Etiological structure of infectious complications and microbial colonization in patients of COVID-19 hospital of a multidisciplinary federal medical institution

BACKGROUND: Despite the proven importance of secondary bacterial infections influencing the severity of viral respiratory diseases, their etiology is still not well understood. There is a gap in knowledge about the nature, frequency, and antimicrobial resistance profiles of bacterial pathogens in the current COVID-19 pandemic.

AIM: To describe the species spectrum of microorganisms in patients of the COVID-19 Hospital on the basis of a multidisciplinary federal medical institution.

MATERIALS AND METHODS: Clinical samples (blood, lower respiratory tract discharge, urine, other biological materials) from patients with COVID-19 who were treated at the COVID-19 Hospital at a multidisciplinary federal medical institution were obtained and processed.

RESULTS: The bacteriological laboratory received 1821 samples of biomaterial from 452 patients, microorganisms were isolated from 620 (38.0%) samples. Most of the biomaterial was represented by blood — 35.9% and discharge from the lower respiratory tract — 31.7%. The structure of microorganisms was dominated by Candida albicans — 19.7%, Staphylococcus aureus — 10.2%, Klebsiella pneumoniae — 10.1%, Enterococcus faecalis — 7.9%. At the beginning of the period of operation of the Hospital, the most frequently identified microorganisms were S. aureus and Haemophilus influenzae — 19.7% and 7.9%, respectively, while in the final period there was a change in the spectrum of microorganisms to nosocomial ESKAPE -pathogens with multiple drug resistance, the structure was dominated by Acinetobacter baumannii — 24.3%. Antibiotic consumption in the hospital increased from 18.3 DDD/100 patient days in 2019 to 28.8 DDD/100 patient days in 2020.

CONCLUSION: Significant colonization of various loci of patients with COVID-19 by fungi of the genus Candida was revealed. There has been a change in the microbial spectrum of infectious agents from community-acquired (H. influenzae and S. pneumoniae) to nosocomial ESKAPE pathogens with multiple drug resistance. The consumption of antibiotics has increased significantly.