Deep sequencing of microbial communities in cystic fibrosis airways

Tânia Duarte

Tânia Duarte, The University of Queensland


Cystic fibrosis (CF) is a life-shortening genetic disorder leading, particularly, to chronic lung disease. We studied airway microbiome at multiple timepoints in sputa of 6 patients subsequent to antibiotic intervention using both short (Illumina) and long (Oxford Nanopore) reads, and both WGS and 16S rRNA gene sequencing. Using sketchy, we were able to rapidly and accurately identify specific strains and resistant profiles of S. aureus infections from raw nanopore reads. By combining short and long-read sequencing data, we were able to generate high-quality assemblies of the most abundant species. This study demonstrates the potential for nanopore sequencing to be used in routine monitoring of infection dynamics for CF patients.


Tania is a Ph.D candidate at the Institute for Molecular Bioscience in The University of Queensland studying cystic fibrosis patients’ airways. She is interested in metagenomics, real-time and long-reads Oxford Nanopore sequencing, and anything that can help CF patients have a better quality of life, including fighting antimicrobial resistance. Tania is passionate about science in general, photography and latin dance.