Genomic Insights into Poultry-Associated Staphylococcus Aureus from Haripur, Pakistan

Staphylococcus aureus (S. aureus), a significant pathogen in both humans and livestock, has been a critical concern in poultry farming due to the rise in antibiotic resistance and zoonotic spillover. The study investigated the genetic diversity and antibiotic resistance profiles of S. aureus isolates collected from poultry farms in Haripur city of Khyber Pakhtunkhwa, Pakistan. A total of 317 samples including chicken nasal passages, cloacae, skin surfaces as well as chicken's feed and litter were collected from four poultry farms and eight slaughter houses. A total of 24 S. aureus isolates were obtained using standard microbiological procedures followed by whole genome sequencing (WGS). The WGS analysis revealed that majority of isolates belonged to sequence type (ST) ST291 (n = 18) and ST88 (n = 6). Furthermore, the genomic analysis identified the presence of various antibiotic resistance genes against several different antibiotic classes including β-lactams [blaZ], quinolones [gyrA_S84L, parC_S80F], fosfomycin [glpT-A100V, glpT_F3I], tetracycline, [tet(38), tet(K)], and erythromycin [erm(C)] as well as diverse range of virulence genes associated with adhesion [clfB, spa, ebp, sdrD, sdrF], biofilm formation [icaA, icaB, icaC, icaD, icaR, isdG], toxin production [geh, hlb, hlgA, hly/hla, lukF-PV, lukS-PV], and immune evasion [aur, coa, sak, sbi, scn]. All isolates possessed mobile genetic elements, including plasmids, insertion sequences, and prophages, suggesting the potential spread of virulence or antibiotic-resistance genes to bacterial populations. The study emphasizes the need for effective biosecurity measures and prudent antibiotic use in poultry farming to mitigate the risk of zoonotic transmission and public health threats.