Background

Synanthropic filth flies thrive in human and animal habitats, posing health risks through the transmission of infectious agents. They breed on organic waste, including animal feces, making them carriers of various pathogens. In Egypt, where livestock farming is common and poor sanitation, these flies may contribute to zoonotic disease transmission. The current study investigates parasitic infections in filth flies from three livestock farms in Assiut Governorate, Upper Egypt, highlighting their role as vectors for zoonotic infections, particularly Cryptosporidium, via morphological and molecular tools.

Methods

A total of 12,749 flies were collected from the study sites via sweep nets. After taxonomic identification, the flies were examined microscopically for parasites using various concentration and staining techniques. Positive samples were further confirmed for infections, particularly for Cryptosporidium parasites, via nested PCR and sequence analysis targeting the COWP and SSU rRNA genes.

Results

This study revealed the presence of several fly species from seven dipteran families, particularly the family Muscidae, primarily Musca domestica, which presented a high parasite infestation rate of 96.6%. This study revealed a high prevalence of various protozoans and helminths in the collected flies. Cryptosporidium was the most prevalent parasite (64.4–100%), infecting all fly species. Entamoeba and Balantidium were also significant, especially in M. domestica (22.6–90.1%, 8.9–100%), Fannia canicularis (10.5–74.4%, 44.2–88.2%), and Borborillus vitripennis (11.1–50%, 37.2–91.4%). Giardia, Trichuris, and Trichostrongylidae had low to moderate prevalence in multiple fly species. Mites are commonly detected on fly exoskeletons, with high infestation rates observed in Musca domestica (77–100%) and Physiphora alceae (66.7–100%). The present study also reported sporadic infections with Trichomonas, Toxocara vitulorum, and pseudoscorpions, along with notable midge larval infestations (52.1%), mainly at site B. Parasitic infections were highest in autumn and spring, with the lowest rates in winter. Molecular identification confirmed the presence of the zoonotic species Cryptosporidium parvum and Cladotanytarsus gedanicus.

Conclusion

This study revealed that zoonotic parasites exist in flies and pose potential risks when they are found near humans. Cryptosporidium parvum is the prevalent parasite causing diarrhea outbreaks in animals. This is the first genetic evidence of Cladotanytarsus gedanicus midge from Upper Egypt.