Background: Cysteine proteases of
Clonorchis sinensis are potential diagnostic antigens, yet the performance of individual members within this diverse enzyme family requires systematic evaluation. This study aimed to assess the diagnostic potential of four recombinant cysteine proteases (r
CsCP1–4) for human clonorchiasis. Methods: An indirect ELISA was developed to measure serum reactivity (IgG, IgG subclasses, IgA) against r
CsCP1–4. The assay was validated using 180 microscopy-confirmed positive and 148 negative control sera. Samples were randomly split into training and validation sets (7.5:2.5). Diagnostic performance of single antigens and their combinations was evaluated using univariate and multivariate logistic regression and compared with a commercial kit. Key metrics included the area under the curve (AUC), sensitivity, specificity, accuracy, F1-score, and Kappa coefficient. Results: Four single antigen–antibody pairs showed high performance: r
CsCP1-IgG4 (AUC = 0.928), r
CsCP2-IgA (AUC = 0.863), r
CsCP3-IgG1 (AUC = 0.920), and r
CsCP4-IgG4 (AUC = 0.958). Among these, r
CsCP1-IgG4, r
CsCP3-IgG1, and r
CsCP4-IgG4 outperformed the commercial kit, achieving higher sensitivity (92.0%, 96.0%, 96.0% vs. 86.0%), specificity (87.5%, 81.3%, 90.6% vs. 78.1%), accuracy (92.0%, 88.9%, 94.1% vs. 86.0%), and F1-scores (0.902, 0.902, 0.939 vs. 0.829). The Kappa values for r
CsCP1-IgG4 (0.768) and r
CsCP4-IgG4 (0.773) indicated substantial agreement with the microscopic standard. Multi-antigen combinations (triple or quadruple) further enhanced performance, achieving sensitivity and specificity > 98% with an AUC approaching 1.0. Conclusions: This study identifies r
CsCP1 and r
CsCP4, particularly in combination with IgG4 detection, as highly promising diagnostic targets for clonorchiasis. Multi-antigen combinations significantly improved diagnostic performance compared to single-antigen assays, offering a strategy for high-precision diagnosis. Furthermore, the efficacy of the r
CsCP2-IgA pair suggests that detecting fecal secretory IgA could be a novel avenue for non-invasive, self-testing applications.
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