodinra.inra.fr/ft/52027B95-6F29-4771-8598-12C1B18923E5
http://prodinra.inra.fr/record/367226
https://doi.org/10.1128/mSystems.00032-16
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record_format openpolar
spelling ftinraparis:oai:prodinra.inra.fr:367226 2023-05-15T18:05:38+02:00 16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife razzauti sanfeliu, maria Bard, Emilie Bernard, Maria Brouat, Carine Charbonnel, Nathalie Dehne Garcia, Alexandre Loiseau, Anne Tatard, Caroline Tamisier, Lucie Taussat, Muriel Vignes, Hélène Galan, Maxime Cosson, Jean-Francois Bik, Holly 2016 application/pdf http://prodinra.inra.fr/ft/52027B95-6F29-4771-8598-12C1B18923E5 http://prodinra.inra.fr/record/367226 https://doi.org/10.1128/mSystems.00032-16 eng eng https://creativecommons.org/licenses/by-sa/3.0/ CC-BY-SA mSystems 4 (1), 1-22. (2016) Biodiversité et Ecologie Biodiversity and Ecology bacteria;emerging infectious diseases;high-throughput sequencing;metabarcoding;molecular epidemiology;rodents;West Africa;zoonoses ARTICLE 2016 ftinraparis https://doi.org/10.1128/mSystems.00032-16 2019-07-16T22:25:38Z 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 these parameters 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 dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs. Article in Journal/Newspaper Rattus rattus Institut National de la Recherche Agronomique: ProdINRA mSystems 1 4
institution Open Polar
collection Institut National de la Recherche Agronomique: ProdINRA
op_collection_id ftinraparis
language English
topic Biodiversité et Ecologie
Biodiversity and Ecology
bacteria;emerging infectious diseases;high-throughput sequencing;metabarcoding;molecular epidemiology;rodents;West Africa;zoonoses
spellingShingle Biodiversité et Ecologie
Biodiversity and Ecology
bacteria;emerging infectious diseases;high-throughput sequencing;metabarcoding;molecular epidemiology;rodents;West Africa;zoonoses
razzauti sanfeliu, maria
Bard, Emilie
Bernard, Maria
Brouat, Carine
Charbonnel, Nathalie
Dehne Garcia, Alexandre
Loiseau, Anne
Tatard, Caroline
Tamisier, Lucie
Taussat, Muriel
Vignes, Hélène
16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife
topic_facet Biodiversité et Ecologie
Biodiversity and Ecology
bacteria;emerging infectious diseases;high-throughput sequencing;metabarcoding;molecular epidemiology;rodents;West Africa;zoonoses
description 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 these parameters 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 dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs.
author2 Galan, Maxime
Cosson, Jean-Francois
Bik, Holly
format Article in Journal/Newspaper
author razzauti sanfeliu, maria
Bard, Emilie
Bernard, Maria
Brouat, Carine
Charbonnel, Nathalie
Dehne Garcia, Alexandre
Loiseau, Anne
Tatard, Caroline
Tamisier, Lucie
Taussat, Muriel
Vignes, Hélène
author_facet razzauti sanfeliu, maria
Bard, Emilie
Bernard, Maria
Brouat, Carine
Charbonnel, Nathalie
Dehne Garcia, Alexandre
Loiseau, Anne
Tatard, Caroline
Tamisier, Lucie
Taussat, Muriel
Vignes, Hélène
author_sort razzauti sanfeliu, maria
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
publishDate 2016
url http://prodinra.inra.fr/ft/52027B95-6F29-4771-8598-12C1B18923E5
http://prodinra.inra.fr/record/367226
https://doi.org/10.1128/mSystems.00032-16
genre Rattus rattus
genre_facet Rattus rattus
op_source mSystems 4 (1), 1-22. (2016)
op_rights https://creativecommons.org/licenses/by-sa/3.0/
op_rightsnorm CC-BY-SA
op_doi https://doi.org/10.1128/mSystems.00032-16
container_title mSystems
container_volume 1
container_issue 4
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