Etiological pattern of community-acquired pneumonia related to the new coronavirus infection COVID-19 pandemic in the Saratov Region

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Abstract

Community-acquired pneumonia is a polyetiological infectious disease of bacterial or viral nature. In most cases, it is caused by pathogens such as Streptococcus pneumoniae, Mycoplasma pneumoniae, Haemophilus influenzae, Chlamydophila pneumoniae, Staphylococcus aureus, Legionella spp. However, despite that a wide range of modern diagnostic methods have been introduced into laboratory practice, the etiology of the disease can be determined only in 40–60% of cases. Here, we analyzed the causative agents of community-acquired pneumonia and relevant markers samples of clinical material collected from patients undergoing treatment in the medical facilities of the city of Saratov and the Saratov Region during the period from July to August, 2020, coupled to increase number of cases of new coronavirus infection COVID-19. Clinical material (oropharyngeal swabs, saliva, sputum, blood and blood serum) was obtained from 129 patients and investigated by using microbiological, immunoserological and molecular genetic methods. For this, there were used transport and nutrient media, diagnostic drugs, reagents, discs with antibacterial domestic and foreign drugs registered in the Russian Federation. As a result, 82 (63.6%) patients were found to have markers of the pathogen COVID-19 (viral RNA or specific antibodies of IgM and/or IgG classes), whereas 42% of cases had overlapped RT-PCR and ELISA data. There was a predominance of severe clinical forms of the disease in the group of patients with pneumonia caused by SARS-CoV-2 virus (17.1%), compared with pneumonia of another etiology (12.8%). No marked differences in specific pattern of the accompanying microflora and its sensitivity to antibacterial agents were observed in persons with/without markers of COVID-19. While being examined by bacteriological methods, S. aureus, K. pneumoniae, S. pneumoniae, M. pneumoniae, Acinetobacter spp., both in monoculture and in associations, were isolated from samples of clinical material collected from the majority of patients. In 49.6% of cases, pathogenic microflora, including pathogens causing community-acquired pneumonia, has not been identified, which may be due to the use of antibacterial drugs before the collection of clinical material and treatment applied due to comorbid chronic diseases.

About the authors

S. A. Portenko

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Author for correspondence.
Email: portenko_sa@microbe.ru
ORCID iD: 0000-0002-8334-9173

Svetlana A. Portenko - PhD (Biology), Head of the Department of Infectious Diseases Diagnostics, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

410005, Saratov, Universitetskaya str., 46.

Phone: +7 927 223-29-92.

Russian Federation

E. S. Kazakova

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: rusrapi@microbe.ru
ORCID iD: 0000-0002-8424-3864

PhD (Biology), Head Researcher, Department of Infectious Diseases Diagnostics, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

E. V. Naidenova

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: katim2003@mail.ru
ORCID iD: 0000-0001-6474-3696

PhD (Biology), Senior Researcher, Department of Infectious Diseases Diagnostics, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

N. A. Osina

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: davidova_n_work@mail.ru
ORCID iD: 0000-0003-0954-5683

PhD (Biology), Head of the Microbiology Department, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

M. V. Proskuriakova

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: proma89@mail.ru
ORCID iD: 0000-0002-7171-855X

Researcher, Department of Infectious Diseases Diagnostics, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

A. D. Katyshev

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: rusrapi@microbe.ru
ORCID iD: 0000-0002-8260-4670

Junior Researcher, Microbiology Department, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

E. A. Sharkova

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: rusrapi@microbe.ru
ORCID iD: 0000-0001-5807-0368

Junior Researcher, Department of Infectious Diseases Diagnostics, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

O. V. Kedrova

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: rusrapi@microbe.ru
ORCID iD: 0000-0001-7400-8599

PhD (Medicine), Academic Secretary, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

E. A. Chumachkova

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: rusrapi@microbe.ru

Researcher, Epidemiology Department, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

M. R. Shamyunov

Saratov Polyclinic Hospital No. 5

Email: gkb5sar@mail.ru

PhD (Medicine), Head Physician, Saratov Polyclinic Hospital No. 5.

Saratov.

Russian Federation

V. F. Kharitonova

Saratov Children’s Infectious Clinical Hospital No. 5

Email: sar5dikb@mail.ru

PhD (Medicine), Head Physician, Saratov Chlidren’s Infectious Clinical Hospital No. 5.

Saratov.

Russian Federation

L. A. Gureva

Saratov Polyclinic No. 2

Email: sekretar@sargp2.ru

Head Physician, Saratov Polyclinic No. 2.

Saratov.

Russian Federation

N. Yu. Popova

City Perinatal Center

Email: guzpcsar@mail.ru

PhD (Medicine), Head Physician, City Perinatal Center.

Saratov.

Russian Federation

L. V. Maksimova

Saratov City Clinical Hospital No. 10

Email: lpu10gkb@mail.ru

PhD (Medicine), Head Physician, Saratov City Clinical Hospital No. 10.

Saratov.

Russian Federation

S. A. Bugorkova

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: rusrapi@microbe.ru
ORCID iD: 0000-0001-7548-4845

PhD, MD (Medicine), Head of the Immunology Department, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

S. A. Scherbakova

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: rusrapi@microbe.ru
ORCID iD: 0000-0003-1143-4069

PhD, MD (Biology), Deputy Director for Scientific and Experimental Work, Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

V. V. Kutyrev

Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor

Email: rusrapi@microbe.ru
ORCID iD: 0000-0003-3788-3452

PhD, MD (Medicine), Professor, RAS Full Member, Director of the Russian Research Anti-Plague Institute “Microbe” of Rospotrebnadzor.

Saratov.

Russian Federation

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Copyright (c) 2021 Portenko S.A., Kazakova E.S., Naidenova E.V., Osina N.A., Proskuriakova M.V., Katyshev A.D., Sharkova E.A., Kedrova O.V., Chumachkova E.A., Shamyunov M.R., Kharitonova V.F., Gureva L.A., Popova N.Y., Maksimova L.V., Bugorkova S.A., Scherbakova S.A., Kutyrev V.V.

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