Description of Genotyping Methods: Spoligotyping
Spacer oligonucleotide typing is a hybridization assay that detects variability in the direct repeat (DR) region in the DNA of M. tuberculosis. The DR region consists of multiple copies of a conserved 36-base-pair sequence (the direct repeats) separated by multiple unique spacer sequences (the standard spoligotyping assay uses 43). Different M. tuberculosis strains have various complements of the 43 spacers, and these different complements form the basis of the assay (Kamerbeek 1997).
The standard spoligotyping assay is performed by using a membrane. In this format, each of the 43 spacers produces either a dark band (indicating the presence of the spacer) or no band (indicating the absence of spacer). As Figure 1. shows, for each M. tuberculosis isolate, the spoligotyping assay produces a series of bands, much like a bar code.
Figure 1. Two examples of spoligotype results showing the original banding patterns as well as the steps involved in converting the banding pattern results to the final octal code designation. The octal designation is the form of the result that is reported by the genotyping laboratories to TB programs.
MSc. Nguyen Hoang Bach
Carlo Urbani Center, Hue College of Medicine and Pharmacy
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