Beyond the primer: anatomical site and cyst viability drive the molecular detection of Taenia saginata in slaughterhouse samples

Abstract Background Bovine cysticercosis, caused by the larval stage of Taenia saginata , results in significant economic losses for the beef industry due to carcass condemnation. While routine post-mortem inspection is mandatory, visual diagnosis lacks specificity, particularly for degenerated or calcified cysts. This study primarily aimed to evaluate how anatomical site and cyst viability influence the molecular confirmation of suspected lesions. As a secondary methodological objective, we assessed the performance of three conventional PCR assays—a widely used large subunit (LSU) rRNA target (328 bp), a previously described Cytochrome c oxidase subunit 1 (COX1) target (253 bp), and a novel COX1 target (428 bp) designed herein—to ensure primer selection did not bias our findings. A total of 232 suspect macroscopic lesions (180 calcified cysts, 12 viable cysts, and 40 non-specific lesions) were collected from cattle slaughtered in Mato Grosso do Sul, Brazil. Results Our results demonstrated no statistically significant difference in diagnostic sensitivity among the three primer sets ( p > 0.05), indicating that molecular confirmation is not limited by primer selection. Instead, molecular detection was profoundly driven by cyst viability and anatomical location ( p < 0.001). While viable cysts yielded high positivity rates (up to 66.7%; 95% CI: 34.9%–90.1%), detection in calcified lesions dropped to approximately 28.9% due to severe DNA degradation. Crucially, calcified hepatic lesions exhibited drastically lower PCR positivity (11.4%–15.2%) compared to those in the heart (46.0%–54.0%) and head muscles (50.0%–60.0%). Conclusions These findings indicate that the anatomical location of a lesion heavily dictates molecular detection rates. While visual inspection of hepatic tissue often conflicts with molecular results, negative PCR in the liver does not necessarily indicate the absence of infection. Rather, this discrepancy highlights a critical limitation in detecting highly degraded DNA, likely driven by rapid clearance within the enzymatically aggressive hepatic parenchyma, combined with the potential misclassification of non-parasitic granulomas. Due to the high rate of false negatives in calcified cysts, conventional PCR cannot be safely recommended for real-time carcass clearance. Instead, to improve diagnostic accuracy, epidemiological surveillance and retrospective sanitary audits should prioritize suspect lesions in the heart and striated muscles over those found in the liver.