PMID- 22163313
OWN - NLM
STAT- MEDLINE
DCOM- 20120720
LR  - 20211021
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 6
IP  - 12
DP  - 2011
TI  - Whole genome sequence analysis of Cryptococcus gattii from the Pacific Northwest 
      reveals unexpected diversity.
PG  - e28550
LID - 10.1371/journal.pone.0028550 [doi]
LID - e28550
AB  - 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.
FAU - Gillece, John D
AU  - Gillece JD
AD  - Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, 
      Arizona, United States of America.
FAU - Schupp, James M
AU  - Schupp JM
FAU - Balajee, S Arunmozhi
AU  - Balajee SA
FAU - Harris, Julie
AU  - Harris J
FAU - Pearson, Talima
AU  - Pearson T
FAU - Yan, Yongpan
AU  - Yan Y
FAU - Keim, Paul
AU  - Keim P
FAU - DeBess, Emilio
AU  - DeBess E
FAU - Marsden-Haug, Nicola
AU  - Marsden-Haug N
FAU - Wohrle, Ron
AU  - Wohrle R
FAU - Engelthaler, David M
AU  - Engelthaler DM
FAU - Lockhart, Shawn R
AU  - Lockhart SR
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, P.H.S.
DEP - 20111207
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
SB  - IM
MH  - Biodiversity
MH  - Cryptococcosis/*microbiology
MH  - Cryptococcus gattii/*genetics
MH  - Genetic Variation
MH  - Genome
MH  - Genome, Fungal
MH  - Genotype
MH  - Geography
MH  - Phylogeny
MH  - Pneumonia/*microbiology
MH  - Polymorphism, Single Nucleotide
MH  - Sequence Analysis, DNA
MH  - Species Specificity
PMC - PMC3233577
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2011/12/14 06:00
MHDA- 2012/07/21 06:00
PMCR- 2011/12/07
CRDT- 2011/12/14 06:00
PHST- 2011/04/19 00:00 [received]
PHST- 2011/11/10 00:00 [accepted]
PHST- 2011/12/14 06:00 [entrez]
PHST- 2011/12/14 06:00 [pubmed]
PHST- 2012/07/21 06:00 [medline]
PHST- 2011/12/07 00:00 [pmc-release]
AID - PONE-D-11-06852 [pii]
AID - 10.1371/journal.pone.0028550 [doi]
PST - ppublish
SO  - PLoS One. 2011;6(12):e28550. doi: 10.1371/journal.pone.0028550. Epub 2011 Dec 7.