Different Strains Of Mycobacterium Tuberculosis Research Articles

MutVis: Automated framework for analysis and visualization of mutational signatures in pathogenic bacterial strains.

In recent years, mutational signature analysis has become a routine practice in cancer genomics for classification and diagnosis. Characterizing mutational signatures across species or within genomes of a bacteria helps in understanding their evolution and adaptation. However, an integrated framework for analysis and visualization of mutational signatures in bacterial genome is lacking. Hence, we aim to develop an integrated, automated, open-source and user-friendly framework called MutVis to analyze mutational signatures from bacterial whole genome next generation sequencing data. The current framework integrates various publicly available packages using Snakemake workflow management software, Python and R scripting. MutVis supports variant calling, transition (Ti) and transversion (Tv) graphical representation, generation of mutational count matrix, graphical visualization of base-pair substitution spectrum (BPSs) and mutation signatures extraction. TvTi plots provide the 6 base substitution classification for both genome and gene level. Further resolution of base pair substitution classification is provided as 96-profile BPSs plot. Mutation signatures is derived based on the characteristic pattern observed in BPSs using non-negative matrix factorization. Relative contribution of signatures is given as hierarchically clustered heatmap. This provides information on active signatures in the individual given sample and classify samples according to signature contributions. We demonstrated the MutVis framework using geographically different strains of Mycobacterium tuberculosis, downloaded from PATRIC TB-ARC Antibiotic Resistance Catalog (n=963). The current framework can be used to study mutation biases and characteristic mutational signatures in bacterial genomes and is freely available at https://github.com/AkshathaPrasanna/MutVis.

Biochemical evaluation and molecular docking studies on encapsulated astaxanthin for the growth inhibition of Mycobacterium tuberculosis

Astaxanthin,, a tetraterpenoid compound was formulated as liposomes and screened for anti-tubercular activity against different strains of Mycobacterium tuberculosis: MTB, MDR-TB and H37Rv isolated from the patient sputum samples. Minimum inhibitory concentration (MIC) was determined by proportion-based method. The molecular docking analysis of astaxanthin with various mycobacterial drug target proteins were performed using in silico tools. Encapsulated astaxanthin showed better inhibition of M. tuberculosis with MIC value of 500μg/mL against all the selected strains. The docking analysis provided the interacting amino acid residues of selected mycobacterial enzymes and mode of ligand-protein interaction. Based on the present study, it was concluded that encapsulated astaxanthin could be a better cost effective natural compound for the treatment of tuberculosis among the patients which will combat side effects in comparison with the first line AntiTB drugs like rifampicin and isoniazid.

Three-dimensional in situ morphometrics of Mycobacterium tuberculosis infection within lesions by optical mesoscopy and novel acid-fast staining

Tuberculosis (TB) preclinical testing relies on in vivo models including the mouse aerosol challenge model. The only method of determining colony morphometrics of TB infection in a tissue in situ is two-dimensional (2D) histopathology. 2D measurements consider heterogeneity within a single observable section but not above and below, which could contain critical information. Here we describe a novel approach, using optical clearing and a novel staining procedure with confocal microscopy and mesoscopy, for three-dimensional (3D) measurement of TB infection within lesions at sub-cellular resolution over a large field of view. We show TB morphometrics can be determined within lesion pathology, and differences in infection with different strains of Mycobacterium tuberculosis. Mesoscopy combined with the novel CUBIC Acid-Fast (CAF) staining procedure enables a quantitative approach to measure TB infection and allows 3D analysis of infection, providing a framework which could be used in the analysis of TB infection in situ.

Differential Responses by Human Macrophages to Infection With Mycobacterium tuberculosis and Non-tuberculous Mycobacteria.

Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacteria (NTM) are formidable causes of lung diseases throughout the world. While MTB is considered to be more virulent than NTM, host factors also play a key role in disease development. To elucidate whether there are differential immune responses to various mycobacteria, THP-1 macrophages were temporally infected with MTB H37Rv or with four different NTM species. We found that cells infected with MTB had greater bacterial burden and p65 nuclear factor-kappa B (NF-κB) activation than cells infected with NTM. There was also differential expression of mRNA for interleukin-1-β (IL-1β), IL-8, IL-10, and tumor necrosis factor-alpha (TNF-α) with no distinct pattern of mRNA expression among the different mycobacteria. In contrast, at the protein level, some generalizations can be made of the cytokines and chemokines expressed. Compared to uninfected cells, the rapid-growing Mycobacterium smegmatis but not Mycobacterium abscessus induced significantly greater pro-inflammatory cytokines and IL-10, whereas both NTM individually induced greater levels of chemokines. Compared to uninfected control cells, the two slow-growing NTM and MTB differentially induced cytokine expression with Mycobacterium avium inducing more pro-inflammatory cytokines and IL-10, whereas M. avium, Mycobacterium intracellulare, and MTB inducing greater but similar levels of chemokines. MTB-infected THP-1 cells also demonstrated lower level of phagosome–lysosome fusion and apoptosis than NTM-infected cells while there were differences in these macrophage functions among the NTM species. Interestingly, M. intracellulare, M. avium, and MTB have similar levels of autophagosome formation, but the levels displayed by all three were lower than for M. smegmatis and M. abscessus. This study demonstrates the differences in bacterial burden and macrophage effector functions among several clinically relevant mycobacterial species. Such disparities may, in part, account for differences in clinical outcomes among patients infected with various species of NTM as has been seen for different strains of MTB.

Matrix Metalloproteinases as Markers of Acute Inflammation Process in the Pulmonary Tuberculosis

The main factors of pathogenesis in the pulmonary tuberculosis are not only the bacterial virulence and sensitivity of the host immune system to the pathogen, but also the degree of destruction of the lung tissue. Such destruction processes lead to the development of caverns, in most cases requiring surgical interventions besides the drug therapy. Identification of special biochemical markers allowing to assess the necessity of surgery or therapy prolongation remains a challenge. We consider promising markers—metalloproteinases—analyzing the data obtained from patients with pulmonary tuberculosis infected by different strains of Mycobacterium tuberculosis. We argue that the presence of drug-resistant strains in lungs leading to complicated clinical prognosis could be justified not only by the difference in medians of biomarkers concentration (as determined by the Mann–Whitney test for small samples), but also by the qualitative difference in their probability distributions (as detected by the Kolmogorov–Smirnov test). Our results and the provided raw data could be used for further development of precise biochemical data-based diagnostic and prognostic tools for pulmonary tuberculosis.

Computational approach for siRNA Based RNA Interference of ATP synthase subunit alpha coding gene of different strains of Mycobacterium tuberculosis

Computational approach for siRNA Based RNA Interference of ATP synthase subunit alpha coding gene of different strains of Mycobacterium tuberculosis

Genotypic diversity of Mycobacterium tuberculosis isolates from North-Central Indian population

ABSTRACTBackground: Different strains of Mycobacterium tuberculosis (MTB) are known to have different epidemiological and clinical characteristics. Some of them are widely distributed and associated with drug resistance, whereas others are locally predominated. Molecular epidemiological investigations have always been beneficial in identifying new strains and studying their transmission dynamics. Sahariya a primitive tribe of North Madhya Pradesh, India, has already been reported to have high prevalence of tuberculosis (TB) than their non-tribal neighbours. However, the information about MTB genotypes prevalent in Sahariya tribe and their non-tribal neighbours is not available.Methods: A total of 214 clinical isolates representing Sahariya tribe and non-tribes were analyzed by spoligotyping and MIRU-VNTR typing.Results: The EAI3_IND/SIT11 genotype was observed as major genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. A 3.04 fold higher risk of getting TB with EAI3_IND/SIT11 genotype was observed in Sahariya as compared to the non-tribal population. The EAI_IND/SIT11 genotype also found to have more number of MDR-TB cases in Sahariya as well as true and possible transmission links. In Sahariya tribe, 3 clusters (6 isolates) reflected true transmission links, whereas 8 clusters consisted of 26 isolates revealed possible transmission links within the same geographical location or nearby houses.Conclusion: The present study highlighted the predominance of EAI3_IND/SIT11 genotype in Sahariya tribe followed by CAS1_Delhi/SIT26 genotype. Combined approach of MIRU-VNTR typing and spoligotyping was observed more favourable in discrimination of MTB genotypes. Further, longitudinal studies using whole genome sequencing can provide more insights into genetic diversity, drug resistance and transmission dynamics of these prevalent genotypes.

Comparative Study of the Molecular Basis of Pathogenicity of M. bovis Strains in a Mouse Model.

