[1]Aagaard CS, Hoang TTKT, Vingsbo-Lundberg C, et al., 2009. Quality and vaccine efficacy of CD4⁺ T cell responses directed to dominant and subdominant epitopes in ESAT-6 from Mycobacterium tuberculosis. J Immunol, 183(4):2659-2668.

[2]Abdallah AM, van Pittius NCG, Champion PAD, et al., 2007. Type VII secretion—mycobacteria show the way. Nat Rev Microbiol, 5(11):883-891.

[3]Adlakha N, Vir P, Verma I, 2012. Effect of mycobacterial secretory proteins on the cellular integrity and cytokine profile of type II alveolar epithelial cells. Lung India, 29(4):313-318.

[4]Aguilar-Ayala DA, Tilleman L, van Nieuwerburgh F, et al., 2017. The transcriptome of Mycobacterium tuberculosis in a lipid-rich dormancy model through RNAseq analysis. Sci Rep, 7:17665.

[5]Aitken JM, Borody TJ, Agrawal G, 2019. A revaluation of the use of conventional Ziehl-Neelsen stain for detection of non-tuberculous mycobacteria. N Z J Med Lab Sci, 73(2):85.

[6]Amanfu W, 2006. The situation of tuberculosis and tuberculosis control in animals of economic interest. Tuberculosis, 86(3-4):330-335.

[7]Bakhori NM, Yusof NA, Abdullah J, et al., 2020. Surface enhanced CdSe/ZnS QD/SiNP electrochemical immunosensor for the detection of Mycobacterium tuberculosis by combination of CFP10-ESAT6 for better diagnostic specificity. Materials (Basel), 13(1):149.

[8]Banuls AL, Sanou A, van Anh NT, et al., 2015. Mycobacterium tuberculosis: ecology and evolution of a human bacterium. J Med Microbiol, 64(11):1261-1269.

[9]Beatty WL, Russell DG, 2000. Identification of mycobacterial surface proteins released into subcellular compartments of infected macrophages. Infect Immun, 68(12):6997-7002.

[10]Belay M, Legesse M, Mihret A, et al., 2015. Pro- and anti-inflammatory cytokines against Rv2031 are elevated during latent tuberculosis: a study in cohorts of tuberculosis patients, household contacts and community controls in an endemic setting. PLoS ONE, 10(4):e0124134.

[11]Bishai WR, 2000. Rekindling old controversy on elusive lair of latent tuberculosis. Lancet, 356(9248):2113-2114.

[12]Boshoff HIM, Lun DS, 2010. Systems biology approaches to understanding mycobacterial survival mechanisms. Drug Discov Today Dis Mech, 7(1):e75-e82.

[13]Bourassa L, 2018. The NanoDisk-MS assay: a new frontier in biomarker-based tuberculosis diagnostics? Clin Chem, 64(5):763-765.

[14]Brennan MJ, Delogu G, 2002. The PE multigene family: a ‘molecular mantra’ for mycobacteria. Trends Microbiol, 10(5):246-249.

[15]Brennan PJ, 2003. Structure, function, and biogenesis of the cell wall of Mycobacterium tuberculosis. Tuberculosis, 83(1-3):91-97.

[16]Brennan PJ, Nikaido H, 1995. The envelope of mycobacteria. Ann Rev Biochem, 64(1):29-63.

[17]Briken V, Porcelli SA, Besra GS, et al., 2004. Mycobacterial lipoarabinomannan and related lipoglycans: from biogenesis to modulation of the immune response. Mol Microbiol, 53(2):391-403.

[18]Brock M, Hanlon D, Zhao MW, et al., 2020. Detection of mycobacterial lipoarabinomannan in serum for diagnosis of active tuberculosis. Diagn Microbiol Infect Dis, 96(2):114937.

[19]Broger T, Tsionksy M, Mathew A, et al., 2019. Sensitive electrochemiluminescence (ECL) immunoassays for detecting lipoarabinomannan (LAM) and ESAT-6 in urine and serum from tuberculosis patients. PLoS ONE, 14(4):e0215443.

