Anaplasma phagocytophilum is the widest spread tick-borne pathogen in animals in Europe and also severely affects the human health. It has been well-documented that in vertebrates A. phagocytophilum infects the granulocytes, whereas in ticks the midgut, hemocytes and salivary glands have been shown as the infection sites. Although pathogen infection does not appear to harm the tick, several studies using “omics” technologies revealed that A. phagocytophilum infection induces transcriptional reprograming and proteome modulation in tick cells. These changes are very likely relevant to the evolutionary adaptation of this pathogen to its multi-host lifestyle. Previously, we showed that the cellular components and processes affected by A. phagocytophilum infection include, but are not limited to the cytoskeleton, apoptosis, metabolism, cell immunity and epigenetics.