It is widely accepted that different strains of Mycobacterium tuberculosis have variable degrees of pathogenicity and induce different immune responses in infected hosts. Similarly, different strains of Mycobacterium bovis have been identified but there is a lack of information regarding the degree of pathogenicity of these strains and their ability to provoke host immune responses. Therefore, in the current study, we used a mouse model to evaluate various factors involved in the severity of disease progression and the induction of immune responses by two strains of M. bovis isolated from cattle. Mice were infected with both strains of M. bovis at different colony-forming unit (CFU) via inhalation. Gross and histological findings revealed more severe lesions in the lung and spleen of mice infected with M. bovis N strain than those infected with M. bovis C68004 strain. In addition, high levels of interferon-γ (IFN-γ), interleukin-17 (IL-17), and IL-22 production were observed in the serum samples of mice infected with M. bovis N strain. Comparative genomic analysis showed the existence of 750 single nucleotide polymorphisms and 145 small insertions/deletions between the two strains. After matching with the Virulence Factors Database, mutations were found in 29 genes, which relate to 17 virulence factors. Moreover, we found an increased number of virulent factors in M. bovis N strain as compared to M. bovis C68004 strain. Taken together, our data reveal that variation in the level of pathogenicity is due to the mutation in the virulence factors of M. bovis N strain. Therefore, a better understanding of the mechanisms of mutation in the virulence factors will ultimately contribute to the development of new strategies for the control of M. bovis infection.

Mycobacterium tuberculosis strains from ancient and modern lineages induce distinct patterns of immune responses.

It is possible that the difference in virulence and prevalence of different strains of Mycobacterium tuberculosis is related to the diverse immune response they evoke in the host. Outbreak strains have been shown to subvert the innate immune response as a potential host evasion mechanism. However, the immunological outcome of the interactions of different clinical strains with different host cells is still not understood. Extremely Drug Resistant (XDR) Beijing, a modern lineage clinical strain and a comparator ancient lineage strain, EAI-5, were selected for the present study. The early induction of proinflammatory cytokines in human peripheral blood monocyte derived macrophages (MDM), monocyte derived dendritic cells (MDDC) and whole blood (WB) infected by selected clinical isolates and laboratory strains H37Rv and BCG were assessed. The two clinical strains exhibited distinct patterns of cytokine induction. The ancient lineage strain induced substantially higher expression of all proinflammatory cytokines like TNF-α, IL-1β, IL-12 and chemokines like MCP-1, IL-8. However, the modern lineage strain exhibited suppressed response for the same. Further, the immune responses to two strains were conserved in infected MDM, MDDC and WB i.e. showing similar patterns of response across multiple human hosts. However, the differential response pattern was not observed when bacterial sonicates were used instead of live mycobacteria. The lineage specific patterns in induction of proinflammatory cytokines and chemokines by different M. tuberculosis strains remain similar in macrophage and dendritic cells isolated from different individuals. The present study also confirms that whole cell sonicates of different lineages of M. tuberculosis fail to induce such lineage specific response.

In vitro bactericidal activities of two novel dihydropyridine derivatives against Mycobacterium tuberculosis.

Introducing new and effective antitubercular agents is important in tuberculosis control programs. In this study, the in vitro antitubercular activity of two novel 1,4-dihydropyridine derivatives (F-27, Cl-33) were screened against a total of 113 different strains of Mycobacterium tuberculosis (77 susceptible and 36 resistant clinical isolates). The in vitro activities of these compounds were evaluated based on the modified broth macro-dilution assay. Compound F-27 showed more than 90% growth inhibition at the range of 2 to 8 μg/mL (minimum inhibitory concentration [MIC]90: 4.13 ± 0.45 µg/mL; p < 0.01), and complete growth inhibition was observed at the range of 8 to 32 μg/mL (minimum bactericidal concentration [MBC]: 11.2 ± 1.65 µg/mL; p < 0.01) against susceptible strains. However, 92% of the resistant strains showed some degree of susceptibility against this compound (MIC90 range: 16 to 64 µg/mL; mean: 40.4 ± 8 µg/mL; p < 0.01). It was found that although there is a linear relationship between the inhibitory activity of F-27 and isoniazid against resistant strains at low concentrations (r = 0.484, p < 0.001), there was no relationship between resistance to isoniazid and F-27 at higher concentrations (r = 0.019, p > 0.1). This may emphasize no cross-resistance between F-27 and isoniazid. Considering the sufficient sample size of the study and based on the excellent antimycobacterial activity of F-27, it could be concluded that F-27 is a potent candidate as a lead compound, and may be considered for development of a new antitubercular agent.

