Clinical metagenomic approach for pathogen recovery from bronchoalveolar lavage using MinION

Reliable and accurate detection of fungal pathogens is essential for early imitation of appropriate antifungal therapies. Conventional diagnostic methods have limitations such as low sensitivity, prior knowledge of the putative pathogen and restricted ability to detect several pathogens simultaneously. Next-generation sequencing is a powerful culture independent tool for the identification and profiling of mixed microbial communities regardless of the ability of member organisms to be grown on media. The fungal microbiome (mycobiome) of bronchoalveolar lavage (BAL) and sputum is not well characterized, particularly in relation to infectious fungal diseases such as candidiasis, aspergillosis or pneumocystis pneumonia (PCP). We aimed to describe and compare the mycobiome of BAL and sputum using long read sequencing directly from the clinical sample.