@article{fdi:010070141,
  title = {16{S} r{RNA} amplicon sequencing forepidemiological surveys of bacteria in wildlife},
  author = {{G}alan, {M}. and {R}azzauti, {M}. and {B}ard, {E}. and {B}ernard, {M}. and {B}rouat, {C}arine and {C}harbonnel, {N}. and {D}ehne-{G}arcia, {A}. and {L}oiseau, {A}. and {T}amisier, {L}. and {V}ayssier-{T}aussat, {M}. and {V}ignes, {H}. and {C}osson, {J}.{F}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}he human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. {H}ighly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. {W}e investigated the potential for recent developments in 16{S} r{RNA} 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 {W}est {A}frica. {I}n 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. {H}owever, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by {HTS} methods. {W}e present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. {W}e demonstrated the application of this strategy using 711 commensal rodents, including 208 {M}us musculus domesticus, 189 {R}attus rattus, 93 {M}astomys natalensis, and 221 {M}astomys erythroleucus, collected from 24 villages in {S}enegal. {S}even major genera of pathogenic bacteria were detected in their spleens: {B}orrelia, {B}artonella, {M}ycoplasma, {E}hrlichia, {R}ickettsia, {S}treptobacillus, and {O}rientia. {M}ycoplasma, {E}hrlichia, {R}ickettsia, {S}treptobacillus, and {O}rientia have never before been detected in {W}est {A}frican rodents. {B}acterial 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. {T}he 16{S} r{RNA} 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. {T}his approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs.},
  keywords = {{AFRIQUE} {DE} {L}'{OUEST}},
  booktitle = {},
  journal = {{MS}ystems},
  volume = {1},
  numero = {4},
  pages = {art. no e00032--00016 [22  en ligne]},
  ISSN = {2379-5077},
  year = {2016},
  DOI = {10.1128/m{S}ystems.00032-16},
  URL = {https://www.documentation.ird.fr/hor/fdi:010070141},
}