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Background Cytauxzoon  spp. infection is believed to be a newly emerging tick-borne disease in felids in Europe, with three species of the haemoparasite having recently been differentiated in wild felids. In Switzerland, rare infections have been documented in domestic cats in the west and northwest of the country, the first of which was in 2014. The aims of the present study were: (i) to characterize a  Cytauxzoon  spp. hotspot in domestic cats in central Switzerland; (ii) to elucidate the geographic distribution of  Cytauxzoon  spp. in domestic cats in Switzerland; (iii) to assess suspected high-risk populations, such as stray and anaemic cats; and (iv) to investigate the newly emerging nature of the infection.  Cytauxzoon  spp. were further differentiated using mitochondrial gene sequencing. Methods The overall study included samples from 13 cats from two households in central Switzerland (study A), 881 cats from all regions of Switzerland (study B), 91 stray cats from a hotspot region in the northwest of Switzerland and 501 anaemic cats from across Switzerland (study C), and 65 Swiss domestic cats sampled in 2003 and 34 European wildcats from eastern France sampled in the period 1995–1996 (study D). The samples were analysed for  Cytauxzoon  spp. using real-time TaqMan quantitative PCR, and positive samples were subjected to  18S  rRNA, cytochrome  b  ( CytB ) and cytochrome  c  oxidase subunit I ( COI ) gene sequencing. Results In study A, six of 13 cats from two neighbouring households in central Switzerland tested postive for  Cytauxzoon  spp.; two of the six infected cats died from bacterial infections. In studies B and C, only one of the 881 cats (0.1%; 95% confidence interval [CI]: 0–0.3%) in the countrywide survey and one of the 501 anaemic cats (0.2%; 95% CI: 0–0.6%) tested postive for  Cytauxzoon  spp. while eight of the 91 stray cats in the northwest of Switzerland tested positive (8.8%; 95% CI: 3.0–14.6%). In study D,  Cytauxzoon  spp. was detected in one of the 65 domestic cat samples from 2003 (1.5%; 95% CI: 0–4.5%) and in ten of the 34 European wildcat samples from 1995 to 1996 (29%; 95% CI: 14.2–44.7%). The isolates showed ≥ 98.6% sequence identities among the  18S  rRNA,  CytB  and  COI  genes, respectively, and fell in the subclade  Cytauxzoon europaeus  based on  CytB  and  COI  gene phylogenetic analyses. Conclusions The study challenges the newly emerging nature of  Cytauxzoon  spp. in central Europe and confirms that isolates from domestic cats in Switzerland and European wild felids belong to the same species. Graphical Abstract

Cytauxzoon europaeus infections in domestic cats in Switzerland and in European wildcats in France: a tale that started more than two decades ago