Microbial landscape and cytokine profile of sputum of patients with COVID-19 complicated by pneumonia

Introduction: One of the complications of coronavirus infection (COVID-19) is lung damage with the development of pneumonia. The addition of bacterial and fungal microflora can complicate the course of the disease up to an extremely unfavorable outcome. Before the COVID-19 pandemic, the dominant causative agent of bacterial pneumonia was Streptococcus pneumoniae, accounting for 50% to 80% of cases.Bacteria of the genus Staphylococcus, the family Enterobacteriacae, non-fermenting gram-negative bacteria and some others also play a role in the structure of pathogens of bacterial pneumonia.The COVID-19 pandemic has significantly changed the structure of bacterial agents, potential pathogens of pneumonia. Commonly used treatment regimens for complicated forms of coronavirus infection have led to a change in the microbial landscape of pneumonia pathogens and an increase the proportion of multidrug-resistant strains. Methods: We examined 111 sputum samples from patients with COVID-19 complicated by pneumonia who received treatment in medical organizations in Rostov-on-Don in 2022-2023. Isolates were identified using MALDI-TOF MS (Microflex Biotyper Bruker Germany). Sensitivity to antimicrobial drugs was determined by the disk diffusion method. The level of cytokines (IL-6, IF-gamma, IL-4, IL-10) in sputum samples was determined by ELISA. Results: The microbial landscape was represented by the following microorganisms: Streptococcus spp., Staphylococcus spp., Rothia spp., Corynebacterium spp., Klebsiella spp., Neisseria spp. Clostridium spp., Lactobacillus spp., atypical for this biotope, was found.Analysis of the results showed the predominant role of Candida spp. (47.0%), Streptococcus spp. (35.7%), Staphylococcus spp. (25.4%)The isolated strains were resistant to 2nd generation fluoroquinolones and nitrofurans (57.0% of cultures); to 2nd generation aminoglycosides (56.0%); to azalides, macrolides, 3rd generation cephalosporins, carbapenems (54.0%); to semisynthetic penicillin's of the 2nd generation (39.0%). Fungi of the genus Candida were sensitive only to nystatin (80%).Analysis of the amount of cytokines in sputum samples of patients with COVID-19 complicated by pneumonia showed that the level of IF-γ was 89.6 pg/ml, IL-4 – 3.6 pg/ml, IL-6 – 23.9%, IL-10 – 22.1 pg/ml, respectively. Discussion: The microbial landscape of sputum microbiota in patients with COVID-19 was dominated by gram-positive coccal flora, due to bacteria of the genus Streptococcus and Staphylococcus, pan-resistant to antibiotics. Yeast-like fungi are not typical pathogens of pneumonia and were sensitive only to nystatin. Their identification was the result of antibiotic treatment. The addition of microbial agents in patients with a complicated COVID-19 contributes to the development of an imbalance of cytokines in the body as a whole and in sputum at the local level. Conclusion: Microorganisms associated with SARS-CoV-2 exhibit multiple drug resistance, which reduces the effectiveness of etiotropic therapy.Overproduction of IF-γ was detected in the sputum of patients. Further study of the cytokine profile in sputum may indirectly help predict the severity and outcome of the disease.