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Background  Rodents are important reservoirs for zoonotic vector-borne agents. Thus, the distribution of rodents and their vicinity to humans and companion animals may have an important impact on human and animal health. However, the reservoir potential of some rodent genera, e.g.  Microtus , has not yet been precisely examined concerning tick-borne pathogens in Central Europe. Therefore, we examined small mammals from Germany and the Czech Republic for the following vector-borne pathogens:  Babesia  spp.,  Bartonella  spp.,  Anaplasma phagocytophilum , “ Candidatus  Neoehrlichia mikurensis” (CNM) and  Coxiella burnetii . Spleen DNA from 321 small mammals belonging to four genera,  Myodes  ( n  = 78),  Apodemus  ( n  = 56),  Microtus  ( n  = 149),  Sorex  ( n  = 38), collected during 2014 in Germany and the Czech Republic were available for this study. DNA samples were examined for the presence of  Babesia  and  Bartonella  DNA by conventional PCR targeting the  18S  rRNA gene and the 16S–23S rRNA intergenic spacer region, respectively. For the detection of CNM,  A. phagocytophilum  and  C. burnetii  real-time PCR assays were performed.    Results   Bartonella  spp. DNA was detected in 216 specimens (67.3%) with 102/174 (58.6%) positive in Germany and 114/147 (77.6%) in the Czech Republic. The prevalence in each genus was 44.9% for  Myodes , 63.2% for  Sorex , 77.2% for  Microtus  and 75% for  Apodemus.  Four  Bartonella  species, i.e.  Bartonella  sp. N40,  B. grahamii ,  B. taylorii  and  B. doshiae , as well as uncultured bartonellae, were detected. The  Bartonella  species diversity was higher in rodents than in shrews. In total, 27/321 (8.4%) small mammals were positive for CNM and 3/321 (0.9%) for  A. phagocytophilum  ( S. coronatus  and  M. glareolus ). All samples were negative for  Babesia  spp. and  Coxiella  spp.    Conclusions  While the detected high prevalence for  Bartonella  in  Apodemus  and  Myodes  spp. is confirmatory with previous findings, the prevalence in  Microtus  spp. was unexpectedly high. This indicates that individuals belonging to this genus may be regarded as potential reservoirs. Interestingly, only  Sorex  spp. and  M. glareolus  were positive for  A. phagocytophilum  in the present study, suggesting a possible importance of the latter for the maintenance of certain  A. phagocytophilum  strains in nature.    Electronic supplementary material  The online version of this article (10.1186/s13071-019-3576-7) contains supplementary material, which is available to authorized users.

Highly prevalent bartonellae and other vector-borne pathogens in small mammal species from the Czech Republic and Germany