Daily Respiratory Research Analysis
Three impactful respiratory studies span stewardship, models, and diagnostics: long-term azithromycin in HIV-associated chronic lung disease reduced gut microbial diversity with effects persisting after cessation; a human precision-cut lung slice acid injury–repair model enables translational discovery and drug testing; and an extraction-free CRISPR workflow detects SARS-CoV-2 from dry swabs and viral transport media, offering rapid, low-cost testing.
Summary
Three impactful respiratory studies span stewardship, models, and diagnostics: long-term azithromycin in HIV-associated chronic lung disease reduced gut microbial diversity with effects persisting after cessation; a human precision-cut lung slice acid injury–repair model enables translational discovery and drug testing; and an extraction-free CRISPR workflow detects SARS-CoV-2 from dry swabs and viral transport media, offering rapid, low-cost testing.
Research Themes
- Antibiotic stewardship and microbiome effects in chronic lung disease
- Translational human ex vivo models of lung injury and repair
- Rapid, extraction-free CRISPR diagnostics for respiratory viruses
Selected Articles
1. Effect of long-term azithromycin treatment on gut microbial diversity in children and adolescents with HIV-associated chronic lung disease.
In a double-blind, placebo-controlled trial of children and adolescents with HIV-associated chronic lung disease, once-weekly azithromycin for 48 weeks reduced gut bacterial alpha-diversity and altered the abundance of 27 genera compared with placebo. Network connectivity among genera was lower with azithromycin, and Campylobacter depletion persisted 6 months post-cessation. These findings highlight durable microbiome impacts of long-term macrolide therapy.
Impact: This randomized trial quantifies sustained gut microbiome perturbations from long-term azithromycin in a high-risk respiratory population, informing antibiotic stewardship in chronic lung disease.
Clinical Implications: Clinicians should balance exacerbation reduction against potential long-lasting microbiome disruption when considering long-term azithromycin in pediatric HIV-associated chronic lung disease, monitor for consequences (e.g., dysbiosis, resistance), and prioritize stewardship and individualized duration.
Key Findings
- After 48 weeks, bacterial alpha-diversity was significantly lower in the azithromycin group versus placebo.
- Twenty-seven bacterial genera showed differential abundance between groups at 48 weeks.
- Microbial interconnectivity networks were more interconnected in placebo than in azithromycin at 48 weeks.
- Correlations between top differentially abundant genera and plasma biomarkers seen at inclusion were no longer significant at 48 weeks.
- Campylobacter depletion persisted 6 months after stopping azithromycin.
Methodological Strengths
- Double-blind, placebo-controlled randomized design with longitudinal sampling at 0, 48, and 72 weeks
- Use of 16S rRNA sequencing and multiplex plasma biomarker profiling
- Multisite recruitment (Zimbabwe and Malawi), enhancing external validity within target population
Limitations
- Microbiome assessed from rectal swabs, which may not fully represent stool microbiota
- 16S rRNA profiling limits taxonomic resolution and lacks functional/metagenomic data
- Generalizability beyond children/adolescents with HIV-associated chronic lung disease is uncertain
- Antimicrobial resistance outcomes were not directly measured
Future Directions: Integrate metagenomics and resistome profiling, assess clinical consequences of dysbiosis, and test stewardship-informed dosing/duration strategies to mitigate microbiome disruption while preserving respiratory benefits.
2. A human PCLS model of lung injury and repair for discovery and pharmaceutical research.
Investigators adapted the acid injury–repair model to human precision-cut lung slices, creating a translational ex vivo platform. Acid injury did not alter overall proliferation but significantly increased alveolar type II/progenitor markers (proSP-C, HTII) in injured regions, and multiple repair-relevant cell types (lipofibroblasts, endothelial cells) were identifiable. The model mimics heterogeneous injury and supports mechanistic and drug screening studies.
Impact: Provides a human tissue-based injury–repair system bridging in vitro and in vivo models, enabling mechanistic studies and preclinical screening in authentic 3D lung microenvironments.
Clinical Implications: While not immediately practice-changing, this human ex vivo platform can accelerate development and validation of therapeutics aimed at enhancing lung repair and may improve translational fidelity of preclinical findings.
Key Findings
- Human precision-cut lung slices were successfully adapted to the acid injury–repair (AIR) model (hAIR).
- Acid injury did not change overall proliferation (Ki67) but increased the proportion of proSP-C and HTII-positive cells in injured regions.
- Repair-relevant non-epithelial populations (lipofibroblasts and endothelial cells) were identified and tracked within hAIR.
- The model establishes adjacent injured and uninjured regions, mimicking heterogeneous lung injury patterns.
Methodological Strengths
- Use of human resected lung tissue and 3D precision-cut lung slices with localized injury
- Multiplex cell marker immunostaining (Ki67, proSP-C, HTII, ADRP, ERG) enabling cell-type–specific analyses
- Parallel viability assessment (MTT, Live/Dead) to support tissue integrity over culture
Limitations
- Short culture timeframe (48 h) captures early repair only; longer-term dynamics not assessed
- Acid injury may not represent all clinical injury etiologies (e.g., infection, mechanical, toxin)
- Donor number and variability were not specified, limiting generalizability and statistical inference
Future Directions: Extend culture duration and functional readouts, incorporate diverse injury stimuli, quantify donor variability, and apply the platform for preclinical testing of pro-repair therapeutics.
3. RNA extraction-free CRISPR-based SARS-CoV-2 detection in viral transport medium and dry swab-a comparative analysis: Short title: Extraction-free CRISPR-based Covid detection.
An extraction-free workflow combining proteinase K/heat treatment, RT-LAMP, and CRISPR detected SARS-CoV-2 directly from both viral transport medium and dry swabs. Detection was more efficient for dry swabs than for VTM. This approach can reduce cost and turnaround time and may be adaptable to other respiratory pathogens.
Impact: Demonstrates a practical, extraction-free CRISPR diagnostic workflow across common sample types, addressing throughput and accessibility constraints during respiratory outbreaks.
Clinical Implications: Laboratories could implement extraction-free CRISPR workflows, especially for dry swabs, to expand rapid testing capacity in low-resource settings; however, formal validation of diagnostic accuracy versus RT-PCR is needed prior to adoption.
Key Findings
- SARS-CoV-2 was detectable without RNA extraction from both dry swabs and two commercial VTM preparations using proteinase K/heat, RT-LAMP, and CRISPR.
- Detection efficiency was higher for dry swab samples than for VTM samples.
- The workflow is presented as adaptable to other respiratory diseases.
Methodological Strengths
- Direct comparison of two common specimen types (dry swab vs VTM) within an extraction-free workflow
- Use of orthogonal amplification (RT-LAMP) and CRISPR detection to enhance sensitivity
- Simple sample pre-processing (proteinase K and heat) enabling low-cost implementation
Limitations
- Diagnostic performance metrics (sensitivity/specificity) relative to RT-PCR were not fully quantified
- Sample size and patient characteristics were not specified, limiting inference
- Only two VTM brands were tested, so generalizability to other media is unknown
Future Directions: Undertake large-scale clinical validation across diverse VTMs and respiratory pathogens, define analytical limits of detection, and integrate into point-of-care platforms.