Evidence for genetic divergence in ribosomal RNA genes in mycobacteria

DNA was isolated from Mycobacterium phlei and from M. smegmatis. Each DNA sample was restricted with endonucleases, the fragments were separated by agarose gel electrophoresis and transferred to nitrocellulose film. Fragments of DNA containing rRNA sequences were identified by means of 125I-labelled rRNA of M. phlei or of M. smegmatis. The distributions of restriction endonuclease sites within the rRNA gene(s) and flanking sequences were found to be characteristic for each of the two species. Hybridizations with heterologous probes indicate that although M. phlei rRNA and M. smegmatis rRNA share regions of sequence homology, they are probably not identical in primary structure. The results suggest that the rRNA genes might prove to be useful taxonomic markers for mycobacteria

Mutations in RpoB Gene and Their Association with Rifampicin-resistance Levels in Clinical Isolates of Mycobacterium Tuberculosis

Present study was aimed to identify most frequent mutations in rpoB gene region and to evaluate the association between mutations in rpoB gene and resistance levels to Rifampicin in clinical isolates of Mycobacterium tuberculosis of different geographical regions of India. A total of 100 clinical isolates of Mycobacterium tuberculosis were included in this study. Drug susceptibility testing against first line anti-tuberculosis drugs was performed on LJ medium by conventional minimal inhibitory concentration (MIC) method and the mutation(s) in rpoB gene of M. tuberculosis isolates were analyzed by sequencing method. Of the 100 M. tuberculosis isolates, 31 (31.0%) and 18 (18.0%) were found resistant and susceptible for all four first-line anti-tuberculosis drugs. The genetic mutations were observed in 96% (72/75) rifampicin-resistant M. tuberculosis isolates, while 4% (3/75) of rifampicin-resistant isolates did not have any mutation in rpoB gene. The mutation TCG531TTG (Ser531Leu) was found as most common and frequent mutation in 69.3% (52/75) of rifampicin-resistant isolates of M. tuberculosis with MIC level (≥ 512mg/l). The mutation at codon 511 was associated with low degree (128mg/l) of rifampicin-resistance, deletions at codons 514-516 or substitution at codon 516 were found to be associated with moderate degree (256mg/l) of rifampicin-resistance and mutations at codon 526, 531 were associated with the high degree (512mg/l) of rifampicin-resistance in M. tuberculosis isolates of Indian origin. The findings of this study will be useful for the development of raid and more specific indigenous molecular tools for the early diagnosis of multidrug-resistant tuberculosis in the country

Assessment of the N-PCR Assay in Diagnosis of Pleural Tuberculosis: Detection of M.tuberculosis in Pleural Fluid and Sputum Collected in Tandem

The nonspecific clinical presentation and paucibacillary nature of tuberculous pleuritis remains a challenge for diagnosis. Diagnosis of tuberculous pleural effusion depends on the demonstration of the presence of tubercle bacilli in the sputum, pleural fluid, or pleural biopsy specimen, or demonstration of granuloma in pleura by histological examination. We examined the clinical utility of the diagnosis of pleural tuberculosis using the in house N-PCR assay, AFB smear microscopy and culture. Besides pleural fluid the inclusion of sputum in the efficacy of diagnosis of pleural tuberculosis was scrutinized.Pleural fluid and sputum samples of 58 tuberculous and 42 non-tuberculous pleural effusion patients were processed for AFB smear microscopy, culture and the N-PCR assay. Mycobacteria were detected exclusively in tuberculous pleural effusion samples. None of the non-tuberculous pleural effusion samples were positive for mycobacteria. Comparative analysis showed that the N-PCR assay had the highest sensitivity. Inclusion of sputum along with pleural fluid increased N-PCR sensitivity from 51.7 to 70.6% (p<0.0001).This improved sensitivity was reflected in AFB smear microscopy and isolation by culture. The sensitivity enhanced on inclusion of sputum from 3.4 (p = 0.50) to 10.3% (p = 0.038) for AFB smear microscopy and for isolation of mycobacteria from 10.3(p = 0.03) to 22.4% (p = 0.0005). Thirteen isolates were obtained from 58 pleural tuberculosis patients. Eleven mycobacterial isolates were identified as M. tuberculosis and two as M. fortuitum and M. chelonae. Complete concordance was seen between the biochemical identification of isolates and the N-PCR identification of mycobacterial species prior to isolation.To the best of our knowledge this is the first PCR based report on utility of sputum for diagnosis of pleural tuberculosis. The present study demonstrates that a combination of pleural fluid with sputum sample and N-PCR improved the diagnosis of pleural tuberculosis

Predominance of Ancestral Lineages of Mycobacterium tuberculosis in India

Molecular epidemiologic findings suggest an ancient focus of TB

A Toolbox for Tuberculosis Diagnosis: An Indian Multicentric Study (2006-2008): Microbiological Results

