eOTUs present in one category and absent from the other.

<p>eOTUs present in one category and absent from the other.</p

Taxa of differential abundance between the control and CF lower airway.

<p>Circular Phylogenetic Tree was rendered in iToL and illustrates abundance changes between eOTUs present in the control lower (inner ring) and CF lower (outer ring) airways. The colour saturation indicates the degree of difference from the mean control lower value for the eOTU; where dark blue indicates a HybScore difference of −52326, white  = 0 (no change from mean control lower), dark red  = +61480. Two eOTUs remained of significantly differential abundance following Benjamini-Hochberg correction; <i>Prevotella veroralis</i> (*) and a CW040 (**). Following a permutation test, 62 taxa were found to be of significantly differential abundance, <i>Corynebacterium</i> (***) is highlighted. A detailed list of the 59 taxa of significantly differential abundance between categories is provided in the supplementary data (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109798#pone.0109798.s001" target="_blank">S2 File</a>).</p

Bacterial community structures in the control lower airways and the CF upper and lower airways.

<p>Principle coordinate analysis (PCoA) plots of A) UniFrac distances and B) weighted UniFrac distances of all airway microbial communities were created in R. Each community from each sample is represented as a filled circle and coloured by sample type and/or patient cohort; CF lower (CF BAL; red), CF upper (CF SWB; blue) and control lower (CN BAL; yellow) airway samples. The x-axis and y-axis represent 2-dimensions of percentage variation explained by the PCoA. Ellipses were included for visualisation purposes.</p

Richness of the microbial communities present in the control lower airways and the CF upper and lower airways.

<p>Box and Whiskers plot of Shannon's diversity indices for microbial communities present in the control lower airway, CF lower airway and the CF upper airway. * represents statistical significance (p = 0.001; two-tailed t test).</p

Adonis scores for correlations between CF community diversity and discrete variables.

<p><i>The CFTR mutation category was Not Applicable (N/A) as all but one patient was F508del homozygous.</i></p><p><i>* Discrete variables that passed the Adonis test (p<0.05).</i></p><p>Adonis scores for correlations between CF community diversity and discrete variables.</p

Baseline demographic and clinical characteristics of all patients included in the study.

<p><i>PA  =  Pseudomonas aeruginosa, SP  =  Streptococcus pneumoniae, MC  =  Moraxella Catarrhalis, SA  =  Staphylococcus aureus, HI  =  Haemophilus influenzae, NF  =  Normal Flora, ICS  =  Inhaled corticosteroids, HS  =  Hypertonic Saline.</i></p><p><i>0 = 0 CFU/ml, 1 = 1 to 100 CFU/ml, 2 = 100 to 10,000 CFU/ml and 3 = >10,000 CFU/ml.</i></p><p>Baseline demographic and clinical characteristics of all patients included in the study.</p

Clustered multidrug-resistant Bordetella petrii in adult cystic fibrosis patients in Ireland: case report and review of antimicrobial therapies

Introduction: Bordetella petrii is an emerging pathogen. Whilst association with cystic fibrosis (CF) has been described previously, this is the first report to our knowledge of multidrug-resistant B. petrii incidence in an Irish CF patient population. Case presentation: Using a case series of four adult CF patients with varying baselines of health, one of whom was asymptomatic, this report attempts correlation of B. petrii colonization, by one common strain, with incidence of acute exacerbation of symptoms. As definitive guidelines for antimicrobial sensitivity/resistance do not exist for B. petrii, we completed a systematic review of available literature to collate evidence of antimicrobial efficacy against B. petrii. Comparison with the isolates in this study indicated B. petrii sensitivity to piperacillin/ tazobactam and minocycline but resistance to antimicrobials in the macrolide, other b-lactam and fluoroquinolone groups. Conclusion: To our knowledge, this is the first report of multiple CF patients sharing a strain of B. petrii. Furthermore, B. petrii may be under-identified in CF patients and should be considered when evaluating exacerbation of CF symptoms

Additional file 1: of Quantitative analysis of dynamic 18F-FDG PET/CT for measurement of lung inflammation

Supplemental data for quantitative analysis of dynamic 18F-FDG PET/CT for measurement of lung inflammation. (DOCX 318 kb

The basophil surface marker CD203c identifies Aspergillus species sensitization in patients with cystic fibrosis.

BACKGROUND: Colonization by Aspergillus fumigatus in patients with cystic fibrosis (CF) can cause A fumigatus sensitization and/or allergic bronchopulmonary aspergillosis (ABPA), which affects pulmonary function and clinical outcomes. Recent studies show that specific allergens upregulate the surface-expressed basophil marker CD203c in sensitized subjects, a response that can be readily measured by using flow cytometry. OBJECTIVE: We sought to identify A fumigatus sensitization in patients with CF by using the basophil activation test (BAT). METHODS: Patients with CF attending Beaumont Hospital were screened for study inclusion. BAT was used to identify A fumigatus sensitization. Serologic (total and A fumigatus-specific IgE), pulmonary function, and body mass index measurements were performed. RESULTS: The BAT discriminates A fumigatus-sensitized from nonsensitized patients with CF. Persistent isolation of A fumigatus in sputum is a significant risk factor for A fumigatus sensitization. Levels of the A fumigatus-stimulated basophil activation marker CD203c inversely correlated with pulmonary function and body mass index in A fumigatus-sensitized but not nonsensitized patients with CF. Total and A fumigatus-specific IgE, but not IgG, levels are increased in A fumigatus-sensitized patients with CF and ABPA when compared with those in A fumigatus-sensitized and nonsensitized patients with CF without ABPA. Itraconazole treatment did not affect A fumigatus sensitization. CONCLUSION: Combining the BAT with routine serologic testing allows classification of patients with CF into 3 groups: nonsensitized, A fumigatus-sensitized, and ABPA. Accurate and prompt identification of A fumigatus-associated clinical status might allow early and targeted therapeutic intervention, potentially improving clinical outcomes.</p