Schistosoma japonicum is a zoonotic trematode that infects both humans and animals in endemic areas of Indonesia. This cross-sectional study aimed to determine the prevalence of S. japonicum infection in cattle and water buffalo and to compare molecular and microscopic diagnostic approaches. A total of 89 fecal samples (51 cattle and 38 water buffalo) were collected from endemic villages in Central Sulawesi, Indonesia. Samples were examined using the Kato–Katz technique and real-time polymerase chain reaction (qPCR). Infection prevalence was calculated for each species, and differences between host species were analyzed using the chi-square or Fisher’s exact test. Diagnostic agreement between methods was assessed using McNemar’s test and Cohen’s kappa coefficient. qPCR detected S. japonicum DNA in 52.9% (27/51) of cattle and 5.3% (2/38) of water buffalo, whereas Kato–Katz identified infections in 21.6% (11/51) of cattle and 2.6% (1/38) of water buffalo. Overall, qPCR detected 29 infections compared with 12 detected by Kato–Katz. Infection prevalence was significantly higher in cattle than in water buffalo (p < 0.001). Diagnostic agreement between qPCR and Kato–Katz was moderate (κ = 0.49). When qPCR was used as the reference comparator, Kato–Katz detected 41.4% of qPCR-positive samples. These findings suggest that cattle may have a greater epidemiological contribution to environmental contamination than water buffalo in the study area. Molecular diagnostics detected substantially more infections than microscopy and may improve surveillance sensitivity in endemic settings.
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