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The limitations of Second Line Probe Assay (SL-LPA) are:
- It detects resistance due to mutation in gyrA, gyrB, rrs, and eis genes; resistances originating from mutations of other genes or gene regions as well as other drug resistance cannot be determined.
- Individual strains in mixed samples cannot be differentiated, which hampers the interpretation of the test.
- It cannot be used to monitor drug treatment, as DNA is detected from viable and non-viable bacteria.
- The results are qualitative, the intensity of bands does not give an estimate of bacterial load in the sample.
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