Use of antibiotics without following standard guidelines is routine practice in developing countries which is giving rise to genetic divergence and increased drug resistance. The current study analyzed genetic divergence and drug resistance by S. aureus and therapeutic efficacy of novel antibiotic combinations. The study revealed that 42.30% (minimum 20%-maximum 70%) of milk samples are positive for S. aureus. Study also revealed seven SNPs in the S. aureus nuc gene (c.53A>G, c.61A>G, c.73T>C, c.93C>A, c.217C>T, c.280T>C, and c.331T>A). Local isolates Staph-2 and Staph-3 were closely related to Bos taurus nuc gene (bovine S. aureus), while Staph-1 was closely related to Homo sapiens (human S. aureus) indicating shifting of host. Change of two amino acids and staphylococcal nuclease conserved domain was observed in all local isolates of S. aureus. The isoelectric points predicted by protParam of Staph-1, Staph-2, and Staph-3 proteins were 9.30, 9.20, and 9.20, respectively. The antibiotic susceptibility profile of S. aureus presented highest resistance against penicillin (46.67%) and glycopeptide (43.33%). When a single antibiotic regimen was adopted in a field trial, the highest efficacy was reported in the case of oxytetracycline (80%) while lowest was presented by azithromycin. Among antibiotics’ combined regimen, the highest efficacy (80%) was presented by gentamicin with oxytetracycline: cefotaxime with vancomycin; and ciprofloxacin with vancomycin. The current study concluded rising percentages of S. aureus from dairy milk, proofs of genetic host shifts, and altered responses of in on field therapeutics.