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Accordingly, in this study, small mammals were captured using snap traps in Wulan County and Ge\u2019ermu City, Qaidam Basin, China. Spleen and brain tissues were collected and cultured to isolate <jats:italic>Bartonella<\/jats:italic> strains. The suspected positive colonies were detected with polymerase chain reaction amplification and sequencing of <jats:italic>gltA<\/jats:italic>, <jats:italic>ftsZ<\/jats:italic>, RNA polymerase beta subunit (<jats:italic>rpoB<\/jats:italic>) and <jats:italic>ribC<\/jats:italic> genes. Among 101 small mammals, 39 were positive for <jats:italic>Bartonella<\/jats:italic>, with the infection rate of 38.61%. The infection rate in different tissues (spleens and brains) (<jats:italic>\u03c7<\/jats:italic><jats:sup>2<\/jats:sup>\u2009=\u20090.112, <jats:italic>P<\/jats:italic>\u2009=\u20090.738) and gender (<jats:italic>\u03c7<\/jats:italic><jats:sup>2<\/jats:sup>\u2009=\u20091.927, <jats:italic>P<\/jats:italic>\u2009=\u20090.165) of small mammals did not have statistical difference, but that in different habitats had statistical difference (<jats:italic>\u03c7<\/jats:italic><jats:sup>2<\/jats:sup>\u2009=\u200910.361, <jats:italic>P<\/jats:italic>\u2009=\u20090.016). Through genetic evolution analysis, 40 <jats:italic>Bartonella<\/jats:italic> strains were identified (two different <jats:italic>Bartonella<\/jats:italic> species were detected in one small mammal), including <jats:italic>B. grahamii<\/jats:italic> (30), <jats:italic>B. jaculi<\/jats:italic> (3), <jats:italic>B. krasnovii<\/jats:italic> (3) and Candidatus <jats:italic>B. gerbillinarum<\/jats:italic> (4), which showed rodent-specific characteristics. <jats:italic>B. grahamii<\/jats:italic> was the dominant epidemic strain (accounted for 75.0%). Furthermore, phylogenetic analysis showed that <jats:italic>B. grahamii<\/jats:italic> in the Qaidam Basin, might be close to the strains isolated from Japan and China<jats:italic>.<\/jats:italic> Overall, we observed a high prevalence of <jats:italic>Bartonella<\/jats:italic> infection in small mammals in the Qaidam Basin. <jats:italic>B. grahamii<\/jats:italic> may cause human disease, and the pathogenicity of the others <jats:italic>Bartonella<\/jats:italic> species needs further study, the corresponding prevention and control measures should be taken into consideration.<\/jats:p>","DOI":"10.1038\/s41598-021-81508-w","type":"journal-article","created":{"date-parts":[[2021,1,18]],"date-time":"2021-01-18T11:03:30Z","timestamp":1610967810000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Genetic diversity of Bartonella species in small mammals in the Qaidam Basin, western China"],"prefix":"10.1038","volume":"11","author":[{"given":"Huaxiang","family":"Rao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shoujiang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuping","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongmei","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,1,18]]},"reference":[{"key":"81508_CR1","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.ijid.2008.04.002","volume":"13","author":"E Mogollon-Pasapera","year":"2009","unstructured":"Mogollon-Pasapera, E., Otvos, L. 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