[20]Bulterys MA, Wagner B, Redard-Jacot M, et al., 2019. Point-of-Care Urine LAM tests for tuberculosis diagnosis: a mini-review. J Clin Med, 9:111.

[21]https://doi.org/10.20944/preprints201912.0002.v1

[22]Chiappini E, Bella CD, Bonsignori F, et al., 2012. Potential role of M. tuberculosis specific IFN-γ and IL-2 ELISPOT assays in discriminating children with active or latent tuberculosis. PLoS ONE, 7(9):e46041.

[23]Cole ST, Brosch R, Parkhill J, et al., 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature, 393(6685):537-544.

[24]Comas I, Chakravartti J, Small PM, et al., 2010. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet, 42(6):498-503.

[25]da Costa AC, de Oliveira Costa-Júnior A, de Oliveira FM, et al., 2014. A new recombinant BCG vaccine induces specific Th17 and Th1 effector cells with higher protective efficacy against tuberculosis. PLoS ONE, 9(11):e112848.

[26]da Costa AC, de Resende DP, de Santos BDP, et al., 2017. Modulation of macrophage responses by CMX, a fusion protein composed of Ag85C, MPT51, and HspX from Mycobacterium tuberculosis. Front Microbiol, 8:623.

[27]Dai ZH, Liu ZQ, Xiu BS, et al., 2017. A multiple-antigen detection assay for tuberculosis diagnosis based on broadly reactive polyclonal antibodies. Iran J Basic Med Sci, 20(4):360-367.

[28]https://doi.org/10.22038/IJBMS.2017.8575

[29]Delogu G, Brennan MJ, 1999. Functional domains present in the mycobacterial hemagglutinin, HBHA. J Bacteriol, 181(24):7464-7469.

[30]Delogu G, Sali M, Fadda G, 2013. The biology of Mycobacterium tuberculosis infection. Mediterr J Hematol Infect Dis, 5(1):e2013070.

[31]Denkinger CM, Pai M, Patel M, et al., 2013. Gamma interferon release assay for monitoring of treatment response for active tuberculosis: an explosion in the spaghetti factory. J Clin Microbiol, 51(2):607-610.

[32]Dheda K, Barry CE, Maartens G, 2016. Tuberculosis. Lancet, 387(10024):1211-1226.

[33]Dillon DC, Alderson MR, Day CH, et al., 2000. Molecular and immunological characterization of Mycobacterium tuberculosis CFP-10, an immunodiagnostic antigen missing in Mycobacterium bovis BCG. J Clin Microbiol, 38(9):3285-3290.

[34]Diogo GR, Hart P, Copland A, et al., 2019. Immunization with Mycobacterium tuberculosis antigens encapsulated in phosphatidylserine liposomes improves protection afforded by BCG. Front Immunol, 10:1349.

[35]Dmitriev BA, Ehlers S, Rietschel ET, et al., 2000. Molecular mechanics of the mycobacterial cell wall: from horizontal layers to vertical scaffolds. Int J Med Microbiol, 290(3):251-258.

[36]Egan AJF, Maya‐Martinez R, Ayala I, et al., 2018. Induced conformational changes activate the peptidoglycan synthase PBP1B. Mol Microbiol, 110(3):335-356.

[37]Ehlers MRW, Daffé M, 1998. Interactions between Mycobacterium tuberculosis and host cells: are mycobacterial sugars the key? Trends Microbiol, 6(8):328-335.

[38]Ernst JD, 1998. Macrophage receptors for Mycobacterium tuberculosis. Infect Immun, 66(4):1277-1281.

[39]Feinberg H, Jégouzo SAF, Rowntree TJW, et al., 2013. Mechanism for recognition of an unusual mycobacterial glycolipid by the macrophage receptor mincle. J Biol Chem, 288(40):28457-28465.

[40]Fenton MJ, Vermeulen MW, 1996. Immunopathology of tuberculosis: roles of macrophages and monocytes. Infect Immun, 64(3):683-690.

[41]Fine PEM, 2001. BCG: the challenge continues. Scand J Infect Dis, 33(1):58-60.

