ArticleJournal of infection and public health2023
Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia.
Article in Journal of infection and public health, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it, 13 citations in OpenAlex.
- Microbiome and One Health in GCC countries: current status, research gaps, and future directions.Frontiers in microbiology · 2026Pooled it
- High prevalence and clinical impact of microbial co-detection in hospitalized children with human parainfluenza virus type 1.Microbiology spectrum · 2026Article
- Metatranscriptomic analysis of upper and lower respiratory tract microbiomes in patients with tuberculosis and community-acquired pneumonia.BMC infectious diseases · 2026Article
- A Retrospective Study on Coinfections, Antimicrobial Resistance, and Mortality Risk Among COVID-19 Patients (2020-2021) with Consideration of Long-COVID Outcomes.Microorganisms · 2025Article
- Recent Changes in the Epidemiology of Group AMicroorganisms · 2025Review
- The intricate interplay among microbiota, mucosal immunity, and viral infection in the respiratory tract.Journal of translational medicine · 2025Review
- Isolation, identification, and sensitivity profile ofFrontiers in pediatrics · 2025Article
- The differential gut microbiota and their MetaCyc pathways in IBRV infected Angus calves.Frontiers in microbiology · 2025Article
- Article
- Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities.Microbiology spectrum · 2024Article
- Oropharyngeal Microbiome Analysis in Patients with Varying SARS-CoV-2 Infection Severity: A Prospective Cohort Study.Journal of personalized medicine · 2024Article
- Microbiome and intestinal pathophysiology in post-acute sequelae of COVID-19.Genes & diseases · 2023Review
- Review
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInfection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health.
methodsA total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 6S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens.
resultsNo significant (p > 0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p < 0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7 %) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1.
conclusionsOverall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.
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