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Seminal Candida Papers

Strain Information

Candida albicans Strains

SC5314

Genotype: wild type

Notes: Wild-type strain used in the systematic sequencing project, the reference sequence stored in CGD. The original strain background from which most of the common laboratory strains are derived. This strain is virulent in a mouse model of systemic infection and is frequently used as a wild-type control. In their 2004 Genome Biology paper on C. albicans genome sequence, Frank Odds, Al Brown and Neil Gow explain the origins of SC5314: "Strain SC5314 was used in the 1980s by scientists at the E.R. Squibb company (now Bristol-Myers Squibb, see Note1) for their pioneering studies of C. albicans molecular biology. It was engineered by Fonzi and Irwin to provide the uridine autotrophic mutant that has been essential to most subsequent molecular genetic research into C. albicans. The strain is usually described merely as a 'clinical isolate', but it is worth setting on record that SC5314 was originally isolated from a patient with generalized Candida infection by Margarita Silva-Hutner (see Note 2) at the Department of Dermatology, Columbia College of Physicians and Surgeons (New York, USA). The original isolate number was 1775 and the strain is identical with strain NYOH#4657 in the New York State Department of Health collection. (This information was provided by Joan Fung-Tome at Bristol-Myers Squibb as a personal communication.) SC5314 belongs to the predominant clade of closely related C. albicans strains that represents almost 40% of all isolates worldwide, as determined by DNA fingerprinting and multi-locus sequence typing (A. Tavanti, A.D. Davidson, N.A.R.G., M.C.J. Maiden and F.C.O., unpublished observations)."

Note 1: The earliest publications that used SC5314 came in 1968 from Squibb Institute for Medical Research.

Note 2: The documentation of the work done by Margarita Silva-Hutner and her lab is preserved at Columbia University Archival Collections.

References: Odds et al., 2004. Genome Biol. 2004; 5(7): 230; Fonzi and Irwin, 1993. 1993 Jul;134(3):717-28; Aszalos et al., 1968. J Antibiot (Tokyo). 1968 Oct;21(10):611-5; Maestrone and Semar, 1968. Naturwissenschaften. 1968 Feb;55(2):87-8; Meyers et al., 1968. Appl Microbiol. 1968 Apr;16(4):603-8.

BWP17

Genotype: ura3::imm434/ura3::imm434 iro1/iro1::imm434 his1::hisG/his1::hisG arg4/arg4

Notes: Isogenic to the SC5314 strain. Uridine, histidine and arginine auxotroph derived from the RM1000 strain by deletion of the ARG4 gene. This strain has a heterozygous deletion on chromosome 5 that was inherited from the RM1000 parental strain.

References: Wilson et al., 1999. J Bacteriol. 1999 Mar;181(6):1868-74.

CAF2-1

Genotype: URA3/ura3::imm434 IRO1/iro1::imm434

Notes: URA3 heterozygous strain derived from the SC5314 strain. The 3-prime end of one copy of the IRO1 gene that resides adjacent to URA3 was inadvertently deleted during the construction of this strain. This strain is virulent in a mouse model of systemic infection and is frequently used as a wild-type control.

References: Fonzi and Irwin, 1993. Genetics 1993 Jul;134(3):717-28.

CAI4

Genotype: ura3::imm434/ura3::imm434 iro1/iro1::imm434

Notes: Isogenic to the SC5314 strain. Uridine auxotroph constructed by deletion of the second copy of URA3. The second copy of IRO1 was inadvertently deleted upon strain construction. As a result, the strain and its descendants have no functional copy of IRO1. This strain is avirulent in a mouse model of systemic infection unless complemented with URA3.

References: Fonzi and Irwin, 1993. Genetics 1993 Jul;134(3):717-28; Garcia et al., 2001. Yeast. 2001 Mar 15;18(4):301-11.

CAI8

Genotype: ura3::imm434/ura3::imm434 iro1/iro1::imm434 ade2::hisG/ade2::hisG

Notes: Isogenic to the SC5314 strain. Derived from the CAF2-1 strain by deletion of URA3 and both copies of ADE2 using the URA-blaster method.

