Introduction: Cystic fibrosis (CF) is the most common life-shortening genetic disorder in Australians. CF leads to several clinical outcomes, particularly chronic lung disease, which causes the highest rate of mortality in CF patients. It remains unclear how microbes can deeply infect the CF airways and why the immune response is ineffective in eradicating them . Traditional culture methods for pathogen identification are laborious and insensitive to microbial community diversity .
Methods: This study performed deep (“metagenomic”) Illumina and Oxford Nanopore Technologies sequencing of the microbial communities in CF sputa to understand their microbial composition, and to identify potential links between persistence and antimicrobial resistance (AMR). Due to high human DNA contamination (~99%) in CF sputa, methods for enriching microbial DNA using saponin were investigated .
Results: Our metagenomic approach identified Pseudomonas aeruginosa as the most abundant pathogen based on either total DNA (99% human contamination) or microbial enriched DNA, consistent with culture results. In addition, AMR genes and strain mixtures within species were identified using both sequencing platforms. Using the saponin method, the human DNA was depleted by ~50-80%, enabling greater detection of microbial reads.
Conclusions: Our results provide exciting preliminary data showing that metagenomic sequencing is a powerful method for characterising microbial populations in the CF airway microbiome. Future studies will use our depletion methods prior to metagenomic sequencing to examine microbial changes over time and in response to treatment, with the aim of better understanding microbial populations, persistence and evolution, and ultimately, informing patient treatment.