The Dynamics of Disease Progression in Cystic Fibrosis

Long-Term Follow-Up of Health-Related Quality of Life and Short-Term Intervention with CFTR Modulator Therapy in Adults with Cystic Fibrosis: Evaluation of Changes over Several Years with or without 33 Weeks of CFTR Modulator Therapy

BACKGROUND

Longitudinal data on changes in health-related quality of life (HRQoL) in adult people with cystic fibrosis (pwCF) and the longitudinal effects of Elexacaftor/Tezacaftor/Ivacaftor therapy (ETI) on HRQoL or HRQoL domains are currently scarce. This study aimed to investigate the effects of ETI on HRQoL and compare them with those of pwCF who did not receive highly effective CFTR modulators over a longer period.

METHODS

Baseline assessment and follow-up data for 5.6 years in pwCF with (n = 21) and 6.5 years in pwCF without (n = 6) ETI (≥18 years) were evaluated. The assessment of HRQoL and clinical parameters was identical at both time points. HRQoL was assessed using the CFQ-R, and clinical outcomes included BMI, ppFEV1, and FEV1 z-score.

RESULTS

ETI was found to improve all HRQoL domains at more than four points over time, and their increases were significant except for vitality, digestion, treatment burden, and social functioning (p < 0.05). Without ETI, psychosocial domains remained almost constant, whereas most physical domains decreased over time.

CONCLUSIONS

The results of the present study show that ETI therapy has a positive effect on HRQoL and clinical outcomes over time but not in pwCF without ETI treatment. Furthermore, our results suggest that disease progression over time affects the physical domains of HRQoL more than the psychosocial domains. Due to the small sample size and the heterogeneity of the study population (CFTR mutation genotype), the results should be interpreted with some caution.

OUP accepted manuscript

Objective

The study sought to investigate the disease state–dependent risk profiles of patient demographics and medical comorbidities associated with adverse outcomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections.

Materials and Methods

A covariate-dependent, continuous-time hidden Markov model with 4 states (moderate, severe, discharged, and deceased) was used to model the dynamic progression of COVID-19 during the course of hospitalization. All model parameters were estimated using the electronic health records of 1362 patients from ProMedica Health System admitted between March 20, 2020 and December 29, 2020 with a positive nasopharyngeal PCR test for SARS-CoV-2. Demographic characteristics, comorbidities, vital signs, and laboratory test results were retrospectively evaluated to infer a patient’s clinical progression.

Results

The association between patient-level covariates and risk of progression was found to be disease state dependent. Specifically, while being male, being Black or having a medical comorbidity were all associated with an increased risk of progressing from the moderate disease state to the severe disease state, these same factors were associated with a decreased risk of progressing from the severe disease state to the deceased state.

Discussion

Recent studies have not included analyses of the temporal progression of COVID-19, making the current study a unique modeling-based approach to understand the dynamics of COVID-19 in hospitalized patients.

Conclusion

Dynamic risk stratification models have the potential to improve clinical outcomes not only in COVID-19, but also in a myriad of other acute and chronic diseases that, to date, have largely been assessed only by static modeling techniques.

Aspergillus fumigatus In-Host HOG Pathway Mutation for Cystic Fibrosis Lung Microenvironment Persistence

