Table 2.

Molecular methods and proteomics for the identification and genotyping of Candida tropicalis.

	Method	Principle	Advantages	Disadvantages	References
Proteomics	Protein profile by mass spectrophotometry	Uses an ionizing matrix and has been assembled to automated methods of microorganisms identification such as MALDI Biotyper and VITEK-MS and several other mass spectrometer	Simple methodology of easy sample preparation and short time for analysis, more efficient than the conventional methods, accurate identification	Higher cost of equipment, necessity for specialized training; possible lack of a robust database	Chao et al., 2014; Angeletti et al., 2015; Panda et al., 2015; Sariguzel et al., 2015; Keceli et al., 2016; Stefaniuk et al., 2016
Molecular identification	Molecular rDNA sequencing	Based on the ability of DNA polymerase to copy a DNA strand from the template in the presence of a primer. The inclusion of fluorescent markers with different colors allows the differentiation of the chains truncated by the respective fluorescence	Robust technique, automated, Higher accuracy, gold standard identification	Requirement for specialized equipment, expensive reagents, and highly trained personnel	Pincus et al., 2007
	PNA-FISH	Based on the use peptide nucleic acid probes directed to specific rRNA species of the main Candida species tagged with fluorescent dyes	High sensitivity and specificity	There may be some problem in discriminating closely related microorganisms	Stender, 2003; Hall et al., 2012; Stone et al., 2013; Calderaro et al., 2014; Gorton et al., 2014; Aydemir et al., 2016
Genotyping	Randomly Amplified Polymorphic DNA (RAPD)	Based on the amplification of DNA fragments by polymerase chain reaction (PCR) by using shortprimers containing random sequences	Fast, simple and low-cost method for detecting polymorphisms; Does not require radioactively labeled probes; use of arbitrary primers, no need of initial genetic or genomic information, and the requirement of only tiny quantities of target DNA	Dominant technique; low reproducibility and low discriminatory power; difficult standardization, possible problems of interpretation	Wu et al., 2014; Almeida et al., 2015
	Microsatellites analysis	Based on the amplification by PCR of small tandem sequence repeats from 2 to 6 highly polymorphic nucleotides, present on chromosomal telomeric regions	Easy execution, reproducible, appropriate for large-scale epidemiological studies, good discriminatory power;	Technical challenges during the construction of enriched libraries and species-specific primers
	Multilocus Sequence Typing (MLST)	Based on the amplification of 6–10 housekeeping genes by PCR, with further PCR products purification and gene sequencing. Gene sequencing generates the sequence type (ST) for haploid organisms and diploid sequence types (DST) for the diploids microorganisms, which also may be compared to a database	Robust technique with high discriminatory power, excellent reproducibility, easy standardization; data that can be shared and compared between different laboratories easily through the Internet	Requirement for specialized equipment, expensive reagents, and highly trained personnel; phylogenetic relationships and resolution of clones can be masked by the use of slowly evolving housekeeping genes	Maiden et al., 1998; Tavanti et al., 2005; Odds and Jacobsen, 2008; Chen et al., 2009; Wu et al., 2012