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Background Borrelia burgdorferi (sensu lato) and rickettsiae of the spotted fever group are zoonotic tick-borne pathogens. While small mammals are confirmed reservoirs for certain Borrelia spp., little is known about the reservoirs for tick-borne rickettsiae. Between 2012 and 2014, ticks were collected from the vegetation and small mammals which were trapped in Saxony, Germany. DNA extracted from ticks and the small mammals’ skin was analyzed for the presence of Rickettsia spp. and B. burgdorferi (s.l.) by qPCR targeting the gltA and p41 genes, respectively. Partial sequencing of the rickettsial ompB gene and an MLST of B. burgdorferi (s.l.) were conducted for species determination.ResultsIn total, 673 small mammals belonging to eight species (Apodemus agrarius, n = 7; A. flavicollis, n = 214; Microtus arvalis, n = 8; Microtus agrestis, n = 1; Mustela nivalis, n = 2; Myodes glareolus, n = 435; Sorex araneus, n = 5; and Talpa europaea, n = 1) were collected and examined. In total, 916 questing ticks belonging to three species (Ixodes ricinus, n = 741; Dermacentor reticulatus, n = 174; and I. trianguliceps, n = 1) were collected. Of these, 474 ticks were further investigated. The prevalence for Rickettsia spp. and B. burgdorferi (s.l.) in the investigated small mammals was 25.3 and 31.2%, respectively. The chance of encountering Rickettsia spp. in M. glareolus was seven times higher for specimens infested with D. reticulatus than for those which were free of D. reticulatus (OR: 7.0; 95% CI: 3.3–14.7; P < 0.001). In total, 11.4% of questing I. ricinus and 70.5% of D. reticulatus were positive for Rickettsia spp. DNA of B. burgdorferi (s.l.) was detected only in I. ricinus (5.5%). Sequence analysis revealed 9 R. helvetica, 5 R. raoultii, and 1 R. felis obtained from 15 small mammal samples.ConclusionSmall mammals may serve as reservoirs for Rickettsia spp. and B. burgdorferi (s.l.). While the prevalence for Rickettsia spp. in M. glareolus is most likely depending on the abundance of attached D. reticulatus, the prevalence for B. burgdorferi (s.l.) in small mammals is independent of tick abundance. Dermacentor reticulatus may be the main vector of certain Rickettsia spp. but not for Borrelia spp.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-017-2053-4) contains supplementary material, which is available to authorized users.

Leptospira- positive bank voles are focally positively associated with PUUV infection in bank voles and with human hantavirus cases. It should be considered that shrews may serve as Leptospira spp. reservoirs.