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ORIGINAL RESEARCH ARTICLE

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

Kunda Ndashe1* ,  Mulemba Tillika Samutela2 ,  Walter Muleya3 ,  Katendi Changula1 ,  John Yabe1,4 ,  Ladslav Moonga1 ,  Ngonda Saasa5 ,  Benjamin Mubemba6 ,  Edgar Simulundu7 ,  Bernard Mudenda Hang’ombe8
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1 Department of Paraclinical Studies, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
2 Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
3 Department of Biomedical Sciences, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
4 Department of Veterinary Paraclinical Studies, School of Veterinary Medicine, University of Namibia, Windhoek, Namibia
5 Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
6 Department of Wildlife Sciences, School of Natural Resources, Copperbelt University, Kitwe, Copperbelt, Zambia
7 Zambia National Public Health Institute, Lusaka, Zambia
8 Directorate of Research and Innovation, Copperbelt University, Kitwe, Copperbelt, Zambia
MI, 026020008 https://doi.org/10.36922/MI026020008
Received: 9 January 2026 | Revised: 2 March 2026 | Accepted: 1 April 2026 | Published online: 8 May 2026
© 2026 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
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Abstract

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.

Keywords
Nile tilapia
Oxford nanopore sequencing
Metagenomics
Bacterial community
Antimicrobial resistance
Funding
None.
Conflict of interest
The authors declare that they have no conflicts of interest.
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Microbes & Immunity, Electronic ISSN: 3029-2883 Print ISSN: 3041-0886, Published by AccScience Publishing
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