Представлены результаты исследования микробного пейзажа содержимого нижних дыхательных путей при внебольничной пневмонии, ассоциированной с COVID-19. Показано, что в структуре бактерий выделенных от пациентов с диагнозом внебольничная пневмония превалируют грамположительные кокки, преимущественно бактерии рода Streptococcus. По частоте обнаружения бактерий семейства Enterobacteriaceae и неферментирующих грамотрицательных бактерий в сравниваемых группах (SARS-COV-2 «обнаружен» / «не обнаружен») статистически значимых различий не отмечено.

Introduction. Many aspects of the pathogenesis and pathomorphology of pneumonia associated with novel coronavirus require a comprehensive study using modern diagnostic methods.The aim of the study was to study the microbiota of the lower respiratory tract in community-acquired pneumonia associated with SARS-CoV-2, to assess the antibiotic and phage resistance of circulating strains of microorganisms.Materials and methods. The analysis of biosamples from 486 patients undergoing inpatient treatment in five mono-hospitals in Tyumen and Tyumen region with a diagnosis of moderate and severe community-acquired pneumonia was carried out. In almost 90% of cases patients received oxygen therapy, about 8% of patients were connected to ventilators. The inoculation of the cultures with clinical samples was carried out for six months (from April to October 2020). The isolated bacterial strains were identified by mass spectrometry. The resistance to antimicrobial drugs and bacteriophages was assessed for identified isolated.Results. Gram-positive cocci, mainly opportunistic microorganisms of the genus Streptococcus and Candida fungi predominated in the microbiota of the lower respiratory tract of patients diagnosed with community-acquired pneumonia associated with SARS-CoV-2. At the same time, bacteria of the Enterobacteriaceae family and nonfermenting gram-negative bacteria were less common compared to patients without coronavirus infection. In the structure of pathogens, the leading position was occupied by the bacteria K. pneumoniae and Acinetobacter spp. The analysis of the sensitivity of microorganisms to antimicrobial drugs showed the highest resistance rates in strains of Acinetobacter spp., Enterococcus spp., Coagulase-negative Staphylococcus. It has been established that in the group of patients with community-acquired pneumonia associated with SARS-CoV-2, the risk of infection with Streptococcus spp. with high level of antibiotic resistance was 1.5 times higher, and taking into account the 95% confidence interval, the value of this indicator ranged from 1.1 to 2.1 times.Conclusion. The data obtained indicate that the microbiota of the lower respiratory tract in community-acquired pneumonia associated with SARS-CoV-2 is represented mainly by bacteria of the genus Streptococcus, which have a high level of resistance to antimicrobial drugs.

The aim of this work was to identify the causative agent of community-acquired pneumonia and coinfection using PCR study of biomaterial from patients.Materials and methods. PCR testing of 268 samples from 258 patients was carried out to identify RNA/DNA of viral and bacterial pathogens of respiratory infections.Results and discussion. In 43.3 % of samples SARS-CoV-2 RNA was detected, in 4.5 % – RNA/DNA of acute respiratory viral infections pathogens, in one sample – DNA of Mycoplasma pneumoniae. Co-infection was detected only in patients of the anti-tuberculosis dispensary (SARS-CoV-2 and Mycobacterium tuberculosis). In the examined patients with pneumonia, SARS-CoV-2 RNA was significantly more often detected in biomaterial from the lower respiratory tract (52 %) than in respiratory smears (8.5 %). In the first week from the onset of the disease, 19.2 % of positive samples were found, in the second – 56.5 %.

The article presents a clinical case of a new coronavirus infection against the background of chronic opisthorchiasis in a resident of the Tyumen region.

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