Qualitative and quantitative evaluation of computed tomography changes in adults with cystic fibrosis treated with elexacaftor-tezacaftor-ivacaftor: a retrospective observational study

Introduction: The availability of highly effective triple cystic fibrosis transmembrane conductance regulator (CFTR) modulator combination therapy with elexacaftor–tezacaftor–ivacaftor (ETI) has improved pulmonary outcomes and quality of life of people with cystic fibrosis (pwCF). The aim of this study was to assess computed tomography (CT) changes under ETI visually with the Brody score and quantitatively with dedicated software, and to correlate CT measures with parameters of clinical response.Methods: Twenty two adult pwCF with two consecutive CT scans before and after ETI treatment initiation were retrospectively included. CT was assessed visually employing the Brody score and quantitatively by YACTA, a well-evaluated scientific software computing airway dimensions and lung parenchyma with wall percentage (WP), wall thickness (WT), lumen area (LA), bronchiectasis index (BI), lung volume and mean lung density (MLD) as parameters. Changes in CT metrics were evaluated and the visual and quantitative parameters were correlated with each other and with clinical changes in sweat chloride concentration, spirometry [percent predicted of forced expiratory volume in one second (ppFEV1)] and body mass index (BMI).Results: The mean (SD) Brody score improved with ETI [55 (12) vs. 38 (15); p < 0.001], incl. sub-scores for mucus plugging, peribronchial thickening, and parenchymal changes (all p < 0.001), but not for bronchiectasis (p = 0.281). Quantitatve WP (p < 0.001) and WT (p = 0.004) were reduced, conversely LA increased (p = 0.003), and BI improved (p = 0.012). Lung volume increased (p < 0.001), and MLD decreased (p < 0.001) through a reduction of ground glass opacity areas (p < 0.001). Changes of the Brody score correlated with those of quantitative parameters, exemplarily WT with the sub-score for mucus plugging (r = 0.730, p < 0.001) and peribronchial thickening (r = 0.552, p = 0.008). Changes of CT parameters correlated with those of clinical response parameters, in particular ppFEV1 with the Brody score (r = −0.606, p = 0.003) and with WT (r = −0.538, p = 0.010).Discussion: Morphological treatment response to ETI can be assessed using the Brody score as well as quantitative CT parameters. Changes in CT correlated with clinical improvements. The quantitative analysis with YACTA proved to be an objective, reproducible and simple method for monitoring lung disease, particularly with regard to future interventional clinical trials

Changes in cystic fibrosis transmembrane conductance regulator protein expression prior to and during elexacaftor-tezacaftor-ivacaftor therapy

Background: Defects in expression, maturation or function of the epithelial membrane glycoprotein CFTR are causative for the progressive disease cystic fibrosis. Recently, molecular therapeutics that improve CFTR maturation and functional defects have been approved. We aimed to verify whether we could detect an improvement of CFTR protein expression and maturation by triple therapy with elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA).Methods: Rectal suction biopsies of 21 p.Phe508del homozygous or compound heterozygous CF patients obtained pre- and during treatment with ELX/TEZ/IVA were analyzed by CFTR Western blot that was optimized to distinguish CFTR glycoisoforms.Findings: CFTR western immunoblot analysis revealed that—compared to baseline—the levels of CFTR protein increased by at least twofold in eight out of 12 patients upon treatment with ELX/TEZ/IVA compared to baseline (p < 0.02). However, polydispersity of the mutant CFTR protein was lower than that of the fully glycosylated wild type CFTR Golgi isoform, indicating an incompletely glycosylated p.Phe508el CFTR protein isoform C* in patients with CF which persists after ELX/TEZ/IVA treatment.Interpretation: Treatment with ELX/TEZ/IVA increased protein expression by facilitating the posttranslational processing of mutant CFTR but apparently did not succeed in generating the polydisperse spectrum of N-linked oligosaccharides that is characteristic for the wild type CFTR band C glycoisoform. Our results caution that the lower amounts or immature glycosylation of the C* glycoisoform observed in patients’ biomaterial might not translate to fully restored function of mutant CFTR necessary for long-term provision of clinical benefit

Towards individualized diagnostics of biofilm-associated infections: a case study

