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Background   Anaplasma phagocytophilum  is a zoonotic tick-borne intracellular alpha-proteobacterium causing tick-borne fever, which leads to significant economic losses in domestic ruminants in Europe. Its epidemiological cycles are complex and reservoir host species of bovine strains have not yet been identified. Given that little genetic information is available on strains circulating within a defined bovine environment, our objective was to assess the genetic diversity of  A. phagocytophilum  obtained from the same farms over time.    Methods  Blood samplings were performed several times in two European herds. In the French herd, 169 EDTA-blood samples were obtained from 115 cows (32 were sampled two to four times). In the German herd, 20 cows were sampled six times (120 EDTA-blood samples). The presence of  A. phagocytophilum  DNA was assessed using a qPCR targeting  msp2 . The positive DNA samples underwent MLST at nine genetic markers ( typA ,  ctrA ,  msp4 ,  pleD ,  recG ,  polA ,  groEL ,  gyrA , and  ankA ). For each locus, sequences were aligned with available bacterial sequences derived from cattle, horse, dog, and roe deer hosts, and concatenated neighbor joining trees were constructed using three to six loci.    Results  Around 20% (57/289) of samples were positive. Forty positive samples from 23 French and six German cows (11 of them being positive at two time points) were sequenced. Six loci ( typA ,  ctrA ,  msp4 ,  pleD ,  recG , and  polA ) allowed to build concatenated phylogenetic trees, which led to two distinct groups of bovine variants in the French herd (hereafter called A and B), whereas only group A was detected in the German herd. In 42% of French samples, double chromatogram peaks were encountered in up to four loci. Eleven cows were found infected three weeks to 17 months after first sampling and harboured a new variant belonging to one or the other group.    Conclusions  Our results demonstrate the occurrence of two major bovine strain groups and the simultaneous infection of single cows by more than one  A. phagocytophilum  strain. This challenges the role of cattle as reservoirs for  A. phagocytophilum.  This role may be facilitated via long-term bacterial persistence in individual cows and active circulation at the herd scale.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2661-7) contains supplementary material, which is available to authorized users.

Co-circulation of different A. phagocytophilum variants within cattle herds and possible reservoir role for cattle