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A total of 226 blood samples were collected from cattle, goats, and sheep with a history of abortion. Molecular analysis was conducted using PCR and sequencing of the internal transcribed spacer (ITS) region of the rRNA gene. The results revealed the prevalence of <jats:italic>T. gondii<\/jats:italic> in cattle at 12.33% (9\/73), while goats and sheep tested negative. In contrast, 14.92% (10\/67) of goat samples tested positive for <jats:italic>Microsporidia<\/jats:italic> spp., with no cases detected in cattle or sheep. No infections with <jats:italic>Sarcocystis<\/jats:italic> spp. or <jats:italic>N. caninum<\/jats:italic> were identified in any tested animals. Across all examined livestock, the overall prevalence of <jats:italic>T. gondii<\/jats:italic> was 3.98% (9\/226), while <jats:italic>Microsporidium<\/jats:italic> spp. exhibited a slightly higher prevalence at 4.42% (10\/226). Molecular sequencing identified three novel <jats:italic>T. gondii<\/jats:italic> strains in cattle recorded in the GenBank database under accession numbers MZ197902, MZ197903, and MZ197904, showing 99.9% genetic similarity to reference strains. Additionally, three novel strains of <jats:italic>Enterocytozoon bieneusi<\/jats:italic> (MZ197781, MZ197782, and MZ197783) were detected in goats. Phylogenetic analysis indicated a close evolutionary relationship between these newly identified <jats:italic>E. bieneusi<\/jats:italic> strains and known genotypes, suggesting a high degree of genetic conservation. These findings underscore the ongoing risks of <jats:italic>T. gondii<\/jats:italic> and <jats:italic>E. bieneusi<\/jats:italic> to livestock and public health. Continued surveillance is necessary to assess the zoonotic potential of these novel strains to aid in effective management strategies.<\/jats:p>","DOI":"10.1007\/s11259-025-10698-9","type":"journal-article","created":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T09:12:22Z","timestamp":1742375542000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["First identification and molecular characterization of protozoan parasites associated with abortion in ruminants from South Sinai Governorate, Egypt"],"prefix":"10.1007","volume":"49","author":[{"given":"Safaa Mohamed","family":"Barghash","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1631-8606","authenticated-orcid":false,"given":"Al-Shaimaa Mohsen","family":"Sadek","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,3,19]]},"reference":[{"issue":"11","key":"10698_CR1","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1016\/j.apjtm.2015.10.015","volume":"8","author":"IF Abou-El-Naga","year":"2015","unstructured":"Abou-El-Naga IF (2015) Demographic, socioeconomic and environmental changes affecting circulation of neglected tropical diseases in Egypt. 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