# Molecular Techniques and Target Selection for the Identification of _Candida_ spp. in Oral Samples
## 3 Molecular Identification of _Candida_ spp.  
A definitive diagnosis of candidiasis does not rely merely on its detection in the oral cavity. Since Candida spp. are commensal organisms, a negative culture result, for example, has a greater diagnostic significance than a positive culture result. Conversely, a positive culture result for Candida does not mean that the patient has oral candidiasis. Furthermore, a negative result is only relevant if the techniques used can identify all members of the genus.  
Several Polymerase Chain Reaction (PCR) and non-PCR-based methods are used for the molecular identification of Candida spp. The search for a precise, fast, and low-cost identification of fungal species is a great challenge in mycology [47], especially when dealing with species complexes. Phenotypic-based identification is frequently inconclusive.  
Techniques based on PCR usually target fungal pathogens by using species-specific probes or primers [47; 48; 49]. Conventional PCR, semi-nested and nested PCR, PCR-enzyme immunoassay, various types of real-time PCR, and multiplex PCR have all been used for the in vitro detection of _Candida_ species, both qualitative and quantitatively [50]. PCR-based methodologies are often applied in the diagnosis of fungal infections, although they can differ considerably in terms of the outcome. These techniques can be applied for the detection of antifungal resistance-inducing mutations, the quantification of fungal load, and the antifungal therapy surveillance and pathogenesis of _Candida_ infection [51]. The PCR-based approaches rely on broad or genus-specific primers that amplify conserved rRNA regions that are sequenced afterwards [52; 53] or subjected to other techniques such as analysis of polymorphic sequences (RFLP: Restriction Fragment Length Polymorphism; AFLP: Amplified Fragment Length Polymorphism; RAPD: Random Amplification of Polymorphic DNA; STR: Short Tandem Repeats) [54; 55], high-resolution melting analy  
\begin{table}
\begin{tabular}{c c c c c c c c c c c} \hline \hline  & \multicolumn{6}{c}{**Blood Samples**} & \multicolumn{6}{c}{**Oral Samples**} \\ \hline  & \multicolumn{6}{c}{**Azoles**} & \multicolumn{6}{c}{**Echinocandins**} & \multicolumn{6}{c}{**Azoles**} \\ \cline{2-11}  & **AmB** & **FLU** & **ITRA** & **VOR** & **POS** & **MICA** & **CASP** & **AmB** & **FLU** & **VOR** \\ \hline _C. albicans_ & S & R & S & I & I-R & S-I & S-I & S & S & S \\ \hline _C. tropicalis_ & S & R & S & S-I & I-R & S & S-I & S & S & S \\ \hline _C. parapysilosis_ & S & R & S & S-I & S & S & S & - & - & - \\ \hline _C. glabrata_ & S-I & R & I & S-I & I-R & S-I & S & S & S & S \\ \hline _C. krusei_ & S & R & S-I-R & S & S & S & S & S & R & S \\ \hline _C. lusitaniae_ & S & I & S & S & S & S & S & - & - & - \\ \hline _C. auris_ & S-I & R & R & R & - & R & R & - & - & - \\ \hline \hline \end{tabular}
\end{table}
Table 1: Susceptibility patterns of _Candida_ species from blood and oral samples. AmB amphoteric B, FLU fluconazole, IFRA itraconazole, VOR voriconazole, POS posaconazole, MICA micafungin; CAPS caspfungin, S-susceptible, I-intermediate, R-resistant [43; 44; 45; 46].  
sis (HRMA) [46; 54; 56; 57], microarray-based detection [58; 59], and capillary electrophoresis [60]. Capillary electrophoresis is better suited than classical electrophoresis for DNA separation due to its superior speed, efficiency, sensitivity, and simpler suitability for automation [61]. However, the use of this technique creates the need for complex equipment adding complexity to equipment maintenance and specialized personnel.  
Existing PCR protocols require enhancements in sensitivity, standardization, and swiftness, as well as a decrease in complexity, in order to be applicable for routine clinical diagnostics [48]. There is a considerable lack of information related to protocols and techniques to identify Candida spp. from oral samples, especially when compared to blood.