Parasite diversity and community structure in invasive Nile tilapia (Oreochromis niloticus) in aquaculture systems of the Upper Tana River, Kenya

Aquaculture systems can influence how hosts and parasites interact, particularly when using widely introduced species such as Nile tilapia ( Oreochromis niloticus ). Although this species is farmed globally and hosts many parasite species, scientific understanding of the effects they have on fish, the environment and humans remains fragmented. In the Upper Tana River region of Kenya, O. niloticus is both a dominant aquaculture species and a well-established non-native fish. However, parasite communities in farmed systems in this region are still poorly described. This study investigated parasite diversity, community structure, the role of environmental conditions and production systems across small scale and large scale tilapia farms. We examined 157 fish for both internal and external parasites. We found diverse parasite taxa including monopisthocotylans, digeneans, copepods, nematodes, and acanthocephalans. Monopisthocotylans were the most prevalent taxa with high infection intensities. Parasite diversity differed significantly between farm types, with higher richness (p = 0.0118), Shannon diversity (p = 0.010), and Simpson diversity (p = 0.0152) in large-scale farms. Parasite community composition also differed between farm types (PERMANOVA: F = 3.22, R² = 0.21, p = 0.033). In contrast, environmental variables (temperature, pH, conductivity, and total dissolved solids) showed weak associations with parasite infection metrics. Histopathological analyses showed that infected fish had significantly higher gill lesion severity than non-infected individuals (p = 0.002). Lesion severity increased with parasite species richness and was generally higher in fish from large scale farms. These results suggest that production system characteristics play a stronger role than measured water quality variables in shaping parasite communities of farmed O. niloticus . They also show that parasite infections can affect fish health while remaining largely overlooked in farm management. Improving fish health therefore requires routine parasite monitoring and closer integration of ecological knowledge into farm-level practices. This is especially important in widely translocated, invasive species such as Nile tilapia, as baseline knowledge of the parasitological aspects of aquaculture-environment interactions is needed to assess the risks of parasite transmission between invasive and native species.