Whole-genome investigations of Salmonella enterica isolates from poultry meat uncovered multidrug-resistant and outbreak-associated serovars circulating in Accra, Ghana

Abstract

Abstract Background Salmonella enterica ( S. enterica ) is a prominent foodborne pathogen associated with severe and potentially fatal infections in humans. This study investigated the prevalence, antimicrobial resistance (AMR) profiles, genetic diversity, and AMR mechanisms of S. enterica serovars isolated from poultry meat from various vendors in Ghana. Methods Poultry meat samples were collected from markets, retail shops, poultry farms, and live poultry retailers. Salmonella isolates were identified using Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-ToF-MS). Antimicrobial susceptibility testing (AST) was conducted using the Kirby-Bauer disk diffusion method. Whole Genome Sequencing was performed on the Illumina NextSeq platform and data analyzed using bioinformatic tools. Results Of the 246 poultry meat samples investigated, Salmonella spp was detected in 71 (29%). AST revealed resistance to tetracycline (44%), trimethoprim/sulphamethoxazole (18%), and ciprofloxacin (14%), ampicillin (8%), gentamicin (8%), chloramphenicol (4%), ceftazidime (1%), and meropenem (1%). Multi-drug resistant (MDR) phenotypes were observed among 30% of the isolates. WGS identified resistance genes for tetracycline (tetA ; 42%), sulfonamides, ( sul ; 38%), quinolones ( qnr ; 31%), trimethoprim ( dfrA1 ; 20%), beta-lactams ( bla TEM−1B ; 8%), and chloramphenicol ( cmIA1 ; 4%). Among the twenty-four serovars were detected, S . Typhimurium, and S. Derby were predominant (n = 7, 29%), followed by S . Liverpool (n = 6), and S . Hato (n = 5). Three of the S. Typhimurium belonged to the outbreak-associated clone ST19. Other significant STs included ST11 ( S. Enteritidis) , ST96 ( S . Schwarzengrund), ST314 ( S . Kentucky), ST1954 ( S . Chester), and ST308 ( S . Poona). Col and Inc plasmid replicons responsible for multiple resistance gene transfers were detected along with virulence genes associated with adhesins, transport, and secretion systems. Conclusion The detection of MDR and outbreak-associated Salmonella enterica serovars in poultry meat sold in Accra underscores a significant threat to public health and food safety. These findings highlight the urgent need for heightened public awareness and sustained surveillance efforts to mitigate and monitor the risk of foodborne infections.