Background: The comparative diagnostic accuracy of mean and lowest Ct values needs to be evaluated for the assessment of mycobacterial burden in tubercular cases. Mutation in any codon of 81 base-pair core regions prevents the hybridization of one or more of five overlapping Probes A-Ein Xpert MTB/RIF assay indicated by “missing probe. Molecular epidemiology of missing probes may prove useful in tracing the source of infection and selection of a more suitable drug regimen for treatment.

Methods: This study included 65 rifampicin resistant cases and an equal number of rifampicin sensitive cases detected by Xpert MTB/RIF assay. Only samples tested positive for tubercular bacilli were included. The information regarding the tubercular load, Ct values of five probes targeting the rpoB gene, lowest Ct value among the five probes, missing probe in rifampicin resistant cases and time taken for the entire cycle were recorded in each case.

Results: Lowest Ct is a stronger indicator of tubercular load than the mean Ct value. E probe was found to be missing in majority (64.6%) of the cases, followed by A (6.2%), B and D (4.6%), C (1.5%) probes. In 7.6% cases, more than one probe was missing. None of the probe was missing in 10.6% of rifampicin resistant cases.

Conclusions: 

Lowest Ct value was found to be a better tool than mean Ct value for the determination of mycobacterium burden. Molecular epidemiology of missing probes could be useful in the development of new probes for the detection of rifampicin resistance.