The AREST CF experience in biobanking - More than just tissues, tubes and time

Differential cell counts using center-point networks achieves human-level accuracy and efficiency over segmentation

Differential cell counts is a challenging task when applying computer vision algorithms to pathology. Existing approaches to train cell recognition require high availability of multi-class segmentation and/or bounding box annotations and suffer in performance when objects are tightly clustered. We present differential count network ("DCNet"), an annotation efficient modality that utilises keypoint detection to locate in brightfield images the centre points of cells (not nuclei) and their cell class. The single centre point annotation for DCNet lowered burden for experts to generate ground truth data by 77.1% compared to bounding box labeling. Yet centre point annotation still enabled high accuracy when training DCNet on a multi-class algorithm on whole cell features, matching human experts in all 5 object classes in average precision and outperforming humans in consistency. The efficacy and efficiency of the DCNet end-to-end system represents a significant progress toward an open source, fully computationally approach to differential cell count based diagnosis that can be adapted to any pathology need.

Changes in airway inflammation with pseudomonas eradication in early cystic fibrosis

BACKGROUND

Neutrophil elastase is a significant risk factor for structural lung disease in cystic fibrosis, and Pseudomonas aeruginosa airway infection is linked with neutrophilic inflammation and substantial respiratory morbidity. We aimed to evaluate how neutrophil elastase (NE) activity changes after P. aeruginosa eradication and influences early disease outcomes.

METHODS

We assessed participants in the AREST CF cohort between 2000 and 2018 who had P. aeruginosa cultured from their routine annual bronchoalveolar lavage (BAL) fluid and who underwent eradication treatment and a post eradication BAL. Factors associated with persistent P. aeruginosa infection, persistent neutrophilic inflammation following eradication and worse structural lung disease one year post-eradication were evaluated.

RESULTS

Eighty-eight episodes (3 months to 6 years old) of P. aeruginosa infection were studied. Eradication was successful in 84.1% of episodes. Median activity of NE was significantly reduced post-eradication from 9.15 to 3.4 nM (p = 0.008) but persisted in 33 subjects. High post-eradication NE levels were associated with an increased risk for P. aeruginosa infection in the next annual visit (odds ratio=1.7, 95% confidence interval 1.1-2.7, p = 0.014). Post-eradication NE levels (difference, 0.8; 95% confidence interval, 0.1-1.5) and baseline bronchiectasis computed tomography (CT) score (difference, 0.4; 95% confidence interval, 0.1-0.8) were the best predictors of bronchiectasis progression within 1 year (backward stepwise linear regression model, R²= 0.608, P<0.001), independent of eradication.

CONCLUSION

In children with CF, NE activity may persist following successful P. aeruginosa eradication and is significantly associated with bronchiectasis progression. Evaluating strategies to diminish neutrophilic inflammation is essential for improving long-term outcomes.

Overcoming Challenges to Make Bacteriophage Therapy Standard Clinical Treatment Practice for Cystic Fibrosis

Individuals with cystic fibrosis (CF) are given antimicrobials as prophylaxis against bacterial lung infection, which contributes to the growing emergence of multidrug resistant (MDR) pathogens isolated. Pathogens such as Pseudomonas aeruginosa that are commonly isolated from individuals with CF are armed with an arsenal of protective and virulence mechanisms, complicating eradication and treatment strategies. While translation of phage therapy into standard care for CF has been explored, challenges such as the lack of an appropriate animal model demonstrating safety in vivo exist. In this review, we have discussed and provided some insights in the use of primary airway epithelial cells to represent the mucoenvironment of the CF lungs to demonstrate safety and efficacy of phage therapy. The combination of phage therapy and antimicrobials is gaining attention and has the potential to delay the onset of MDR infections. It is evident that efforts to translate phage therapy into standard clinical practice have gained traction in the past 5 years. Ultimately, collaboration, transparency in data publications and standardized policies are needed for clinical translation.

Elimination of Australian epidemic strain (AES1) pseudomonas aeruginosa in a pediatric cystic fibrosis center

INTRODUCTION

In this cohort study spanning an 18-year period, we evaluated the prevalence and associated mortality rate of epidemic strains of pseudomonas aeruginosa (PsA), especially Australian Epidemic Strain Type 1 (AES1), in a pediatric cystic fibrosis center practicing cohort segregation and early PsA eradication.

METHODS

Cohort segregation was introduced in January 2000. PsA clonal strain was determined by pulse-field-gel-electrophoresis (PFGE) at the time of routine collection of airway specimens. Children with PsA underwent eradication treatment with anti-pseudomonal antibiotics over 2-3 months. We analyzed changes in prevalence and mortality from 1999 to 2016.

RESULTS

The prevalence of AES1 declined from 69 (20%) in 1999 to 16 (5.4%) in 2006, to 1 (0.4%) in 2016. The prevalence of PsA overall diminished less over the same period, from 128 (37%) patients in 1999 to 57 (23%) in 2016. New acquisition of AES1 became less common over time, with no new cases identified from 2011. Those who contracted AES1 had a greater risk of death than those who did not (Odds Ratio 4.9, 95%CI 2.5-9.6). Patients with other AES PsA types were uncommon (AES2 n = 5, AES5 n = 2, AES14 n = 3, AES19 n = 1).

CONCLUSIONS

Cohort segregation was associated with reduction in AES1 prevalence ascertained by PFGE surveillance for patients in a single large pediatric cystic fibrosis center. Other alterations in practice such as early eradication treatment may also have contributed to reduced PsA prevalence. These factors combined with the transition of chronically infected patients over time to adult centers has eliminated AES1 from our clinic, with an accompanying mortality decrease.