Molecular Genetic Analysis of the Causative Agents of COVID-19–Associated Bacterial Pneumonia in Hospitals of Rostov-on-Don

Abstract

Introduction: Hospital-acquired bacterial superinfections in COVID-19 patients are one of the main reasons of a severer course of the disease, a higher risk of adverse outcomes, and, consequently, a longer hospital stay. Much attention is, therefore, paid to the study of genetic markers enabling identification of clonal relationships between different isolates of the causative agents of bacterial co-infections, which, in their turn, help distinguish between hospital- and community-acquired cases of infectious diseases. Objective: To study the genetic diversity and clonal relationships of A. baumannii and P. aeruginosa isolated from patients with a novel coronavirus disease (COVID-19) in Rostov-on-Don. Materials and methods: We tested biological specimens from 217 in- and outpatients with community-acquired pneumonia in the city of Rostov-on-Don. Whole-genome sequencing of A. baumannii and P. aeruginosa strains was performed using a MiSeq sequencer (Illumina, USA). SNP markers were selected using proprietary software written in Java and Python. Cluster analysis and dendrogram construction were performed using the author's software using the UPGMA method. The MEGA 5 software was used to build the dendrogram. Results: We established the spectrum of bacteria causing the development of secondary infection associated with COVID-19. Results of the whole-genome sequencing of 10 pneumonia pathogens isolated from patients with the novel coronavirus disease revealed clonality of individual strains. The nosocomial origin of two isolates of P. aeruginosa and two of A. baumannii was demonstrated and confirmed by the analysis of their plasmid composition. Secondary bacterial infection in COVID-19 patients may be attributed to the pathological development of the dominant microflora of the upper respiratory tract mucosa, which provides normal biocenosis in healthy people, or non-compliance with basic principles of hospital hygiene and infection control precautions. Conclusion: The research helped determine the etiological structure of pneumonia in patients with COVID-19. Whole-genome sequencing and the following bioinformatic analysis revealed the nosocomial origin of a number of strains of P. aeruginosa and A. baumanii.