On-site sequencing of Polyporales sp. isolated from a rare lung fungal infection using Oxford nanopore flongle

Abstract

Fungal infection is rarely reported in immunocompetent retroviral disease patients. We report a first case of a 42-year-old man with underlying retroviral disease on Highly Active Antiretroviral Therapy (HAART) who was infected with pulmonary Polyporales sp. Despite undetected viral load with high CD4 count, the patient was found to have unexplained significant loss of weight and appetite. Subsequently, CT thorax revealed multiple lung nodules at the lateral segment of the right middle lobe of lung. Bronchoscopy was carried out and showed a black patch at the right bronchus intermedius, lateral segment of the middle lobe which did not disappear upon bronchial flush or wash. The fungal culture was first described as Cladosporium sp. based on colony appearance and morphology under light microscopy examination. Due to the rarity of thisinfection, we recovered the sample from paraffin embedded tissue block and then re-cultured on Sabouraud agar at 300 Celcius. The total genomic DNA was then extracted by using the DNeasy Blood and Tissue kit. Full-length genome sequencing was carried out using Flongle platform for long read protocols which resulted as Polyporales sp. This finding will definitely add a novel value for precision diagnosis and clinical surveillance of a rare fungal infection.