ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2022
Bacterial and Viral Respiratory Tract Microbiota and Host Characteristics in Adults With Lower Respiratory Tract Infections: A Case-Control Study.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 34 citations in OpenAlex.
- Nasopharyngeal microbiota profiles and lytA-PCR status in adult pneumococcal pneumonia: distinct microbial communities and diagnostic implications.Pneumonia (Nathan Qld.) · 2026Article
- Characterization of Nasopharyngeal Microbiota Dysbiosis in Children withMicroorganisms · 2026Article
- How to identify respiratory pathogens in primary health care - a review on the benefits, prospects and pitfalls in using point of care tests.Infection · 2025Review
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- Towards novel BIOmarkers to diagnose SEPsis (BIOSEP) in the emergency room: a protocol for a multicentre, prospective cohort study.BMJ open · 2025Article
- Seasonal Dynamics of Microbial Communities in PMAnimals : an open access journal from MDPI · 2025Article
- Profiling the nasopharyngeal Microbiome in patients with community-acquired pneumonia caused by Streptococcus pneumoniae: diagnostic challenges and ecological insights.Medical microbiology and immunology · 2025Article
- Can some algorithms of machine learning identify osteoporosis patients after training and testing some clinical information about patients?BMC medical informatics and decision making · 2025Article
- Infectious and Commensal Bacteria in Rheumatoid Arthritis-Role in the Outset and Progression of the Disease.International journal of molecular sciences · 2024Review
- The shifting lipidomic landscape of blood monocytes and neutrophils during pneumonia.JCI insight · 2024Article
- The salivary microbiota of patients with acute lower respiratory tract infection-A multicenter cohort study.PloS one · 2024Article
- Impact of influenza virus infection on lung microbiome in adults with severe pneumonia.Annals of clinical microbiology and antimicrobials · 2023Article
- Investigation of Upper Respiratory Carriage of Bacterial Pathogens among University Students in Kampar, Malaysia.Tropical medicine and infectious disease · 2023Article
- Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection.Scientific reports · 2023Article
- The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures.Clinical microbiology reviews · 2022Review
- SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding.Scientific reports · 2022Article
- The Platelet Lipidome Is Altered in Patients with COVID-19 and Correlates with Platelet Reactivity.Thrombosis and haemostasis · 2022Article
- Lung Microbiota of Critically Ill Patients with COVID-19 Are Associated with Nonresolving Acute Respiratory Distress Syndrome.American journal of respiratory and critical care medicine · 2022Observational
- Rectal microbiota are coupled with altered cytokine production capacity following community-acquired pneumonia hospitalization.iScience · 2022Article
- Impact of COVID-19 Lockdown on the Nasopharyngeal Microbiota of Children and Adults Self-Confined at Home.Viruses · 2022Article
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundViruses and bacteria from the nasopharynx are capable of causing community-acquired pneumonia (CAP), which can be difficult to diagnose. We aimed to investigate whether shifts in the composition of these nasopharyngeal microbial communities can be used as diagnostic biomarkers for CAP in adults.
methodsWe collected nasopharyngeal swabs from adult CAP patients and controls without infection in a prospective multicenter case-control study design. We generated bacterial and viral profiles using 16S ribosomal RNA gene sequencing and multiplex polymerase chain reaction (PCR), respectively. Bacterial, viral, and clinical data were subsequently used as inputs for extremely randomized trees classification models aiming to distinguish subjects with CAP from healthy controls.
resultsWe enrolled 117 cases and 48 control subjects. Cases displayed significant beta diversity differences in nasopharyngeal microbiota (P = .016, R2 = .01) compared to healthy controls. Our extremely randomized trees classification models accurately discriminated CAP caused by bacteria (area under the curve [AUC] .83), viruses (AUC .95) or mixed origin (AUC .81) from healthy control subjects. We validated this approach using a dataset of nasopharyngeal samples from 140 influenza patients and 38 controls, which yielded highly accurate (AUC .93) separation between cases and controls.
conclusionsRelative proportions of different bacteria and viruses in the nasopharynx can be leveraged to diagnose CAP and identify etiologic agent(s) in adult patients. Such data can inform the development of a microbiota-based diagnostic panel used to identify CAP patients and causative agents from nasopharyngeal samples, potentially improving diagnostic specificity, efficiency, and antimicrobial stewardship practices.
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