Computational protocol: Genotyping Candida albicans from Candida Leukoplakia and Non Candida Leukoplakia Shows No Enrichment of Multilocus Sequence Typing Clades but Enrichment of ABC Genotype C in Candida Leukoplakia

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Protocol publication

[…] Twenty-five C. albicans isolates from CL lesions and 19 isolates from NCL lesions, from separate patients in each case (with the exception of two isolates, CL12 and CL122 which were recovered from separate CL lesions in patient 12), were subjected to MLST as described previously . For comparison, MLST was also performed on 34 oral carriage (OC) C. albicans isolates recovered from oral rinse samples of 34 separate control healthy subjects attending the DDUH Accident and Emergency Department. All DNA sequencing reactions were performed commercially by Source Bioscience LifeSciences (Dublin, Ireland) using ABI 3730xl DNA analysers and dye-labelled terminators (Applied Biosystems, Foster City, CA, USA). Sequences were analysed using BioNumerics version 5.0 software (Applied Maths NV, Saint-Martens-Latem, Belgium) and the online C. albicans MLST database (http://calbicans.mlst.net). All MLST data generated in the present study have been deposited in the C. albicans MLST database (http://calbicans.mlst.net).The genetic relatedness of the isolates investigated in the present study to each other and to selected strains from the online MLST database was evaluated using the software program MEGA version 5 to generate dendrograms based on the unweighted-pair group method with arithmetic averages (UPGMA) . The UPGMA clustering algorithm defines MLST clades that correlate well with those previously defined by DNA fingerprinting using the C. albicans-specific repetitive sequence-containing Ca3 probe .The online Based Upon Related (eBURST) algorithm (http://eburst.mlst.net) was used to subdivide MLST allelic profile datasets into hypothetical non-overlapping groups of clonal complexes (CCs) composed of a single putative founder diploid sequence type (DST) and its closely related descendant DSTs , . […]

Pipeline specifications

Software tools BioNumerics, MEGA, BURST
Databases MLST.net
Application WGS analysis
Organisms Candida albicans, Homo sapiens
Diseases Brain Diseases, Neoplasms