High-Frequency Genetic Contents Variations in Clinical Candida albicans Isolates

Abstract

Candida albicans is the most common fungal pathogen, causing skin and mucosal infections in generally healthy individuals, life-threatening infections in immunocompromised patients, and leading to death in up to 50% of patients with bloodstream infections. 1,2)C. albicans is known for its unstable genome. The instability of the chromosome copy number of entire chromosomes, as well as the large portions of chromosomes was extensively studied with laboratory and freshly isolated strains using pulse-field gene electrophoresis (PFGE) as reviewed by Rustchenko,3) Rustchenko and Sherman,4) and Selmecki et al. 5) Combined with Southern blot analysis, PFGE allowed limited analysis of gene copy number, and also could be extended to the analysis of chromosome deletions and other rearrangements. [6][7][8][9][10][11][12][13][14][15] Recently, array technology opened a new dimension in the study of genome instability. Array comparative genomic hybridization (array CGH) allows the detection of genomic variations across a whole genome. When the CGH intensity data are plotted as a function of position on the genetic map, aneuploidy of chromosomes or chromosomal segments are readily identified. The availability of the C. albicans strain SC5314 genome sequence has allowed the construction of microarrays for the analysis of gene copy number. Berman's laboratory largely used array CGH to demonstrate aneuploidies in C. albicans derivatives of the sequencing strain SC5314, several laboratory strains, as well as clinical isolates, as reviewed by Selmecki et al. 5)Also, Thewes et al. 16) used array CGH to elucidate the genomic diversity among C. albicans less virulent strain ATCC10231 and the reference sequencing strain SC5314 in the hope to uncover genetic basis of pathogenicity. Although some variable genes were identified, this study was limited to a single strain.Despite the extensive effort of various laboratories, a comprehensive study, which would include various strains and which would focus on the DNA sequence and gene copy number variability is still lacking, although this approach was applied to other organisms, including Saccharomyces cerevisiae. 17,18) In order to fill this need, we examined the genomic contents of eight clinical isolates, as compared to the SC5314 reference strain, using array CGH. The Cluster Along Chromosomes (CLAC) algorithm was employed to identify variable genes. Medical School; Rochester, N.Y., 14642, U.S.A.: and c Department of Pharmacology, School of Pharmacy, Second Military Medical University; Shanghai 200433, China. Received October 25, 2010; accepted January 24, 2011; published online February 16, 2011 Genome plasticity is a hallmark of Candida albicans and is believed to be an adaptation strategy. But the extent of such genomic variability is not well investigated. In this study, genetic contents of clinical C. albicans isolates were investigated at whole-genome level with array-based comparative genomic hybridization (array CGH) technology. It was revealed that C. albicans possess...

Genetic and phenotypic intra-species variation in Candida albicans

“…This is consistent with earlier studies that revealed karyotypic variation in multiple C. albicans isolates (Suzuki et al 1982;Rustchenko-Bulgac 1991;Perepnikhatka et al 1999;Selmecki et al 2006;Rustchenko 2007;Bouchonville et al 2009;Yang et al 2011). In the current study, seven of the 21 strains contained trisomic chromosomes, with Chr 4 and Chr 7 being trisomic in multiple isolates.…”

“…Analysis of the 21 C. albicans genomes revealed gene copy number variation, including transposons that have previously been shown to be active and to have differential representation between strains Holton et al 2001;Yang et al 2011). Variable copy number was also observed for the CYP5 gene that encodes a cytoplasmic cyclophilin.…”

Transposition of the Zorro2 Retrotransposon Is Activated by Miconazole in <i>Candida albicans</i>

“…We previously revealed that the copy numbers of ORF19.7274 and ORF19.7275 of the Zorro2 retrotransposon were increased in several clinical isolates compared with SC5314 by array-based comparative genomic hybridization analysis. 21) In this study, the transcription of Zorro2 was found up-regulated in strains in response to shorttime MCZ stress. Additional copies of Zorro2 were observed in the genome of derivative strains under long-term treatment of MCZ, suggesting that the Zorro2 has been transposed in the derivative strains with resistance to azole drugs.…”

“…Previous studies have reported that retrotransposons, including Tca2, Tca5, Zorro1 and Zorro3, can be activated by temperature changes in C. albicans, [15][16][17]20) but no evidence has yet been provided to prove the transcription or transposition activity for Zorro2 in C. albicans. In this study, we showed that the Zorro2 retrotransposon in C. albicans was transcriptionally activated and transposed in response to MCZ, probably caused by the induction of endogenous ROS.…”

Kinetics of oral colonization by Candida spp. during topical corticotherapy for oral lichen planus

“…Quantification of DNA copies from five Candida species was performed by qPCR with previously described primers , derived from the ITS2 regions of C. albicans, C. glabrata , C. parapsilosis , C. dubliniensis and C. tropicalis . Reactions were carried out with SYBR Green Master Mix (Applied Biosystems, Foster City, CA, USA), in a StepOne™ Real‐Time PCR System (Applied Biosystems) with one cycle of 10 min at 95°C; 40 cycles of 15 s at 95°C, 1 min at 60°C; and a final extension cycle at 72°C for 15 s.…”