Duplex droplet digital PCR method for the detection of Enterocytozoon hepatopenaei and Vibrio parahaemolyticus acute hepatopancreatic necrosis disease

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

This study provides a comprehensive summary of the findings regarding the application and diagnostic efficacy of droplet digital PCR (ddPCR) in detecting viral and bacterial pathogens in aquaculture. Utilizing a systematic search of four databases up to 6 November 2023, we identified studies where ddPCR was deployed for pathogen detection in aquaculture settings, adhering to Preferred Reporting Items for Systematic Reviews and Meta-analysis of Diagnostic Test Accuracy guidelines. From the collected data, 16 studies retrieved, seven were included in a meta-analysis, encompassing 1121 biological samples from various fish species. The detection limits reported ranged markedly from 0.07 to 34 copies/μL. A direct comparison of the diagnostic performance between ddPCR with quantitative PCR (qPCR) proved challenging due to limited data, thus only a pooled sensitivity analysis was feasible. The results showed a pooled sensitivity of 0.750 (95% confidence interval [CI]: 0.487-0.944) for ddPCR, compared to 0.461 (95% CI: 0.294-0.632) for qPCR, with no statistically significant difference in sensitivity between the two methods (p = .5884). Notably, significant heterogeneity was observed among the studies (I2 = 93%-97%, p < .01), with the year of publication significantly influencing this heterogeneity (p < .001), but not the country of origin (p = .49). No publication bias was detected, and the studies generally exhibited a low risk of bias according to QUADAS-C criteria. While ddPCR and qPCR showed comparable sensitivities in pathogen detection, ddPCR's capability to precisely quantify pathogens without the need for standard curves highlights its potential utility. This characteristic could significantly enhance the accuracy and reliability of pathogen detection in aquaculture.

Enterocytozoon hepatopenaei Infection in Shrimp: Diagnosis, Interventions, and Food Safety Guidelines

The emergence of disease in shrimp has governed much concern in food safety and security among consumers with the recent reports on hepatopancreatic microsporidiosis (HPM) caused by Enterocytozoon hepatopenaei (EHP). The microsporidians present in shrimp remain a silent pathogen that prevents optimal shrimp growth. However, the biggest threat is in its food safety concerns, which is the primary focus in ensuring food biosecurity and biosafety. Hence, the objective of this review is to summarise the current knowledge of EHP and its infection in shrimp with food safety concerns. This paper provides an analysis of the diagnostic methods for detecting EHP infections in shrimp aquaculture. Interventions with current molecular biology and biotechnology would be the second approach to addressing EHP diseases. Finally, a systematic guideline for shrimp food safety using diagnostic and intervention is proposed. Thus, this review was aimed to shed light on effective methods for the diagnosis and prevention of EHP infection in shrimp. We also include information on molecular and genomics tools as well as innate immune biomolecules as future targets in the intervention strategies on the microsporidsosis life cycle in shrimp and its environment. Overall, this will result in reduced disease outbreaks in shrimp aquaculture, ensuring the shrimp food safety in the future.

Development of a droplet digital PCR assay for the sensitive detection of iridovirus in Andrias davidianus

Chinese giant salamander iridovirus (GSIV) is the first known and causative viral pathogen in Andrias davidianus. Developing a sensitive, accurate and specific assay to detect GSIV in samples is essential to prevent the further spread of the pathogen. In this study, we established a droplet digital PCR (ddPCR) assay that targeted the mcp gene of GSIV, enabling rapid and quantitative detection of the virus. We determined that the optimal annealing temperature, primer concentration and probe concentration were 57.1°C, 50 nM and 500 nM, respectively. We analysed the specificity and sensitivity of the ddPCR assay and found that five common aquatic animal viruses, including Cyprinid herpesvirus 2 (CyHV-2), infectious spleen and kidney necrosis virus (ISKNV), Koi herpesvirus (KHV) and Carp Edema Virus (CEV) displayed negative results based on this GSIV ddPCR assay. The assay can detect GSIV with the lowest detection limit of 3.7 copies per reaction. To evaluate the sensitivity and accuracy of the ddPCR assay, we tested different infected tissue samples with both the ddPCR and TaqMan real-time PCR assays. Our results showed that the ddPCR assay detected GSIV in all samples with 100% positivity, while the TaqMan real-time PCR assay detected GSIV in only 82.1% of samples. The established ddPCR method provided several advantages in detecting GISV, including high sensitivity, high precision and absolute quantification, making it a powerful tool for detection of possible and potential GSIV infection, even in samples with low viral load.