ArticleJournal of clinical microbiology2015
Rapid Detection of Emerging Pathogens and Loss of Microbial Diversity Associated with Severe Lung Disease in Cystic Fibrosis.
Article in Journal of clinical microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it, 105 citations in OpenAlex.
- Bacteria of the lung microbiome and health biomarkers in chronic airway disease: a systematic review and meta-analysis.NPJ biofilms and microbiomes · 2026Pooled it
- The CF-Sputum Induction Trial (CF-SpIT) to assess lower airway bacterial sampling in young children with cystic fibrosis: a prospective internally controlled interventional trial.The Lancet. Respiratory medicine · 2018Trial
- A polyvalent phage shapes bacterial dynamics.Journal of virology · 2026Article
- Article
- Article
- Airway Microbiome in Children with Cystic Fibrosis: A Review of Microbial Shifts and Therapeutic Impacts.Medicina (Kaunas, Lithuania) · 2025Review
- The cystic fibrosis pathogenJournal of medical microbiology · 2025Article
- Differences in sputum microbiota based on cure status of patients with nontuberculous mycobacterial pulmonary disease.The Korean journal of internal medicine · 2025Article
- Article
- Distinctive salivary oral microbiome in patients with burning mouth syndrome depending on pain intensity compared to healthy subjects.Journal of dental sciences · 2025Article
- Non-Tuberculous Mycobacteria: Single Center Analyses of Risk Factors, Management and Mortality Outcomes of Adults with HIV.Diagnostics (Basel, Switzerland) · 2024Article
- Elevated risk of adverse effects from foodborne contaminants and drugs in inflammatory bowel disease: a review.Archives of toxicology · 2024Review
- Changing profile of bacterial infection and microbiome in cystic fibrosis: when to use antibiotics in the era of CFTR-modulator therapy.European respiratory review : an official journal of the European Respiratory Society · 2024Review
- Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.International journal of molecular sciences · 2024Article
- Antibiotic Resistance in Patients with Cystic Fibrosis: Past, Present, and Future.Antibiotics (Basel, Switzerland) · 2023Review
- Article
- Low Diversity and Instability of the Sinus Microbiota over Time in Adults with Cystic Fibrosis.Microbiology spectrum · 2022Article
- A clinicians' review of the respiratory microbiome.Breathe (Sheffield, England) · 2022Review
- Commensal Bacteria in the Cystic Fibrosis Airway Microbiome ReduceFrontiers in cellular and infection microbiology · 2022Article
- Mild Cystic Fibrosis Lung Disease Is Associated with Bacterial Community Stability.Microbiology spectrum · 2021Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Respiratory infection in cystic fibrosis (CF) is polymicrobial, but standard sputum microbiology does not account for the lung microbiome or detect changes in microbial diversity associated with disease. As a clinically applicable CF microbiome surveillance scheme, total sputum nucleic acids isolated by a standard high-throughput robotic method for accredited viral diagnosis were profiled for bacterial diversity using ribosomal intergenic spacer analysis (RISA) PCR. Conventional culture and RISA were performed on 200 paired sputum samples from 93 CF adults; pyrosequencing of the 16S rRNA gene was applied to 59 patients to systematically determine bacterial diversity. Compared to the microbiology data, RISA profiles clustered into two groups: the emerging nonfermenting Gram-negative organisms (eNFGN) and Pseudomonas groups. Patients who were culture positive for Burkholderia, Achromobacter, Stenotrophomonas, and Ralstonia clustered within the eNFGN group. Pseudomonas group RISA profiles were associated with Pseudomonas aeruginosa culture-positive patients. Sequence analysis confirmed the abundance of eNFGN genera and Pseudomonas within these respective groups. Low bacterial diversity was associated with severe lung disease (P < 0.001) and the presence of Burkholderia (P < 0.001). An absence of Streptococcus (P < 0.05) occurred in individuals with lung function in the lowest quartile. In summary, nucleic acids isolated from CF sputum can serve as a single template for both molecular virology and bacteriology, with a RISA PCR rapidly detecting the presence of dominant eNFGN pathogens or P. aeruginosa missed by culture (11% of cases). We provide guidance for how this straightforward CF microbiota profiling scheme may be adopted by clinical laboratories.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.