Relevance of commercial amplification methods for direct detection of Mycobacterium tuberculosis complex in clinical samples.

Mycobacteria are a group of acid-fast, aerobic, slow-growing organisms whose genus includes more than 90 different species. The causative agents of tuberculosis (TB), which is currently considered a global emergency, with more than 2 million people dying every year and 8 million new cases, belong to the Mycobacterium tuberculosis complex (MTB). Moreover, although of lesser public health importance, many other species referred to as nontuberculous mycobacteria (NTM) have also been associated with human disease with increasing frequency worldwide (65). As MTB is highly infectious for humans, it is of paramount importance that TB be diagnosed as early as possible to stop the spread of the disease. Active TB is currently diagnosed by conventional laboratory procedures including specimen digestion and decontamination, microscopic examination for the presence of acid-fast bacilli (AFB), isolation by culture on solid and/or liquid media, and identification and drug susceptibility testing of the recovered isolate. Because of the slow growth of mycobacteria, the above-reported laboratory procedures may require turnaround times of 3 to 4 weeks or longer. During the last decade, several molecular methods have been developed for direct detection and identification of MTB in clinical specimens. These methods, being able to potentially reduce the diagnostic time from weeks to days, have been acquiring greater and greater relevance in the field of laboratory TB diagnosis. The basic principle of any molecular diagnostic test is the detection of a specific nucleic acid sequence by hybridization to a complementary sequence, a probe, followed by detection of the hybrid. However, the sensitivity of nucleic acid probe tests that do not involve amplification is much lower than that of amplified ones. Any portion of nucleic acid can be copied by using the specific polymerase, provided that some sequence data are known for the setup of appropriate primers. In general, amplification of target nucleic acid sequences is composed of three parts: denaturation, primer annealing, and primer extension. Discovery of PCRs in 1986 made this process reiterative, leading to an exponential increase in the production of the amplified target. Soon after, alternative amplification techniques were developed and patented by companies, which used different enzymes and strategies, but they are all based on reiterative reactions. Many different amplification targets including both DNA or RNA fragments have been proposed. The target most frequently amplified in MTB is the IS6110 (31) repetitive element, of which 10 to 16 copies are present in most clinical isolates. Numerous techniques for nucleic acid extraction have been proposed, as have different types of controls for monitoring the efficacy of nucleic acid extraction and amplification procedures. Currently, the U.S. Food and Drug Administration (FDA) requires that culture (still considered the “gold standard” for TB diagnosis) must be done in conjunction with the performance of each amplification-based test. In this paper, we review and discuss the currently available commercial methods which are capable of detecting MTB directly from clinical samples.