Dual-probe assay for rapid detection of drug-resistant Mycobacterium tuberculosis by real-time PCR

Mutations in particular nucleotides of genes coding for drug targets or drug-converting enzymes lead to drug resistance in Mycobacterium tuberculosis. For rapid detection of drug-resistant M. tuberculosis in clinical specimens, a simple and applicable method is needed. Eight TaqMan minor groove binder (MGB) probes, which discriminate one-base mismatches, were designed (dual-probe assay with four reaction tubes). The target of six MGB probes was the rpoB gene, which is involved in rifampin resistance; five probes were designed to detect for mutation sites within an 81-bp hot spot of the rpoB gene, and one probe was designed as a tuberculosis (TB) control outside the rpoB gene hot-spot. We also designed probes to examine codon 315 of katG and codon 306 of embB for mutations associated with resistance to isoniazid and ethambutol, respectively. Our system was M. tuberculosis complex specific, because neither nontuberculous mycobacteria nor bacteria other than mycobacteria reacted with the system. Detection limits in direct and preamplified analyses were 250 and 10 fg of genomic DNA, respectively. The system could detect mutations of the rpoB, katG, and embB genes in DNAs extracted from 45 laboratory strains and from sputum samples of 27 patients with pulmonary TB. This system was much faster (3 h from DNA preparation) than conventional drug susceptibility testing (3 weeks). Results from the dual-MGB-probe assay were consistent with DNA sequencing. Because the dual-probe assay system is simple, rapid, and accurate, it can be applied to detect drug-resistant M. tuberculosis in clinical laboratories.     

A more reliable PCR for detection of Mycobacterium tuberculosis in clinical samples.

Diagnostic techniques based on PCR have two major problems: false-positive reactions due to contamination with DNA fragments from previous PCRs (amplicons) and false-negative reactions caused by inhibitors that interfere with the PCR. We have improved our previously reported PCR based on the amplification of a fragment of the Mycobacterium tuberculosis complex-specific insertion element IS6110 with respect to both problems. False-positive reactions caused by amplicon contamination were prevented by the use of uracil-N-glycosylase and dUTP instead of dTTP. We selected a new set of primers outside the region spanned by the formerly used primers to avoid false-positive reactions caused by dTTP-containing amplicons still present in the laboratory. With this new primer set, 16 copies of the IS6110 insertion element, the equivalent of two bacteria, could be amplified 10(10) times in 40 cycles, resulting in a mean efficiency of 77% per cycle. To detect the presence of inhibitors of the Taq polymerase, which may cause false-negative reactions, part of each sample was spiked with M. tuberculosis DNA. The DNA purification method using guanidinium thiocyanate and diatoms effectively removed most or all inhibitors of the PCR. However, this was not suitable for blood samples, for which we developed a proteinase K treatment followed by phenol-chloroform extraction. This method permitted detection of 20 M. tuberculosis bacteria per ml of whole blood. Various laboratory procedures were introduced to reduce failure or inhibition of PCR and avoid DNA cross contamination. We have tested 218 different clinical specimens obtained from patients suspected of having tuberculosis. The samples included sputum (n=145), tissue biopsy samples (n=25), cerebrospinal fluid (n=15), blood (n=14), pleural fluid (n=9), feces, (n=7), fluid from fistulae (n=2), and pus from a wound (n=1). The results obtained by PCR were consistent with those obtained with culture, which is the "gold standard." We demonstrate that PCR is a useful technique for the rapid diagnosis of tuberculosis at various sites.     

