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Background Tuberculosis (TB) though primarily affects the lungs it may also affect the other parts of the body and referred as extra pulmonary (EPTB). This study is focused on understanding the genetic diversity and molecular epidemiology of Mycobacterium tuberculosis (M.tb) among tuberculous lymphadenitis (TBL), a form of EPTB patients identified in Chennai, Tamil Nadu. Methods The genetic diversity was identified by performing spoligotyping on the M.tb clinical isolates that were recovered from lymph node samples. A total of 71 M.tb isolates were recovered from extra pulmonary lymph node samples and subjected to Drug susceptibility testing and spoligotyping was carried out. In addition, immunological characterization from blood of same individuals from whom M.tb was isolated was carried out between the two major lineages groups East African Indian 3 (EAI3) and non-EAI3 strains by ELISA. The results of spoligotyping patterns were compared with the world Spoligotyping Database of Institute Pasteur de Guadeloupe (SpolDB4). Results We found 41 spoligotype patterns and their associated lineages. Out of 41 spoligotype pattern, only 22 patterns are available in the spoldB4 database with Spoligotype international Type (SIT) number and remaining patterns were orphan strains without SIT number. The most predominant spoligotype lineage that was found in lymph node sample in this region of India was EAI (36), followed by central Asian strain (CAS) (6), T1 (5), Beijing (3), Latin American & Mediterranean (LAM) (2), U (1), X2 (1) and orphan (22). In addition to EAI, CAS and Beijing, our study identified the presence of orphan and unique spoligotyping patterns in Chennai region. We observed six drug resistant isolates. Out of six drug resistant isolates, four were resistant to isoniazid drug and associated with EAI family. Moreover, we observed increased levels of type 2 and type 17 cytokine profiles between EAI3 and non-EAI family, infected individuals. Conclusions The study confirms that EAI lineage to be the most predominant lineages in EPTB patients with lymphadenitis and were found to have increased type 1 and type 17 proinflammatory cytokine profiles.

The end TB strategy reinforces the essentiality of readily accessible biomarkers for early tuberculosis diagnosis. Exploration of microRNA (miRNA) and pathway analysis opens an avenue for the discovery of possible therapeutic targets. miRNA is a small, non-coding oligonucleotide characterized by the mechanism of gene regulation, transcription, and immunomodulation. Studies on miRNA define their importance as an immune marker for active disease progression and as an immunomodulator for innate mechanisms, such as apoptosis and autophagy. Monocyte research is highly advancing toward TB pathogenesis and biomarker efficiency because of its innate and adaptive response connectivity. The combination of monocytes/macrophages and their relative miRNA expression furnish newer insight on the unresolved mechanism for Mycobacterium survival, exploitation of host defense, latent infection, and disease resistance. This review deals with miRNA from monocytes, their relative expression in different disease stages of TB, multiple gene regulating mechanisms in shaping immunity against tuberculosis, and their functionality as biomarker and host-mediated therapeutics. Future collaborative efforts involving multidisciplinary approach in various ethnic population with multiple factors (age, gender, mycobacterial strain, disease stage, other chronic lung infections, and inflammatory disease criteria) on these short miRNAs from body fluids and cells could predict the valuable miRNA biosignature network as a potent tool for biomarkers and host-directed therapy.

Introduction Differentiation between relapse and reinfection in cases with tuberculosis (TB) recurrence has important implications for public health, especially in patients with human immunodeficiency virus (HIV) co-infection. We compared Mycobacterial Interspersed Repeat Unit (MIRU) typing and spoligotyping with whole genome sequencing (WGS) to differentiate between relapse and reinfection in patients (HIV-positive and HIV-negative) with TB recurrence. We also assessed the value of WGS to track acquired drug resistance in those with relapse after successful treatment. Method Forty-one paired M. tuberculosis isolates collected from 20 HIV-positive and 21 HIV-negative patients were subjected to WGS in addition to spoligotyping and MIRU typing. Phylogenetic and Single Nucleotide Substitution (SNP) clustering analyses were performed to determine whether recurrences were due to relapse or re-infection. Results Comparison of M. tuberculosis genomes indicated that 95% of TB recurrences in the HIV-negative cohort were due to relapse, while the majority of TB recurrences (75%) in the HIV-positive cohort was due to reinfection (P = 0.0001). New drug resistance mutations were acquired in 5/24 cases (20.8%) that experienced relapse. Conclusions WGS provided increased resolution, but differentiation between relapse and reinfection was broadly consistent with MIRU and spoligotyping. The high contribution of reinfection among HIV infected patients experiencing TB recurrence warrants further study to explore risk factors for TB exposure.