The prevalence of Aspergillus fumigatus colonization in individuals with cystic fibrosis (CF) and subsequent fungal persistence in the lung is increasingly recognized. However, there is no consensus for clinical management of A. fumigatus in CF individuals, due largely to uncertainty surrounding A. fumigatus CF pathogenesis and virulence mechanisms. To address this gap in knowledge, a longitudinal series of A. fumigatus isolates from an individual with CF were collected over 4.5 years. Isolate genotypes were defined with whole-genome sequencing that revealed both transitory and persistent A. fumigatus in the lung. Persistent lineage isolates grew most readily in a low-oxygen culture environment, and conidia were more sensitive to oxidative stress-inducing conditions than those from nonpersistent isolates. Closely related persistent isolates harbored a unique allele of the high-osmolarity glycerol (HOG) pathway mitogen-activated protein kinase kinase, Pbs2 (pbs2C2). Data suggest this novel pbs2C2 allele arose in vivo and is necessary for the fungal response to osmotic stress in a low-oxygen environment through hyperactivation of the HOG (SakA) signaling pathway. Hyperactivation of the HOG pathway through pbs2C2 comes at the cost of decreased conidial stress resistance in the presence of atmospheric oxygen levels. These novel findings shed light on pathoadaptive mechanisms of A. fumigatus in CF, lay the foundation for identifying persistent A. fumigatus isolates that may require antifungal therapy, and highlight considerations for successful culture of persistent Aspergillus CF isolates. IMPORTANCE Aspergillus fumigatus infection causes a spectrum of clinical manifestations. For individuals with cystic fibrosis (CF), allergic bronchopulmonary aspergillosis (ABPA) is an established complication, but there is a growing appreciation for A. fumigatus airway persistence in CF disease progression. There currently is little consensus for clinical management of A. fumigatus long-term culture positivity in CF. A better understanding of A. fumigatus pathogenesis mechanisms in CF is expected to yield insights into when antifungal therapies are warranted. Here, a 4.5-year longitudinal collection of A. fumigatus isolates from a patient with CF identified a persistent lineage that harbors a unique allele of the Pbs2 mitogen-activated protein kinase kinase (MAPKK) necessary for unique CF-relevant stress phenotypes. Importantly for A. fumigatus CF patient diagnostics, this allele provides increased fitness under CF lung-like conditions at a cost of reduced in vitro growth under standard laboratory conditions. These data illustrate a molecular mechanism for A. fumigatus CF lung persistence with implications for diagnostics and antifungal therapy.

Effects of music therapy as an adjunct to chest physiotherapy in children with cystic fibrosis: A randomized controlled trial

Airway clearance therapy (ACT) is considered an important approach to improve airway clearance in children with cystic fibrosis (CF). Daily ACT administration requires substantial commitments of time and energy that complicate ACT and reduce its benefits. It is crucial to establish ACT as a positive routine. Music therapy (MT) is an aspect of integrative strategies to ameliorate the psycho-emotional consequences of chronic diseases, and a MT intervention could help children with CF between the ages of 2 and 17 develop a positive response. The aim of this randomized controlled trial was to evaluate the effects of specifically composed and recorded instrumental music as an adjunct to ACT. We compared the use of specifically composed music (Treated Group, TG), music that the patient liked (Placebo Group, PG), and no music (Control Group, CG) during the usual ACT routine in children with CF aged from 2 to 17. The primary outcomes, i.e., enjoyment and perception of time, were evaluated via validated questionnaires. The secondary outcome, i.e., efficiency, was evaluated in terms of avoided healthcare resources. Enjoyment increased after the use of the specifically composed music (children +0.9 units/parents +1.7 units; p<0.05) compared to enjoyment with no music (0 units) and familiar music (+0.5 units). Perception of time was 11.1 min (±3.9) less than the actual time in the TG (p<0.05), 3.9 min (±4.2) more than the actual time in the PG and unchanged in the CG. The potential cost saving related to respiratory exacerbations was €6,704.87, while the cost increased to €33,524.35 in the CG and to €13,409.74 in the PG. In conclusion, the specifically composed, played and compiled instrumental recorded music is an effective adjunct to ACT to establish a positive response and is an efficient option in terms of avoided costs.

Trial registered as ISRCTN11161411. ISRCTN registry (www.isrctn.com).

