| Summary: | Human babesiosis in Europe has been attributed to infection with <i>Babesia divergens</i> and, to a lesser extent, with <i>Babesia venatorum</i> and <i>Babesia microti,</i> which are all transmitted to humans through a bite of <i>Ixodes ricinus</i>. These <i>Babesia</i> species circulate in the Netherlands, but autochthonous human babesiosis cases have not been reported so far. To gain more insight into the natural sources of these <i>Babesia</i> species, their presence in reservoir hosts and in <i>I. ricinus</i> was examined. Moreover, part of the ticks were tested for co-infections with other tick borne pathogens. In a cross-sectional study, qPCR-detection was used to determine the presence of <i>Babesia</i> species in 4611 tissue samples from 27 mammalian species and 13 bird species. Reverse line blotting (RLB) and qPCR detection of <i>Babesia</i> species were used to test 25,849 questing <i>I. ricinus</i>. Fragments of the 18S rDNA and cytochrome c oxidase subunit I (COI) gene from PCR-positive isolates were sequenced for confirmation and species identification and species-specific PCR reactions were performed on samples with suspected mixed infections. <i>Babesia microti</i> was found in two widespread rodent species: <i>Myodes glareolus</i> and <i>Apodemus sylvaticus</i>, whereas <i>B. divergens</i> was detected in the geographically restricted <i>Cervus elaphus</i> and <i>Bison bonasus</i>, and occasionally in free-ranging <i>Ovis aries</i>. <i>B. venatorum</i> was detected in the ubiquitous <i>Capreolus capreolus</i>, and occasionally in free-ranging <i>O. aries</i>. <i>S</i>pecies-specific PCR revealed co-infections in <i>C. capreolus</i> and <i>C. elaphus,</i> resulting in higher prevalence of <i>B. venatorum</i> and <i>B. divergens</i> than disclosed by qPCR detection, followed by 18S rDNA and COI sequencing. The non-zoonotic <i>Babesia</i> species found were <i>Babesia capreoli</i>, <i>Babesia vulpes, Babesia</i> sp. deer clade<i>,</i> and badger-associated <i>Babesia</i> species. The infection rate of zoonotic <i>Babesia</i> species in questing <i>I. ricinus</i> ticks was higher for <i>Babesia</i> clade I (2.6%) than <i>Babesia</i> clade X (1.9%). Co-infection of <i>B. microti</i> with <i>Borrelia burgdorferi</i> sensu lato and <i>Neoehrlichia mikurensis</i> in questing nymphs occurred more than expected, which reflects their mutual reservoir hosts, and suggests the possibility of co-transmission of these three pathogens to humans during a tick bite. The ubiquitous spread and abundance of <i>B. microti</i> and <i>B. venatorum</i> in their reservoir hosts and questing ticks imply some level of human exposure through tick bites. The restricted distribution of the wild reservoir hosts for <i>B. divergens</i> and its low infection rate in ticks might contribute to the absence of reported autochthonous cases of human babesiosis in the Netherlands.
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