Environmental fungal sensitisation associates with poorer clinical outcomes in COPD

Indoor air and surface sampling for metagenomic sequencing: A subset of COPD patients (n=11) were recruited for home environmental sampling which included (a) indoor (bedroom) air sampling (b) outdoor (balcony) air sampling and (c) surface swab obtained from either an air-conditioning filter or fan from the patient's bedroom. Air samples were concurrently obtained from the patient's bedroom and balcony using filter-based air samplers SASS3100 (Research International, USA) with a flow rate of 100 L/min for 8 consecutive hours. In addition, a surface (either air-conditioner or fan where applicable) were swabbed and subjected to metagenomic sequencing. The surfaces (air conditioner or fan) were swabbed using 4N6Floq (Copan, USA) swabs pre-moistened with 0.1% PBS-Triton-X100. DNA was then extracted from the swabs using the DNeasy PowerWater kit as per manufacturer's instructions. Extraction blanks and sterile swabs were processed in parallel as controls. Sequencing was performed using the Illumina HiSeq 2500 platform (Illumina, USA) and library preparation including sequencing methodologies were performed using published protocols (Gusareva et al PNAS 2019).