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Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) is a clinically prevalent bacterium and is resistant to many drugs. Genetic factors such as <i>mec</i> genes are considered to be responsible for this resistance. Recently, <i>Staphylococcal</i> Cassette Chromosome <i>mec</i> (<i>SCCmec</i>) element mutations produced <i>mecC</i>, a new genetic variant that encodes a transpeptidase enzyme (63% similarity with <i>mecA</i>-encoded PBP2a). This cross-sectional study was conducted to establish the prevalence of the <i>mecA</i> and <i>mecC</i> genes among phenotypically identified MRSA and their effectiveness against different antibiotics in clinical specimens. The prevalence of <i>Staphylococcus aureus</i> was 10.2% (<i>n</i> = 102) in the total number of clinical specimens collected (<i>n</i> = 1000). However, the prevalence of MRSA was 6.3% (<i>n</i> = 63) of the total samples collected, while it was 61.8% among total <i>Staphylococcus aureus</i> isolates. <i>mec</i> genes were confirmed in 96.8% (<i>n</i> = 61) isolates of MRSA, while 3.2% (<i>n</i> = 2) were found to be negative for <i>mec</i> genes. The combination of <i>mecA</i> and <i>mecC</i> was detected in 57.1% (<i>n</i> = 36) of the MRSA isolates. The prevalence of lone <i>mecA</i> was 31.8% (<i>n</i> = 20) and that of lone <i>mecC</i> was 7.9% (<i>n</i> = 5) among all the MRSA samples. Penicillin and amoxicillin/clavulanic acid were the most resistant antibiotics followed by norfloxacin (91.2%), levofloxacin (87.1%), ciprofloxacin (83.9%), azithromycin (78.6%), erythromycin (77.4%), moxifloxacin (69.8%), and sulfamethoxazole/trimethoprim (54.9%)<b>.</b> On the other hand, vancomycin and teicoplanin (98.4%) were more effective drugs against MRSA followed by linezolid (96.7%), clindamycin (84.6%), chloramphenicol (83.7%), fusidic acid (70.6%), gentamicin (67.7%), and tetracycline (56.8%). In conclusion, a significant prevalence of <i>mecA</i> and <i>mecC</i> has been found among MRSA isolated from clinical specimens, which is likely responsible for antibiotic resistance in MRSA in our clinical settings. However, vancomycin, teicoplanin, and linezolid were found the top three most effective drugs against MRSA in our clinical settings. Thus, MRSA endemics in local areas require routine molecular and epidemiological investigation.