Analysis of coexisting pathogens in nasopharyngeal swabs from COVID-19.

Publisher: Frontiers Media SA Country of Publication: Switzerland NLM ID: 101585359 Publication Model: eCollection Cited Medium: Internet ISSN: 2235-2988 (Electronic) Linking ISSN: 22352988 NLM ISO Abbreviation: Front Cell Infect Microbiol Subsets: MEDLINE

Original Publication: Lausanne : Frontiers Media SA

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

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.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2023 Gao, Yu, Cao, Yang, Li, Lan, Tang, Huang, Luan, Liu, Yu, Jian, Zha, Fan, Bai, Luo, He and Deng.)

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

Date Created: 20230710 Date Completed: 20230711 Latest Revision: 20230718

20231215

PMC10325643

10.3389/fcimb.2023.1140548

37424777