Prevalence of Staphylococcus aureus in the Oral Microbiome of Children with Orofacial Clefts: A Comparative Study using PCR and Vitek Assays

Background and Objective: Cleft lip and palate (CLP) are among the most common congenital craniofacial anomalies, arising during early intrauterine development and affecting a substantial number of newborns worldwide. Individuals with oral clefts are prone to bacterial colonization, increasing the risk of infection and antibiotic resistance. The detection of methicillin-resistant Staphylococcus aureus is therefore clinically important. This study aimed to identify the presence of the mecA gene in S. aureus isolates obtained from patients with cleft lip and cleft palate and to evaluate the agreement between molecular and automated diagnostic methods. Materials and Methods: A laboratory-based analytical study was conducted on S. aureus isolates recovered from patients with oral clefts. Bacterial identification was performed using the Vitek automated system. Genomic DNA was extracted, and polymerase chain reaction was carried out to detect the mecA gene, followed by agarose gel electrophoresis. The diagnostic performance of PCR and Vitek was compared, and agreement between the two methods was assessed using the kappa coefficient. Data were analyzed in SPSS, with PCR-Vitek agreement assessed by Cohen’s kappa and cleft-S. aureus associations by ORs (95% CI; p<0.05). Results: The PCR analysis demonstrated distinct amplification bands corresponding to the mecA gene in several S. aureus isolates, confirming the presence of methicillin resistance. The Vitek system showed comparable identification results, with a notable level of agreement between the two diagnostic approaches. The findings indicate a considerable prevalence of mecA-positive S. aureus among individuals with cleft lip and palate, suggesting an increased risk of antibiotic-resistant infections in this population. Conclusion: The study highlights the relevance of combining molecular and automated diagnostic tools for accurate detection of methicillin-resistant S. aureus in patients with oral clefts. Early identification of resistance markers such as mecA can support effective infection control and guide appropriate antimicrobial therapy. Further studies with larger sample sizes are recommended to strengthen clinical correlations and resistance surveillance.