Bacterial community profiles of diseased Nile tilapia livers revealed by shotgun metagenomics

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Bacterial diseases remain a major constraint to Nile tilapia (Oreochromis niloticus) aquaculture, where conventional bacterial culture-based methods often underestimate pathogen diversity and delay timely interventions. In the present study, both conventional bacterial culture and shotgun metagenomic sequencing using the Oxford nanopore device were used independently to characterize the bacterial community in liver samples from diseased tilapia collected from cage farms on Lake Kariba, Zambia. Further, the resulting sequence data were also used to ascertain the presence of antimicrobial resistance (AMR) genes. Conventional bacterial culture approaches identified a limited set of bacterial genera, including Aeromonas, Streptococcus, Pseudomonas, Lactococcus, and Acinetobacter. In contrast, metagenomic sequencing detected 78 bacterial species spanning 17 phyla and over 150 genera, highlighting substantially higher microbial diversity. Dominant species included Pseudomonas nitroreducens, Staphylococcus aureus, and Lactococcus garvieae, whereas Salmonella enterica was detected at a lower abundance across samples, with variation in prevalence across samples. Additionally, several opportunistic and fastidious bacteria undetectable by culture were identified, demonstrating the broader resolution of the metagenomic approach in disease investigations. Screening for AMR determinants revealed multiple resistance genes, including parE, mdsA, mprF, gyrA, and rpoB, associated with multidrug resistance in S. aureus, Escherichia coli, and S. enterica. These findings underscore the advantages of metagenomics for comprehensive bacterial profiling, co-infection detection, and surveillance of resistance genes in aquaculture systems. This culture-independent approach provides a rapid and detailed diagnostic tool to support early intervention and sustainable disease management in tilapia farming.

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