An Aptamer Linked Immobilized Sorbent Assay (ALISA) to Detect Circulatory IFN-α, an Inflammatory Protein among Tuberculosis Patients.

Dysregulation of IFN-α is the basis for pathogenesis of autoimmune as well as infectious diseases. Identifying inflammatory signatures in peripheral blood of patients is an approach for monitoring active infection. Hence, estimation of type I IFNs as an inflammatory biomarker to scrutinize disease status after treatment is useful. Accordingly, an Aptamer Linked Immobilized Sorbent Assay (ALISA) for the detection of IFN-α in serum samples was developed. Sixteen aptamers were screened for their ability to bind IFN-α. Aptamer IFNα-3 exhibited specificity for IFN-α with no cross-reactivity with interferons ß and γ and human serum albumin. The disassociation constant (Kd) was determined to be 3.96 ± 0.36 nM, and the limit of detection was ∼2 ng. The characterized IFNα-3 aptamer was used in ALISA to screen tuberculosis (TB) patients' sera. An elevated IFN-α level in sera derived from untreated TB patients (median = 0.31), compared to nontuberculous household contacts (median = 0.13) and healthy volunteers (median = 0.12), and further a decline in IFN-α level among treated patients (median = 0.13) were seen. The ALISA assay facilitates direct estimation of inflammatory protein(s) in circulation unlike mRNA estimation by real time PCR. Designing of aptamers similar to the IFNα-3 aptamer provides a novel approach to assess other inflammatory protein(s) in patients before, during, and after completion of treatment and would denote clinical improvement in successfully treated patients.

Identification of hot and cold spots in genome of Mycobacterium tuberculosis using Shewhart Control Charts.

The organization of genomic sequences is dynamic and undergoes change during the process of evolution. Many of the variations arise spontaneously and the observed genomic changes can either be distributed uniformly throughout the genome or be preferentially localized to some regions (hot spots) compared to others. Conversely cold spots may tend to accumulate very few variations or none at all. In order to identify such regions statistically, we have developed a method based on Shewhart Control Chart. The method was used for identification of hot and cold spots of single-nucleotide variations (SNVs) in Mycobacterium tuberculosis genomes. The predictions have been validated by sequencing some of these regions derived from clinical isolates. This method can be used for analysis of other genome sequences particularly infectious microbes.

Anchor-based whole genome phylogeny (ABWGP): a tool for inferring evolutionary relationship among closely related microorganisms [corrected].

Phenotypic behavior of a group of organisms can be studied using a range of molecular evolutionary tools that help to determine evolutionary relationships. Traditionally a gene or a set of gene sequences was used for generating phylogenetic trees. Incomplete evolutionary information in few selected genes causes problems in phylogenetic tree construction. Whole genomes are used as remedy. Now, the task is to identify the suitable parameters to extract the hidden information from whole genome sequences that truly represent evolutionary information. In this study we explored a random anchor (a stretch of 100 nucleotides) based approach (ABWGP) for finding distance between any two genomes, and used the distance estimates to compute evolutionary trees. A number of strains and species of Mycobacteria were used for this study. Anchor-derived parameters, such as cumulative normalized score, anchor order and indels were computed in a pair-wise manner, and the scores were used to compute distance/phylogenetic trees. The strength of branching was determined by bootstrap analysis. The terminal branches are clearly discernable using the distance estimates described here. In general, different measures gave similar trees except the trees based on indels. Overall the tree topology reflected the known biology of the organisms. This was also true for different strains of Escherichia coli. A new whole genome-based approach has been described here for studying evolutionary relationships among bacterial strains and species.

Disparity in circulating peripheral blood dendritic cell subsets and cytokine profile of pulmonary tuberculosis patients compared with healthy family contacts.

