8. Armstrong JA, Hart PD. Phagosome-lysosome interactions in cultured macrophages infected with virulent tubercle bacilli. Reversal of the usual nonfusion pattern and observations on bacterial survival. J Exp Med. 1975; 142(1):1-16. https://doi.org/10.1084/jem.142.1.1 PMID: 807671

9. Simeone R, Bobard A, Lippmann J, Bitter W, Majlessi L, Brosch R, et al. Phagosomal rupture by Mycobacterium tuberculosis results in toxicity and host cell death. PLoS Pathog. 2012; 8(2):e1002507. https://doi.org/10.1371/journal.ppat.1002507 PMID: 22319448

10. van der Wel N, Hava D, Houben D, Fluitsma D, van Zon M, Pierson J, et al. M. tuberculosis and M. leprae translocate from the phagolysosome to the cytosol in myeloid cells. Cell. 2007; 129(7):1287-1298. https://doi.org/10.1016/j.cell.2007.05.059 PMID: 17604718

11. Khadela A, Chavda VP, Postwala H, Shah Y, Mistry P, Apostolopoulos V. Epigenetics in Tuberculosis: Immunomodulation of Host Immune Response. Vaccines (Basel). 2022; 10(10):1740. https://doi.org/10.3390/vaccines10101740 PMID: 36298605

12. Pacis A, Mailhot-Leonard F, Tailleux L, Randolph HE, Yotova V, Dumaine A, et al. Gene activation precedes DNA demethylation in response to infection in human dendritic cells. Proc Natl Acad Sci U S A. 2019; 116(14):6938-6943. https://doi.org/10.1073/pnas.1814700116 PMID: 30886108

13. Siddle KJ, Tailleux L, Deschamps M, Loh YH, Deluen C, Gicquel B, et al. bacterial infection drives the expression dynamics of microRNAs and their isomiRs. PLoS Genet. 2015; 11(3):e1005064. https://doi.org/10.1371/journal.pgen.1005064 PMID: 25793259

14. Cole J, Morris P, Dickman MJ, Dockrell DH. The therapeutic potential of epigenetic manipulation during infectious diseases. Pharmacol Ther. 2016; 167:85-99. https://doi.org/10.1016/j.pharmthera.2016.07.013 PMID: 27519803

15. Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E, et al. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods. 2009; 6(8):569-575. https://doi.org/10.1038/nmeth.1351 PMID: 19644458

16. Alonso H, Aguilo JI, Samper S, Caminero JA, Campos-Herrero MI, Gicquel B, et al. Deciphering the role of IS6110 in a highly transmissible Mycobacterium tuberculosis Beijing strain, GC1237. Tuberculosis (Edinburgh, Scotland). 2011; 91(2):117-126. https://doi.org/10.1016/j.tube.2010.12.007 PMID: 21256084

17. Polena H, Boudou F, Tilleul S, Dubois-Colas N, Lecointe C, Rakotosamimanana N, et al. Mycobacterium tuberculosis exploits the formation of new blood vessels for its dissemination. Sci Rep. 2016; 6:33162. https://doi.org/10.1038/srep33162 PMID: 27616470

18. Valway SE, Sanchez MP, Shinnick TF, Orme I, Agerton T, Hoy D, et al. An outbreak involving extensive transmission of a virulent strain of Mycobacterium tuberculosis. N Engl J Med. 1998; 338(10):633-639. https://doi.org/10.1056/NEJM199803053381001 PMID: 9486991

19. Hamilton TA, Zhao C, Pavicic PG Jr, Datta S. Myeloid colony-stimulating factors as regulators of macrophage polarization. Front Immunol. 2014; 5:554. https://doi.org/10.3389/fimmu.2014.00554 PMID: 25484881

20. Moniot S, Forgione M, Lucidi A, Hailu GS, Nebbioso A, Carafa V, et al. Development of 1,2,4-Oxadiazoles as Potent and Selective Inhibitors of the Human Deacetylase Sirtuin 2: Structure-Activity Relationship, X-ray Crystal Structure, and Anticancer Activity. J Med Chem. 2017; 60(6):2344-2360. https://doi.org/10.1021/acs.jmedchem.6b01609 PMID: 28240897

21. Bhaskar A, Kumar S, Khan MZ, Singh A, Dwivedi VP, Nandicoori VK. Host sirtuin 2 as an immunotherapeutic target against tuberculosis. eLife. 2020; 9. https://doi.org/10.7554/eLife.55415 PMID: 32697192

22. Fiorentino F, Mautone N, Menna M, D'Acunzo F, Mai A, Rotili D. Sirtuin modulators: past, present, and future perspectives. Future Med Chem. 2022; 14(12):915-939. https://doi.org/10.4155/fmc-2022-0031 PMID: 35583203

23. Troegeler A, Lastrucci C, Duval C, Tanne A, Cougoule C, Maridonneau-Parini I, et al. An efficient siRNA-mediated gene silencing in primary human monocytes, dendritic cells and macrophages. Immuno Cell Biol. 2014; 92(8):699-708. https://doi.org/10.1038/icb.2014.39 PMID: 24890643

24. Cardoso F, Castro F, Moreira-Teixeira L, Sousa J, Torrado E, Silvestre R, et al. Myeloid Sirtuin 2 Expression Does Not Impact Long-Term Mycobacterium tuberculosis Control. PLoS ONE. 2015; 10(7): e0131904. https://doi.org/10.1371/journal.pone.0131904 PMID: 26135889

25. Gu J, Deng JY, