Whole genome sequence analysis of cryptococcus gattii from the pacific northwest reveals unexpected diversity

John D. Gillece, James M. Schupp, S. Arunmozhi Balajee, Julie Harris, Talima R Pearson, Yongpan Yan, Paul S Keim, Emilio DeBess, Nicola Marsden-Haug, Ron Wohrle, David M. Engelthaler, Shawn R. Lockhart

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

A recent emergence of Cryptococcus gattii in the Pacific Northwest involves strains that fall into three primarily clonal molecular subtypes: VGIIa, VGIIb and VGIIc. Multilocus sequence typing (MLST) and variable number tandem repeat analysis appear to identify little diversity within these molecular subtypes. Given the apparent expansion of these subtypes into new geographic areas and their ability to cause disease in immunocompetent individuals, differentiation of isolates belonging to these subtypes could be very important from a public health perspective. We used whole genome sequence typing (WGST) to perform fine-scale phylogenetic analysis on 20 C. gattii isolates, 18 of which are from the VGII molecular type largely responsible for the Pacific Northwest emergence. Analysis both including and excluding (289,586 SNPs and 56,845 SNPs, respectively) molecular types VGI and VGIII isolates resulted in phylogenetic reconstructions consistent, for the most part, with MLST analysis but with far greater resolution among isolates. The WGST analysis presented here resulted in identification of over 100 SNPs among eight VGIIc isolates as well as unique genotypes for each of the VGIIa, VGIIb and VGIIc isolates. Similar levels of genetic diversity were found within each of the molecular subtype isolates, despite the fact that the VGIIb clade is thought to have emerged much earlier. The analysis presented here is the first multi-genome WGST study to focus on the C. gattii molecular subtypes involved in the Pacific Northwest emergence and describes the tools that will further our understanding of this emerging pathogen.

Original languageEnglish (US)
Article numbere28550
JournalPLoS One
Volume6
Issue number12
DOIs
StatePublished - Dec 7 2011

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Cryptococcus gattii
Northwestern United States
Multilocus Sequence Typing
Sequence Analysis
sequence analysis
Genes
Genome
Single Nucleotide Polymorphism
genome
Minisatellite Repeats
minisatellite repeats
phylogeny
Public health
Pathogens
public health
Public Health
Genotype
genetic variation
pathogens
genotype

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Whole genome sequence analysis of cryptococcus gattii from the pacific northwest reveals unexpected diversity. / Gillece, John D.; Schupp, James M.; Balajee, S. Arunmozhi; Harris, Julie; Pearson, Talima R; Yan, Yongpan; Keim, Paul S; DeBess, Emilio; Marsden-Haug, Nicola; Wohrle, Ron; Engelthaler, David M.; Lockhart, Shawn R.

In: PLoS One, Vol. 6, No. 12, e28550, 07.12.2011.

Research output: Contribution to journalArticle

Gillece, JD, Schupp, JM, Balajee, SA, Harris, J, Pearson, TR, Yan, Y, Keim, PS, DeBess, E, Marsden-Haug, N, Wohrle, R, Engelthaler, DM & Lockhart, SR 2011, 'Whole genome sequence analysis of cryptococcus gattii from the pacific northwest reveals unexpected diversity', PLoS One, vol. 6, no. 12, e28550. https://doi.org/10.1371/journal.pone.0028550
Gillece, John D. ; Schupp, James M. ; Balajee, S. Arunmozhi ; Harris, Julie ; Pearson, Talima R ; Yan, Yongpan ; Keim, Paul S ; DeBess, Emilio ; Marsden-Haug, Nicola ; Wohrle, Ron ; Engelthaler, David M. ; Lockhart, Shawn R. / Whole genome sequence analysis of cryptococcus gattii from the pacific northwest reveals unexpected diversity. In: PLoS One. 2011 ; Vol. 6, No. 12.
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