Droplet digital PCR for fish pathogen detection and quantification: A systematic review and meta-analysis

Area of Science:

• Aquatic microbiology
• Molecular diagnostics
• Veterinary medicine

Background:

• Aquaculture faces significant economic losses due to viral and bacterial pathogens.
• Accurate and sensitive pathogen detection is crucial for disease management and prevention in fish farming.
• Quantitative PCR (qPCR) is a common method, but droplet digital PCR (ddPCR) offers potential advantages.

Purpose of the Study:

• To systematically review and meta-analyze the diagnostic efficacy of ddPCR for detecting viral and bacterial pathogens in aquaculture.
• To compare the performance of ddPCR with qPCR in aquaculture pathogen detection.
• To assess the heterogeneity and risk of bias in studies evaluating ddPCR for aquaculture diagnostics.

Main Methods:

• Systematic literature search of four databases up to November 6, 2023.
• Inclusion of 16 studies, with seven undergoing meta-analysis of 1121 biological samples.
• Adherence to Preferred Reporting Items for Systematic Reviews and Meta-analysis of Diagnostic Test Accuracy (PRISMA-DTA) guidelines and QUADAS-C criteria.

Main Results:

• Pooled sensitivity for ddPCR was 0.750 (95% CI: 0.487-0.944), compared to 0.461 (95% CI: 0.294-0.632) for qPCR, with no significant difference (p=0.5884).
• Significant heterogeneity was observed (I²=93%-97%, p<0.01), influenced by publication year but not country.
• Low risk of bias and no detected publication bias across the included studies.

Conclusions:

• ddPCR demonstrates comparable sensitivity to qPCR for aquaculture pathogen detection.
• ddPCR's ability to quantify pathogens precisely without standard curves enhances diagnostic reliability.
• ddPCR holds significant potential for improving accuracy in aquaculture disease surveillance and management.