Simultaneous identification of Mycobacterium genus and Mycobacterium tuberculosis complex in clinical samples by 5'-exonuclease fluorogenic PCR

Early diagnosis of tuberculosis and screening of other mycobacteria is required for the appropriate management of patients. We have therefore developed a 5'-exonuclease fluorogenic PCR assay in a single-tube balanced heminested format that simultaneously detects Mycobacterium tuberculosis complex (MTC) and members of the Mycobacterium genus (MYC) using the 16S ribosomal DNA target directly on clinical samples. One hundred twenty-seven clinical samples (65 smear negative and 62 smear positive) with a positive culture result from 127 patients were tested, including 40 negative control specimens. The finding of both a positive MTC and probe value and a positive MYC probe value confirmed the presence of MTC or mycobacteria with a 100% positive predictive value. However, a negative value for MTC or MYC did not discount the presence of mycobacteria in the specimen. Interestingly, the addition of the MYC probe allowed the diagnosis of an additional 7% of patients with tuberculosis and rapid screening of nontuberculous mycobacteria (NTM). Thus, over 75% of the patients were diagnosed with mycobacterial disease by PCR. The sensitivity was much higher on smear-positive samples (90.3%) than smear-negative samples (49.2%) and was slightly higher for MTC than NTM samples. With regard to the origin of the sample, MTC pulmonary samples gave better results than others. In conclusion, we believe this test may be useful for the rapid detection of mycobacteria in clinical samples and may be a valuable tool when used together with conventional methods and the clinical data available.     

Direct detection and identification of Mycobacterium tuberculosis and Mycobacterium bovis in bovine samples by a novel nested PCR assay: correlation with conventional techniques

Mycobacterium tuberculosis and M. bovis infect animals and humans. Their epidemiologies in developed and developing countries differ, owing to differences in the implementation of preventive measures (World Health Organization, 1999). Identification and differentiation of these closely related mycobacterial species would help to determine the source, reservoirs of infection, and disease burden due to diverse mycobacterial pathogens. The utility of the hupB gene (Rv2986c in M.tuberculosis, or Mb3010c in M.bovis) to differentiate M. tuberculosis and M. bovis was evaluated by a PCR-restriction fragment length polymorphism (RFLP) assay with 56 characterized bovine isolates (S. Prabhakar et al., J. Clin. Microbiol. 42:2724-2732, 2004). The degree of concordance between the PCR-RFLP assay and the microbiological characterization was 99.0% (P < 0.001). A nested PCR (N-PCR) assay was developed, replacing the PCR-RFLP assay for direct detection of M. tuberculosis and M. bovis in bovine samples. The N-PCR products of M. tuberculosis and M. bovis corresponded to 116 and 89 bp, respectively. The detection limit of mycobacterial DNA by N-PCR was 50 fg, equivalent to five tubercle bacilli. M. tuberculosis and/or M. bovis was detected in 55.5% (105/189) of the samples by N-PCR, compared to 9.4% (18/189) by culture. The sensitivities of N-PCR and culture were 97.3 and 29.7, respectively, and their specificities were 22.2 and 77.7%, respectively. The percentages of animals or samples identified as infected with M.tuberculosis or M. bovis by N-PCR and culture reflected the clinical categorizations of the cattle (P of <0.05 to <0.01). Mixed infection by N-PCR was detected in 22 animals, whereas by culture mixed infection was detected in 1 animal.     

Rapid detection of Mycobacterium tuberculosis complex and rifampin resistance in smear-negative clinical samples by use of an integrated real-time PCR method

Sixty-four of 85 (75.3%) smear-negative respiratory (n = 78) and nonrespiratory (n = 7) samples with positive cultures of Mycobacterium tuberculosis complex (MTC) were detected by the GeneXpert system using the Xpert MTB/RIF assay (GX). In addition, GX found rpoB mutations in all six of the rifampin-resistant strains detected. The test was negative in 20 culture-negative and 20 nontuberculous culture-positive samples (100% specificity). GX offers high potential for the diagnosis of tuberculosis due to its capacity for direct detection of MTC, its rapidity, and its simplicity.     

