A Rapid and Sensitive Diagnostic Screening Assay for Detection of Mycobacteria Including Mycobacterium tuberculosis Directly from Sputum without Extraction

Abstract

We report a novel approach utilising a real-time PCR screening assay targeting a 53 bp tandemly repeated element present at various loci within the Mycobacterium tuberculosis (Mtb) genome. Positive samples were identified within a discriminatory melting curve range of 90-94°C, with results obtained in under one hour directly from decontaminated sputum samples without extraction. A panel of 89 smear-positive sputa were used for analytical validation of the assay with 100% concordance, with sensitivity matching that of culture. Cross reactivity was detected within a narrow range of mycobacteria other than tuberculosis (MOTT) (five sputa, three in silico), with the highest sensitivity within M. avium complex (MAC). A year-long head to head evaluation of the test with the GeneXpert platform was carried out with 104 consecutive samples at the Royal Free Hospital, UK. Receiver operating characteristics (ROC) analysis of the data revealed that the two tests are approximately equivalent in sensitivity, with the area under the curve being 0.85 and 0.80 for the GeneXpert and our assay, respectively, indicating that the test would be a cost effective screen prior to GeneXpert testing.

Figure 1

Alignment of loci containing the targeted 53 bp repeat element within a fully sequenced M. tuberculosis genome (H37Rv) and primers used in the study (Mtb detect For and Mtb detect Rev). Sequence labels correspond to the published name of the locus and the repeat number at that locus.

Figure 2

Agarose gel electrophoresis of amplified products from serial dilutions of a known concentration of Mtb DNA (H37Rv).

Figure 3

Melting curve analysis of LC480 amplified serial dilutions of H37Rv DNA.

Figure 4

(a) Receiver operator characteristic curve for Mtb detect and GeneXpert compared to culture as gold standard. (b) Receiver operator characteristic curve for Mtb detect and GeneXpert compared to treatment as gold standard.