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In Gabon, the circulation and maintenance of rodent-borne zoonotic infectious agents are poorly studied and are often limited to one type of pathogen. Among the three existing studies on this topic, two are focused on a zoonotic virus, and the third is focused on rodent<jats:italic>Plasmodium<\/jats:italic>. In this study, we searched for a wide range of bacteria, protozoa and viruses in different organs of rodents from the town of Franceville in Gabon. Samples from one hundred and ninety-eight (198) small mammals captured, including two invasive rodent species, five native rodent species and 19 shrews belonging to the<jats:italic>Soricidae<\/jats:italic>family, were screened. The investigated pathogens were bacteria from the<jats:italic>Rickettsiaceae<\/jats:italic>and<jats:italic>Anaplasmataceae<\/jats:italic>families,<jats:italic>Mycoplasma<\/jats:italic>spp.,<jats:italic>Bartonella<\/jats:italic>spp.,<jats:italic>Borrelia<\/jats:italic>spp.,<jats:italic>Orientia<\/jats:italic>spp.,<jats:italic>Occidentia<\/jats:italic>spp.,<jats:italic>Leptospira<\/jats:italic>spp.,<jats:italic>Streptobacillus moniliformis<\/jats:italic>,<jats:italic>Coxiella burnetii<\/jats:italic>, and<jats:italic>Yersinia pestis;<\/jats:italic>parasites from class<jats:italic>Kinetoplastida<\/jats:italic>spp. (<jats:italic>Leishmania<\/jats:italic>spp.,<jats:italic>Trypanosoma<\/jats:italic>spp.),<jats:italic>Piroplasmidae<\/jats:italic>spp., and<jats:italic>Toxoplasma gondii<\/jats:italic>; and viruses from<jats:italic>Paramyxoviridae<\/jats:italic>,<jats:italic>Hantaviridae<\/jats:italic>,<jats:italic>Flaviviridae<\/jats:italic>and<jats:italic>Mammarenavirus<\/jats:italic>spp. We identified the following pathogenic bacteria:<jats:italic>Anaplasma<\/jats:italic>spp. (8.1%; 16\/198),<jats:italic>Bartonella<\/jats:italic>spp. (6.6%; 13\/198),<jats:italic>Coxiella<\/jats:italic>spp. (5.1%; 10\/198) and<jats:italic>Leptospira<\/jats:italic>spp. (3.5%; 7\/198); and protozoans:<jats:italic>Piroplasma<\/jats:italic>sp. (1%; 2\/198),<jats:italic>Toxoplasma gondii<\/jats:italic>(0.5%; 1\/198), and<jats:italic>Trypanosoma<\/jats:italic>sp. (7%; 14\/198). None of the targeted viral genes were detected. These pathogens were found in Gabonese rodents, mainly<jats:italic>Lophuromys<\/jats:italic>sp.,<jats:italic>Lemniscomys striatus<\/jats:italic>and<jats:italic>Praomys<\/jats:italic>sp. We also identified new genotypes:<jats:italic>Candidatus<\/jats:italic>Bartonella gabonensis and Uncultured<jats:italic>Anaplasma<\/jats:italic>spp. This study shows that rodents in Gabon harbor some human pathogenic bacteria and protozoans. It is necessary to determine whether the identified microorganisms are capable of undergoing zoonotic transmission from rodents to humans and if they may be responsible for human cases of febrile disease of unknown etiology in Gabon.<\/jats:p>","DOI":"10.1371\/journal.pone.0248244","type":"journal-article","created":{"date-parts":[[2021,3,8]],"date-time":"2021-03-08T18:33:24Z","timestamp":1615228404000},"page":"e0248244","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["First investigation of pathogenic bacteria, protozoa and viruses in rodents and shrews in context of forest-savannah-urban areas interface in the city of Franceville (Gabon)"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2443-0067","authenticated-orcid":true,"given":"Joa Bra\u00efthe","family":"Mangombi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadine","family":"N\u2019dilimabaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Bernard","family":"Lekana-Douki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Octavie","family":"Banga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sydney","family":"Maghendji-Nzondo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9774-7669","authenticated-orcid":true,"given":"Mathieu","family":"Bourgarel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Leroy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florence","family":"Fenollar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oleg","family":"Mediannikov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,3,8]]},"reference":[{"issue":"1756","key":"pone.0248244.ref001","article-title":"A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special?","volume":"280","author":"AD Luis","year":"2013","journal-title":"Proc R Soc B Biol Sci"},{"key":"pone.0248244.ref002","first-page":"1","article-title":"Rodent-borne diseases and their risks for public health","author":"BG Meerburg","year":"2009","journal-title":"Crit Rev Microbiol"},{"key":"pone.0248244.ref003","unstructured":"Mills J. 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