IN VITRO STUDY OF URSOLIC ACID COMBINATION FIRST-LINE ANTITUBERCULOSIS DRUGS AGAINST DRUG-SENSITIVE AND DRUG-RESISTANT STRAINS OF Mycobacterium tuberculosis

Objective: The resurgence of tuberculosis (TB) caused by Mycobacterium TB (MTB) is associated with the rapid spread of multidrug-resistant,therefore, the development of new antimycobacterial agents is necessary. The aim of this study was to evaluate the antimycobacterial activity ofursolic acid (UA) when it using alone and combination with TB drugs.Methods: MTB H37Rv strain, streptomycin-rifampicin resistant strain, and isoniazid-ethambutol resistant strain were evaluated by susceptibility testusing a serial number of UA (25-150 µg/mL). Minimum inhibitory concentration (MIC) was read as minimum concentration of drugs that completelyinhibit visible growth of organism. Activities of drug combination of UA with TB drug were determined in Lowenstein-Jensen media by calculatingthe fractional inhibitory concentration index.Results: The results showed that MIC of UA was 50 µg/mL against three different strains of MTB. The combination of UA and TB drugs displayedsynergistic interaction, and no antagonism result from the combination was observed for strains of MTB.Conclusion: These results indicate that UA may serve as a promising lead compound for future antimycobacterial drug development.Keywords: Ursolic acid, Tuberculosis, Drug combination, Susceptibility test

Proteomics Analysis of Three Different Strains of Mycobacterium tuberculosis under In vitro Hypoxia and Evaluation of Hypoxia Associated Antigen’s Specific Memory T Cells in Healthy Household Contacts

In vitro mimicking conditions are thought to reflect the environment experienced by Mycobacterium tuberculosis inside the host granuloma. The majority of in vitro dormancy experimental models use laboratory-adapted strains H37Rv or Erdman instead of prevalent clinical strains involved during disease outbreaks. Thus, we included the most prevalent clinical strains (S7 and S10) of M. tuberculosis from south India in addition to H37Rv for our in vitro oxygen depletion (hypoxia) experimental model. Cytosolic proteins were prepared from hypoxic cultures, resolved by two-dimensional electrophoresis and protein spots were characterized by mass spectrometry. In total, 49 spots were characterized as over-expressed or newly emergent between the three strains. Two antigens (ESAT-6, Lpd) out of the 49 characterized spots were readily available in recombinant form in our lab. Hence, these two genes were overexpressed, purified and used for in vitro stimulation of whole blood collected from healthy household contacts (HHC) and active pulmonary tuberculosis patients (PTB). Multicolor flow cytometry analysis showed high levels of antigen specific CD4+ central memory T cells in the circulation of HHC compared to PTB (p < 0.005 for ESAT-6 and p < 0.0005 for Lpd). This shows proteins that are predicted to be up regulated during in vitro hypoxia in most prevalent clinical strains would indicate possible potential immunogens. In vitro hypoxia experiments with most prevalent clinical strains would also elucidate the probable true representative antigens involved in adaptive mechanisms.

Synthesis, QSAR Model Study and Antimicrobial Evaluation of Esters and Thioester Derivatives of Isonicotinic Acid on the Different Strains of Mycobacterium Tuberculosis

Isoniazid is one of the widely used first-line drugs in the treatment of tuberculosis for many years but the mechanism of the action of the drugs is still not clear. Herein, we report the synthesis, QSAR model study and biological effects of esters and thioester derivative of isonicotinic acid (INA) on different strains of Mycobacterium tuberculosis in an attempt to establish the mode of action of the active form of Isoniazid (INH). The esters of INA are expected to show antibiotic activities against strains of Mycobacterium tuberculosisupon activation by intracellular nonspecific esterases, while thioesters is expected not to show antimicrobial effects and thus served as control. The obtained results indicated that the synthesized esters did not show antimicrobial activity. The conclusion drawn from the result is that either INA is not the active form of INH or that the esters show poor water solubility- in addition to the possibility of acquired during resistance of the strains during culture and testing - all of which could hamper mycobacterial cell up take. This suggests that more studies are needed to search for the possible active form of isoniazid.

In silico identification and characterization of a hypothetical protein of Mycobacterium tuberculosis EAI5 as a potential virulent factor.

