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Studies of tick-borne diseases (TBDs) in Europe focus on pathogens with principal medical importance (e.g. Lyme disease and tick-borne encephalitis), but we have limited epidemiological information on the neglected pathogens, such as the members of the genera Anaplasma, Rickettsia, Babesia and Candidatus Neoehrlichia mikurensis. Here, we integrated an extensive field sampling, laboratory analysis and GIS models to provide first publicly available information on pathogen diversity, prevalence and infection risk for four overlooked zoonot