Molecular-based mycobacterial identification in a clinical laboratory setting: a comparison of two methods

Performance of a molecular assay to detect Mycobacterium tuberculosis complex DNA in clinical specimens: multicenter study in Brazil

BACKGROUND

In high tuberculosis (TB) burden countries, there are few data on the performance of new molecular commercialised assays developed locally.

OBJECTIVE

To evaluate the performance of a new molecular commercialised assay for TB diagnosis (Detect-TB) in three laboratories.

METHODS

A total of 302 sputum samples from an equal number of patients with presumptive diagnosis of pulmonary tuberculosis (PTB) were submitted for routine smear microscopy, culture, and Detect-TB assay at three different sites in Brazil (the cities of Caxias do Sul, São Paulo and Canoas).

FINDINGS

Seventy four (24.7%) TB cases were diagnosed (65 bacteriologically confirmed). When compared to smear microscopy/culture results, the overall sensitivity and specificity of Detect-TB assay was 84.6% (CI 95%; 73.7-91.6) and 93.1% (CI 95%; 89.1-95.8), respectively. When compared to bacteriological and clinical diagnostic criteria, the sensitivity and specificity of Detect-TB assay was 74.3% (CI 95%; 63.3-82.9) and 92.9% (CI 95%; 88.7-95.6), respectively. Among the three sites - Caxias do Sul, São Paulo and Canoas - the sensitivity and specificity were respectively 94.7% and 97.8%; 71.4% and 93.9%, 82.1% and 88.9%.

MAIN CONCLUSIONS

These findings suggest that the Detect-TB assay could be applied routinely in reference laboratories across different regions in Brazil.

Mycobacterium diagnostics: from the primitive to the promising

The field of clinical microbiology has been revolutionised by genomic and proteomic methods, which have facilitated more rapid diagnosis and characterisation of infection in many cases. In contrast, mycobacteriological evolution has tended to retain the traditional methods of smear microscopy for detection of acid-fast bacilli to indicate mycobacteria, along with culture, and in synergy with more modern molecular methods. Thus, efforts have been focused on reducing the time to diagnosis of infection, while increasing the amount of diagnostic information available, including more definitive speciation, and more rapid susceptibility test results. Although smear microscopy remains a mainstay for the laboratory-based diagnosis of mycobacterial infection, molecular testing has vastly reduced the time needed for identification of Mycobacterium tuberculosis in particular, when compared with traditional culture-based techniques. Molecular methods may also yield antimicrobial susceptibility results through testing for the most common resistance-inducing mutations to some of the antimicrobial agents of choice. However, the diversity of resistance mutations already characterised suggests that these currently-available molecular detection systems should be accompanied by culture-based susceptibility testing. This review compares the efficacy of microscopic, phenotypic, proteomic and genotypic methods available for mycobacterial diagnosis. The diversity of methods currently in use reflects the complexity of this area of diagnostic microbiology.

Evaluation of the Speed-Oligo Mycobacteria assay for the identification of nontuberculous mycobacteria

Nontuberculous mycobacteria (NTM) causing human infectious disease have become increasingly common. Rapid and accurate identification to the species level is, therefore, critical. The Speed-Oligo Mycobacteria assay is an oligochromatographic method that was made available recently for the identification and differentiation of mycobacteria. The present study aimed to evaluate the performance of the Speed-Oligo Mycobacteria assay for the identification of NTM. We examined a total of 62 strains (9 type strains, 19 reference strains and 34 clinical isolates) belonging to 13 different species (Mycobacterium intracellulare, M. fortuitum, M. gordonae, M. kansasii, M. marinum, M. peregrinum, M. scrofulaceum, M. abscessus, M. bovis BCG, M. chelonae, M. avium, M. malmoense and M. xenopi). The Speed-Oligo Mycobacteria assay was performed according to the manufacturer's instructions. Discrepant results between Speed-Oligo Mycobacteria and the original identification were reassessed by the Speed-Oligo Mycobacteria assay and resolved by the GenoType Mycobacterium CM assay and by sequencing of 16S rRNA and protein-encoding genes. We found 93.5 % (58/62) concordance for the identification of NTM as compared with the original identification. Three strains were erroneously identified by Speed-Oligo Mycobacteria: one M. kansasii strain was identified as Mycobacterium tuberculosis complex, and one M. chelonae strain and one M. peregrinum strain were both identified as Mycobacterium abscessus. Moreover, one M. chelonae strain was not identified by Speed-Oligo Mycobacteria since it did not react with any species-specific probe. For these strains, sequencing of the genes hsp65, 16S rRNA and rpoB and the GenoType Mycobacterium CM assay were performed. The Speed-Oligo Mycobacteria assay can be a useful tool for the rapid and easy identification of the most common NTM. If applied in clinical practice it could reduce diagnostic delays and contribute to correct clinical and better management of infections caused by NTM.

