New Real-Time PCR Able To Detect in a Single Tube Multiple Rifampin Resistance Mutations and High-Level Isoniazid Resistance Mutations in Mycobacterium tuberculosis

Abstract

The emergence of resistance to antituberculosis drugs is a relevant matter worldwide, but the retrieval of antibiograms for Mycobacterium tuberculosis is severely delayed when phenotypic methods are used. Genotypic methods allow earlier detection of resistance, although conventional approaches are cumbersome or lack sensitivity or specificity. We aimed to design a new real-time PCR method to detect rifampin (RIF)-and isoniazid (INH)-resistant M. tuberculosis strains in a single reaction tube. First, we characterized the resistant isolates in our area of Spain by DNA sequencing. Some mutation was found within the rpoB core region in all the RIF-resistant (RIF r ) strains. Forty-six percent of the INH-resistant (INH r ) strains showed a mutation in katG codon 315, and most of these were associated with high MICs. Eighteen of the RIF r , INH r , and multidrugresistant strains sequenced were tested by our real-time PCR assay; and full concordance of the results of the PCR with the sequencing data was obtained. In addition, a blind test was performed with a panel of 15 different susceptible and resistant strains from throughout Spain, and our results were also in 100% agreement with the sequencing data. Ours is the first assay based on rapid-cycle PCR able to simultaneously detect in a single reaction tube a large variety of mutations associated with RIF resistance (12 different mutations affecting 8 independent codons, including the most prevalent mutations at positions 526 and 531) and the most frequent INH resistance mutations. Our design could be a model for new, rapid genotypic methods able to simultaneously detect a wide variety of antibiotic resistance mutations.The emergence of resistance to antituberculosis (anti-TB) drugs is a relevant matter worldwide and has been reported in several studies (5,18,20). The standard treatment for TB is a multidrug regimen that is based on isoniazid (INH) and rifampin (RIF), the drugs most efficaceous against Mycobacterium tuberculosis infection. The development of resistance to these two drugs, however, means that the efficacy of standard anti-TB treatment is reduced by up to 77% (12).The detection of resistant M. tuberculosis strains is generally performed by phenotypic assays, which require the isolate to be cultured in the presence of the different drugs. This usually means unacceptable delays in the detection of resistance and makes it difficult to adhere to the recommendations of the Centers for Disease Control and Prevention for the reporting of resistance patterns within 28 days of receipt of the specimen in the laboratory (25).Methods that guarantee the early detection of resistant M. tuberculosis strains are required in order to avoid delays in the initiation of effective therapies and to prevent the transmission of multidrug-resistant (MDR) strains, which have been responsible for notorious outbreaks (1, 4, 7).The molecular basis of resistance to anti-TB drugs is becoming clearer (2, 19). More than 95% of RIF-resistant (RIF r ) strains are associated with mutation...

Molecular Analysis of Isoniazid and Rifampin Resistance inMycobacterium tuberculosisIsolates Recovered from Barcelona

“…Understanding the genetic events leading to drug resistance in clinical M. tuberculosis isolates, as well as their prevalence in different geographic areas, makes it possible to develop rapid genetic assays for their detection. 10,32,48 Mutations in an 81-bp "core region" of rpoB gene have been found in approximately 95% of rifampin (RIF)-resistant strains. 7,47 In contrast, resistance to isoniazid (INH) is associated with a variety of mutations affecting one or more genes.…”

Rapid, High-Throughput Detection of Rifampin Resistance and Heteroresistance in Mycobacterium tuberculosis by Use of Sloppy Molecular Beacon Melting Temperature Coding

“…T m assays are well suited for busy diagnostic laboratories, because they can be performed in homogeneous closed systems without the risk of carryover amplicon contamination, are amenable to multiplexing, and are easily adapted to a high-throughput format. Fluorescence resonance energy transfer (FRET) probes, dually labeled probes, TaqMan, and molecular beacon probes have all been used in T m assays to detect drug resistance mutations in M. tuberculosis, as has the high-resolution T m analysis (HRMA) of PCR products using DNA intercalating dyes (9,10,13,18,20,24,26,27). However, M. tuberculosis drug resistance assays which use T m analysis have been largely limited to tests of the most commonly encountered mutations (20,24,27).…”

Direct Detection of Rifampin- and Isoniazid-Resistant Mycobacterium tuberculosis in Auramine-Rhodamine-Positive Sputum Specimens by Real-Time PCR

“…More than 96% of rifampinresistant strains have mutations in an 81-bp "core region" of the rpoB gene, which encodes the ␤ subunit of the RNA polymerase (10,21), and the majority of isoniazid-resistant strains have been found to contain mutations in codon 315 of the katG gene, which encodes the catalase-peroxidase (30), or mutations in the inhA ribosomal binding site (1). Different genotypic approaches have been developed for the detection of resistance in M. tuberculosis (5,7,18,22).…”