The Great ESKAPE: Exploring the Crossroads of Bile and Antibiotic Resistance in Bacterial Pathogens

Throughout the course of infection, many pathogens encounter bactericidal conditions that threaten the viability of the bacteria and impede the establishment of infection. Bile is one of the most innately bactericidal compounds present in humans, functioning to reduce the bacterial burden in the gastrointestinal tract while also aiding in digestion. It is becoming increasingly apparent that pathogens successfully resist the bactericidal conditions of bile, including bacteria that do not normally cause gastrointestinal infections. This review highlights the ability of Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter (ESKAPE), and other enteric pathogens to resist bile and how these interactions can impact the sensitivity of bacteria to various antimicrobial agents. Given that pathogen exposure to bile is an essential component to gastrointestinal transit that cannot be avoided, understanding how bile resistance mechanisms align with antimicrobial resistance is vital to our ability to develop new, successful therapeutics in an age of widespread and increasing antimicrobial resistance.

Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations

Pseudomonas aeruginosa is an opportunistic pathogen that chronically infects the lungs of individuals with cystic fibrosis (CF) by forming antibiotic-resistant biofilms. Emergence of phenotypically diverse isolates within CF P. aeruginosa populations has previously been reported; however, the impact of heterogeneity on social behaviors and community function is poorly understood. Here we describe how this heterogeneity impacts on behavioral traits by evolving the strain PAO1 in biofilms grown in a synthetic sputum medium for 50 days. We measured social trait production and antibiotic tolerance, and used a metagenomic approach to analyze and assess genomic changes over the duration of the evolution experiment. We found that (i) evolutionary trajectories were reproducible in independently evolving populations; (ii) over 60% of genomic diversity occurred within the first 10 days of selection. We then focused on quorum sensing (QS), a well-studied P. aeruginosa trait that is commonly mutated in strains isolated from CF lungs. We found that at the population level, (i) evolution in sputum medium selected for decreased the production of QS and QS-dependent traits; (ii) there was a significant correlation between lasR mutant frequency, the loss of protease, and the 3O-C12-HSL signal, and an increase in resistance to clinically relevant β-lactam antibiotics, despite no previous antibiotic exposure. Overall, our findings provide insights into the effect of allelic polymorphism on community functions in diverse P. aeruginosa populations. Further, we demonstrate that P. aeruginosa population and evolutionary dynamics can impact on traits important for virulence and can lead to increased tolerance to β-lactam antibiotics.

Evaluation of a five-year predicted survival model for cystic fibrosis in later time periods

We evaluated a multivariable logistic regression model predicting 5-year survival derived from a 1993-1997 cohort from the United States Cystic Fibrosis (CF) Foundation Patient Registry to assess whether therapies introduced since 1993 have altered applicability in cohorts, non-overlapping in time, from 1993-1998, 1999-2004, 2005-2010 and 2011-2016. We applied Kaplan-Meier statistics to assess unadjusted survival. We tested logistic regression model discrimination using the C-index and calibration using Hosmer-Lemeshow tests to examine original model performance and guide updating as needed. Kaplan-Meier age-adjusted 5-year probability of death in the CF population decreased substantially during 1993-2016. Patients in successive cohorts were generally healthier at entry, with higher average age, weight and lung function and fewer pulmonary exacerbations annually. CF-related diabetes prevalence, however, steadily increased. Newly derived multivariable logistic regression models for 5-year survival in new cohorts had similar estimated coefficients to the originals. The original model exhibited excellent calibration and discrimination when applied to later cohorts despite improved survival and remains useful for predicting 5-year survival. All models may be used to stratify patients for new studies, and the original coefficients may be useful as a baseline to search for additional but rare events that affect survival in CF.

Association between lung function, thoracoabdominal mobility and posture in cystic fibrosis: pilot study