Molecular strain identification of the Mycobacterium tuberculosis complex in archival tissue samples

AIMS: To investigate the use of different molecular analyses that can identify distinct strains of human pathogenic mycobacteria in formalin fixed and paraffin wax embedded archival tissue samples to see whether it is possible to differentiate between the members of the Mycobacterium tuberculosis complex (M tuberculosis, M bovis, M africanum, M microti, or M canettii) and/or substrains in a high number of samples. This would be of interest for identifying individual infection traits and superinfection by different mycobacterial strains. METHODS: Forty nine archival tissue samples with clinically and/or histologically suspected tuberculosis infection were subjected to molecular DNA analysis. RESULTS: The molecular analysis revealed the presence of M tuberculosis complex DNA in 20 samples, whereas acid fast bacilli could be detected by Ziehl-Neelsen staining in only eight samples. All IS6110 positive samples were further characterised by spoligotyping and seven cases provided M tuberculosis specific signatures, whereas M bovis specific signatures were obtained in four cases. The analysis of mtp40, oxyR, and pncA partial gene sequences confirmed the presence of M tuberculosis in six cases and M bovis in one case. The amplification and sequencing of four further genetic regions (katG, gyrA, TbD1, RD9) characterised six "modern" M tuberculosis strains belonging to genetic groups 2 or 3. CONCLUSION: This study provides clear evidence that archival paraffin wax embedded material can be used for further studies on the strain identification of M tuberculosis complex strains and can therefore unequivocally be used for the study of the epidemiology and evolution of tuberculosis pathogens.     

用于PCR检测的临床标本和石蜡切片的简便处理法

本文以套式ＰＣＲ检测ＨＣＭＶ为例研究了用于ＰＣＲ检测的全血和血清，口腔和宫颈粘液，羊水，新鲜组织及石蜡切片等标本的多种处理方法，并对各种方法的特点进行比较，这些方法的特点是简便快速，所需试剂和仪器低廉适合于基层医院推广使用。     

Direct detection of Mycobacterium tuberculosis complex in clinical samples from patients in Norway by ligase chain reaction.

Our aim was to investigate the use of DNA amplification with the ligase chain reaction (LCR) for detection of the Mycobacterium tuberculosis complex directly in human clinical specimens. The LCR assay employed was the Abbott LCx MTB Assay, which uses the gene encoding protein antigen b as the target template. Four hundred eighty-two samples from 457 patients in one clinical microbiology laboratory in Norway were processed by routine culture analysis (BACTEC culture), direct microscopy (Ziehl-Neelsen staining) and LCR. Of the 118 specimens containing cultivable M. tuberculosis, 106 (90.6%) were detected by LCR. Among the 364 culture-negative specimens, 356 samples were negative also by LCR and 8 (1.6%) were positive by LCR. In five of the eight LCR-positive and culture-negative samples, another sample from the same patient was M. tuberculosis culture positive and/or the patient had symptoms of tuberculosis. In comparison with culture, the sensitivity of LCR was 96.7% for smear-positive samples and 72.0% for smear-negative samples, respectively. For all samples combined, the sensitivity, specificity, and positive and negative predictive values were 90.2, 99.2, 97.4, and 96.7%, respectively. Challenging the M. tuberculosis LCR test with DNAs and cultures from strains of Mycobacterium ulcerans and Mycobacterium marinum, which are the mycobacterial species most closely related to the M. tuberculosis complex, resulted in all-negative test results. The sensitivity, specificity, and positive and negative predictive values of BACTEC culture in comparison with the LCR test and clinical criteria were 95.9, 100, 100, and 98.6%, respectively. A certain prioritization of samples subjected to the LCR assay should be based on clinical indications and risks with regard to infection transmission and patient isolation policy. More automation and lower expenses are generally desired for nucleic acid amplification kits. However, this M. tuberculosis LCR assay represents a valuable tool in routine mycobacterial diagnostics.     

Multiplex polymerase chain reaction for rapid detection of atypical mycobacteria and Mycobacterium tuberculosis complex.

A three-step polymerase chain reaction (PCR) method was developed for the detection and typing of mycobacterial DNA in clinical samples and fixed tissue specimens. The first step was to rule out or prove the presence of DNA of Mycobacterium tuberculosis complex. An amplified fragment from the insertion sequence (IS) 6110 was used for this purpose. Patients negative for IS 6110 were evaluated for a fragment of the 65 kDa-antigen, present in all mycobacteria. In positive patients, a multiplex PCR was performed for M. gordonae, M. avium, M. kansasii, M. fortuitum, and M. malmoense, combined in one PCR run. As another control, to prove mycobacterial DNA, PCR was used for the gene coding for the 16S ribosomal RNA also found in all mycobacteria. Appropriate negative controls were included. Different clinical samples were compared for an efficient amplification of these different mycobacterial DNA fragments. Different mycobacteria can be identified within one day in either unfixed cytologic and bacteriologic samples, or formalin-fixed paraffin-embedded tissue samples. Therefore, this method is a quick, cost efficient, and reliable tool to identify mycobacteria other than the tuberculosis complex.     

