Computer-assisted methods for assessing strain relatedness in Candida albicans by fingerprinting with the moderately repetitive sequence Ca3

Abstract

When used to probe EcoRI-digested Candida albicans DNA, the moderately repetitive sequence Ca3 generated a Southern blot hybridization pattern which included 15 to 25 bands, depending upon the strain. The pattern was stable through 400 generations in each of three independent strains but variable between most of 46 unrelated tester strains, making it a very effective probe for discrimination between strains. Computerassisted methods (Dendron) were developed for storage of Ca3 patterns in data files, calculation of similarity (SAB) values between strains based upon band positions and intensities, and generation of histograms and dendrograms based on SAB values for all strains or any subset of strains in large epidemiological studies. In testing the effectiveness of the system, it was found that (i) multiple isolates from different body locations of the same healthy individual could represent either the same strain or different strains, (ii) isolates from oral lesions of a husband and wife represented the same strain, (iii) strains isolated from the mouths of 10 healthy individuals on the same day and in the same geographical location were as dissimilar on average as the 46 unrelated tester strains, and (iv) strains isolated from seven immunocompromised patients hospitalized over a 2.5-month period in the same hospital were highly similar, indicating nosocomial origin. The apparent effectiveness of these fingerprinting methods and the Dendron program suggests that interlaboratory procedures for fingerprinting should be standardized and all patterns should be analyzed and stored in a common and accessible data base for broad epidemiological analysis.

Comparative study of the genepath group 4 reagent system and other chef systems for karyotype analysis of candida spp

“…The power of the molecular subtype analysis can be improved by the use of computer-assisted analytical techniques which also provides dendrograms for vizualizing clustering of strains with similar band patterns (32,33,35). When this technique was applied to the set of C .…”

“…The banding pattern data for each strain were normalized against an internal standard. The Dendron program computed the similarity coefficients Sm for every pairs of strains on the bases of the positions (molecular weight) of bands in the DNA pattern (32,33). The system also provided dendograms which reflected the relatedness among strains based on similarity values calculated by the unweighted group pair method (32).…”

Molecular methods for strain typing of Candida albicans : a review

“…Ease of performance and feasibility refers to the cost of specialized equipment and reagents, the facility to implement the technique in routine use, the technical complexity of the procedure and the ease of result interpretation. Moreover, data should be suitable for computerized analysis and storage, which is needed for the construction of databases (Schmid et al 1990;Singh et al 2006).…”

“…When used to probe Southern blots of EcoRI-digested DNA, Ca3 identifies over 20 bands of various intensities that include invariable (monomorphic), moderately variable and hypervariable bands (Schmid et al 1990). The Ca3 probe has been demonstrated to be highly effective in the analysis of C. albicans populations and has identified five major clades (named I, II, III, SA and E) of closely related strain types (Schmid et al 1995;Pujol et al 1997Pujol et al , 2002Blignaut et al 2002;Soll and Pujol 2003).…”

“…Moreover, Ca3 hybridization has proven to be reproducible and amenable to computer-assisted analysis. Databases have been established for subsequent retrospective and comparative studies (Schmid et al 1990;Schr€ oppel et al 1994;Lockhart et al 1996).…”