Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities

• Published in: Microbiology spectrum Vol. 12; no. 5; p. e0416623
• Main Authors: Aljabr, Waleed, Dandachi, Iman, Abbas, Basma, Karkashan, Alaa, Al-Amari, Ahod, AlShahrani, Dayel
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 02.05.2024
• Subjects: Adult; Aged; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; COVID-19; COVID-19 - diagnosis; COVID-19 - epidemiology; COVID-19 - microbiology; COVID-19 - virology; disease severity; Female; High-Throughput Nucleotide Sequencing; Humans; Male; Metagenome; Metagenomics - methods; metatranscriptomics; microbiome; Microbiota - genetics; Middle Aged; Nasopharynx - microbiology; Nasopharynx - virology; Research Article; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Severity of Illness Index; Streptococcus pneumoniae - classification; Streptococcus pneumoniae - genetics; Streptococcus pneumoniae - isolation & purification; Virology; COVID-19; metatranscriptomics; disease severity; microbiome
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.04166-23

In this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia , Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.