Fixed orthodontic treatment can alter the oral environment, potentially increasing cariogenic bacteria levels. This study aimed to utilize real-time polymerase chain reaction (qPCR) to quantify salivary levels of cariogenic bacteria in patients undergoing orthodontic treatment with fixed appliances. This case-control study was conducted in Erbil, Iraq, from April 2024 to August 2024. One hundred participants were included in the study by random sampling method and equally divided into two groups: case group ororthodontic group and control group. The orthodontic group included participants with fixed orthodontic brackets, while the control group included participants without current or past orthodontic treatment with matching age and sex as the orthodontic group. Data were collected via questionnaires, clinical examinations, and saliva sampling. Salivary samples were analyzed using real-time PCR to detect Streptococcus mutans (SM) and Lactobacillus (LB) spp. levels. The age ranged from 18 to 30 years, and the mean age of participants was 23.96 ± 3.64 years. No significant differences were observed between the two groups across most parameters, except in the use of fluoride therapy, where the control group demonstrated better usage (p≤0.003). Real-time PCR results indicated a significant difference in the levels of LB and SM between patients with fixed orthodontics and the control group (p≤0.001). However, no significant differences were found in decay indices such as decayed, missing, and filled teeth; decayed, missing, and filled surfaces; and plaque index in this study. The quantity and levels of LB and SM were higher in the orthodontic group compared to the control group. Despite the elevated bacterial levels in the orthodontic group, there was no significant difference in decay and plaque indices between the two groups.
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