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Background    Anaplasma phagocytophilum  is a tick-transmitted Gram-negative obligate intracellular bacterium able to infect a wide variety of wild and domestic animals worldwide. Based on the genetic diversity observed with different molecular markers, several host-specific lineages have been identified. Roe deer is one of the most important reservoirs of this bacterium and hosts different genetic groups sometimes found on domestic animals. We therefore developed an  ankA  cluster-specific nested PCR (nPCR) to evaluate the prevalence of the three different  ankA  genetic groups described in roe deer (clusters II, III and IV) at three locations in France and the level of co-infections.    Results  The specificity of the three nPCRs was assessed by partially sequencing 35 amplicons of  ankA  genes obtained from the different nested PCRs. All three genetic lineages were detected in roe deer from all three geographical locations. Of the infected deer population, 60.7% were co-infected by two or three different genetic variants. Co-infections varied from 42.9 to 70.6% of the infected population depending on the local infection prevalences (from 33.3 to 73.9%). All types of mixed infections occurred, suggesting the absence of a strict variant exclusion by another variant.    Conclusions  Mixed infections by two or three genetic variants of  A. phagocytopilum  are a common feature in roe deer. Genetic variants (cluster IV) also found in domestic ruminants (cattle and sheep) were present in all the roe deer populations analyzed, suggesting a shared epidemiological cycle.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-017-2316-0) contains supplementary material, which is available to authorized users.

parasites and vectors

Detecting and characterizing mixed infections with genetic variants of Anaplasma phagocytophilum in roe deer (Capreolus capreolus) by developing an ankA cluster-specific nested PCR