Detection of Penaeus vannamei Pathogens from Water and Sediment eDNA Using a Universal Conventional PCR Approach

Environmental DNA (eDNA) offers a promising, non-invasive approach for monitoring infectious agents in aquaculture. While molecular techniques for detecting shrimp pathogens are well established in host tissues, there is a lack of standardized protocols for pathogen detection from environmental samples using conventional PCR. In this study, we developed and validated a universal conventional PCR protocol for monitoring DNA from major viral and bacterial shrimp pathogens within pond water and sediment samples. The method was applied to two commercial shrimp farms in Mexico, where eDNA was extracted from field-collected water and sediment. Using published primer sets, we successfully amplified DNA sequences corresponding to six key pathogens—Infectious hypodermal and hematopoietic necrosis virus (IHHNV), Baculovirus penaei (BP), Monodon baculovirus (MBV), Shrimp hemocyte iridescent virus (SHIV), Candidatus Hepatobacter penaei (NHP-B), and Acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio spp.—in environmental samples. Sequencing of PCR amplicons confirmed 93–100% identity to previously reported pathogen strains, highlighting the method’s reliability. Pathogen detection rates varied by site, sample type, and date, with the percentage of positive samples ranging from 11.1% to 77.7%. Notably, this is the first report of SHIV DNA detection from environmental samples in the Americas, highlighting its value for pathogen surveillance even in the absence of documented outbreaks. This protocol offers a cost-effective and scalable tool for pathogen surveillance in shrimp aquaculture, enhancing early disease detection and contributing to improved biosecurity and risk assessment frameworks.