Geographically, most tuberculosis (TB) cases in 2018 were reported from India. This TB burden is compounded by MDR-TB and XDR-TB. The strategies for the management and control of TB in the community depend on an understanding of the mode of spread of the different strains of TB isolates in the community. To determine the distribution and trends of M. tb strains over the time period in the community due to treatment, we carried out the present study on changes over two decades. Design/Methods. A total of 1218 M. tb isolates (year: 2001–2018) from Tiruvallur, India, were genotyped by spoligotyping after DNA extraction and subjected to anti-TB drug susceptibility testing for the first-line anti-TB drugs. Results. On analysis with the SpolDB4 database, majority (2001–2003: 53.32% and 2015–2018: 46.3%) of the isolates belonged to East African Indian (EAI) lineage, and the orphans designated in comparison to SpolDB4 stood 33% among 2001–2003 strain collection and 46.3% among 2015–2018 strain collection. 10.2% (2001–2003) and 9.26% (2015 to 2018) of isolates were monoresistant to isoniazid (H). MDR strains were less common among EAI strains (3.2%) compared to non-EAI strains (10.32%). Conclusions. EAI is the most predominant lineage in Tiruvallur, despite the presence of highly transmissible lineages like Beijing for the last two decades. The prevalence of MDR-TB is below the national average of 2-3% among the new TB cases in the last two decades. The reason can be attributed to the well-established nature of the locally circulating strains in this region which are not associated with drug resistance.

According to the WHO report 2019, Tuberculosis (TB) is an ancient disease of humanity that is curable. TB has caused significant morbidity and mortality even in 2018. The etiological agent of TB, Mycobacterium tuberculosis (MTB) exploits its virulence factors to escape from host immunity and therapeutic drugs. Host Directed Therapy (HDT) is an adjunctive therapy where repurposed drugs, small molecules, vitamins, cytokines, and monoclonal antibodies are used to overcome the pathogen exploited pathways in the host. One of the HDTs, i.e. induction of autophagy is a highly regulated intracellular self-degradative process in which pathogens are sequestered in double-layered autophagosomes and targeted to the lysosome for degradation. Apart from the pathogen clearance, autophagy involves the release of nutrients during starvation, removal of damaged organelles and aggregated proteins, antigen presentation, tumor suppression, and anti-aging mechanisms. Xenophagy is a type of selective autophagy against microbes induced by ubiquitin receptors (p62/SQSTM1, NDP52, NBR1, OPTN, Parkin and Smurf proteins) after pathogen recognition. ULK1/2, Beclin-1, ATG5-ATG12-ATG16 L and LC-II-PE complexes along with two nutrient-sensing protein complexes, mTOR and AMPK activate autophagy mechanisms to limit infection. Pattern Recognition Receptors (PRRs) such as TLR2, recognize lipopolysaccharide (LPS) of MTB and triggers vitamin D3 activating enzymes. Activated vitamin D3 induces the synthesis of antimicrobial peptide, LL-37, which further enhances xenophagy. Apart from vitamin D, few micronutrients such as zinc and iron also regulate autophagy. In this review, we discuss current knowledge, advances and perspectives of autophagy against TB.

Drug-resistant tuberculosis (TB), one of the leading causes of death worldwide, arises mainly from spontaneous mutations in the genome of Mycobacterium tuberculosis. There is an urgent need to understand the mechanisms by which the mutations confer resistance in order to identify new drug targets and to design new drugs. Previous studies have reported numerous mutations that confer resistance to anti-TB drugs, but there has been little systematic analysis to understand their genetic background and the potential impacts on the drug target stability and/or interactions. Here, we report the analysis of whole-genome sequence data for 98 clinical M. tuberculosis isolates from a city in southern India. The collection was screened for phenotypic resistance and sequenced to mine the genetic mutations conferring resistance to isoniazid and rifampicin. The most frequent mutation among isoniazid and rifampicin isolates was S315T in katG and S450L in rpoB respectively. The impacts of mutations on protein stability, protein-protein interactions and protein-ligand interactions were analysed using both statistical and machine-learning approaches. Drug-resistant mutations were predicted not only to target active sites in an orthosteric manner, but also to act through allosteric mechanisms arising from distant sites, sometimes at the protein-protein interface.

