Evaluation of real-time PCR of patient pleural effusion for diagnosis of tuberculosis

Background: Pleural tuberculosis (TB) diagnosis often requires invasive procedures such as pleural biopsy. The aim of this study was to evaluate the role of real-time polymerase chain reaction (PCR) for the IS6110 sequence of M. tuberculosis in pleural fluid specimens as a rapid and non-invasive test for pleural TB diagnosis. Findings: For this cross-sectional study, 150 consecutive patients with pleural effusion diagnosed by chest radiography, who were referred for diagnostic thoracocentesis and pleural biopsy and met eligibility criteria, had a pleural fluid specimen submitted for real-time PCR testing. Overall, 98 patients had pleural TB and 52 had pleural effusion secondary to other disease. TB diagnosis was obtained using acid-fast bacilli (AFB) smear or culture for mycobacteria and/or histopathologic examination in 94 cases and by clinical findings in 4 cases. Sensitivity, specificity, positive and negative predictive values of PCR testing for pleural TB diagnosis were 42.8% (95% CI 38.4 - 44.8), 94.2% (95% CI 85.8 - 98.0), 93.3% (95% CI 83.6 - 97.7), and 48.5% (95% CI 44.2 - 50.4), respectively. The realtime PCR test improved TB detection from 30.6% to 42.9% when compared to AFB smear and culture methods performed on pleural fluid specimens, although the best sensitivity was achieved by combining the results of culture and histopathology of pleural tissue specimens. Conclusion: The real-time PCR test of pleural fluid specimens is a useful and non-invasive additional assay for fast diagnosis of pleural TB

Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil

Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genome Sequencing (WGS) holds the potential to produce high-resolution epidemiological data in a high-throughput manner. Florianópolis, the state capital of Santa Catarina (SC) in south Brazil, shows a high TB incidence (46.0/100,000). Here we carried out a WGS-based evaluation of the M.tb strain diversity, drug-resistance and ongoing transmission in the capital metropolitan region. Resistance to isoniazid, rifampicin, streptomycin was identified respectively in 4.0% (n = 6), 2.0% (n = 3) and 1.3% (n = 2) of the 151 studied strains by WGS. Besides, resistance to pyrazinamide and ethambutol was detected in 0.7% (n = 1) and reistance to ethionamide and fluoroquinolone (FQ) in 1.3% (n = 2), while a single (0.7%) multidrug-resistant (MDR) strain was identified. SNP-based typing classified all isolates into M.tb Lineage 4, with high proportion of sublineages LAM (60.3%), T (16.4%) and Haarlem (7.9%). The average core-genome distance between isolates was 420.3 SNPs, with 43.7% of all isolates grouped across 22 genomic clusters thereby showing the presence of important ongoing TB transmission events. Most clusters were geographically distributed across the study setting which highlights the need for an urgent interruption of these large transmission chains. The data conveyed by this study shows the presence of important and uncontrolled TB transmission in the metropolitan area and provides precise data to support TB control measures in this region.publishersversionpublishe

Colorimetric microwell plate reverse-hybridization assay for Mycobacterium tuberculosis detection

Direct smear examination using Ziehl-Neelsen staining for pulmonary tuberculosis (PTB) diagnosis is inexpensive and easy to use, but has the major limitation of low sensitivity. Rapid molecular methods are becoming more widely available in centralized laboratories, but they depend on timely reporting of results and strict quality assurance obtainable only from costly commercial kits available in high burden nations. This study describes a pre-commercial colorimetric method, Detect-TB, for detecting Mycobacterium tuberculosis DNA in which an oligonucleotide probe is fixed onto wells of microwell plates and hybridized with biotinylated polymerase chain reaction amplification products derived from clinical samples. The probe is capable of hybridising with the IS6110 insertion element and was used to specifically recognise the M. tuberculosis complex. When combined with an improved silica-based DNA extraction method, the sensitivity of the test was 50 colony-forming units of the M. tuberculosis reference strain H37Rv. The results that were in agreement with reference detection methods were observed in 95.2% (453/476) of samples included in the analysis. Sensitivity and specificity for 301 induced sputum samples and 175 spontaneous sputum samples were 85% and 98%, and 94% and 100%, respectively. This colorimetric method showed similar specificity to that described for commercially available kits and may provide an important contribution for PTB diagnosis

Detecção da mutação mais freqüente no códon 315 do gene katG relacionada com a resistência à isoniazida em isolados de Mycobacterium tuberculosis

