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. 2016. 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife. mSystems, 1 (4):00032-16, 22 p.

https://doi.org/10.1128/mSystems.00032-16

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Url - jeu de données - Entrepôt autre : https://datadryad.org/stash/dataset/doi:10.5061/dryad.m3p7d / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/nuccore/KU697337 / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/nuccore/KU697350

Résumé : 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.

Mots-clés Agrovoc : maladie infectieuse, Enquête pathologique, séquence d'arn, zoonose, transmission des maladies, surveillance épidémiologique, relation homme-faune, bactérie pathogène, agent pathogène, rongeur, Rattus, séquençage à haut débit