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Background   Anaplasma phagocytophilum  is currently regarded as a single species. However, molecular studies indicate that it can be subdivided into ecotypes, each with distinct but overlapping transmission cycle. Here, we evaluate the interactions between and within clusters of haplotypes of the bacterium isolated from vertebrates and ticks, using phylogenetic and network-based methods.    Methods  The presence of  A. phagocytophilum  DNA was determined in ticks and vertebrate tissue samples. A fragment of the  groEl  gene was amplified and sequenced from qPCR-positive lysates. Additional  groEl  sequences from ticks and vertebrate reservoirs were obtained from GenBank and through literature searches, resulting in a dataset consisting of 1623  A. phagocytophilum  field isolates. Phylogenetic analyses were used to infer clusters of haplotypes and to assess phylogenetic clustering of  A. phagocytophilum  in vertebrates or ticks. Network-based methods were used to resolve host-vector interactions and their relative importance in the segregating communities of haplotypes.    Results  Phylogenetic analyses resulted in 199 haplotypes within eight network-derived clusters, which were allocated to four ecotypes. The interactions of haplotypes between ticks, vertebrates and geographical origin, were visualized and quantified from networks. A high number of haplotypes were recorded in the tick  Ixodes ricinus . Communities of  A. phagocytophilum  recorded from Korea, Japan, Far Eastern Russia, as well as those associated with rodents had no links with the larger set of isolates associated with  I. ricinus , suggesting different evolutionary pressures. Rodents appeared to have a range of haplotypes associated with either  Ixodes trianguliceps  or  Ixodes persulcatus  and  Ixodes pavlovskyi . Haplotypes found in rodents in Russia had low similarities with those recorded in rodents in other regions and shaped separate communities.    Conclusions  The  groEl  gene fragment of  A. phagocytophilum  provides information about spatial segregation and associations of haplotypes to particular vector-host interactions. Further research is needed to understand the circulation of this bacterium in the gap between Europe and Asia before the overview of the speciation features of this bacterium is complete. Environmental traits may also play a role in the evolution of  A. phagocytophilum  in ecotypes through yet unknown relationships.    Electronic supplementary material  The online version of this article (10.1186/s13071-019-3583-8) contains supplementary material, which is available to authorized users.

Anaplasma phagocytophilum evolves in geographical and biotic niches of vertebrates and ticks