Tuberculosis, a life threatening disease caused by different strains of Mycobacterium tuberculosis is creating an alarming condition due to the emergence of increasing multi drug resistance (MDR) trait. In this study, in silico approach was used for the identification of a conserved novel virulent factor in Mycobacterium tuberculosis EAI5 (Accession no.CP006578) which can also act as potential therapeutic target. Systematic comparative search of genes that are common to strain EAI5 and other human pathogenic strains of M. tuberculosis enlisted 408 genes. These were absent in the non-pathogenic Mycobacterium smegmatis MC2155 and in the human genome. Among those genes, only the protein coding hypothetical genes (97 out of 408) and their corresponding products were selected for further exploration. Of these, 11 proteins were found to have notable conserved domains, of which one hypothetical protein (NCBI Acc No. AGQ35418.1) was selected for further in silico exploration which was found to have two functional domains, one having phosphatidylinositol specific phospholipase C (PI-PLC) activity while the other short domain with weak lectin binding activity. As PI-PLC contributes virulence property in some pathogenic bacteria with a broad range of activities, different bioinformatic tools were used to explore its physicochemical and other important properties which indicated its secretary nature. This PI-PLC was previously not reported as drug/vaccine target to the best of our knowledge. Its predicted 3D structure can be explored for development of inhibitor for novel therapeutic strategies against MDR-TB.

Preparation, standardization and in vitro safety testing of Mycobacterium nosodes (Emtact- polyvalent nosode)

Most of the nosodes in the homeopathic pharmacopeia have been sourced from obscure pathological material over a century ago; of which no scientific documentation is available. A method for preparation and standardization of univalent and polyvalent Mycobacterium nosodes (labeled as Emtact), using different strains of Mycobacterium tuberculosis was developed. The committee comprising microbiologists, scientist, pharmacist, homeopaths and clinicians had reviewed and approved the method of preparation of nosode. Preparation of the nosode was based on the reference in the Homeopathy Pharmacopoeia of India (HPI), group N-IV. Strains of M. tuberculosis viz. Standard strain H37Rv, multi-drug resistant (MDR) M. tuberculosis, Mycobacterium bovis (BCG vaccine) and Mycobacterium avium were identified, procured and documented. Twenty billion viable cells for each strain were taken for Original Stock Nosode (OSN). The original stock was prepared by suspending the microbial cells into water for injection (WFI) (1ml). As per the Indian Pharmacopoeia (IP) monograph, sterility testing was done for different potencies. Polymerase Chain Reaction (PCR) was performed for 30c potency for detection of any DNA material of the source organisms. A polyvalent (multi-strain) and univalent M. tuberculosis nosodes were prepared for research and clinical use. No growth of Mycobacterium was observed in any of the samples above 5c potency. The in-vitro testing for nosode (30c) was found to be free from any organism and DNA material. Mycobacterium nosodes sourced from individual strain and polyvalent Emtact nosode invitro testing results found to be satisfactory for its handling and utilization. The nosode seems to be safe and may be tested further invivo to explore its therapeutic application.

Sorting Inactivated Cells Using Cell-Imprinted Polymer Thin Films

Previous work showed that cell imprinting in a poly(dimethylsiloxane) film produced artificial receptors to cells by template-assisted rearrangement of functional groups on the surface of the polymer thin film which facilitated cell capture in the polymer surface indentations by size, shape, and, most importantly, chemical recognition. We report here that inactivation of cells by treatment with formaldehyde (4%), glutaraldehyde (2%), or a combination of the two leads to markedly improved capture selectivity (a factor of 3) when cells to be analyzed are inactivated in the same manner. The enhanced capture efficiency compared to living cells results from two factors: (1) rigidification of the cell surface through cross-linking of amine groups by the aldehyde; and (2) elimination of chemicals excreted from living cells which interfere with the fidelity of the cell-imprinting process. Moreover, cell inactivation has the advantage of removing biohazard risks associated with working with virulent bacteria. These results are demonstrated using different strains of Mycobacterium tuberculosis.

Zanthoxylum capense constituents with antimycobacterial activity against Mycobacterium tuberculosis in vitro and ex vivo within human macrophages

