Analysis of coexisting pathogens in nasopharyngeal swabs from COVID-19

Front Cell Infect Microbiol. 2023 Jun 22:13:1140548. doi: 10.3389/fcimb.2023.1140548. eCollection 2023.

Abstract

Background: The impact of COVID-19 on the world is still ongoing, and it is currently under regular management. Although most infected people have flu-like symptoms and can cure themselves, coexisting pathogens in COVID-19 patients should not be taken lightly. The present study sought to investigate the coexisting pathogens in SARS-CoV-2 infected patients and identify the variety and abundance of dangerous microbes to guide treatment strategies with a better understanding of the untested factors.

Methods: We extracted total DNA and RNA in COVID-19 patient specimens from nasopharyngeal swabs to construct a metagenomic library and utilize Next Generation Sequencing (NGS) to discover chief bacteria, fungi, and viruses in the body of patients. High-throughput sequencing data from Illumina Hiseq 4000 were analyzed using Krona taxonomic methodology for species diversity.

Results: We studied 56 samples to detect SARS-CoV-2 and other pathogens and analyzed the species diversity and community composition of these samples after sequencing. Our results showed some threatening pathogens such as Mycoplasma pneumoniae, Klebsiella pneumoniae, Streptococcus pneumoniae, and some previously reported pathogens. SARS-CoV-2 combined with bacterial infection is more common. The results of heat map analysis showed that the abundance of bacteria was mostly more than 1000 and that of viruses was generally less than 500. The pathogens most likely to cause SARS-CoV-2 coinfection or superinfection include Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Klebsiella pneumoniae, and Human gammaherpesvirus 4.

Conclusions: The current coinfection and superinfection status is not optimistic. Bacteria are the major threat group that increases the risk of complications and death in COVID-19 patients and attention should be paid to the use and control of antibiotics. Our study investigated the main types of respiratory pathogens prone to coexisting or superinfection in COVID-19 patients, which is valuable for identifying and treating SARS-CoV-2.

Keywords: SARS-CoV-2; co-infection; high-throughput sequencing; metagenomics; respiratory pathogens.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics
  • COVID-19*
  • Coinfection* / microbiology
  • Humans
  • Klebsiella pneumoniae
  • Nasopharynx / microbiology
  • SARS-CoV-2 / genetics
  • Streptococcus pneumoniae
  • Superinfection*
  • Viruses* / genetics

Grants and funding

This work was supported by grants from the National Natural Science Foundation of China (NO. 32170119), the CAMS Innovation Fund for Medical Sciences (CIFMS) (No. CAMS-2016-I2M-3-025), Major Medical Innovation Projects of Sichuan Health Committee-Innovative Research of Key Technologies about COVID-19 Patients’ Medical Treatment and Key Research and Development Projects of Science and Technology Department of Sichuan Province (No. 2019YFS0319), 2020 Major medical innovation project of Sichuan Provincial Health Commission (No. 20ZDCX002), Sichuan Provincial Regional Innovation Cooperation Project (No. 2023YFQ0075), the National Science Fund for Young Scholars (No. 31600116), and the Research Fund of Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province (No. FB20-03).