New Test Developed to Diagnose Virulent Lung Fungus

The emergence of distinct populations of Cryptococcus gattii in the temperate North American Pacific Northwest (PNW) was surprising, as this species was previously thought to be confined to tropical and semitropical regions.

C. gattii, is a pathogenic fungus that is highly adaptive and warrants global public health vigilance, and the dominant emergent population displays increased virulence and caused primary pulmonary disease, as opposed to the predominantly neurologic disease seen previously elsewhere.


Scientists at Northern Arizona University (Flagstaff, AZ, USA) working with an international team from 15 countries performed whole-genome sequencing on 118 C. gattii isolates, including the PNW subtypes and the global diversity of molecular type VGII, to better ascertain the natural source and genomic adaptations leading to the emergence of infection in the PNW.

The genomes of all 118 C. gattii isolates were sequenced using HiSeq, MiSeq, or GAIIx sequencing technology (Illumina; San Diego, CA, USA). High-molecular-weight DNA was extracted using the ZR Fungal/Bacterial DNA MiniPrep kit (Zymo Research; Irvine, CA, USA). Prior to sequencing, the libraries were quantified with quantitative PCR (qPCR) on the ABI 7900HT (Life Technologies Corporation; Carlsbad, CA, USA). Single nucleotide polymorphisms variant detection, multilocus sequence typing (MLST), and phylogenetic analysis were also performed.

The team found that there were most likely multiple distinct North American introductions of at least two of the three PNW VGII subtypes. Gene content varies between the VGII subtypes and C. gattii has developed a number of evolutionary strategies that allow for continual niche adaptation. Paul Keim, PhD, one of the study's senior authors, said “By closely analyzing the genomes of dozens of outbreak strains, as well as globally diverse strains, we were able to closely compare and determine the genomic differences that may cause their clinical and ecological changes.”

The new tests developed for this study by the Translational Genomics Research Institute (Flagstaff, AZ, USA) are making it easier to detect this and other fungi, and could lead to better monitoring and treatments. The same tools used in this study were also used to investigate the cause of a fungal meningitis outbreak associated with steroid back injections, and the recent outbreak of Valley Fever. The study was published on July 15, 2014, in the journal mBIO.

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Northern Arizona University 
Illumina
Zymo Research