The genomes of 16 clinical Mycobacterium tuberculosis isolates were subjected to whole-genome sequencing to identify mutations related to resistance to one or more anti-Mycobacterium drugs. The sequence data will help in understanding the genomic characteristics of M. tuberculosis isolates and their resistance mutations prevalent in South India.

The CYP2R1 gene express the enzyme 25-hydroxylase, involved in the synthesis of major circulating vitamin D metabolite 25-hydroxyvitaminD [25(OH)D]. CYP2R1 gene variants have been reported to be associated with altered 25(OH)D level and associated with the development of active disease including tuberculosis (TB). The aim of the present study was to understand the association of rs10741657 (G/A) and rs2060793(A/G) CYP2R1 gene polymorphisms with tuberculosis susceptibility/protection in 104 Healthy controls (HCs) and 105 pulmonary tuberculosis (PTB) patients and to understand the influence of gene variants on 25(OH)D levels in South Indian population. Genotyping was performed by polymerase chain reaction trailed by restriction fragment length polymorphism (PCR-RFLP) method. Plasma samples were used for 25(OH)D level estimation by ELISA method. In rs10741657, under a dominant model (GG vs AG + AA), “AG” and “AA” genotypes as well as in rs2060793 under an overdominant model (GA vs GG + AA), “GA” genotype were significantly associated with protection to pulmonary tuberculosis. Based on sex, rs10741657 “AG” was significantly associated with protection and “GG” was significantly associated with susceptibility to TB in males. A sufficient vitamin D level was found with rs10741657 “AA” and “AG” genotypes and “GG” genotype associated with 81.8% of vitamin D deficiency in PTB individuals. In conclusion, rs10741657 “AG” and “AA” genotypes were associated with higher 25(OH)D levels and protection to TB. The lower 25(OH)D levels associated with rs10741657 “GG” genotype individuals may be recommended for higher vitamin D supplementation for better outcome from the disease. Further studies with large sample size are needed to confirm this study finding.

Tuberculosis (TB), a bacterialinfectious disease caused by Mycobacterium tuberculosis (M.tb), which causes significant mortality in humans worldwide. Current treatment regimen involve the administration of multiple antibiotics over the course of several months that contributes to patient non-compliance leading to relapse and the development of drug-resistant M.tb (MDR and XDR) strains. Together, these facts highlight the need for the development of shorter TB treatment regimens. Host-directed therapy (HDT) is a new and emerging concept that aims to augment host immune response using drugs/compounds with or without adjunct antibiotics against M.tb infection. Autophagy is a natural catabolic mechanism of the cell that involves delivering the cytosolic constituents to the lysosomes for degradation and recycling the components; thereby maintaining the cellular and energy homoeostasis of a cell. However, over the past decade, an improved understanding of the role of autophagy in immunity has led to autophagy activation by using drugs or agents. This autophagy manipulation may represent a promising host-directed therapeutic strategy for human TB. However, current clinical knowledge on implementing autophagy activation by drugs or agents, as a stand-alone HDT or as an adjunct with antibiotics to treat human TB is insufficient. In recent years, many reports on high-throughput drug screening and measurement of autophagic flux by fluorescence, high-content microscopy, flow cytometry, microplate reader and immunoblotting have been published for the discovery of drugs that modulate autophagy. In this review, we discuss the commonly used chemical screening approaches in mammalian cells for the discovery of autophagy activating drugs against M.tbinfection. We also summarize the various autophagy-activating agents, both pre-clinical candidates and compounds approved for advanced clinical investigation during mycobacterial infection. Finally, we discuss the opportunities and challenges in using autophagy activation as HDT strategy to improve TB outcome and shorten treatment regimen.

