Whole-Genome Characterization of Gram-Negative Bacteria in Pig Production Systems at Okada, Edo State, Nigeria: A One Health Approach

Pig farming significantly supports livestock agriculture, food security, livelihoods, household income, and employment across developing countries, including Nigeria. This study charac terized Gram-negative bacteria from pig production systems at Okada, Edo State, Nigeria, using a One Health approach of integrating animal, environmental and human-associated compartments. A total of 356 samples were collected and examined from the three compart ments comprising, 132 pig-associated (37.08%), 124 environmental (34.83%), and 100 hu man-associated (28.09%). Cultural and biochemical examinations yielded 48 Gram-negative isolates, with 22 (45.83%) from pigs, 14 (29.17%) from environmental sources, and 12 (25.00%) from humans. The isolates comprised Proteus, Enterobacter, Pseudomonas, Esche richia, Klebsiella, Bordetella, Morganella, Providencia and Citrobacter, with Proteus predom inating (13; 27.08%). Although bacterial genera varied numerically among compartments, Pearson’s chi-square test showed no significant association between bacterial genus and com partment (χ² = 11.25, p = 0.79). Whole-genome shotgun sequencing generated high-quality data, with mean reads exceeding 17 million and Q30 scores, with 95.50–96.50% of reads re tained after filtering. Krona analysis showed predominance of Proteobacteria, Gammaprote obacteria and Enterobacterales across the compartments. Proteus spp (> 20%) and Bordetella trematum(16%), were prominent among pig-associated sequences; Proteus spp (>22%) and Escherichia coli(14%), predominated among human-associated sequences; environmental profiles were more heterogeneous, with E. coli, Citrobacter freundii, Klebsiella variicola each contributing approximately 9%. Seventeen species and a genus Halomonas were identified, with nine species shared across the three compartments. Cochran’s Q test showed no signifi cant difference in species representation (Q = 1.14, p = 0.57). Jaccard similarity was highest between environmental and human-associated compartments (0.733), indicating substantial taxonomic connectivity. Overall, the findings support integrated One Health surveillance of Gram-negative bacteria in pig production.