Anais do Congresso Paranaense de Microbiologia
IV Congress of Microbiology in Paraná

The ongoing outbreak of COVID-19 has caused many deaths and affected millions of people worldwide. As a respiratory viral infection, it can compromise the respiratory system severely causing an imbalance in the homeostasis of the organism. Therefore, microbiota that regularly lives in the nasopharynx host can cause a secondary bacterial infection that can aggravate the clinical condition of the patient. For this reason, it may be desirable a diagnostic tool that can evaluate the presence of potentially pathogenic bacteria in the nasopharynx of COVID-19 patients to be requested along with the RT-PCR for SARS-CoV-2. In this way, clinicians may have more information about the patient, which can aid in a better therapeutic approach, since the overuse of antibiotics can promote the selection of resistant bacterial strains. In this study, we evaluate a multiplex real-time PCR (qPCR) methodology using SYBR Green to detect three important pathogens that inhabit the nasopharynx: Haemophilus influenzae, Streptococcus pneumoniae, and Neisseria meningitidis. The selected genes are exclusive of these bacteria, and the primers are routinely used for bacterial meningitis diagnoses applied for cerebrospinal fluid and serum samples. The multiplex SYBR Green qPCR was applied to detect these bacteria in approximately 200 samples of nasopharyngeal and oropharyngeal swabs from suspected patients of COVID-19, which were received for SARS-CoV-2 detection, as part of the diagnostic routine. The study was approved by the institutional ethical committee (CAAE: 45285921.7.0000.0059). The main bacterium observed was H. influenzae in 53.6% of the samples. The presence of two or three bacteria was observed in 9% of the samples and 35.5% were negative for all three pathogens evaluated. There was no statistical difference between groups SARS-CoV-2 positive and negative, identified by the RT-PCR, or groups with the flu-like syndrome and severe acute respiratory syndrome. Our findings show the prevalence of H. influenzae in the studied patients, which could lead to an aggravation of the clinical conditions of the patient. We highlighted that infection with SARS-CoV-2 does not change the naso and oropharyngeal human microbiota, considering these three important bacteria. This is an important finding, suggesting that the infection with this virus is not likely to induce an imbalance in the microbiota, at least for these three, which could trigger secondary bacterial infections. Therefore, studies like this one are important for the identification of clinically relevant bacteria that cause meningitis and pneumonia in individuals who are carriers and could be potentially transmitters to unvaccinated people.