Abstract Introduction: Deterioration of lung function is the main cause of mortality in cystic fibrosis (CF), so it is essential to study different related factors. Objective: To assess the association of pulmonary function with thoracoabdominal mobility and postural alignment in individuals with CF. Method: A cross-sectional study was performed in individuals with CF (8-17 years). Pulmonary function was assessed by spirometry. Thoracoabdominal mobility and postural alignment were evaluated by photogrammetry using the Postural Assessment Software (PAS/Sapo). Pearson correlation coefficient analysis was performed, and p < 0.05 was considered significant. Results: The following spirometric variables showed a decrease compared to predicted values: FEV1, FEV1/FVC, PEF and FEF25-75%. Postural assessment showed alterations in head horizontal alignment (HHA; 2.71 ± 2.23o), acromion horizontal alignment (AHA; 1.33 ± 1.35o), anterior superior iliac spine (ASIS) horizontal alignment (ASISHA; 1.11 ± 0.89o), angle between acromia and ASIS (AAASIS; 0.89 ± 0.39o), scapula horizontal asymmetry - T3 (SHAT3; 16.95 ± 12.03%), and asymmetry of the projection of the center of gravity within the base of support in the frontal (11.45 ± 8.10%) and sagittal (48.98 ± 18.55%) planes. A strong positive correlation was found between pulmonary function and thoracoabdominal mobility in the variables anteroposterior mobility of the upper chest (APMUC) and FVC (r = 0.818, p = 0.024), APMUC and FEV1 (r = 0.874, p = 0.010), and APMUC and FEF25-75% (r = 0.797, p = 0.032). A strong negative correlation was detected between FEV1/FVC and AHA (r = -0.761, p = 0.047). Conclusion: Our study showed in CF a reduction in pulmonary function, strong positive correlation between APMUC and pulmonary function, high prevalence of kyphoscoliosis and strong negative correlation between AHA and pulmonary function.

Palivizumab and Long-term Outcomes in Cystic Fibrosis

BACKGROUND

The American Academy of Pediatrics does not recommend routine use of palivizumab prophylaxis for infants with cystic fibrosis (CF) but recommends consideration in infants with clinical evidence of chronic lung disease or nutritional compromise. However, the beneficial impact of palivizumab on longer-term outcomes is uncertain.

METHODS

We used Cystic Fibrosis Foundation Patient Registry data to assess the association of receiving palivizumab during the first 2 years of life with longer-term outcomes, including lung function at 7 years old, time to first positive Pseudomonas respiratory culture, and pulmonary-related hospitalizations during the first 7 years of life. Eligible infants were born from 2008 to 2015 and diagnosed with CF during the first 6 months of life. Demographic and clinical confounders of association between palivizumab receipt and outcomes were explored. We created propensity scores to adjust for potential confounding by indication (ie, sicker infants were more likely to receive palivizumab). For each outcome, we performed regression analyses adjusted by propensity scores.

RESULTS

The sample included 4267 infants; 1588 (37%) received palivizumab. Mean percent forced expiratory volume in 1 second predicted at 7 years old was similar among those who did (98.2; 95% confidence interval: 96.9-99.5) and did not (97.3; 95% confidence interval: 96.1-98.5) received palivizumab, adjusting for propensity scores. Time to first positive Pseudomonas aeruginosa culture and annual risk of hospitalization were similar among those who did and did not receive palivizumab.

CONCLUSIONS

At the population level, palivizumab receipt was not associated with improved longer-term outcomes in children with CF.

Pharmacokinetics of Continuous Infusion Beta-lactams in the Treatment of Acute Pulmonary Exacerbations in Adult Patients With Cystic Fibrosis

BACKGROUND

Several clinical trials have shown the efficacy of continuous infusion beta-lactam (BL) antibiotics in patients with cystic fibrosis (CF); however, little is known about pharmacokinetic changes during the treatment of an acute pulmonary exacerbation (APE). Identifying and understanding these changes may assist in optimizing antibiotic dosing during APE treatment.

METHODS

This study was a retrospective cohort study of 162 adult patients with CF admitted to the University of Utah Hospital between January 1, 2008, and May 15, 2014, for treatment of an APE with both a continuous infusion BL and IV tobramycin. We extracted the administered doses of continuous infusion BLs and tobramycin along with serum drug concentrations and calculated medication clearance rates. The primary outcome was change in clearance rates of continuous infusion BLs between day 2 and day 7 of APE treatment.

