Objective:

To investigate the prevalence of antimicrobial resistance genes in the lower airway microbiome of patients with chronic lung disease compared to healthy controls, highlighting the clinical significance of these findings.

Key Findings:

• Tetracycline resistance genes were found in 33% of samples, beta-lactam and macrolide resistance genes in 26% each, with statistical significance noted.
• Antimicrobial resistance genes were present in 38% of healthy controls, 39% of asthma patients, 51% of COPD patients, 65% of sarcoidosis patients, and 83% of IPF patients, with significant differences.
• Patients with sarcoidosis and IPF had significantly higher odds of harboring resistance genes compared to controls.
• Recent antibiotic exposure was linked to a higher burden of resistance genes, with statistical significance.

Interpretation:

The study indicates a higher prevalence of antimicrobial resistance genes in chronic lung disease patients, particularly in sarcoidosis and IPF, emphasizing the implications for clinical practice and the impact of antibiotic use on the microbiome.

Limitations:

• Cross-sectional design limits causal interpretation, affecting the ability to draw definitive conclusions.
• Small sample sizes in certain disease groups restrict subgroup analyses, potentially skewing results.
• Self-reported antibiotic exposure lacks specificity, which may affect the accuracy of findings.
• Single lung lobe sampling may not represent the entire pulmonary microbiome, limiting generalizability.

Conclusion:

The findings emphasize the influence of antibiotic use on the presence of resistance mechanisms in the microbiome of patients with chronic lung diseases, underscoring the need for careful antibiotic stewardship.