Tilapia lake virus (TiLV) is a highly virulent pathogen that has caused substantial mortality in tilapia farms, particularly those with open-water systems. However, TiLV can also emerge and persist in closed environments, such as recirculating aquaculture systems (RAS), where environmental accumulation and repeated exposure may intensify infection and sustain outbreaks. In this case study, we conducted three field experiments to better understand TiLV dynamics among Nile tilapia in RAS. In experiment I, we quantified the TiLV levels in the fish, water, and sediment to compare outbreak and no-outbreak conditions and found that the TiLV concentrations in liver samples and the water were significantly higher in the outbreak ponds and positively correlated with increased fish mortality. In experiment II, we used a side-by-side field trial to evaluate the protective efficacy of a TiLV vaccine and its effects on the viral loads in the fish and aquatic environment during outbreaks. The vaccinated fish showed substantially lower cumulative mortality (16.7%) than the unvaccinated controls (37.7%), with a relative percent survival of 55.6%. Additionally, the TiLV concentrations in the pond water of the vaccinated group were significantly lower. In experiment III, we compared the TiLV patterns between RAS and non-RAS operations to determine how water recirculation influences viral accumulation and outbreak severity. The results revealed limited viral accumulation and shorter disease outbreak duration in the non-RAS. Overall, our findings showed that the TiLV levels in the rearing water were closely linked with disease severity in the RAS-based tilapia hatcheries. Continuous water recirculation allowed the virus to build up in the system, which led to more prolonged outbreaks, while the non-RAS conditions with regular water discharge showed lower viral loads and faster recovery. The vaccinated fish had better survival rates and released less virus into the water, which helped reduce infection pressure across the ponds. Together, these results suggest that combining vaccination with good water management and molecular monitoring can provide a practical, noninvasive way to detect and control TiLV outbreaks in intensive farming systems.

Source water quality deterioration from microbial contamination is a severe problem confronting drinking water suppliers worldwide and has been addressed in the widely adopted Water Safety Plan framework to ensure the reliability and provision of high-quality drinking water. Microbial source tracking (MST) is used to examine different microbial pollution sources via specific intestinal markers for humans and different types of animals. However, the application of MST in tropical surface water catchments that provide raw water for drinking water supplies is limited. We analyzed a set of MST markers, namely, three cultivable bacteriophages and four molecular PCR and qPCR assays, together with 17 microbial and physicochemical parameters, to identify fecal pollution from general, human-, swine-, and cattle-specific sources. Seventy-two river water samples at six sampling sites were collected over 12 sampling events during wet and dry seasons. We found persistent fecal contamination via the general fecal marker GenBac3 (100% detection; 2.10–5.42 log10 copies/100 mL), with humans (crAssphage; 74% detection; 1.62–3.81 log10 copies/100 mL) and swine (Pig-2-Bac; 25% detection; 1.92–2.91 log10 copies/100 mL) comprising the major and minor contamination sources, respectively. Higher microbial contamination was observed during the wet season (p < 0.05). The conventional PCR screening used for the general and human markers showed 94.4% and 69.8% agreement with the respective qPCR results. Coliphage could be a screening parameter for the human qPCR marker (90.6% and 68.4% positive and negative predictive values; Spearman’s rank correlation coefficient = 0.66; p < 0.05). The total and fecal coliforms exceeding 20,000 and 4,000 MPN/100 mL standard values significantly increased the likelihood of detection via the crAssphage marker: odds ratios and 95% confidence intervals 15.75 (4.43–55.98) and 5.65 (1.39–23.05), respectively. Our study demonstrates the potential benefits of MST monitoring and its incorporation into the water safety frameworks of drinking water suppliers worldwide.