Molecular Detection of Giardia duodenalis in a Symptomatic Domestic Sheep Flock and Preliminary Surveillance in Wild Mouflon (Ovis gmelini ophion) in Cyprus

(1) Background: Giardia duodenalis is a common protozoan parasite infecting various mammalian hosts, yet data on its prevalence in Cypriot ruminants, including the endemic and protected mouflon (Ovis gmelini ophion), remain absent. This study aimed to evaluate the prevalence and molecular characteristics of Giardia species (sp.) in domestic and wild ruminants in Cyprus to assess potential risks to wildlife. (2) Methods: We analysed 146 faecal samples—comprising 32 domestic sheep, 10 domestic and 34 free-ranging goats, and 70 wild mouflons—using nested polymerase chain reaction (PCR) and multi-locus sequence typing of the ssrRNA, tpi, bg, and gdh genes. (3) Results: Giardia was detected in only 1 of the 42 domestic ruminant samples (1/32 sheep; 3.1%), which was characterized as G. duodenalis assemblage E. No Giardia DNA was detected in the the domestic goats (0/10), wild mouflons (0/70) or the free-ranging goats (0/34) co-inhabiting the forest environment. (4) Conclusions: This study provides the first molecular report of Giardia sp. in domestic sheep in the Republic of Cyprus. While the parasite is present in domestic ruminants, the findings suggest a low positivity rate and no immediate evidence of transmission to the endangered mouflon. Further research with a larger sample size is recommended to confirm these observations and guide future conservation strategies.