[42]Forrellad MA, Klepp LI, Gioffré A, et al., 2013. Virulence factors of the Mycobacterium tuberculosis complex. Virulence, 4(1):3-66.

[43]Früh K, Picker L, 2017. CD8+ T cell programming by cytomegalovirus vectors: applications in prophylactic and therapeutic vaccination. Curr Opin Immunol, 47:52-56.

[44]Garnier T, Eiglmeier K, Camus JC, et al., 2003. The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci USA, 100(13):7877-7882.

[45]Gatfield J, Pieters J, 2000. Essential role for cholesterol in entry of mycobacteria into macrophages. Science, 288(5471):1647-1651.

[46]Ghon A, 1923. The primary complex in human tuberculosis and its significance. Am Rev Tuberc, 7(5):314-317.

[47]Gomez-Gonzalez PJ, Andreu N, Phelan JE, et al., 2019. An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome. Sci Rep, 9:5204.

[48]Gordejo FJR, Vermeersch JP, 2006. Towards eradication of bovine tuberculosis in the European Union. Vet Microbiol, 112(2-4):101-109.

[49]Guerin ME, Korduláková J, Alzari PM, et al., 2010. Molecular basis of phosphatidyl-myo-inositol mannoside biosynthesis and regulation in mycobacteria. J Biol Chem, 285(44):33577-33583.

[50]Heithoff DM, Conner CP, Hanna PC, et al., 1997. Bacterial infection as assessed by in vivo gene expression. Proc Natl Acad Sci, 94(3):934-939.

[51]Hernández-Pando R, Jeyanathan M, Mengistu G, et al., 2000. Persistence of DNA from Mycobacterium tuberculosis in superficially normal lung tissue during latent infection. Lancet, 356(9248):2133-2138.

[52]Huebner RE, Schein MF, Bass JB Jr, 1993. The tuberculin skin test. Clin Infect Dis, 17(6):968-975.

[53]Iantomasi R, Sali M, Cascioferro A, et al., 2012. PE_PGRS30 is required for the full virulence of Mycobacterium tuberculosis. Cell Microbiol, 14(3):356-367.

[54]Ireton GC, Greenwald R, Liang H, et al., 2010. Identification of Mycobacterium tuberculosis antigens of high serodiagnostic value. Clin Vaccine Immunol, 17(10):1539-1547.

[55]Jankute M, Cox JAG, Harrison J, et al., 2015. Assembly of the mycobacterial cell wall. Ann Rev Microbiol, 69:405-423.

[56]Jena L, Kashikar S, Kumar S, et al., 2013. Comparative proteomic analysis of Mycobacterium tuberculosis strain H37Rv versus H37Ra. Int J Mycobacteriol, 2(4):220-226.

[57]Jhingan GD, Kumari S, Jamwal SV, et al., 2016. Comparative proteomic analyses of avirulent, virulent, and clinical strains of Mycobacterium tuberculosis identify strain-specific patterns. J Biol Chem, 291(27):14257-14273.

[58]Kalscheuer R, Palacios A, Anso I, et al., 2019. The Mycobacterium tuberculosis capsule: a cell structure with key implications in pathogenesis. Biochem J, 476(14):1995-2016.

[59]Katial RK, Hershey J, Purohit-Seth T, et al., 2001. Cell-mediated immune response to tuberculosis antigens: comparison of skin testing and measurement of in vitro gamma interferon production in whole-blood culture. Clin Diagn Lab Immunol, 8(2):339-345.

[60]Kaufmann SHE, 2020. Vaccination against tuberculosis: revamping BCG by molecular genetics guided by immunology. Front Immunol, 11:316.

[61]Kawasaki M, Echiverri C, Raymond L, et al., 2019. Lipoarabinomannan in sputum to detect bacterial load and treatment response in patients with pulmonary tuberculosis: analytic validation and evaluation in two cohorts. PLoS Med, 16(4):e1002780.

[62]Kendall SL, Withers M, Soffair CN, et al., 2007. A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis. Mol Microbiol, 65(3):684-699.

[63]Lawn SD, Kerkhoff AD, Vogt M, et al., 2012. Diagnostic accuracy of a low-cost, urine antigen, point-of-care screening assay for HIV-associated pulmonary tuberculosis before antiretroviral therapy: a descriptive study. Lancet Infect Dis, 12(3):201-209.

[64]Lawn SD, Kerkhoff AD, Nicol MP, et al., 2015. Underestimation of the true specificity of the urine lipoarabinomannan point-of-care diagnostic assay for HIV-associated tuberculosis. J Acquir Immune Defic Syndr, 69(4):e144-e146.

[65]Liu C, Zhao Z, Fan J, et al., 2017. Quantification of circulating Mycobacterium tuberculosis antigen peptides allows rapid diagnosis of active disease and treatment monitoring. Proc Natl Acad Sci USA, 114(15):3969-3974.

[66]Liu J, Jaijyan DK, Tang QY, et al., 2019. Promising cytomegalovirus-based vaccine vector induces robust CD8⁺ T-cell response. Int J Mol Sci, 20(18):4457.

[67]Lorenzi JC, Trombone AP, Rocha CD, et al., 2010. Intranasal vaccination with messenger RNA as a new approach in gene therapy: use against tuberculosis. BMC Biotechnol, 10:77.

[68]Mack U, Migliori GB, Sester M, et al., 2009. LTBI: latent tuberculosis infection or lasting immune responses to M. tuberculosis? A TBNET consensus statement. Eur Respir J, 33(5):956-973.

[69]Manca C, Lyashchenko K, Wiker HG, et al., 1997. Molecular cloning, purification, and serological characterization of MPT63, a novel antigen secreted by Mycobacterium tuberculosis. Infect Immun, 65(1):16-23.

[70]Mateos J, Estévez O, González-Fernández Á, et al., 2020. Serum proteomics of active tuberculosis patients and contacts reveals unique processes activated during Mycobacterium tuberculosis infection. Sci Rep, 10:3844.

[71]Means TK, Wang SY, Lien E, et al., 1999. Human Toll-like receptors mediate cellular activation by Mycobacterium tuberculosis. J Immunol, 163(7):3920-3927.

[72]Meier NR, Jacobsen M, Ottenhoff THM, et al., 2018. A systematic review on novel Mycobacterium tuberculosis antigens and their discriminatory potential for the diagnosis of latent and active tuberculosis. Front Immunol, 9:2476.

[73]Mekalanos JJ, 1992. Environmental signals controlling expression of virulence determinants in bacteria. J Bacteriol, 174(1):1-7.

[74]Monkongdee P, McCarthy KD, Cain KP, et al., 2009. Yield of acid-fast smear and mycobacterial culture for tuberculosis diagnosis in people with human immunodeficiency virus. Am J Respir Crit Care Med, 180(9):903-908.

[75]Morandi M, Sali M, Manganelli R, et al., 2013. Exploiting the mycobacterial cell wall to design improved vaccines against tuberculosis. J Infect Dev Ctries, 7(3):169-181.

[76]Murphy DJ, Brown JR, 2008. Novel drug target strategies against Mycobacterium tuberculosis. Curr Opin Microbiol, 11(5):422-427.

[77]Mustafa AS, Skeiky YA, Al-Attiyah R, et al., 2006. Immunogenicity of Mycobacterium tuberculosis antigens in Mycobacterium bovis BCG-vaccinated and M. bovis-infected cattle. Infect Immun, 74(8):4566-4572.

[78]Nurwidya F, Handayani D, Burhan E, et al., 2018. Molecular diagnosis of tuberculosis. Chonnam Med J, 54(1):1-9.

[79]Ong E, He YQ, Yang ZH, 2020. Epitope promiscuity and population coverage of Mycobacterium tuberculosis protein antigens in current subunit vaccines under development. Infect Genet Evol, 80:104186.

[80]Pandey RP, Kumar S, Ahmad S, et al., 2020. Use Chou’s 5-steps rule to evaluate protective efficacy induced by antigenic proteins of Mycobacterium tuberculosis encapsulated in chitosan nanoparticles. Life Sci, 256:117961.

