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Background  Rickettsiae are emerging pathogens causing public health problems in many countries around the world.  Rickettsia  spp. are found in association with a wide range of arthropods which feed on different species of animals. However, the distribution and natural cycle of  Rickettsia  species and their association with different arthropod vectors are not fully established. The aim of this study was to investigate the presence and prevalence of  Rickettsia  spp. in ticks, mites and fleas parasitizing different species of small mammals in Lithuania and to molecularly characterize the  Rickettsia  spp. obtained from different ectoparasites.    Results  A total of 1261 ectoparasites (596  Ixodes ricinus  ticks, 550 mites of five species and 115 fleas of eight species) collected from 238 rodents in Lithuania during 2013–2014 were investigated for the presence of  Rickettsia  pathogens. Infection rates were calculated as the maximum likelihood estimation (MLE) with 95% confidence intervals (CI). The infection rate varied among ectoparasites and was found highest in fleas 43.5%, followed by  I. ricinus  ticks (MLE = 26.5%; 95% CI: 22.2–31.3%) and then mites (MLE = 9.3%; 95% CI: 7.0–12.2%). Sequence analysis of partial  gltA  and  17kDa  genes revealed the presence of  Rickettsia helvetica ,  R. felis ,  R. monacensis ,  Rickettsia  sp .  and rickettsial endosymbionts. Four  Rickettsia  spp. were identified in fleas, while three  Rickettsia  spp. were identified in Laelapidae mites and only one ( R. helvetica ) in  I. ricinus  ticks.    Conclusions  To our knowledge, this is the first report of the occurrence and molecular characterization of  Rickettsia  spp. in 11 species of ectoparasites of small rodents in Lithuania. The present data extend the knowledge on the distribution of  Rickettsia  spp. and their association with different arthropod vectors. Prior to our study,  R. felis  had never been identified in Lithuania. To our knowledge, this is also the first report of  R. felis  in  L. agilis  and  H. microti  mites and in  Ct. agyrtes  and  H. talpae  fleas, as well as the first detection of  R. monacensis  in  Ct. agyrtes  fleas.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2947-9) contains supplementary material, which is available to authorized users.

Prevalence and diversity of Rickettsia species in ectoparasites collected from small rodents in Lithuania