Data from: 16S rRNA amplicon sequencing for epidemiological 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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ftdryad:oai:v1.datadryad.org:10255/dryad.113695 2023-05-15T18:05:42+02:00 Data from: 16S rRNA amplicon sequencing for epidemiological 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 Senegal West Africa 2016-07-19T20:06:42Z http://hdl.handle.net/10255/dryad.113695 https://doi.org/10.5061/dryad.m3p7d unknown doi:10.5061/dryad.m3p7d/1 doi:10.5061/dryad.m3p7d/2 doi:10.5061/dryad.m3p7d/3 doi:10.5061/dryad.m3p7d/4 doi:10.5061/dryad.m3p7d/5 doi:10.5061/dryad.m3p7d/6 doi:10.5061/dryad.m3p7d/7 doi:10.5061/dryad.m3p7d/8 doi:10.5061/dryad.m3p7d/9 doi:10.5061/dryad.m3p7d/10 doi:10.5061/dryad.m3p7d/11 doi:10.5061/dryad.m3p7d/12 doi:10.5061/dryad.m3p7d/13 doi:10.5061/dryad.m3p7d/14 doi:10.1128/mSystems.00032-16 doi:10.5061/dryad.m3p7d Galan M, Razzauti M, Bard E, Bernard M, Brouat C, Charbonnel N, Dehne-Garcia A, Loiseau A, Tatard C, Tamisier L, Vayssier-Taussat M, Vignes H, Cosson J (2016) 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife. mSystems 1(4): e00032-16. http://hdl.handle.net/10255/dryad.113695 Zoonoses Rodents West Africa metagenomics 16S rRNA amplicon sequencing MiSeq Next-generation sequencing NGS High-throughput sequencing HTS Metabarcoding Epidemiology Disease monitoring Article 2016 ftdryad https://doi.org/10.5061/dryad.m3p7d https://doi.org/10.5061/dryad.m3p7d/1 https://doi.org/10.5061/dryad.m3p7d/2 https://doi.org/10.5061/dryad.m3p7d/3 https://doi.org/10.5061/dryad.m3p7d/4 https://doi.org/10.5061/dryad.m3p7d/5 https://doi.org/1 2020-01-01T15:33:36Z 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 molecular 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 Dryad Digital Repository (Duke University) |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
Zoonoses Rodents West Africa metagenomics 16S rRNA amplicon sequencing MiSeq Next-generation sequencing NGS High-throughput sequencing HTS Metabarcoding Epidemiology Disease monitoring |
spellingShingle |
Zoonoses Rodents West Africa metagenomics 16S rRNA amplicon sequencing MiSeq Next-generation sequencing NGS High-throughput sequencing HTS Metabarcoding Epidemiology Disease monitoring 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 Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife |
topic_facet |
Zoonoses Rodents West Africa metagenomics 16S rRNA amplicon sequencing MiSeq Next-generation sequencing NGS High-throughput sequencing HTS Metabarcoding Epidemiology Disease monitoring |
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 molecular 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. |
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 |
Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife |
title_short |
Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife |
title_full |
Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife |
title_fullStr |
Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife |
title_full_unstemmed |
Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife |
title_sort |
data from: 16s rrna amplicon sequencing for epidemiological surveys of bacteria in wildlife |
publishDate |
2016 |
url |
http://hdl.handle.net/10255/dryad.113695 https://doi.org/10.5061/dryad.m3p7d |
op_coverage |
Senegal West Africa |
genre |
Rattus rattus |
genre_facet |
Rattus rattus |
op_relation |
doi:10.5061/dryad.m3p7d/1 doi:10.5061/dryad.m3p7d/2 doi:10.5061/dryad.m3p7d/3 doi:10.5061/dryad.m3p7d/4 doi:10.5061/dryad.m3p7d/5 doi:10.5061/dryad.m3p7d/6 doi:10.5061/dryad.m3p7d/7 doi:10.5061/dryad.m3p7d/8 doi:10.5061/dryad.m3p7d/9 doi:10.5061/dryad.m3p7d/10 doi:10.5061/dryad.m3p7d/11 doi:10.5061/dryad.m3p7d/12 doi:10.5061/dryad.m3p7d/13 doi:10.5061/dryad.m3p7d/14 doi:10.1128/mSystems.00032-16 doi:10.5061/dryad.m3p7d Galan M, Razzauti M, Bard E, Bernard M, Brouat C, Charbonnel N, Dehne-Garcia A, Loiseau A, Tatard C, Tamisier L, Vayssier-Taussat M, Vignes H, Cosson J (2016) 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife. mSystems 1(4): e00032-16. http://hdl.handle.net/10255/dryad.113695 |
op_doi |
https://doi.org/10.5061/dryad.m3p7d https://doi.org/10.5061/dryad.m3p7d/1 https://doi.org/10.5061/dryad.m3p7d/2 https://doi.org/10.5061/dryad.m3p7d/3 https://doi.org/10.5061/dryad.m3p7d/4 https://doi.org/10.5061/dryad.m3p7d/5 https://doi.org/1 |
_version_ |
1766177211807694848 |