Limper, A.H.

Abstract RATIONALE: Understanding co-isolation patterns between fungi and other potentially pathogenic microorganisms in the airways of bronchiectasis patients is important for uncovering possible microbial interactions and informing treatment. Although numerous organisms have been identified in respiratory cultures, the specific patterns of their co-isolation are underexplored. OBJECTIVES: To examine the patterns of co-isolation between fungi and bacteria or mycobacteria in respiratory samples from patients with bronchiectasis across a large national health system. METHODS: We reviewed 58,170 respiratory culture tests from 8,194 patients with bronchiectasis (identified using ICD-10-CM codes J47.0, J47.1, and J47.9) across Mayo Clinic. These tests were analyzed for fungal, bacterial, and mycobacterial growth, focusing on co-isolation from the same sample. Chi-square statistics were used to compute p-values. RESULTS: Of all 18,983 samples cultured for fungi, 59% were positive. Of these, 72% yielded yeasts and 40% molds. Among the 11,372 samples cultured for both fungi and bacteria, 681 (6%) showed co-isolation, representing 54% of positive bacterial cultures. The odds of bacterial co-isolation with fungi were 1.4 (95% CI: 1.3-1.6; p < 0.01), driven by yeasts (OR: 1.5, 95% CI: 1.3-1.7; p < 0.01), rather than molds (OR: 1.0, 95% CI: 0.9-1.2; p = 0.8). Pseudomonas species, the most common bacterial isolate, had a higher likelihood of co-isolation with fungi (OR: 1.6, 95% CI: 1.3-1.9; p < 0.01), particularly yeasts (OR: 1.6, 95% CI: 1.4-2.0; p < 0.01). Molds, including those from genera such as aspergillus and penicillium, did not show a significant association with the isolation of pseudomonas. On the other hand, among the 15,859 samples cultured for both fungi and mycobacteria, 1352 (9%) showed co-isolation, representing 62% of positive mycobacterial cultures. Odds of co-isolation were 1.7 (95% CI: 1.5-1.8; p < 0.01). Molds showed a stronger association with isolation of mycobacteria (OR: 1.7, 95% CI: 1.5-1.9; p < 0.01) compared to bacteria, while yeasts also had elevated odds (OR: 1.4, 95% CI: 1.2-1.5). CONCLUSIONS: Distinct patterns of fungal co-isolation with bacteria and mycobacteria have been observed in bronchiectasis, which may influence key aspects of the disease, such as inflammation and mucociliary dysfunction. Advanced metagenomic and immunoprofiling techniques could provide deeper insights into these co-isolation patterns while considering other factors like clinical demographics, previous antibiotic exposure, and disease severity. Understanding whether altering the mycobiome could modify these aspects and improve outcomes remains an important avenue for research.