References: Fonzi and Irwin, 1993. Genetics 1993 Jul;134(3):717-28.

P37005

Genotype: MTLa/MTLa

Notes: Wild-type clinical isolate. Naturally homozygous for the MTLa mating type locus.

References: Lockhart et al., 2002. Genetics. 2002 Oct;162(2):737-45.

Red3/6

Genotype: ade2/ade2

Notes: Isogenic to the WO-1 strain. Adenine auxotroph derived from the WO-1 strain by chemical mutagenesis using MNNG.

References: Srikantha et al., 1995. Mol Cell Biol. 1995 Mar;15(3):1797-805.

RM1000

Genotype: ura3::imm434/ura3::imm434 iro1/iro1::imm434 his1::hisG/his1::hisG

Notes: Isogenic to the SC5314 strain. Derived from the CAI4 strain by deletion of the HIS1 gene using the URA-blaster method (see Fonzi and Irwin, 1993 for details of this method). The standard RM1000 strain was found to have a heterozygous deletion on chromosome 5. RM1000#2 is an isolate that has been shown to have wild-type copies of chromosome 5.

References: Negredo et al., 1997. Microbiology. 1997 Feb;143 ( Pt 2):297-302.

SN87

Genotype: ura3::imm434::URA3/ura3::imm434 iro1::IRO1/iro1::imm434 his1::hisG/his1::hisG leu2/leu2

Notes: Isogenic to the SC5314 strain. Histidine and leucine auxotroph derived from the RM1000#2 strain by deletion of the LEU2 gene. This strain is virulent in a mouse model of systemic infection.

References: Noble and Johnson, 2005. Eukaryot Cell. 2005 Feb;4(2):298-309.

SN95

Genotype: ura3::imm434::URA3/ura3iro1IRO1/iro1his1his1arg4/arg4

Notes: Isogenic to the SC5314 strain. Histidine and arginine auxotroph derived from the RM1000#2 strain by deletion of the ARG4 gene. This strain is virulent in a mouse model of systemic infection.

References: Noble and Johnson, 2005. Eukaryot Cell. 2005 Feb;4(2):298-309.

SN152

Genotype: ura3/::imm434::URA3/ura3::imm434 iro1::IRO1/iro1::imm434 his1::hisG/his1::hisG leu2/leu2 arg4/arg4

Notes: Isogenic to the SC5314 strain. Histidine, leucine and arginine auxotroph derived from the RM1000#2 strain by deletion of the LEU2 and ARG4 genes. This strain is virulent in a mouse model of systemic infection.

References: Noble and Johnson, 2005. Eukaryot Cell. 2005 Feb;4(2):298-309.

SN250

Genotype: his1Δ/his1Δ, leu2Δ::C.dubliniensis HIS1 /leu2Δ::C.maltosa LEU2, arg4Δ /arg4Δ, URA3/ura3Δ::imm434, IRO1/iro1Δ::imm434

Notes: Isogenic to the SC5314 strain. Derived from SN87 by integration of C. dubliniensis HIS1 and C. maltosa LEU2 at the disrupted leu2 loci and then deleted for arg4. Derived from SN87 and QMY23.

References: Noble et al., 2010. Nat Genet. 2010 Jul;42(7):590-8; 

Mitrovich et al., 2007. Genome Res. 2007 Apr;17(4):492-502.

WO-1

Genotype: MTLalpha

Notes: Wild-type clinical isolate that switches between white and opaque phenotypes at high frequency. The MTLa locus is absent in this strain (for more information see Lockhart et al., 2002). This strain has been sequenced by the Broad Institute (http://www.broadinstitute.org/annotation/genome/candida_group/GenomeDescriptions.html)

References: Slutsky et al., 1987. J Bacteriol. 1987 Jan;169(1):189-97; Lockhart et al., 2002. Genetics. 2002 Oct;162(2):737-45.