Contribution of PCR for detection of Mycobacterium tuberculosis complex in respiratory and nonrespiratory specimens

AIM OF THE STUDY: To evaluate the sensitivity of PCR versus culture of complex tuberculosis mycobacteria and to determine the delay between PCR results and identification of mycobacteria in culture. MATERIALS AND METHODS: Ninety-nine pulmonary and 66 extrapulmonary specimens were analyzed. Samples were inoculated on liquid (MGIT, Bactec) and solid media (Coletsos) and respectively incubated 6 and 12 weeks. Identification was performed by reverse hybridization of PCR products to their complementary probes immobilized on membrane strips (Genotype MTBC, HAIN). Specimens DNA detection was realized by PCR (Cobas Amplicor Mycobacterium tuberculosis test, Roche). RESULTS: Sensitivity of PCR for acid fast bacilli smear positive pulmonary (50/50) and extrapulmonary (7/7) specimens was 100%. Delay between PCR result and identification was 11 days for pulmonary specimens and 8 days for extrapulmonary specimens. Sensitivity of PCR for smear negative samples was, respectively, of 78.7% (37/47) and 51.8% (29/56) for pulmonary and extrapulmonary specimens. In case of PCR positive result of a smear negative sample, a gap of respectively 13 and 12 days was obtained for pulmonary and extrapulmonary specimens compared to identification. CONCLUSION: Positive PCR result for respiratory specimens allows a gap of 11 to 13 days in diagnosis in comparison with identification of mycobacteria in culture.     

Substances interfering with direct detection of Mycobacterium tuberculosis in clinical specimens by PCR: effects of bovine serum albumin.

Interfering substances have been reported to inhibit PCR assays for the direct detection of Mycobacterium tuberculosis in clinical specimens. Using an internal control, we determined that 52% of respiratory specimens interfered with our PCR assay. On the basis of these findings, we tried to circumvent the problem by simply diluting prepared sediments. With sediment from a routinely processed sputum known to be inhibitory to PCR, one aliquot was prepared in a routine manner for PCR. Remaining sediment was diluted in phosphate-buffered saline, Middlebrook 7H10 broth, or BACTEC 12B broth; an internal control was added to all reaction mixtures and controls. Internal control was detected only in the sample diluted with BACTEC 12B medium. Components of the BACTEC 12B medium including PANTA reagent (polymyxin B, amphotericin B, nalidixic acid, trimethoprim, and azlocillin), reconstituting fluid, 0.2% glycerol, 0.05% Tween 80, and 0.05% bovine serum albumin (BSA) were tested in a similar manner. Only 0.05% BSA resulted in amplification of the internal control DNA. Varying concentrations of BSA were added to 11 aliquots of a respiratory sediment known to be inhibitory to the PCR. Internal control was detected in all reaction mixtures containing 0.00038 to 0.1% BSA. To determine the ability of BSA to override inhibition, respiratory specimens were run in triplicate: undiluted, diluted 1:2 with BACTEC 12B medium, or diluted with 0.026% BSA. For 21 of 22 inhibitory specimens, BSA was able to override the presence of interfering substances. These data suggest that the presence of BSA in a PCR assay is critical for the direct detection of M. tuberculosis in respiratory specimens.     

Characterization of a DNA probe for detection of Mycobacterium tuberculosis complex in clinical samples by polymerase chain reaction.