Vitamin D deficiency is often associated with tuberculosis susceptibility. Variants of vitamin D binding protein gene are reported to be associated with blood circulating concentration of 25(OH)D levels. The aim of the present study was to understand the association of rs7041 (G/T) and rs4588 (C/A) polymorphisms with tuberculosis susceptibility/protection in 125 Healthy controls (HCs) and 125 pulmonary tuberculosis (PTB) patients and to understand whether the gene variants have any influence on 25(OH)D levels in South Indian population. The genotyping for both the polymorphisms were done by polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) method. 25(OH)D levels were estimated by ELISA method. The results revealed that under codominant model, rs4588 ‘CA' genotype significantly associated with TB susceptibility [OR: 1.47 (0.85–2.55); p = 0.049] and associated with 47.4% 25(OH)D deficiency in PTB patients. Whereas, under recessive model (‘AA' vs ‘CC' + ‘CA') rs4588 ‘AA' genotype significantly associated with TB protection [OR: 0.14 (0.02–1.29); p = 0.042]. Whereas in rs7041 polymorphism, under overdominant model (‘TG' vs ‘GG+’TT'), no association was found. Increased 25(OH)D levels were found with rs7041 “GG”, and rs4588 “CC” genotype in HCs and PTB patients. Haplotypes ‘TA' and ‘TC' associated with susceptibility to TB in males compared with females [‘TA' - OR: 4.18 (1.84–9.49); ‘TC' - OR: 3.63 (1.34–9.84)]. The results suggest that the heterozygous genotype rs4588 “CA” significantly associated with susceptibility while rs4588 “AA” genotype significantly associated with TB protection. Gene variants with 25(OH)D deficiency revealed no significant association due to limited sample size. However, in rs7041 “TG” and rs4588 “CA” genotype was associated with 61.1% and 47.4% 25(OH)D deficiency (OR > 2.0) in PTB patients. Future studies with larger sample size are needed to confirm this study finding.

Objectives The emergence of drug-resistant tuberculosis (TB) poses a serious challenge to existing anti-TB therapies. Hence, there is a direct need for identification of new drugs and effective combination regimens. Methods In this study, minimum inhibitory concentrations (MICs) of the anti-TB drugs bedaquiline (BDQ), delamanid (DEL) and moxifloxacin (MFX) were evaluated using a resazurin microtiter assay (REMA) against five drug-resistant clinicalMycobacterium tuberculosis (MTB) isolates as well as the drug-susceptible reference strain H37Rv. In addition, their fractional inhibitory concentration indices (FICIs) were evaluated using a REMA-based calorimetric chequerboard assay to assess their interaction profiles against the MTB isolates. Results The FICI indicated that BDQ acted synergistically with DEL against isoniazid (INH)-monoresistant, rifampicin (RIF)-monoresistant and extensively drug-resistant (XDR) clinical MTB isolates. In addition, the combination of DEL acted synergistically with MFX against INH-monoresistant, RIF-monoresistant and XDR clinical MTB isolates. Moreover, the combination of BDQ and MFX showed a synergistic effect against RIF-monoresistant and pre-XDR clinical MTB isolates. DEL at 0.125 × MIC (i.e. 0.015 μg/mL) used in combination with BDQ at 0.25 × MIC (i.e. 0.015 μg/mL) had a stronger bactericidal effect against the XDR-TB clinical isolate than DEL alone at 1 × MIC (i.e. 0.125 μg/mL). Conclusion Synergistic and additive effects between these two-drug combinations offer an attractive chemotherapeutic regimen against drug-resistant clinical MTB isolates.

The Mycobacterium tuberculosis (Mtb) Lineage 4 strains CDC1551 and H37Rv develop tolerance to multiple antibiotics upon macrophage residence. Genetic mutation of the efflux pump Rv1258c in CDC1551 abolishes rifampin tolerance but not isoniazid tolerance. Here we show that clinical isolates from the other predominant Mtb lineages developed macrophage-induced isoniazid tolerance. Furthermore, all lineages developed rifampin tolerance except Lineage 2 Beijing strains, which are natural Rv1258c mutants. Thus macrophage-induced antibiotic tolerance is featured across the majority of Mtb lineages. Our findings further link Rv1258c to rifampin tolerance among clinical isolates.

Monocytes are critical defense components that play an important role in the primary innate immune response. The heterogeneous nature of monocytes and their ability to differentiate into either monocyte-derived macrophages or monocyte-derived dendritic cells allows them to serve as a bridge between the innate and adaptive immune responses. Current studies of monocytes based on immunofluorescence, single-cell RNA sequencing and whole mass spectrometry finger printing reveals different classification systems for monocyte subsets. In humans, three circulating monocyte subsets are classified based on relative expression levels of CD14 and CD16 surface proteins, namely classical, intermediate and non-classical subsets. Transcriptomic analyses of these subsets help to define their distinct functional properties. Tuberculosis (TB) is a disease instigated by the deadly pathogen Mycobacterium tuberculosis. Current research on monocytes in TB has indicated that there are alterations in the frequency of intermediate and non-classical subsets suggesting their impact in bacterial persistence. In this review, we will focus on these monocyte subsets, including their classification, frequency distribution, cytokine profiles, role as a biomarker and will comment on future directions for understanding the salient phenotypic and functional properties relevant to TB pathogenesis.