WUM5A

Genotype: MTLalpha/MTLalpha ura3-1Δ::FRT/ura3-2Δ::FRT

Notes: Isogenic to the WO-1 strain. Uridine auxotroph constructed by deletion of both copies of URA3.

References: Strauss et al. 2001. J Bacteriol. 2001 Jun;183(12):3761-9.

Candida glabrata (Nakaseomyces glabratus) Strains

B

Genotype: Wild type

Notes: Clinical isolate from a case of vaginitis that did not respond to fluconazole or boric acid treatment; it is virulent in a murine model of vaginitis. This strain was called LF 547.92 in the original publication.

References: Fidel et al., 1996. J Infect Dis. 1996 Feb;173(2):425-31.

BG2

Genotype: Wild type

Notes: Clinical isolate from a case of vaginitis that did not respond to fluconazole or boric acid treatment; it is virulent in a murine model of vaginitis

References: Cormack and Falkow, 1999. Genetics. 1999 Mar;151(3):979-87.

BG14

Genotype: ura3-delta(-285 +932)::Tn903NeoR

Notes: A ura3 derivative of the wild-type B2 clinical isolate.

References: Cormack and Falkow, 1999. Genetics. 1999 Mar;151(3):979-87.

BG462

Genotype: URA3

Notes: A derivative of the B2 clinical isolate with the URA3 gene restored

References: De Las Peñas, et al., 2003. Genes Dev. 2003 Sep 15;17(18):2245-58.

CBS138 (ATCC 2001)

Genotype: Wild type

Notes: Type strain for the Genolevures C. glabrata sequencing project. This strain has also been called NRRL-Y-65 and IFO 0622.

References: Dujon et al., 2004. Nature. 2004 Jul 1;430(6995):35-44; Koszul, et al., 2003. FEBS Lett. 2003 Jan 16;534(1-3):39-48.

2001T

Genotype: trp1

Notes: A trp1 auxotrophic strain derived from the CBS138 (ATCC 2001) wild-type strain.

References: Kitada et al., 1995. Gene. 1995 Nov 20;165(2):203-6.

2001HT

Genotype: his3 trp1::ScURA3

Notes: A his3 trp1 auxotrophic strain derived from 200T, a derivative of the CBS138 (ATCC 2001) wild-type strain.

References: Kitada et al., 1995. Gene. 1995 Nov 20;165(2):203-6.

NCCLS84 (ATCC 90030)

Genotype: Wild type

Notes: Wild-type strain

References: Espinel-Ingroff et al., 1992. J Clin Microbiol. 1992 Dec;30(12):3138-45

84u

Genotype: ura3

Notes: A ura3 derivative of the wild-type NCCLS84 (ATCC90030) strain.

References: Tsai et al., 2006. Antimicrob Agents Chemother. 2006 Apr;50(4):1384-92.

Candida parapsilosis Strains

ATCC 22019

Genotype: heterozygous MET/met

Notes: Application of parasexual genetic methods was used to determine that C. parapsilosis strain ATCC 22019 is is heterozygous MET/met

References: Whelan and Kwon-Chung, 1988. J Med Vet Mycol 1988 Jun;26(3):163-71.

CDC317

Genotype: Wild type

Notes: Reference strain used for the C. parapsilosis sequencing project. This isolate came from the hands of a hospital worker, who was the source for an outbreak of infection in a Mississippi community hospital in 2001.

References: Kuhn et al., 2004. Emerg Infect Dis. 2004 Jun;10(6):1074-81; Clark et al., 2004. J Clin Microbiol. 2004 Oct;42(10):4468-72.

CLIB214 (CBS 604; ATCC 22019; NRRL Y-12969)

Genotype: Wild type

Notes: Type strain, originally isolated from a patient with diarrhea in Puerto Rico by Ashford (1928). This strain is dependent on oxidative metabolism for growth since it lacks a fermentative pathway.

