Background: Staphylococcus aureus is a major zoonotic and foodborne pathogen with substantial One Health implications, yet its prevalence, resistance, and virulence potential within the aquaculture sector in Nigeria remains poorly characterized. Objectives: To supplement existing information, this current study investigated the prevalence, clonal distribution, antimicrobial resistance, and virulence gene profiles of S. aureus isolates from fish, fish water, and occupationally exposed fish handlers in Anambra State, Southeast Nigeria. Methods: A total of 607 samples—comprising 465 surface swabs from raw and processed fish, 36 fish water samples, and 106 nasal swabs from fish handlers—were processed using selective culture, biochemical tests, antimicrobial susceptibility testing, DNA microarray analysis, spa typing, and SCCmec typing. Results: S. aureus was recovered from 16.5% (100/607) of the samples. Fourteen (14%) isolates were methicillin-resistant (MRSA), harboring mecA and SCCmec types IV and V, with a combined MRSA prevalence of 2.3%. Multidrug resistance was observed in 52.2% of isolates (mean Multiple Antimicrobial Resistance index: 0.23), with 19 resistance genes spanning nine antimicrobial classes—including heavy metal and biocide resistance. Twenty-eight spa types across 13 clonal complexes (CCs) were identified, with CC1, CC5, and CC8 predominating. The detection of shared spa types between fish and handlers indicates potential cross-contamination. Detected virulence genes included those for accessory gene regulators (agrI-IV), Pantone–Valentine leucocidin (lukFS-PV), toxic shock syndrome (tsst-1), hemolysins (hla, hlb, hld/hlIII, hlgA), biofilm formation (icaA, icaD), immune evasion (chp, scn, sak), enterotoxins (sea, seb, sec, sed, egc, and others), exfoliative toxins (etA, etB), epidermal cells differentiation (edinA, edinB), and capsular types (cap5, cap8). Conclusions: This study reveals that the aquaculture sector in Southeast Nigeria serves as a significant reservoir of genetically diverse, multidrug-resistant S. aureus strains with robust virulence profiles. These findings highlight the necessity of integrated One Health surveillance and targeted interventions addressing antimicrobial use and hygiene practices within aquatic food systems.

Non-typhoidal Salmonella (NTS) is an important poultry-associated pathogen with major One Health and economic impacts, but data on its epidemiology and antimicrobial resistance in Nigeria remain limited. This study investigated the prevalence, serovar distribution, clonal relatedness, and antimicrobial resistance of NTS along the poultry production chain in Enugu State, southeastern Nigeria. A total of 2400 samples were collected, comprising feces (cecal content)/cloacal swabs from chickens (n = 1100), eggs (n = 400), chicken meat (n = 600), and stool samples from poultry workers (n = 300). Isolation and identification were performed using standard bacteriological methods, with confirmation by serotyping and polymerase chain reaction (PCR) targeting the invA gene. Genetic relatedness was assessed using enterobacterial repetitive intergenic consensus (ERIC)-PCR, and antimicrobial susceptibility was determined by the disk diffusion method. Overall, 47 (2.0%) Salmonella enterica isolates were recovered from 2400 samples, with the highest prevalence observed in eggs (3.5%), followed by human stool (3.3%), chicken meat (1.8%), and chicken feces (1.1%). Only 35 (11.8%) of the 297 sampled farms were positive for Salmonella, and recovery rates differed significantly (p = 0.0065) among sample sources. Five serotypes were identified, dominated by S. Typhimurium (57.4%), followed by S. Enteritidis (14.9%), S. Anatum (12.8%), S. Stanley (8.5%), and S. Agona (6.3%). ERIC-PCR revealed multiple clonal clusters, many containing isolates from mixed sources, indicating circulation of related strains between poultry and humans. All isolates were resistant to ampicillin, with high resistance to tetracycline (76.6%), sulphamethoxazole–trimethoprim (51.1%), and fluoroquinolones. Overall, 80.9% of isolates were multidrug-resistant, with a mean Multiple Antibiotic Resistance Index of 0.29, highest among isolates from chicken feces. Although the prevalence of NTS was low, the presence of genetically related multidrug-resistant strains across the production chain underscores the role of poultry as a reservoir for zoonotic transmission and highlights the need for coordinated One Health surveillance and antimicrobial stewardship strategies in Nigeria.