RESULTS

The BL clearance rate increased 20.7% (95% CI, 11.42 to 32.49; P < .001), whereas the tobramycin clearance rate decreased 6.3% (95% CI, -12.29 to -4.45; P < .001). The mean percent predicted FEV1 increased between admission and discharge by 12.2% (95% CI, -13.81 to -10.55; P < .001).

CONCLUSIONS

Clinicians should monitor BL levels along with aminoglycoside levels and make dose adjustments to maximize the chance of optimal antibiotic treatment. Continuous infusion BL and tobramycin clearance can change dramatically during the treatment of an APE, which may necessitate significant changes in dosing to achieve optimal antibiotic levels. Clearance rates of these antibiotics may change in opposite directions, requiring specific monitoring of each medication.

Predicting disease progression in cystic fibrosis

INTRODUCTION

Progressive lung disease is the major cause of morbidity and mortality in patients with cystic fibrosis (CF). Methods of correctly predicting the future progression of lung disease in patients with CF are essential for directing aggressive treatment to prevent loss of lung function and end stage respiratory failure. Areas covered: This review addresses predictors of respiratory disease progression in patients with CF. We searched Web of Science and Medline, with no restriction on publication date, with the search terms 'cystic fibrosis' and 'disease progression', 'lung function decline', 'prognosis', 'prediction/predictive', 'prediction/prognostic scores', 'risk factors', 'outcome measures/endpoints/disease surrogate', 'longitudinal/long term', 'statistical model', and 'survival'. Expert commentary: Forced expiratory volume in 1 sec (FEV₁) and rate of FEV₁ decline, remain the most significant predictors of mortality in patients with CF while CT scores and airway secretion biomarkers are the main predictors of early CF lung disease. Comprehensive scores incorporating clinical, lung function, imaging and laboratory data will become essential in the future for predicting disease progression and for use in clinical trials. Early interventions may delay the progression of structural lung disease.

Microbial Interactions in the Cystic Fibrosis Airway

Interactions in the airway ecology of cystic fibrosis may alter organism persistence and clinical outcomes. Better understanding of such interactions could guide clinical decisions. We used generalized estimating equations to fit logistic regression models to longitudinal 2-year patient cohorts in the Cystic Fibrosis Foundation Patient Registry, 2003 to 2011, in order to study associations between the airway organisms present in each calendar year and their presence in the subsequent year. Models were adjusted for clinical characteristics and multiple observations per patient. Adjusted models were tested for sensitivity to cystic fibrosis-specific treatments. The study included 28,042 patients aged 6 years and older from 257 accredited U.S. care centers and affiliates. These patients had produced sputum specimens for at least two consecutive years that were cultured for methicillin-sensitive Staphylococcus aureus, methicillin-resistant S. aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, and Candida and Aspergillus species. We analyzed 99.8% of 538,458 sputum cultures from the patients during the study period. Methicillin-sensitive S. aureus was negatively associated with subsequent Paeruginosa. Paeruginosa was negatively associated with subsequent B. cepacia complex, Axylosoxidans, and Smaltophilia. Bcepacia complex was negatively associated with the future presence of all bacteria studied, as well as with that of Aspergillus species. Paeruginosa, B. cepacia complex, and S. maltophilia were each reciprocally and positively associated with Aspergillus species. Independently of patient characteristics, the organisms studied interact and alter the outcomes of treatment decisions, sometimes in unexpected ways. By inhibiting P. aeruginosa, methicillin-sensitive S. aureus may delay lung disease progression. Paeruginosa and B. cepacia complex may inhibit other organisms by decreasing airway biodiversity, potentially worsening lung disease.

Airway microbiota in patients with paediatric cystic fibrosis: Relationship with clinical status

INTRODUCTION

New massive sequencing techniques make it possible to determine the composition of airway microbiota in patients with cystic fibrosis (CF). However, the relationship between the composition of lung microbiome and the clinical status of paediatric patients is still not fully understood.

