Mycobiome subtyping of bronchoalveolar lavage (BAL) in individuals with prior tuberculosis

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Rationale: The clinical relevance of the mycobiome in individuals with prior pulmonary tuberculosis (PTB) is uncertain. Methods: We prospectively recruited and followed up n=63 individuals with suspected PTB based on clinic-radiological features and negative sputum culture. BAL was examined for mycobacterial and fungal microbiology, galactomannan (GM) and ITS (mycobiome) sequencing using an Illumina MiSeq platform. Results: Of the n=63 individuals included, n=7 had active PTB, n=44 had prior PTB and n=12 had no active or past PTB. N=43 (68.2%) had chronic pulmonary aspergillosis (CPA) and no significant difference in CPA prevalence occurred across the three groups. BAL mycobiome beta-diversity revealed significant differences between the three groups (PERMANOVA, adjusted p=0.045), however, no significant difference between those with or without CPA was seen. Unsupervised clustering of prior PTB identified three clusters: C1 characterised by Aspergillus and Cladosporium, associated with elevated BAL GM and lung nodules; C2 with mixed fungal composition; and C3, dominated by Fuscicolla, the youngest individuals and more frequent fever. No difference in active PTB was detected across clusters. Six-month mortality was recorded in n=7 individuals where Aspergillus and Penicillium predominated. Conclusion: Distinct mycobiome subtypes exist in individuals with prior PTB, which vary by symptoms, radiology and BAL GM, highlighting that the post-TB state is heterogenous and that fungal dysbiosis may have clinical relevance in PTB-lung disease related clinical outcomes.

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