References: Ashford, 1928. Am J Trop Med 8:507�538. In: Kurtzman CP, Fell JW, Boekhout T (eds), 2011. The yeasts: a taxonomic study. p. 987-1278, 5th ed. Elsevier, London, United Kingdom; Logue et al., 2005. Eukaryot Cell 4(6):1009-17.

CPL2

Genotype: leu2Δ::FRT/leu2Δ::FRT, his1Δ::FRT/his1Δ::FRT, frt::CdHIS1

Notes: Leucine auxotroph laboratory strain

References: Németh et al., 2021. Virulence. 2021 Dec;12(1):937-950.

GA1

Genotype: Wild type

Notes: Wild-type clinical isolate. The SAT1 flipper method and the Candida albicans IMH3 gene have been used as dominant-selectable markers to construct gene knockouts in this strain.

References: Gácser et al., 2005. FEMS Microbiol Lett. 2005 Apr 1;245(1):117-21; Gácser et al., 2007. J Clin Invest. 2007 Oct;117(10):3049-58.

SR23 (CBS7157)

Genotype: ade- lys-

Notes: An adenine and lysine auxotroph isolated from a contaminated culture of Saccharomyces cerevisiae as a yeast with peculiar physiological features and carrying a linear mitochondrial DNA

References: Kovac et al., 1984. Mol Gen Genet 197:420-424; Nosek et al., 2004. Mol Genet Genomics 272(2):173-80; Mutalová et al., 2024. Microbiol Resour Announc. 2024 Jul 31;13(9):e00347-24.

Candida auris (Candidozyma auris) Strains

AR0382 (B11109)

Genotype: Wild type

Notes: Aggregative strain with high biofilm formation.

References: Vila et al., 2020. mSphere. 2020 Aug 5;5(4):e00760-20; Wang et al., 2024. Nat Commun. 2024 Oct 25;15(1):9212.

AR0387 (B8441)

Genotype: Wild type

Notes: Reference strain; non-aggregative strain with low biofilm formation.

References: Vila et al., 2020. mSphere. 2020 Aug 5;5(4):e00760-20; Wang et al., 2024. Nat Commun. 2024 Oct 25;15(1):9212.

AR0389

Genotype: erg11-Y132F

Notes: Has high drug resistance due to an ERG11 mutation (Y132F) and overexpression of the drug efflux transporter gene CDR1.

References: Shinohara et al., 2024. JAC Antimicrob Resist. 2024 Feb 21;6(1):dlad155.

AR0390 (B11205)

Genotype: erg11-K143R

Notes: Clinical isolate with high fluconazole resistance.

References: Rybak et al., 2021. Microbiol Spectr. 2021 Dec 8;9(3):e01585-21.

B11220

Genotype: Wild type

Notes: Clade II clinical isolate with susceptibility to all antifungal drugs.

References: Yang et al., 2024. Infect Immun. 2024 Jun 11;92(6):e0010324.

B11221

Genotype: Wild type

Notes: Clade III clinical isolate with resistance to caspofungin. Contains an L-rhamnose utilization cluster that appears to allow more ready use of alternate sugars, better drug tolerance, and better survival from host immune cell attack, possibly due to reduced β-(1,3)-glucans at the cell surface.

References: Yang et al., 2024. Infect Immun. 2024 Jun 11;92(6):e0010324.

Candida tropicalis Strains

ATCC 20336 (pK233)

Genotype: Wild type

Notes: This strain excretes alpha,omega-dicarboxylic acids as a by-product when cultured on n-alkanes or fatty acids as the carbon source.

References: Craft et al., 2003. Appl Environ Microbiol 69(10):5983-91.

ATCC 20913

Genotype: ura3/ura3

Notes: A uracil auxotroph derived from C. tropicalis ATCC 20336 by random mutagenesis.

References: Haas et al., 1990. J Bacteriol 172(8):4571-7.

ATCC 750

Genotype: Wild type

Notes: A wild-type fluconazole susceptible strain.

References: Barchiesi et al., 2000. Antimicrob Agents Chemother 44(6):1578-84.

