Molecular Fingerprints to Identify Candida Species

Table 2

Summary of loci used for individual MLST schemes. Data for C. dubliniensis, C. glabrata, C. krusei, and C. tropicalis are from McManus et al. [50], Dodgson et al. [42], Jacobsen et al. [51], and Tavanti et al. [52], respectively.

Species	Locus	Gene product	Primers	Sequenced fragment size (bp)	Genotypes/site
C. dubliniensis	CdAAT1a	Aspartate aminotransferase	F: ATCAAACTACTAAATTTTTGAC	373	1.25
			R: CGGCAACATGATTAGCCC
	CdACC1	Acetyl-coenzyme A carboxylase	F: GCCAGAGAAATTTTGATCCAATGT	407	1.33
			R: TTCATCAACATCATCCAAGTG
	CdADP1	ATP-dependent permease	F: GAGCCAAGTATGAATGACTTG	443	1.2
			R: TTGATCAACAAACCCGATAAT
	CdPMIb	Mannose phosphate isomerase	F: ACCAGAAATGGCC	375	3.5
			R: GCAGCCATACATTCAATTAT
	CdRPN2	26S proteasome regulatory subunit	F: TTTATGCATGCTGGTACTACTGATG	302	1
			R: TAACCCCATACTCAAAGCAGCAGCCT
	CdSYA1	Alanyl-RNA synthetase	F: AGAAGAATAGTTGCTCTTACTG	391	1
			R: GTTGCCCTTACCACCAGCTTT
	CdVPS13	Vacuolar protein sorting 13	F: CGTTGAGAGATATTCGACTT	403	1.33
			R: ACGGATCGATCGCCAATCC
	CdZWF1b	Glucose-6-phosphate dehydrogenase	F: GTTTCATTTGATCCTGAAGC	491	0.86
			R: GCCATTGATAAGTACCTGGAT
C. glabrata	CgFKS	1,3-𝛽-glucan synthase	F: GTCAAATGCCACAACAACAACCT	589	1.27
			R: AGCACTTCAGCAGCGTCTTCAG
	CgLEU2	3-Isopropylmalate dehydrogenase	F: TTTCTTGTATCCTCCCATTGTTCA	512	1
			R: ATAGGTAAAGGTGGGTTGTGTTGC
	CgNMT1	Myristoyl-coenzyme A, protein N-myristoyltransferase	F: GCCGGTGTGGTGTTGCCTGCTC	607	0.81
			R: CGTTACTGCGGTGCTCGGTGTCG
	CgTRP1	Phosphoribosyl-anthranilate isomerase	F: AATTGTTCCAGCGTTTTTGT	419	1.08
			R: GACCAGTCCAGCTCTTTCAC
	CgUGP1	UTP-glucose-1-phosphate uridylyltransferase	F: TTTCAACACCGACAAGGACACAGA	616	0.75
			R: TCGGACTTCACTAGCAGCAAATCA
	CgURA3	Orotidine-5′-phosphate decarboxylase	F: AGCGAATTGTTGAAGTTGGTTGA	602	0.68
			R: AATTCGGTTGTAAGATGATGTTGC
C. krusei	CkADE2	Phosphoribosylaminoimidazole carboxylase	F: GTCACTTCTCAGTTTGAAGC	470	2.33
			R: ACACCATCTAAAGTAGAGCC
	CkHIS3	Imidazole glycerol phosphate dehydratase	F: GGAGGGGACATATCACTGCC	400	1.75
			R: AATCTTTAATTGCCAAAGCC
	CkLEU2	3-Isopropylmalate dehydrogenase	F: CTGTGAGACCAGAACAGGGG	619	1.89
			R: GCAGAGCCACCCAAGTCTCC
	CkLYS2	L-Aminoadipate-semialdehyde dehydrogenase	F: ATCTGAGAAGCAGTTGGCGC	441	1.90
			R: AGACTTGTAAGAATTATCCC
	CkNMT1	Myristoyl-coenzyme A, protein N-myristoyltransferase	F: CTGATGAAGAAATCACCG	537	2.00
			R: GCTTGATATCATCTTTGTCC
	CkTRP1	Phosphoribosyl-anthranilate isomerase	F: AGCTATGTCGAGCAAAGAGG	380	2.00
			R: ACATCAACGCCACAACACCC
C. tropicalis	CtICL1	Isocitrate lyase	F: CAACAGATTGGTTGCCATCAGAGC	447	0.71
			R: CGAAGTCATCAACAGCCAAAGCAG
	CtMDR1	Multidrug resistance protein	F: TGTTGGCATTCACCCTTCCT	425	1.67
			R: TGGAGCACCAAACAATGGGA
	CtSAPT2	Secreted aspartic protease 2	F: CAACGATCGTGGTGCTG	525	0.51
			R: CACTGGTAGCTGAAGGAG
	CtSAPT4	Secreted aspartic protease 4	F: TGCTTCTCCTACAACTTCACCTCC	390	0.90
			R: ATTCCCATGACTCCCTGAGCAACA
	CtXYR1	D-xylose reductase I or II	F: AGTTGGTTTCGGATGTTG	370	3.00
			R: TCGTAAATCAAAGCACCAGT
	CtZWF1	Glucose-6-phosphate dehydrogenase	F: GGTGCTTCAGGAGATTTAGC	520	0.94
			R: ACCTTCAGTACCAAAAGCTTC

F and R indicate forward and reverse primers, respectively. Genotypes/site indicate the ratio of genotypes to SNPs.