Anaplasma phagocytophilum strain:ecotype I | isolate:SLO-1 Genome sequencing. Anaplasma phagocytophilum strain:ecotype I | isolate:SLO-1

Infection with the tick-borne Anaplasma phagocytophilum can cause human granulocytic anaplasmosis (HGA). In Europe, the genetic cluster called A. phagocytophilum ecotype I is zoonotic. Despite its ubiquitous presence in ticks, livestock and wildlife, the number of reported HGA cases remains low. Here, we isolated and cultivated A. phagocytophilum from a Slovenian HGA patient, and sequenced its complete genome. In addition, we sequenced a fragment of the Anaplasma groEL gene from the blood of HGA patients from France (n=5) and Poland (n=3), and supplemented this with existing molecular epidemiological data. Genetic comparison of whole genomes (n=5), multilocus sequence typing (MLST, n=165), and a single genetic locus (groEL, n=992) revealed that the zoonotic variant forms a small, but distinct cluster within ecotype I, which predominantly circulates between foxes, wild boar, horses, cats, dogs, and Ixodes ricinus. Our findings indicate that the most abundant A. phagocytophilum ecotype I variants are found in a wider variety of wild and domesticated animals, most notably ruminants. These findings provide a straightforward explanation for the low abundance of HGA cases in Europe. We propose that the enzootic cycle, geographic distribution, and the infection rate in questing ticks of the zoonotic variant is investigated to assess the public health risk of HGA in Europe.