Journal
MEDICAL MYCOLOGY
Volume 58, Issue 5, Pages 650-660Publisher
OXFORD UNIV PRESS
DOI: 10.1093/mmy/myz109
Keywords
mycoses; molecular diagnostics; clinical metagenomics; MinION; Pneumocystis
Categories
Funding
- National Health and Medical Research Council of Australia (NHMRC) grant [APP1121936]
- Western Sydney Local Health District Research & Education Network Research Grant Scheme
- Australian Research Council Future Fellowship [FT180100024]
- Hermon Slade Foundation [HSF_17_04]
- Australian Research Council [FT180100024] Funding Source: Australian Research Council
Ask authors/readers for more resources
The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior culturing. The MinION from Oxford Nanopore Technologies offers real-time, direct sequencing of long DNA fragments directly from clinical samples. The aim of this study was to assess the ability of unbiased, genome-wide, long-read, shotgun sequencing using MinION to identify Pneumocystis jirovecii directly from respiratory tract specimens and to characterize the associated mycobiome. Pneumocystis pneumonia (PCP) is a lifethreatening fungal disease caused by P jirovecii. Currently, the diagnosis of PCP relies on direct microscopic or real-time quantitative polymerase chain reaction (PCR) examination of respiratory tract specimens, as P jirovecii cannot be cultured readily in vitro. P jirovecii DNA was detected in bronchoalveolar lavage (BAL) and induced sputum (IS) samples from three patients with confirmed PCP. Other fungi present in the associated mycobiome included known human pathogens (Aspergillus, Cryptococcus, Pichia) as well as commensal species (Candida, Malassezia, Bipolaris). We have established optimized sample preparation conditions for the generation of high-quality data, curated databases, and data analysis tools, which are key to the application of long-read MinION sequencing leading to a fundamental new approach in fungal diagnostics.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available