Biofilm resistance: Moving toward individualized testing A procedure for individualized testing of biofilms might yield more reliable data on antibiotic susceptibility in clinical conditions. Researchers in Germany, led by Mathias Müsken at the Helmholtz Centre for Infection Research, developed a method to analyze the antibiotic resistance of patients’ biofilm samples, using microscopy and cell staining. They studied Pseudomonas aeruginosa biofilms gathered from people with cystic fibrosis. The procedure revealed differences in antibiotic susceptibility between bacteria growing in biofilms and in the free-living state. The findings cast doubt on the general utility of antibiotic resistance profiles derived from standard laboratory studies. The clinical advantages of using the procedure to study the antibiotic susceptibility of patients’ unique biofilms should be investigated further. The researchers suggest individualized testing might increase the effectiveness of treatment for chronically infected patients

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

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

High Individuality of Respiratory Bacterial Communities in a Large Cohort of Adult Cystic Fibrosis Patients under Continuous Antibiotic Treatment.

Routine clinical diagnostics of CF patients focus only on a restricted set of well-known pathogenic species. Recent molecular studies suggest that infections could be polymicrobial with many bacteria not detected by culture-based diagnostics

Multidimensional Scaling (MDS) plots from bacterial community composition observed in 72 sputum samples.

<p>Bubbles indicate relative abundances of the 4 most prevalent OTUs in the cohort: <i>P</i>. <i>aeruginosa</i> in green, <i>S</i>. <i>aureus</i> in orange, alpha-hemolytic <i>Streptococcus</i> (<i>Streptococcus</i> -1) in yellow, <i>R</i>. <i>mucilaginosa</i> in blue. 2D Stress values are given in each plot and reveal moderate stress. <b>(A)</b> Merged bubble plots from all four dominant OTUs, coloured bubbles indicating the individual abundances. <i>P</i>. <i>aeruginosa</i> as well as <i>S</i>. <i>aureus</i> have priority, whereas the abundances for <i>R</i>. <i>mucilaginosa</i> and alpha-hemolytic <i>Streptococcus</i> are in the background. (<b>B)</b> Individual MDS plots for each dominant OTU. Numbers indicate individual patients. Letters are according the order of sputum collection.</p

Comparison of prevalence of bacteria in the cohort identified by deep sequencing (NGS, grey bars) and cultivation for classical diagnostics (black bars).

<p>OTUs are listed on the left according their occurrence observed with deep sequencing. Bacteria present in >50% of all samples were categorized as highly prevalent, bacteria detectable in more than 10% of the cases were considered moderately prevalent and those observed in less than 10% of the cases were categorized as bacteria with low prevalence. Categorization follows detection rates by deep sequencing. For precise identification of bacteria see Table C in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117436#pone.0117436.s001" target="_blank">S1 File</a>. Only 71 sputum samples were taken into account (no data from cultivation for sample #20B). * Streptococcus-1 was compared with alpha-hemolytic streptococci.</p

Multidimensional Scaling (MDS) plots from bacterial community composition observed in 72 sputum samples with superimposed host factors.

<p>For a better orientation in the plot, relative abundances of <i>S</i>. <i>aureus</i> are indicated as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117436#pone.0117436.g001" target="_blank">Fig. 1B</a> (orange circles). <b>(A)</b> Age of patients superimposed on the previous MDS plot calculated for the community compositions of 72 sputum samples. Four age classes were defined for the cohort according to the statistical quartils. Symbols indicate the age of the patient at the time point of sputum collection. <b>(B)</b> Lung function of patients superimposed on the previous MDS plot defined for the community compositions of 72 sputum samples. Four classes of lung functions were calculated according to the statistical quartils of FEV₁ values measured for the patients on the day of sputum collection. Symbols indicate the four classes and samples without associated FEV₁ values. <b>(C)</b> CFTR mutations of patients superimposed on the previous MDS plot calculated for the community compositions of 72 sputum samples. Three classes of identified genotypes were determined for the cohort. Partly or completely unknown genotypes are accordingly labelled representing a fourth class.</p

Maximum relative abundances of the bacterial OTUs determined in individual sputum samples.

<p>Individual relative abundances were determined by deep sequencing. OTU identification was achieved by comparison with SSCP sequences.</p

Dynamics of community composition in three representative individuals (patient #20, #35 and #34) from the sub-cohort of patients that provided samples twice or three times.

<p>Each OTU is indicated by a specific colour and further identified in the figure legend. CF patients are identified by numbers and sputum sample are shown in chronological order, hereby, time intervals to the initial sample are indicated in the plot. All other OTUs summarized in grey represent low abundant species not represented by the taxa indicate in the figure.</p