In-house PCR with DNA extracted directly from positive slides to confirm or exclude the diagnosis of tuberculosis: focus on biosafety

Direct detection of Mycobacterium tuberculosis rifampin resistance in bio-safe stained sputum smears

Direct smear microscopy of sputum forms the mainstay of TB diagnosis in resource-limited settings. Stained sputum smear slides can serve as a ready-made resource to transport sputum for molecular drug susceptibility testing. However, bio-safety is a major concern during transport of sputum/stained slides and for laboratory workers engaged in processing Mycobacterium tuberculosis infected sputum specimens. In this study, a bio-safe USP (Universal Sample Processing) concentration-based sputum processing method (Bio-safe method) was assessed on 87 M. tuberculosis culture positive sputum samples. Samples were processed for Ziehl-Neelsen (ZN) smear, liquid culture and DNA isolation. DNA isolated directly from sputum was subjected to an IS6110 PCR assay. Both sputum DNA and DNA extracted from bio-safe ZN concentrated smear slides were subjected to rpoB PCR and simultaneously assessed by DNA sequencing for determining rifampin (RIF) resistance. All sputum samples were rendered sterile by Bio-safe method. Bio-safe smears exhibited a 5% increment in positivity over direct smear with a 14% increment in smear grade status. All samples were positive for IS6110 and rpoB PCR. Thirty four percent samples were RIF resistant by rpoB PCR product sequencing. A 100% concordance (κ value = 1) was obtained between sequencing results derived from bio-safe smear slides and bio-safe sputum. This study demonstrates that Bio-safe method can address safety issues associated with sputum processing, provide an efficient alternative to sample transport in the form of bio-safe stained concentrated smear slides and can also provide information on drug (RIF) resistance by direct DNA sequencing.

Optimal DNA Isolation Method for Detection of Nontuberculous Mycobacteria by Polymerase Chain Reaction

Background

Nontuberculous mycobacteria (NTM) are a group of opportunistic pathogens and these are widely dispersed in water and soil resources. Identification of mycobacteria isolates by conventional methods including biochemical tests, growth rates, colony pigmentation, and presence of acid-fast bacilli is widely used, but these methods are time-consuming, labor-intensive, and may sometimes remain inconclusive.

Materials and Methods

The DNA was extracted from NTM cultures using CTAB, Chelex, Chelex + Nonidet P-40, FTA^® Elute card, and boiling The quantity and quality of the DNA extracted via these methods were determined using UV-photometer at 260 and 280 nm, and polymerase chain reaction (PCR) amplification of the heat-shock protein 65 gene with serially diluted DNA samples.

Results

The CTAB method showed more positive results at 1:10-1:100,000 at which the DNA amount was substantial. With the Chelex method of DNA extraction, PCR amplification was detected at 1:10 and 1:1000 dilutions.

Conclusions

According to the electrophoresis results, the CTAB and Chelex DNA extraction methods were more successful in comparison with the others as regard producing suitable concentrations of DNA with the minimum use of PCR inhibitor.

Evaluation of the Mean Cost and Activity Based Cost in the Diagnosis of Pulmonary Tuberculosis in the Laboratory Routine of a High-Complexity Hospital in Brazil

At a global level, with the increase in healthcare costs, there is a need to assess the economic impact of the incorporation of new technologies in different health disorders in different countries. There is scarce information regarding costs incurred with the use of current or new diagnostic tests for tuberculosis or from the vantage point of their incorporation within the healthcare systems of high-burden countries. The present study aimed to assess the mean cost and the activity based cost of the laboratory diagnosis for tuberculosis by means of conventional techniques and from the Detect TB^®LabTest molecular test kit in a general high-complexity hospital of the public health system in Brazil. Cost analysis was performed by means of primary data, collected in the Mycobacteria and Molecular Biology Laboratory in 2013. The mean cost and activity based cost were, respectively, U$10.06/U$5.61 for centrifuged bacilloscopy by Ziehl Neelsen (ZN) and Auramine (AU); U$7.42/U$4.15 for direct bacilloscopy by ZN; U$27.38/U$16.50 for culture in a Loweinstein-Jensen solid medium; and U$115.74/U$73.46 for the Detect TB^®LabTest Kit. The calculation of the ABC should be used in making decisions by administrators to be the best method of assessing the costs of conventional techniques and molecular method for providing the real value of the tests. So it is need to calculate the ABC, and not of the mean cost, in various scenarios before incorporating new technologies in health institutions.