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

Gillece, John D. and Schupp, James M. and Balajee, S. Arunmozhi and Harris, Julie and Pearson, Talima and Yan, Yongpan and Keim, Paul and DeBess, Emilio and Marsden-Haug, Nicola and Wohrle, Ron and Engelthaler, David M. and Lockhart, Shawn R. (2011) Whole genome sequence analysis of Cryptococcus gattii from the pacific northwest reveals unexpected diversity. Plos One, 6 (12). pp. 1-7. ISSN 1932-6203

Available under License Creative Commons Public Domain Dedication.

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Publisher’s or external URL: http://dx.doi.org/10.1371/journal.pone.0028550


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.

Item Type: Article
ID number or DOI: 10.1371/journal.pone.0028550
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QR Microbiology > QR355 Virology
Department/Unit: College of Engineering, Forestry, and Natural Science > Biological Sciences
Research Centers > Center for Microbial Genetics and Genomics
Date Deposited: 28 Mar 2016 20:53
URI: http://openknowledge.nau.edu/id/eprint/1726

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