Dendritic cell (DC) subsets, myeloid DCs (mDCs), and plasmacytoid DCs (pDCs) play a fundamental role in immune response to Mycobacterium tuberculosis (M. tuberculosis). Flow-cytometric estimation of DC subsets showed differences in the ratio of these subsets in untreated, smear-positive pulmonary tuberculosis patients compared with healthy family contacts (HFC, p < 0.05). The percentage of pDCs (0.14 +/- 0.01) was higher than mDCs (0.12 +/- 0.01) in patients, whereas in HFC, mDCs (0.15 +/- 0.01) was higher than pDCs (0.1 +/- 0.01). The percentage of mDCs (0.15 +/- 0.01) and pDCs (0.11 +/- 0.01) was restored in treated patients. Alteration in the DC subsets before and after chemotherapy was confirmed in the follow-up of acid-fast bacilli (AFB)-positive patients. This reversal in the percentage of mDC vs pDCs implicates the influence of active disease on circulating DC subsets. The cytokine bead array revealed an inverse relationship in the circulating levels of IL-12 and IFN-gamma. High IL-12 (37.9 +/- 15.2) and low IFN-gamma (11.09 +/- 3.6) was seen in HFCs derived serum samples compared with that of patients (p < 0.05). The higher percentage of mDCs and elevated IL-12 levels was found to be associated with high risk HFCs investigated. Furthermore CpG/LPS-stimulated whole-blood culture of untreated patients expressed high IFN-alpha in pDCs and less IL-12 in mDCs compared with those of treated patients.

Assessment of the N-PCR assay in diagnosis of pleural tuberculosis: detection of M. tuberculosis in pleural fluid and sputum collected in tandem.

BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.

Visual format for detection of Mycobacterium tuberculosis and M. bovis in clinical samples using molecular beacons.

A real-time polymerase chain reaction (PCR) assay for the direct identification of Mycobacterium tuberculosis and M. bovis using molecular beacons was developed. The assay was modified for use in regular thermal cyclers. Molecular beacons that were specific for M. tuberculosis (Tb-B) and M. bovis (Bo-B) were designed. The fluorescence of the target PCR product-molecular beacon probe complex was detected visually using a transilluminator. The results were then compared with those of conventional multiplex PCR (CM-PCR) assays and biochemical identification. The detection limit of Tb-B and Bo-B beacons was 500 fg and 50 fg by the visual format and real-time PCR assay, respectively, compared with 5 pg by CM-PCR assay. Pulmonary and extrapulmonary samples were examined. The agreement between culture and the two assays was very good in sputum samples and fair in extrapulmonary samples. The agreement between clinical diagnoses with the two assays was moderate in extrapulmonary samples. There was very good agreement between CM-PCR and visual format assays for all samples used in the study. Concordance in the identification of isolates by the visual, CM-PCR assay, and biochemical identification was seen. Hence, the use of molecular beacon detection of M. tuberculosis and M. bovis in clinical samples is feasible by setting up two asymmetric PCRs concurrently. The assay is sensitive, specific, simple to interpret, and takes less than 3 hours to complete.

Modulation of gamma interferon receptor 1 by Mycobacterium tuberculosis: a potential immune response evasive mechanism.

Mycobacterium tuberculosis inhibits gamma interferon (IFN-gamma)-mediated antimycobacterial action by adopting diverse mechanisms. IFN-gamma binds to its receptor, IFN-gammaR, in order to initiate proper signaling. We have observed reduced surface expression levels of IFN-gamma receptor 1 (IFN-gammaR1) in untreated pulmonary tuberculosis patients compared to those in healthy individuals (P < 0.01). Following antitubercular therapy, the expression of IFN-gammaR1 was restored in these patients. To delineate the mechanism by which M. tuberculosis modulates IFN-gammaR1, in vitro experiments were designed, wherein the down modulation of IFN-gammaR1 surface expression was observed for CD14+ cells in peripheral blood mononuclear cells (PBMCs) cocultured with live M. tuberculosis compared to that for uninfected cells (P < 0.01). No modulation of IFN-gammaR1 expression was observed for CD14+ cells in PBMCs infected with Mycobacterium smegmatis. A time-dependent decrease in IFN-gammaR1 mRNA expression was observed for PBMCs infected with M. tuberculosis. Similar down modulation of IFN-gammaR1 protein and mRNA expression in phorbol myristate acetate-differentiated THP-1 cells (pdTHP-1) by M. tuberculosis was observed (P < 0.01). Using reporter gene analysis of 5' deletion constructs of the IFN-gammaR1 gene (IFNGR1) promoter, the decrease in IFN-gammaR1 mRNA in M. tuberculosis-infected pdTHP-1 cells was shown to be due to the decreased transcription of IFNGR1. By immunoblotting and electrophoretic mobility shift assays, the down regulation of stimulating protein 1 (Sp1) expression and its recruitment on the phorbol ester-responsive element of the IFNGR1 promoter in M. tuberculosis-infected pdTHP-1 cells was observed. This down regulation of Sp1 in pdTHP-1 cells cocultured with M. tuberculosis may be responsible for the down regulation of IFN-gammaR1 expression, thereby potentially altering its receptivity to IFN-gamma.