NCYC2512

Genotype: Wild type

Notes: A wild-type saline soil isolate from Pakistan that is capable of producing large amounts of alpha,omega-dodecanedioic acid.

References: Rodriguez et al., 1996. Yeast 12(13):1321-9.

1230

Genotype: Wild type

Notes: A wild-type dicarboxylic acid-producing industrial strain.

References: He and Chen, 2005. Yeast 22(6):481-91.

Candida dubliniensis Strains

CD36

Genotype: Wild type

Notes: Type strain, oral isolate from an HIV+ patient in Ireland; also catalogued as NCPF 3949 and CBS-7987.

References: Sullivan et al., 1995. Microbiology (Reading) 1995 Jul:141 ( Pt 7):1507-21.

Protocols and Methods

Candida albicans Protocols and Methods

Candida glabrata (Nakaseomyces glabratus) Protocols and Methods

  • Genetic manipulation of C. glabrata

Candida parapsilosis Protocols and Methods

Candida auris (Candidozyma auris) Protocols and Methods

Candida dubliensis Protocols and Methods

Candida tropicalis Protocols and Methods

Species Comparisons by Topic

Ploidy

Notes: Candida albicans and its close relatives are all on a single phylogenetic branch characterized by diploidy, while the two typical haploid species (C. glabrata and C. auris) are on distinct, distantly related branches for which haploidy is the standard form. Note that the two haploid pathogens are more prone to pleiotropic resistance because only a single mutation is needed in the haploid genome to generate stable change.

References:

Typical diploids

  • C. albicans
  • C. dubliniensis
  • C. parapsilosis
  • C. tropicalis

Typical haploids

  • C. glabrata
  • C. auris

From Munoz et al., 2018


CUG codon usage

Notes: Yeasts of the Candida clade (as opposed to C. glabrata, also known as Nakaseomyces glabratus, which is on the Saccharomyces clade) have undergone an evolutionary reassignment of the CUG codon from leucine to serine. This is due to a novel serine-tRNA (ser-tRNACAG) that contains a guanosine at position 33, a position that is occupied by a pyrimidine (uridine) in nearly all other tRNAs.

References:

Reassigned CUG as serine

  • C. albicans
  • C. dubliniensis
  • C. parapsilosis
  • C. tropicalis
  • C. auris

Standard CUG as leucine

  • C. glabrata


From Butler et al., 2009

Mitochondrial genome

Notes: Candida parapsilosis is unusual in having a mitochondrial genome that is linear and capped by telomeric ends. The close relatives of this species, C. orthopsilosis and C. metapsilosis and Candida subhashii, have a mix of circular and linear mitochondrial genomes. The other Candida spp. are exclusively circular.

References:

Exclusively linear

  • C. parapsilosis

Mix of linear and circular

  • C. orthopsilosis
  • C. metapsilosis
  • C. subhashii

Exclusively circular

  • C. albicans
  • C. dubliniensis
  • C. tropicalis
  • C. auris
  • C. glabrata

From Kosa et al., 2006

Filamentous growth

Notes: Candida spp. vary in filamentous growth as a means of infection/invasion. C. albicans and its close relative C. dubliniensis use true hyphae to penetrate tissues, while C. parapsilosis and C. tropicalis can penetrate tissues by means of pseudohyphae (lacking septa). In contrast, C. glabrata almost never forms filaments and infects in the yeast form. C. auris is an outlier in that it infects both by pseudohyphae and in the yeast form.

Note that the classifications below represent the typical forms for each species, but exceptions are not unusual.


References:


Invasive/infectious by true hyphae

  • C. albicans
  • C. dubliniensis

Invasive/infectious pseudohyphal growth (lacking septa)

  • C. parapsilosis
  • C. tropicalis
  • C. auris

Invasive/infectious as yeast form

  • C. glabrata
  • C. auris


From Kosa et al., 2006

Biofilms

Pathogenicity

Mating/Reproduction

Drug resistance

Respiratory metabolism

Datasets

  • RNA-Seq
  • ChIP-Seq

Community Resources

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