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

• DOI: 10.1128/msystems.00032-16
• Publication Date: 2016-07-20T02:04:09Z
• Authors: Maxime Galan; Maria Razzauti; Emilie Bard; Maria Bernard; Carine Brouat; Nathalie Charbonnel; Alexandre Dehne-G...; Anne Loiseau; Caroline Tatard; Lucie Tamisier; Muriel Vayssier-T...; Helene Vignes; Jean-François Cosson
• Keywords: Amplicon sequencing; Amplicon; Pandemic

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 required use these effective tools such epidemiological contexts. In particular, HTS introduces biases into raw data set might lead incorrect interpretations. We describe here a procedure cleaning before estimating reliable biological parameters, as positivity, prevalence, and coinfection, using 16S rRNA amplicon on an Illumina MiSeq platform. This procedure, applied 711 rodents collected West Africa, detected several bacterial species, including some at high despite their never having been reported Africa. future, approach could be adapted monitoring other microbes protists, fungi, even viruses.