A caracterização das mutações nos genes katG, ahpC e inhA e sua correlação com a resistência à isoniazida em isolados de Mycobacterium tuberculosis tem sido descrita. A mutação S315T no gene katG é a mais freqüentemente encontrada e pode fornecer rápida informação para a seleção do tratamento anti-tuberculose, para a vigilância epidemiológica da resistência e, possivelmente rastrear a transmissão de linhagens resistentes. Dessa forma, o objetivo do trabalho foi o desenvolvimento de um Ensaio de Hibridização Reversa (EHR) para a rápida identificação da mutação no códon 315 do gene katG em M. tuberculosis. Após a padronização da metodologia com 180 DNAs de M. tuberculosis isolados de cultura, o teste foi aplicado a 46 DNAs isolados de amostras clínicas e foram testados para a detecção de mutantes katG315 resistentes à isoniazida. Quando aplicado em DNA de cultura o teste pôde detectar com sucesso a mutação mais comum no katG315 (AGC ACC) em todas as linhagens estudadas em comparação com o seqüenciamento de DNA. Em relação às amostras clínicas, o EHR apresentou concordância com o seqüenciamento em todas as amostras com baciloscopia positiva. O teste desenvolvido apresenta um bom potencial para a rápida identificação da resistência à isoniazida em regiões com uma elevada prevalência de mutantes katG315 entre isolados de M. tuberculosis resistentes à isoniazida.Mutations in katG, ahpC and inhA genes were identified and have been correlated with isoniazid resistance in Mycobacterium tuberculosis isolates, mutation in katG S315T being the most frequent. Rapid detection of this mutation could therefore improve the choice of an adequate anti-TB regimen, epidemiological monitoring of isoniazid resistance and, possibly to track transmission of resistant strains. Reverse Hybridization Assay (RHA) is a simple technique for the rapid identification of katG315 mutation in M. tuberculosis. The assay was standardized with 180 DNAs isolated from cultures of M. tuberculosis and was applied to 46 clinical specimens and tested for the detection of isoniazid-resistant katG315 mutants. When the test was applied to the DNA from cultured M. tuberculosis it was possible to successfully detect the most common mutation at katG315 (AGC ACC) in all isolates studied in comparison with DNA sequencing. For clinical samples, the RHA presented agreement with the sequencing in all samples with smear positive. The developed test presents a good potential for the rapid identification of isoniazid resistance in regions with a high prevalence of katG315 mutants among isoniazid-resistant M. tuberculosis isolates

Detecção da mutação mais freqüente no códon 315 do gene katG relacionada com a resistência à isoniazida em isolados de Mycobacterium tuberculosis

A caracterização das mutações nos genes katG, ahpC e inhA e sua correlação com a resistência à isoniazida em isolados de Mycobacterium tuberculosis tem sido descrita. A mutação S315T no gene katG é a mais freqüentemente encontrada e pode fornecer rápida informação para a seleção do tratamento anti-tuberculose, para a vigilância epidemiológica da resistência e, possivelmente rastrear a transmissão de linhagens resistentes. Dessa forma, o objetivo do trabalho foi o desenvolvimento de um Ensaio de Hibridização Reversa (EHR) para a rápida identificação da mutação no códon 315 do gene katG em M. tuberculosis. Após a padronização da metodologia com 180 DNAs de M. tuberculosis isolados de cultura, o teste foi aplicado a 46 DNAs isolados de amostras clínicas e foram testados para a detecção de mutantes katG315 resistentes à isoniazida. Quando aplicado em DNA de cultura o teste pôde detectar com sucesso a mutação mais comum no katG315 (AGC ACC) em todas as linhagens estudadas em comparação com o seqüenciamento de DNA. Em relação às amostras clínicas, o EHR apresentou concordância com o seqüenciamento em todas as amostras com baciloscopia positiva. O teste desenvolvido apresenta um bom potencial para a rápida identificação da resistência à isoniazida em regiões com uma elevada prevalência de mutantes katG315 entre isolados de M. tuberculosis resistentes à isoniazida.Mutations in katG, ahpC and inhA genes were identified and have been correlated with isoniazid resistance in Mycobacterium tuberculosis isolates, mutation in katG S315T being the most frequent. Rapid detection of this mutation could therefore improve the choice of an adequate anti-TB regimen, epidemiological monitoring of isoniazid resistance and, possibly to track transmission of resistant strains. Reverse Hybridization Assay (RHA) is a simple technique for the rapid identification of katG315 mutation in M. tuberculosis. The assay was standardized with 180 DNAs isolated from cultures of M. tuberculosis and was applied to 46 clinical specimens and tested for the detection of isoniazid-resistant katG315 mutants. When the test was applied to the DNA from cultured M. tuberculosis it was possible to successfully detect the most common mutation at katG315 (AGC ACC) in all isolates studied in comparison with DNA sequencing. For clinical samples, the RHA presented agreement with the sequencing in all samples with smear positive. The developed test presents a good potential for the rapid identification of isoniazid resistance in regions with a high prevalence of katG315 mutants among isoniazid-resistant M. tuberculosis isolates