Characterization of the Nasopharyngeal Microbiota of COVID-19 Patients According to Disease Severity

Purpose: Increasing evidence indicates a possible relationship between the pathogenesis of COVID-19 and the nasopharyngeal microbiota. This study aimed to compare the nasopharyngeal microbiota of COVID-19 patients with different disease severity. Methods & Materials: A comparative study was performed on patients classified into four groups according to their disease severity. A total of 26 patients were recruited for each of the following study groups. Group 1 (G1): patients with a confirmatory diagnosis of SARS-CoV-2 and hospitalized in the ICU. Group 2 (G2): patients with a confirmatory diagnosis of SARS-CoV-2 and hospitalized in regular hospitalization wards. Group 3 (G3): patients with a confirmatory diagnosis of SARS-CoV-2 who were not hospitalized and had mild or no symptoms. Group 4 (G4): healthy patients with a negative result for SARS-CoV-2. The diagnosis of SARS-CoV-2 was performed by reverse-transcriptase polymerase chain reaction (RT-PCR). The nasopharyngeal microbiota was characterized using polymerase chain reaction (PCR) targeting 13 representative bacteria genus. Results: The detection of some bacteria genus was significantly more frequent in the hospitalized groups compared to healthy subjects. This is the case of Lactobacillus with 96.15% in G1, 96.15% in G2, 23.08% in G3 and 15.38% in G4. Similarly, Prevotella presented 96.15% in G1, 80.77 in G2, 0.00% in G3 and 19.23% in G4. Veilonella, Bacteroidetes and Firmicutes presented a similar prevalence. On the other hand, the detection of Eubacterium was more frequent among asymptomatic and healthy subjects, with 3.85% in G1, 19.23% in G2, 50.00% in G3 and 30.77% in G4. The relative abundance of the bacteria was evaluated and Lactobacillus and Veilonella were predominant in both of the hospitalized groups (G1 and G2). On the other hand, Actinobacteria and Eubacterium were predominant in the asymptomatic and healthy groups (G3 and G4) Conclusion: In conclusion a unique nasopharyngeal microbiota profile was found in COVID-19 patients with different disease severity. Lactobacillus, Prevotella, Veilonella, Bacteroidetes and Firmicutes were the predominant bacteria genus in critical and hospitalized patients. While. Eubacterium and Actinobacteria were predominant in the groups of asymptomatic and healthy subjects. Further longitudinal studies are required to determine the prognostic role of the nasopharyngeal microbiota.