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Research Article | Clinical Science and Epidemiology

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

Maxime Galan, Maria Razzauti, Emilie Bard, Maria Bernard, Carine Brouat, Nathalie Charbonnel, Alexandre Dehne-Garcia, Anne Loiseau, Caroline Tatard, Lucie Tamisier, Muriel Vayssier-Taussat, Helene Vignes, Jean-François Cosson
Holly Bik, Editor
Maxime Galan
aINRA, CBGP, Montferrier sur Lez, France
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Maria Razzauti
aINRA, CBGP, Montferrier sur Lez, France
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Emilie Bard
bINRA, EpiA, Clermont-Ferrand, France
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Maria Bernard
cINRA, Sigenae, France
dINRA, GABI, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Carine Brouat
eIRD, CBGP, Montferrier sur Lez, France
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Nathalie Charbonnel
aINRA, CBGP, Montferrier sur Lez, France
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Alexandre Dehne-Garcia
aINRA, CBGP, Montferrier sur Lez, France
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Anne Loiseau
aINRA, CBGP, Montferrier sur Lez, France
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Caroline Tatard
aINRA, CBGP, Montferrier sur Lez, France
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Lucie Tamisier
aINRA, CBGP, Montferrier sur Lez, France
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Muriel Vayssier-Taussat
fINRA, Bipar, Maisons-Alfort, France
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Helene Vignes
gCIRAD, AGAP, Montpellier, France
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Jean-François Cosson
aINRA, CBGP, Montferrier sur Lez, France
fINRA, Bipar, Maisons-Alfort, France
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  • ORCID record for Jean-François Cosson
Holly Bik
New York University
Roles: Editor
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DOI: 10.1128/mSystems.00032-16
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ABSTRACT

Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses. 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 musculusdomesticus, 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. IMPORTANCE Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses.

  • Copyright © 2016 Galan et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license .

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16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife
Maxime Galan, Maria Razzauti, Emilie Bard, Maria Bernard, Carine Brouat, Nathalie Charbonnel, Alexandre Dehne-Garcia, Anne Loiseau, Caroline Tatard, Lucie Tamisier, Muriel Vayssier-Taussat, Helene Vignes, Jean-François Cosson
mSystems Jul 2016, 1 (4) e00032-16; DOI: 10.1128/mSystems.00032-16

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16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife
Maxime Galan, Maria Razzauti, Emilie Bard, Maria Bernard, Carine Brouat, Nathalie Charbonnel, Alexandre Dehne-Garcia, Anne Loiseau, Caroline Tatard, Lucie Tamisier, Muriel Vayssier-Taussat, Helene Vignes, Jean-François Cosson
mSystems Jul 2016, 1 (4) e00032-16; DOI: 10.1128/mSystems.00032-16
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KEYWORDS

NO MESH TERMS ASSIGNED AS OF 10-11-2019
bacteria
emerging infectious diseases
high-throughput sequencing
metabarcoding
molecular epidemiology
next-generation sequencing
rodents
West Africa
zoonoses

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