True Microbiota Involved in Chronic Lung Infection of Cystic Fibrosis Patients Found by Culturing and 16S rRNA Gene Analysis

Rudkjøbing, Vibeke Børsholt; Thomsen, Trine Rolighed; Alhede, Morten; Kragh, Kasper Nørskov; Nielsen, Per Halkjær; Johansen, Ulla; Givskov, Michael; Høiby, Niels; Bjarnsholt, Thomas

doi:10.1128/jcm.06092-11

Cited by 32 publications

(39 citation statements)

References 21 publications

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“…For CF patients, a notably high species diversity for the families Prevotellaceae and Streptococcaceae was recently described, which matches the outcome of our study (31). CF end-stage lungs have been shown to harbor relatively low numbers of species, and 16S rRNA gene analysis of explanted lung tissue samples revealed the same four phyla of the five bacterial classes with more than one OTU found in the current study: Proteobacteria, Bacteroidia, Firmicutes, and Actinobacteria (32). Great similarity was observed between the dominant OTUs in the current and other studies; therefore, the communities in CF airways are presumably greatly influenced by these species, e.g., P. aeruginosa, S. aureus, Rothia mucilaginosa, and Streptococcus spp.…”

Section: Discussionsupporting

confidence: 76%

Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

et al. 2015

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The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult patients with cystic fibrosis (CF) during nonexacerbation periods and under continuous antibiotic treatment. Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and internal transcript spacer), and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were detected only in low numbers. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial richness showed saturation after 50 patients were analyzed. In contrast to bacteria, a large number of fungal species were observed together with high fluctuations over time and among patients. These findings demonstrated that the mycobiome was dominated by transient species, which strongly suggested that the main driving force was their presence in inhaled air rather than colonization. Considering the high exposure of human airways to fungal spores, we concluded that fungi have low colonization abilities in CF, and colonization by pathogenic fungal species may be considered a rare event. A comprehensive understanding of the conditions promoting fungal colonization may offer the opportunity to prevent colonization and substantially reduce or even eliminate fungus-related disease progression in CF.

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Section: Discussionsupporting

confidence: 76%

Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

et al. 2015

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“…However, the experience of patients with CF in our center indicates that classic culture methods sufficiently detects the clinically important bacteria. 73 Moreover, PCR detects a broad variety of bacteria but may blur which bacteria are relevant to treat.…”

Section: *Of a Total Of 8 Patients The Number Of Times The Bacteria mentioning

confidence: 99%

Sinus Bacteriology in Patients with Cystic Fibrosis or Primary Ciliary Dyskinesia: A Systematic Review

Grønhøj

et al. 2017

Am J Rhinol�Allergy

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“…However, with the development of culture-independent molecular screening technique, it is now evident that microbes can also be found residing within the lower respiratory tract, albeit at a lower biomass when compared to the upper respiratory tract [14,26]. There are studies that have demonstrated that the lower airway tract microbiome could be misrepresented due to upper respiratory tract microbial flora contamination during the sample collection process [27,28]. Therefore, microbial study on the lower airway tract is a fledging area of interest with many challenges.…”

Section: Lower Respiratory Tractmentioning

confidence: 99%

“…A significant number of the disease-specific studies are concentrated on cystic fibrosis [27,28,46,48,49,51,52], signifying the need to redirect research efforts on the less well-studied areas such as asthma, COPD and RTI.…”

Section: Overview Of Human Airway Tract Microbiome Studiesmentioning

confidence: 99%

Uncovering the hidden villain within the human respiratory microbiome

Lee¹,

Bent

2014

Diagnosis

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Abstract:Respiratory tract infection increases the risk of secondary bacterial infection and causes mortality. Despite advances in the field of targeted molecular diagnostics, there are still failed attempts in identifying a valid causative etiological agent in a large proportion of respiratory tract infections. To date, a comprehensive list of human respiratory infection-associated eukaryotic viruses has been identified. However, there has been little progress towards the characterisation of the viruses that infect bacteria (phages), which are capable of mediating the transfer of virulence genes into non-pathogenic bacterial species to cause respiratory tract infections. With the advent of next-generation-sequencing, the application of an unbiased comparative metagenomic survey on the viral communities within the human respiratory tract may reveal to us how the phage virome changes between healthy individuals and respiratory tract infection patients. With this useful information, it will be feasible to develop an alternative phage-based diagnostic panel for respiratory tract infections. The review herein presents the current status of human airway microbiome research and highlights potential gaps which can be translated into research possibilities for future work on respiratory tract infection diagnosis.

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True Microbiota Involved in Chronic Lung Infection of Cystic Fibrosis Patients Found by Culturing and 16S rRNA Gene Analysis

Cited by 32 publications

References 21 publications

Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

Sinus Bacteriology in Patients with Cystic Fibrosis or Primary Ciliary Dyskinesia: A Systematic Review

Uncovering the hidden villain within the human respiratory microbiome

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