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Background  Natural foci of tick-borne spotted fever group (SFG) rickettsiae of public health concern have been found in Slovakia, but the role of rodents in their circulation is unclear. Ticks ( Ixodes ricinus ,  Ixodes trianguliceps ,  Dermacentor marginatus ,  Dermacentor reticulatus ,  Haemaphysalis concinna  and  Haemaphysalis inermis ) and tissues of rodents ( Apodemus flavicollis ,  Apodemus sylvaticus ,  Myodes glareolus ,  Microtus arvalis ,  Microtus subterraneus  and  Micromys minutus ) were examined for the presence of SFG rickettsiae and  Coxiella burnetii  by molecular methods. Suburban, natural and rural habitats were monitored to acquire information on the role of ticks and rodents in the agents’ maintenance in various habitat types of Slovakia.    Results  The overall prevalence of rickettsial infection in questing  I. ricinus  and  D. marginatus  was 6.6% and 21.4%, respectively.  Rickettsia helvetica ,  R. monacensis  and non-identified rickettsial species were detected in  I. ricinus , whereas  R. slovaca  and  R. raoultii  were identified in  D. marginatus. Rickettsia  spp.-infected  I. ricinus  occurred during the whole tick questing period.  Rickettsia helvetica  dominated (80.5%) followed by  R. monacensis  (6.5%). The species were present in all studied habitats.  Rickettsia slovaca  (66.7%) and  R. raoultii  (33.3%) were identified in  D. marginatus  from the rural habitat.  Apodemus flavicollis  was the most infested rodent species with  I. ricinus , but  My. glareolus  carried the highest proportion of  Rickettsia -positive  I. ricinus  larvae. Only 0.5% of rodents ( A. flavicollis ) and 5.2% of engorged  I. ricinus  removed from  My. glareolus, A. flavicollis  and  M. arvalis  were  R. helvetica-  and  R. monacensis -positive.  Coxiella burnetii  was not detected in any of the tested samples. We hypothesize that rodents could play a role as carriers of infected ticks and contribute to the maintenance of rickettsial pathogens in natural foci.    Conclusions  Long-term presence of SFG  Rickettsia  spp. was confirmed in questing ticks from different habitat types of Slovakia. The results suggest a human risk for infection with the pathogenic  R. helvetica ,  R. monacensis ,  R. slovaca  and  R. raoultii .    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-017-2094-8) contains supplementary material, which is available to authorized users.

Molecular evidence of Rickettsia spp. in ixodid ticks and rodents in suburban, natural and rural habitats in Slovakia