Detection of specific bacterial gene regions

The high sensitivity gained by real-time PCR allows detection of specific gene or gene regions. Target-specific bacterial genes can be detected even when they are present in very low concentrations, thus permitting detection and/or quantification of minor bacterial subpopulations, bacterial mutations, and drug-resistance strains (Sloan et al., 2004; Costa et al., 2005).

Resistance in Mycobacterium tuberculosis is mostly conferred by point mutations in genes coding for drug targets or drug-converting enzymes (van Doorn et al., 2003; Rindi et al., 2003). The catalase peroxidase gene (katG) is the most commonly targeted gene region for the detection of isoniazid-resistance, with the majority of mutations occurring at codon 315 in 30-90% of isoniazid-resistant strains. Genotypic real-time PCR assays that detect mutations within such regions are predictive of clinical drug resistance and have potential to provide rapid detection of resistance in bacterial isolates (Rindi et al., 2003). Recently developed real-time PCR genotypic assays for detection of isoniazid resistance in Mycobacterium tuberculosis simply detect the mutations C (-15) T and G (-24) T in the regulatory region of the inhA gene (Rindi et al., 2003).

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