Molecular and Epidemiological Investigation of Cryptosporidium Infection in Goat Population from Bouira Province, Algeria

Cryptosporidiosis is a gastrointestinal disease affecting terrestrial and aquatic vertebrates worldwide. This study investigated molecularly and microscopically the prevalence and the diversity of <i>Cryptosporidium</i> spp. in goats across the Bouira communes, Algeria. A total of 559 fecal samples were collected from 70 farms, representing 16.6% of the regional goat population. Samples were analyzed using microscopy (modified Ziehl-Neelsen staining) and molecular methods (i.e., qPCR and nested PCR targeting the 18S rRNA gene, followed by sequencing). Microscopy detected <i>Cryptosporidium</i> in 6.1% of samples, while qPCR revealed a significantly higher prevalence of 13.6% (<i>p</i> < 0.00001), confirming the superior sensitivity of molecular diagnostics. Spatial analysis identified significant clustering (Moran's <i>I</i> = 0.330, <i>p</i> = 0.0003), with communes-level prevalence ranging from 6.7% to 45.7%. Infection rates correlated positively with humidity and rainfall but negatively with temperature. Phylogenetic analysis confirmed <i>Cryptosporidium xiaoi</i> as the sole species circulating, showing 100% genetic similarity to global caprine isolates. Despite <i>C. xiaoi</i>'s host adaptation, a GenBank review highlighted six other zoonotic species infecting goats worldwide, underscoring potential cross-species transmission risks. The study emphasizes the need for PCR-based surveillance to assess true prevalence and zoonotic threats, while climatic findings support targeted interventions in high-risk areas.