[81]Park ST, Kang CM, Husson RN, 2008. Regulation of the SigH stress response regulon by an essential protein kinase in Mycobacterium tuberculosis. Proc Natl Acad Sci USA, 105(35):13105-13110.

[82]Paylor R, 2014. Bovine tuberculosis. In: Mouser P (Ed.), Michigan State University Veterinary Student, Graduate Student. Michigan State University, p.1-3.

[83]Pieters J, Gatfield J, 2002. Hijacking the host: survival of pathogenic mycobacteria inside macrophages. Trends Microbiol, 10(3):142-146.

[84]Pinto SM, Verma R, Advani J, et al., 2018. Integrated multi-omic analysis of Mycobacterium tuberculosis H37Ra redefines virulence attributes. Front Microbiol, 9:1314.

[85]Pollock JM, Andersen P, 1997. Predominant recognition of the ESAT-6 protein in the first phase of interferon with Mycobacterium bovis in cattle. Infect Immun, 65(7):2587-2592.

[86]Pym AS, Brodin P, Brosch R, et al., 2002. Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti. Mol Microbiol, 46(3):709-717.

[87]Pym AS, Brodin P, Majlessi L, et al., 2003. Recombinant BCG exporting ESAT-6 confers enhanced protection against tuberculosis. Nat Med, 9(5):533-539.

[88]Renshaw PS, Panagiotidou P, Whelan A, et al., 2002. Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6· CFP-10 complex: implications for pathogenesis and virulence. J Biol Chem, 277(24):21598-21603.

[89]Renshaw PS, Lightbody KL, Veverka V, et al., 2005. Structure and function of the complex formed by the tuberculosis virulence factors CFP‐10 and ESAT‐6. EMBO J, 24(14):2491-2498.

[90]Rodriguez GM, 2006. Control of iron metabolism in Mycobacterium tuberculosis. Trends Microbiol, 14(7):320-327.

[91]Rustad TR, Harrell MI, Liao RL, et al., 2008. The enduring hypoxic response of Mycobacterium tuberculosis. PLoS ONE, 3(1):e1502.

[92]Ryndak M, Wang SS, Smith I, 2008. PhoP, a key player in Mycobacterium tuberculosis virulence. Trends Microbiol, 16(11):528-534.

[93]Ryu YJ, 2015. Diagnosis of pulmonary tuberculosis: recent advances and diagnostic algorithms. Tuber Respir Dis, 78(2):64-71.

[94]Sable SB, Posey JE, Scriba TJ, 2019. Tuberculosis vaccine development: progress in clinical evaluation. Clin Microbiol Rev, 33(1):e00100-19.

[95]Santos R, Ursu O, Gaulton A, et al., 2017. A comprehensive map of molecular drug targets. Nat Rev Drug Dis, 16(1):19-34.

[96]Schlesinger LS, 1993. Macrophage phagocytosis of virulent but not attenuated strains of Mycobacterium tuberculosis is mediated by mannose receptors in addition to complement receptors. J Immunol, 150(7):2920-2930.

[97]Schlesinger LS, Bellinger-Kawahara CG, Payne NR, et al., 1990. Phagocytosis of Mycobacterium tuberculosis is mediated by human monocyte complement receptors and complement component C3. J Immunol, 144(7):2771-2780.

[98]Seddon JA, Paton J, Nademi Z, et al., 2016. The impact of BCG vaccination on tuberculin skin test responses in children is age dependent: evidence to be considered when screening children for tuberculosis infection. Thorax, 71(10):932-939.

[99]Shah M, Hanrahan C, Wang ZY, et al., 2016. Lateral flow urine lipoarabinomannan assay for detecting active tuberculosis in HIV‐positive adults. Cochrane Database Syst Rev, 2016(5):CD011420.

[100]Sigal GB, Pinter A, Lowary TL, et al., 2018. A novel sensitive immunoassay targeting the 5-methylthio-D-xylofuranose– lipoarabinomannan epitope meets the WHO’s performance target for tuberculosis diagnosis. J Clin Microbiol, 56(12):e01338-18.

[101]Silva VMC, Kanaujia G, Gennaro ML, et al., 2003. Factors associated with humoral response to ESAT-6, 38 kDa and 14 kDa in patients with a spectrum of tuberculosis. Int J Tuber Lung Dis, 7(5):478-484.

[102]Singh A, Crossman DK, Mai D, et al., 2009. Mycobacterium tuberculosis WhiB3 maintains redox homeostasis by regulating virulence lipid anabolism to modulate macrophage response. PLoS Pathog, 5(8):e1000545.

[103]Sinha P, Gupta A, Prakash P, et al., 2016. Differentiation of Mycobacterium tuberculosis complex from non-tubercular mycobacteria by nested multiplex PCR targeting IS6110, MTP40 and 32kD alpha antigen encoding gene fragments. BMC Infect Dis, 16:123.

[104]Smith I, 2003. Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence. Clin Microbiol Rev, 16(3):463-496.

[105]Sreejit G, Ahmed A, Parveen N, et al., 2014. The ESAT-6 protein of Mycobacterium tuberculosis interacts with beta-2-microglobulin (β2M) affecting antigen presentation function of macrophage. PLoS Pathog, 10(10):e1004446.

[106]Su HB, Zhu SL, Zhu L, et al., 2017. Mycobacterium tuberculosis latent antigen Rv2029c from the multistage DNA vaccine A39 drives TH1 responses via TLR-mediated macrophage activation. Front Microbiol, 8:2266.

[107]Swaminathan S, Rekha B, 2010. Pediatric tuberculosis: global overview and challenges. Clin Infect Dis, 50(S3):S184-S194.

[108]Sweeney TE, Braviak L, Tato CM, et al., 2016. Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis. Lancet Respir Med, 4(3):213-224.

[109]Vergne I, Chua J, Singh SB, et al., 2004. Cell biology of Mycobacterium tuberculosis phagosome. Annu Rev Cell Dev Biol, 20:367-394.

[110]Verma R, Pinto SM, Patil AH, et al., 2017. Quantitative proteomic and phosphoproteomic analysis of H37Ra and H37Rv strains of Mycobacterium tuberculosis. J Proteome Res, 16(4):1632-1645.

[111]Vir P, Gupta D, Agarwal R, et al., 2014. Interaction of alveolar epithelial cells with CFP21, a mycobacterial cutinase-like enzyme. Mol Cell Biochem, 396(1-2):187-199.

[112]Voskuil MI, Schnappinger D, Visconti KC, et al., 2003. Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. J Exp Med, 198(5):705-713.

[113]Weiner J III, Kaufmann SHE, 2014. Recent advances towards tuberculosis control: vaccines and biomarkers. J Int Med, 275(5):467-480.

[114]Weiner J, Maertzdorf J, Kaufmann SHE, 2013. The dual role of biomarkers for understanding basic principles and devising novel intervention strategies in tuberculosis. Ann New York Acad Sci, 1283(1):22-29.

[115]WHO (World Health Organization), 2014. High-priority target product profiles for new tuberculosis diagnostics: report of a consensus meeting. Geneva, Switzerland, WHO. https://apps.who.int/iris/handle/10665/135617

[116]WHO, 2015. The use of lateral flow urine lipoarabinomannan assay (LF-LAM) for the diagnosis and screening of active tuberculosis in people living with HIV: policy guidance. WHO. https://apps.who.int/iris/handle/10665/193633

[117]WHO, 2019. Global tuberculosis report 2019. WHO. https://apps.who.int/iris/handle/10665/329368

[118]Wolf AJ, Desvignes L, Linas B, et al., 2008. Initiation of the adaptive immune response to Mycobacterium tuberculosis depends on antigen production in the local lymph node, not the lungs. J Exp Med, 205(1):105-115.

[119]Zhang W, Shu QB, Zhao Z, et al., 2018. Antigen 85B peptidomic analysis allows species-specific mycobacterial identification. Clin Proteomics, 15(1):1.