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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Online Access: | https://doi.org/10.5061/dryad.m3p7d |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::ad9fb26df2d04d228f0e4f9149f800b0 2023-05-15T18:05:15+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 2017-04-29 https://doi.org/10.5061/dryad.m3p7d undefined unknown http://dx.doi.org/10.5061/dryad.m3p7d https://dx.doi.org/10.5061/dryad.m3p7d lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:94081 oai:easy.dans.knaw.nl:easy-dataset:94081 10.5061/dryad.m3p7d 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care Metabarcoding Bartonella high-throughput sequencing Mastomys erythroleucus HTS Mycoplasma MiSeq Epidemiology Orientia Zoonoses Mus musculus domesticus Next-generation sequencing Borrelia 16S rRNA amplicon sequencing Rodents West Africa metagenomics Disease monitoring Streptobacillus NGS Rattus rattus Mastomys natalensis Rickettsia Ehrlichia Senegal envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2017 fttriple https://doi.org/10.5061/dryad.m3p7d 2023-01-22T17:22:29Z 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 ... Dataset Rattus rattus Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care Metabarcoding Bartonella high-throughput sequencing Mastomys erythroleucus HTS Mycoplasma MiSeq Epidemiology Orientia Zoonoses Mus musculus domesticus Next-generation sequencing Borrelia 16S rRNA amplicon sequencing Rodents West Africa metagenomics Disease monitoring Streptobacillus NGS Rattus rattus Mastomys natalensis Rickettsia Ehrlichia Senegal envir geo |
spellingShingle |
Life sciences medicine and health care Metabarcoding Bartonella high-throughput sequencing Mastomys erythroleucus HTS Mycoplasma MiSeq Epidemiology Orientia Zoonoses Mus musculus domesticus Next-generation sequencing Borrelia 16S rRNA amplicon sequencing Rodents West Africa metagenomics Disease monitoring Streptobacillus NGS Rattus rattus Mastomys natalensis Rickettsia Ehrlichia Senegal envir geo 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 |
Life sciences medicine and health care Metabarcoding Bartonella high-throughput sequencing Mastomys erythroleucus HTS Mycoplasma MiSeq Epidemiology Orientia Zoonoses Mus musculus domesticus Next-generation sequencing Borrelia 16S rRNA amplicon sequencing Rodents West Africa metagenomics Disease monitoring Streptobacillus NGS Rattus rattus Mastomys natalensis Rickettsia Ehrlichia Senegal envir geo |
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 ... |
format |
Dataset |
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 |
2017 |
url |
https://doi.org/10.5061/dryad.m3p7d |
genre |
Rattus rattus |
genre_facet |
Rattus rattus |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:94081 oai:easy.dans.knaw.nl:easy-dataset:94081 10.5061/dryad.m3p7d 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.m3p7d https://dx.doi.org/10.5061/dryad.m3p7d |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.m3p7d |
_version_ |
1766176709819760640 |