Evaluation of four molecular methods for the diagnosis of tuberculosis in pulmonary and blood samples from immunocompromised patients

The present study analysed the concordance among four different molecular diagnostic methods for tuberculosis (TB) in pulmonary and blood samples from immunocompromised patients. A total of 165 blood and 194 sputum samples were collected from 181 human immunodeficiency virus (HIV)-infected patients with upper respiratory complaints, regardless of suspicious for TB. The samples were submitted for smear microscopy, culture and molecular tests: a laboratory-developed conventional polymerase chain reaction (PCR) and real-time quantitative PCR (qPCR) and the Gen-Probe and Detect-TB Ampligenix kits. The samples were handled blindly by all the technicians involved, from sample processing to results analysis. For sputum, the sensitivity and specificity were 100% and 96.7% for qPCR, 81.8% and 94.5% for Gen-Probe and 100% and 66.3% for Detect-TB, respectively. qPCR presented the best concordance with sputum culture [kappa (k) = 0.864)], followed by Gen-Probe (k = 0.682). For blood samples, qPCR showed 100% sensitivity and 92.3% specificity, with a substantial correlation with sputum culture (k = 0.754) and with the qPCR results obtained from sputum of the corresponding patient (k = 0.630). Conventional PCR demonstrated the worst results for sputa and blood, with a sensitivity of 100% vs. 88.9% and a specificity of 46.3% vs. 32%, respectively. Commercial or laboratory-developed molecular assays can overcome the difficulties in the diagnosis of TB in paucibacillary patients using conventional methods available in most laboratories.

A multicenter clinical evaluation of Mycobacterium tuberculosis IgG/IgM antibody detection using the colloidal gold method

A specific immunoassay method with the colloidal gold labeling technique has been developed more and more for tuberculosis (TB) diagnosis. The aim of this multicenter clinical evaluation was to evaluate the performance of a new serological diagnostic kit (the Trustline TB IgG/IgM Rapid Test kit) for the detection of Mycobacterium tuberculosis infection in China, with the Aupu TB Ab (IgG) Colloidal Gold Test kit being used as a control. A total of 1,009 specimens were collected from three TB hospitals, including 628 patients with TB, and 219 non-TB and 162 healthy patients as negative controls. According to the clinical diagnostic results, the sensitivities of the Trustline kit and the Aupu kit were 61.3 % and 53.7 %, respectively. Using the bacteriological test results as the "gold standard" to compare the results of the two kits, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Youden index (YI) were 77.60 %, 79.8 %, 73.31 %, 81.50 %, and 0.574 by the Trustline kit, and 67.86 %, 88.9 %, 83.27 %, 77.40 %, and 0.568 by the Aupu kit, respectively. Further, the sensitivity of the Trustline kit and the Aupu kit for the smear staining and the bacterial culture being positive was 75.6 %, 76.6 % and 65.6 %, 66.5 %, and for the negative result, it was 53.8 %, 50.9 % and 47.5 %, 45.0 %, respectively. Additionally, 35 specimens were IgM-positive by the Trustline kit; of these, 30 (4.8 %) were from patients with TB and 5 (1.3 %) were from individuals without TB. The results showed that the experimental test had a much higher sensitivity than the other commercial test and exhibited a good detection rate for M. tuberculosis infection. Therefore, this kit can be used in the supplementary diagnosis and screening of TB.