MATERIAL AND METHODS

A cross-sectional observational study was conducted on induced sputum samples from children with CF and known mutation in the CFTR gene. The bacterial sequences of the 16SrRNA gene were analyzed and their association with various clinical variables studied.

RESULTS

Analysis of the 13 samples obtained showed a core microbiome made up of Staphylococcus spp., Streptococcus spp., Rothia spp., Gemella spp. and Granulicatella spp., with a small number of Pseudomonas spp. The cluster of patients with less biodiversity were found to exhibit a greater number of sequences of Staphylococcus spp., mainly Staphylococcus aureus (p 0.009) and a greater degree of lung damage.

CONCLUSION

An airway microbiome with greater biodiversity may be an indicator of less pronounced disease progression, in which case new therapeutic interventions that prevent reduction in non-pathogenic species of the airway microbiota should be studied.

Rescue therapy within the UK Cystic Fibrosis Registry: An exploration of predictors of intravenous antibiotic use amongst adults with CF

Background and objective

Intravenous (i.v.) antibiotics are needed for rescue when preventative therapy fails to achieve stability among adults with cystic fibrosis (CF). Understanding the distribution of i.v. days can provide insight into the care that adults with CF need. We aim to determine the baseline characteristics that are associated with higher i.v. use, in particular to test the hypothesis that prior‐year i.v. use is associated with future‐year i.v. use.

Methods

This is a cross‐sectional analysis of the 2013–2014 UK CF registry data. Stepwise logistic regression was performed using current‐year i.v. days as the dependent variable, and demographic variables including prior‐year i.v. days as the covariates. Based on these results, study sample was divided into clinically meaningful subgroups using analysis similar to tree‐based method.

Results

Data were available for 4269 adults in 2013 and 4644 adults in 2014. Prior‐year i.v. use was the strongest predictor for current‐year i.v. use followed by forced expiratory volume in 1 s (FEV₁). Adults with high prior‐year i.v. use (>14 days) continued to require high levels of i.v., regardless of FEV₁. Those with high prior‐year i.v. use and FEV₁ ≥70% had higher current‐year i.v. days compared to adults with low prior‐year i.v. use and FEV₁ <40% (28 days, interquartile range (IQR): 11–41 days vs 14 days, IQR: 0–28 days; Mann–Whitney P‐value <0.001 in 2013).

Conclusion

CF people with prior high levels of rescue often continue to need high levels of rescue even if they have good FEV₁. The reasons for this require further investigations.

Intravenous (i.v.) antibiotic is an important treatment option in cystic fibrosis and is also a marker of pulmonary exacerbations. Our study showed that previous‐year i.v. use is a strong predictor of current‐year i.v. use. This finding could help clinicians to identify people most at risk of future exacerbation.

[Interstitial processes of the lungs in childhood]

Interstitial processes in the lungs of children can be due to several underlying diseases. Knowledge of the child's age is important as genetic aberrations play a major role in diseases in the first 2 years, whereas immunological diseases are more common starting in kindergarden age. In general lung diseases are rare in children, which makes the diagnostics difficult and results in a delayed diagnosis. In addition, pediatric pulmonologists are often very reluctant to perform lung biopsies due to a lack of a specialized pathologist. In order to make a contribution to the diagnostics of pediatric pulmonary diseases, pathologists should be specialized in pulmonary pathology, have a good knowledge of genetic methods and fetal lung development, which includes the genetic factors involved in lung growth and differentiation. A close cooperation with the pediatric pulmonologist is necessary and each patient should be discussed jointly on an interstitial lung disease board to promote the quality of diagnostics. The pathologist should be aware that the developing lungs of children are not just a smaller form of adult lungs and often react very differently. In this article, we mainly focus on diffuse infiltration patterns, such as ground glass and reticulonodular infiltrations as described in high-resolution computed tomography (HRCT). Localized interstitial processes, which can sometimes be tumor-like and malformations are not dealt with; however, vascular malformations are included as these often manifest as diffuse interstitial infiltrations and must therefore be taken into consideration for the differential diagnostics.