Mycobacteriophages produce lysins that break down the host cell wall at the end of lytic cycle to release their progenies. The ability to lyse mycobacterial cells makes the lysins significant. Mycobacteriophage Che12 is the first reported temperate phage capable of infecting and lysogenising Mycobacterium tuberculosis. Gp11 of Che12 was found to have Chitinase domain that serves as endolysin (lysin A) for Che12. Structure of gp11 was modeled and evaluated using Ramachandran plot in which 98 % of the residues are in the favored and allowed regions. Che12 lysin A was predicted to act on NAG-NAM-NAG molecules in the peptidoglycan of cell wall. The tautomers of NAG-NAM-NAG molecule were generated and docked with lysin A. The stability and binding affinity of lysin A - NAG-NAM-NAG tautomers were studied using molecular dynamics simulations.

Two actively secreted (38 and 30 kDa) and 1 cytosolic (16 kDa) antigens were purified from Mycobacterium tuberculosis culture filtrate and cytosol, respectively, using a combination of chromatographic and electrophoretic methods. One recombinant antigen (27 kDa) overexpressed in Escherichia coli was also isolated. The diagnostic test characteristics of circulating immune complex (CIC)-bound antibodies to purified protein antigens, singly and in combination, were evaluated in patients with pulmonary tuberculosis. The individual antigens ranged in their sensitivity from 73% to 88%, while considering the IgG response. Addition of IgA results improved the sensitivity. The combination of IgG results for 38, 30, and 16 kDa offered >95% sensitivity and specificity for the smear- and culture-positive tuberculosis, as well as for the smear-negative, culture-positive group. CIC-bound antibodies promise to be a better diagnostic tool than serum antibodies.

Background and aim. Bacteriologic diagnosis of childhood tuberculosis is difficult, and alternate methods are needed. The utility of a serologic test for major secretory antigen (30 kDa) and a cytosolic antigen (16 kDa) of Mycobacterium tuberculosis was evaluated for the diagnosis of tuberculosis in children. Methods. Enzyme-linked immunosorbent assay was used. Specific IgG, IgA and IgM antibodies were measured in the sera from 26 clinically and/or bacteriologically diagnosed cases of childhood tuberculosis and 61 normal children. Results. Anti-IgG antibodies alone, against both 30- and 16-kDa antigens, were detected in 65.4% of patients. However, by combination of all three isotypes, increased sensitivities of 84.6 and 73%, with a specificity of 96.7% each, were obtained for 30- and 16-kDa antigens, respectively. Conclusions. We found good specificity and reasonably good sensitivity for detection of antibodies by enzyme-linked immunosorbent assay to 30-kDa antigen alone. The 16-kDa antigen did not perform as well.

[Abstract] Serodiagnosis of tuberculosis using purified native antigens is one of the approaches for the early detection of TB. The Antigen 85 complex consisting of Ag 85A, 85B and 85C are the most abundant antigens in the culture supernatant of mycobacteria. It has also been shown to be the immunodominant (the property of an antigenic determinant that causes it to be responsible for the major immune response in a host) antigens of CFA (culture filtrate antigens – proteins secreted by mycobacteria into the culture medium). This protocol gives the details for purification of the Ag85 complex from CFA and also the method of isolation of the individual components of the complex by column chromatography.

Two secreted antigens (38 and 30 kDa) and 1 cytosolic antigen (16 kDa) were purified in our laboratory from Mycobacterium tuberculosis culture filtrate and cytosol using chromatographic/electrophoretic methods. One recombinant antigen (27 kDa, MPT51) expressed in Escherichia coli was also isolated. All the 4 antigens were tested individually for detection of serum IgG, IgA, and IgM (a total of 476 sera from 5 groups) by indirect enzyme-linked immunosorbent assay. Keeping the well-reported 38 kDa as the main candidate, the usefulness of the other antigens, which may add to the test positivity in cases not diagnosed by 38 kDa, was analyzed. The individual antigens ranged in their sensitivity from 57% to 67% (IgG). Addition of other antigen results, with that of 38 kDa, offered a sensitivity of 91% in smear- and culture-positive tuberculosis (TB), 78% in smear-negative culture-confirmed TB, and 97% specificity in normal healthy subjects. IgG antibody to multiple antigens (38, 30, and 16 kDa) may be a sensitive, specific, rapid, and cost-effective test to rule-in clinical suspicion of pulmonary TB.