BACKGROUND: The aim of this multicentric prospective study in India was to assess the value of several microbiological tools that contribute to the diagnosis of tuberculosis (TB) according to HIV status. METHODS: Standard microbiological tools on individual specimens were analyzed. RESULTS: Among the 807 patients with active TB, 131 were HIV-infected, 316 HIV-uninfected and 360 had HIV-unknown status. Among the 980 non-active TB subjects, 559 were at low risk and 421 were at high risk of M. tuberculosis (Mtb) exposure. Sensitivity of smear microscopy (SM) was significantly lower in HIV-infected (42.2%) than HIV-uninfected (75.9%) (p = 0.0001) and HIV-unknown pulmonary TB patients (61.4%) (p = 0.004). Specificity was 94.5% in non-TB patients and 100% in health care workers (HCW) and healthy family contacts. Automated liquid culture has significantly higher diagnostic performances than solid culture, measured by sensitivity (74.7% vs. 55.9%) (p = 0.0001) and shorter median time to detection (TTD) (12.0 vs. 34.0 days) (p = 0.0001). Specificity was 100% in HCW and cured-TB patients, but was lower in non-TB patients (89%) due to isolation of Mycobacteria other than tuberculosis (MOTT). TTD by both methods was related to AFB score. Contamination rate was low (1.4%). AccuProbe hybridization technique detected Mtb in almost all culture-positive specimens, but MOTT were found in 4.7% with a significantly higher frequency in HIV-infected (15%) than HIV-uninfected TB patients (0.5%) (p = 0.0007). Pre-test classification significantly increased the diagnostic value of all microbiological tests in pulmonary TB patients (p<0.0001) but to a lesser degree in extrapulmonary TB patients. CONCLUSIONS: Conventional microbiological tools led to results similar to those already described in India special features for HIV-infected TB patients included lower detection by SM and culture. New microbiological assays, such as the automated liquid culture system, showed increased accuracy and speed of detection

Research priorities in Maternal, Newborn, &amp; Child Health &amp; Nutrition for India:An Indian Council of Medical Research-INCLEN Initiative

In India, research prioritization in Maternal, Newborn, and Child Health and Nutrition (MNCHN) themes has traditionally involved only a handful of experts mostly from major cities. The Indian Council of Medical Research (ICMR)-INCLEN collaboration undertook a nationwide exercise engaging faculty from 256 institutions to identify top research priorities in the MNCHN themes for 2016-2025. The Child Health and Nutrition Research Initiative method of priority setting was adapted. The context of the exercise was defined by a National Steering Group (NSG) and guided by four Thematic Research Subcommittees. Research ideas were pooled from 498 experts located in different parts of India, iteratively consolidated into research options, scored by 893 experts against five pre-defined criteria (answerability, relevance, equity, investment and innovation) and weighed by a larger reference group. Ranked lists of priorities were generated for each of the four themes at national and three subnational (regional) levels [Empowered Action Group & North-Eastern States, Southern and Western States, & Northern States (including West Bengal)]. Research priorities differed between regions and from overall national priorities. Delivery domain of research which included implementation research constituted about 70 per cent of the top ten research options under all four themes. The results were endorsed in the NSG meeting. There was unanimity that the research priorities should be considered by different governmental and non-governmental agencies for investment with prioritization on implementation research and issues cutting across themes

Advances in the diagnosis and treatment of leprosy

Leprosy is a chronic infectious disease caused by Mycobacterium leprae that mainly affects the skin and peripheral nerves. Over recent years, many important advances have been made in developing molecular diagnostics, in identifying highly effective drugs and designing multidrug regimens for treatment, and in unravelling the genomic structure and functions of the leprosy bacillus. Using the new information about specific sequences of M. leprae, several gene probes and gene amplification systems for confirming diagnosis and monitoring treatment have been developed. Among these, polymerase chain reaction (PCR)-based methods have been useful in confirming the diagnosis in paucibacillary leprosy (where few bacilli are present). RNA-targeting systems for monitoring the progress of treatment, in situ hybridisation techniques for analysing specimens with nonspecific histological features, and molecular methods for direct detection of rifampicin/dapsone resistance are other major technological advances with immense applied value. Several effective regimens for the treatment of leprosy have been developed, which include rifampicin, clofazimine and dapsone as core drugs. Although these regimens are generally satisfactory, limitations in terms of persisting activity and late reactions/relapses in paucibacillary leprosy, and persistence of dead and/or live organisms in multibacillary forms of the disease, have been observed

Molecular modelling and docking analysis of katG and rpoB gene in MDR-TB isolates from North Central Indian population

Tuberculosis caused by Mycobacterium tuberculosis, requires multi drug therapy approach. Drug resistance in M. tuberculosis is caused by mutations in specific regions in drug target genes. The study aimed to identify mutations in katG and rpoB genes and investigate the drug–drug target interactions. A total of 27 MDR-TB isolates were sequenced for katG and rpoB genes and docking and MIC analysis were performed. Three types of mutations for katG gene (Arg463Leu in all isolates of Sahariya and non-tribes; Asp529Thr and Asp529His, each in two isolates only, in Sahariya) were observed. In rpoB gene, the Ser531Leu change was observed in 17/21 isolates in Sahariya and 3/6 isolates in non-tribes. The docking analysis revealed that the drugs isoniazid and rifampicin bind to different residues in mutant forms than their proposed active sites, making active binding sites rigid and causing resistance. The MIC for isoniazid was found to range from 0.2 to 5 μg/ml in Sahariya tribe, whereas, in non-tribes, it is 0.2 μg/ml and 1 μg/ml. The MIC for rifampicin was observed at 64 μg/ml in both the population groups. The study explored the possible functional variation in isoniazid and rifampicin resistance with respect to the identified mutations. The present results indicate that these mutations affect the drug binding affinity and are causing resistance. Keywords: Sahariya tribe, MDR-TB, Molecular modelling, Dockin