We cloned and sequenced a DNA fragment from Mycobacterium tuberculosis for use in the identification of members of the M. tuberculosis complex. The DNA probe for culture confirmation had a sensitivity and a specificity of 100%. By using primers developed from this probe, the polymerase chain reaction detected 20 mycobacteria by ethidium bromide staining. This polymerase chain reaction system demonstrated 98% sensitivity and 100% specificity for detection of the M. tuberculosis complex in 200 sputum specimens.     

Rapid discrimination of Mycobacterium tuberculosis complex strains by ligation-mediated PCR fingerprint analysis.

A ligation-mediated PCR (LMPCR) method for the amplification of sequences flanking the IS6110 of the Mycobacterium tuberculosis complex has been developed. The method uses one primer specific for IS6110 and a second specific for a linker ligated to SalI-restricted genomic DNA. LMPCR is a rapid screening method, valuable for the fingerprinting of M. tuberculosis complex strains.     

Comparison of Amplicor, in-house PCR, and conventional culture for detection of Mycobacterium tuberculosis in clinical samples.

Five hundred four clinical specimens (337 sputum and 167 bronchial samples) from 340 patients were tested for the presence of M. tuberculosis complex by the Amplicor M. tuberculosis test and by an in-house PCR. The results were compared with those obtained by conventional culture and by direct microscopy. Thirty specimens (from 14 patients) were positive by in-house PCR, 25 (from 13 patients) were positive by the Amplicor M. tuberculosis test, and 24 (from 10 patients) were positive by culture. Cultures from 16 specimens were contaminated with other bacteria. Strong inhibition of in-house PCR was found with three samples. After discordancy analyses, with clinical data as supportive evidence for tuberculosis, 27 true-positive and 458 true-negative samples were defined. On the basis of these figures, the sensitivities of the Amplicor M. tuberculosis test, in-house PCR, culture, and microscopy were 70.4, 92.6, 88.9, and 52.4%, respectively. The specificities of all four tests were higher than 98%. The good performance of the in-house PCR for detection of M. tuberculosis makes it a very useful additional tool in M. tuberculosis diagnostics. In contrast, the Amplicor test needs to be improved. Twenty-three of the Amplicor-negative samples were further tested for inhibition of the Amplicor system by retesting the DNA extracts after the addition of M. tuberculosis DNA. In 15 of these samples, 5 true positives and 10 true negatives, inhibition of the Amplicor test was demonstrated. This might explain the lack of sensitivity of the Amplicor test. If the inhibition problem can be solved, the Amplicor M. tuberculosis test, which is already rapid, very user-friendly, and reasonably priced, may certainly become very useful in microbiological laboratories.     

Evaluation of DNA extraction techniques for detecting Mycobacterium tuberculosis complex organisms in Asian elephant trunk wash samples

Rapid and sensitive diagnostic assays for the detection of tuberculous mycobacteria in elephants are lacking. DNA extraction with PCR analysis is useful for tuberculosis screening in many species but has not been validated on elephant trunk wash samples. We estimated the analytical sensitivity and specificity of three DNA extraction methods to detect Mycobacterium tuberculosis complex organisms in trunk wash specimens. A ZR soil microbe DNA kit (ZR) and a traditional salt and ethanol precipitation (TSEP) approach were evaluated under three different treatment conditions: heat treatment, phenol treatment, and contamination with Mycobacterium avium. A third approach, using a column filtration method, was evaluated for samples contaminated with soil. Trunk wash samples from uninfected elephants were spiked with various concentrations of M. bovis cells and subjected to the described treatment conditions prior to DNA extraction. Extracted DNA was amplified using IS6110-targeted PCR analysis. The ZR and TSEP methods detected as low as 1 to 5 M. bovis cells and 10 M. bovis cells, respectively, per 1.5 ml of trunk wash under all three conditions. Depending on the amount of soil present, the column filtration method detected as low as 5 to 50 M. bovis cells per 1.5 ml of trunk wash. Analytical specificity was assessed by DNA extraction from species of nontuberculous mycobacteria and amplification using the same PCR technique. Only M. bovis DNA was amplified, indicating 100% analytical specificity of this PCR technique. Our results indicate that these DNA extraction techniques offer promise as useful tests for detection of M. tuberculosis complex organisms in elephant trunk wash specimens.