Ethnopharmacological relevanceZanthoxylum capense Thunb. (Rutaceae) is a medicinal plant traditionally used in Mozambique to treat tuberculosis. Aims of the studyThe main aim of the study was to find antimycobacterial lead compounds from Zanthoxylum capense. Another goal was to provide scientific validation for the use of this plant in traditional medicine. Methods and materialsBy bioassay-guided fractionation, 16 compounds were isolated and screened for their in vitro antimycobacterial activity against two different strains of Mycobacterium tuberculosis. Their in vitro cytotoxicity to human THP-1 macrophages was also assessed. The compounds with favourable selectivity index values (SI>10) were further investigated for their ability to inhibit the growth of Mycobacterium tuberculosis H37Rv in an intracellular macrophage model of infection. ResultsThe best results were obtained for a benzophenanthridine alkaloid, decarine (1), and an N-isobutylamide, N-isobutyl-(2E,4E)-2,4-tetradecadienamide (15), which showed high activity against Mycobacterium tuberculosis H37Rv (MIC of 1.6μg/ml), and a low macrophage cytotoxicity (IC50>60μg/ml), indicating considerable selective activity. The benzophenanthridine alkaloid 6-acetonyldihydronitidine (6) revealed cytotoxicity (IC50 1.7μg/ml), despite the determined MIC of 6.2–12.5μg/ml. In infected macrophages, decarine (1) was able to reduce bacterial survival by almost two log units at a concentration of 6.2μg/ml 5 days post-drug exposure. Compound 15 exhibited an intermediate activity at drug concentrations ranging from 6.2 to 25μg/ml. ConclusionsThe high antimycobacterial activity of decarine found, both in vitro and ex vivo against mycobacteria, and the low cytotoxicity towards human macrophages indicate that it may be valuable as a lead scaffold for the development of anti-TB drugs.

The non‐human primate model of tuberculosis

Non-human primates (NHPs) are used to model human disease owing to their remarkably similar genomes, physiology, and immune systems. Recently, there has been an increased interest in modeling tuberculosis (TB) in NHPs. Macaques are susceptible to infection with different strains of Mycobacterium tuberculosis (Mtb), producing the full spectrum of disease conditions, including latent infection, chronic progressive infection, and acute TB, depending on the route and dose of infection. Clearly, NHPs are an excellent model of human TB. While the initial aim of the NHP model was to allow preclinical testing of candidate vaccines and drugs, it is now also being used to study pathogenesis and immune correlates of protection. Recent advances in this field are discussed in this review. Key questions such as the effect of hypoxia on the biology of Mtb and the basis of reactivation of latent TB can now be investigated through the use of this model.

Mixed infection with Beijing and non-Beijing strains in pulmonary tuberculosis in Taiwan: prevalence, risk factors, and dominant strain

Patients with pulmonary tuberculosis (TB) can be simultaneously infected with different strains of Mycobacterium tuberculosis (mixed infection). We investigated the prevalence and risk factors of mixed infection by Beijing and non-Beijing strains in pulmonary TB patients in Taiwan. We developed a quantitative PCR method to simultaneously detect the presence of Beijing and non-Beijing strains. A total of 868 pre-treatment samples (from 868 patients), including 563 sputum samples smear-positive for acid-fast bacilli and 305 liquid medium samples culture-positive for mycobacteria, were tested. Medical records of patients with culture-confirmed pulmonary TB were reviewed. The detection limit of our quantitative PCR method was five copies of target sequences. With mycobacterial culture result as the reference standard, the sensitivity and specificity of our quantitative PCR method were 95% and 98%, respectively. M. tuberculosis strains were isolated in 466 samples, of which 231 (49.6%) were infected with a Beijing strain. Another 14 patients (3.0%) had mixed infection, with the Beijing strain being the dominant strain in 13 (93%). Age <25 years with pulmonary cavities was associated with mixed infection. In patients infected with non-Beijing strains, the bacterial load of non-Beijing strains was lower among those with mixed infection than among those without. Our quantitative PCR method was accurate in detecting Beijing and non-Beijing strains in smear-positive sputum and culture-positive liquid medium samples. Mixed infection was present in pulmonary TB patients (3.0%), especially in those aged <25 years with pulmonary cavities. Beijing strains seem to be more dominant than non-Beijing strains in patients with mixed infection.

SVM Model for Amino Acid Composition Based Prediction of Mycobacterium tuberculosis

The Tuberculosis is the classical human mycobacterial disease, caused by Mycobacterium tuberculosis. The disease primarily affect the lung and causes pulmonary tuberculosis, as well as affect intestine, bone, joints, meninges, lymph nodes, skin and other tissue of the body, causing extra pulmonary tuberculosis. Thus there arises the need to understand the relationships among various parameters of these proteins for prediction of their classes, structures and functionality. The computational approaches for prediction of their classes are fast and economical therefore can be used to complement the existing wet lab techniques. Realizing their importance, in this paper an attempt has been made to correlate them with their amino acid composition and predict them with fair accuracy. This is a novel method where Mycobacterium Tuberculosis has been classified on the basis of amino acid composition using Support Vector Machine. The SVM has been implemented using SVM Light package. The method discriminates different strains of Mycobacterium Tuberculosis. The performance of the method was evaluated using 10-fold cross-validation where accuracy of 100% was obtained.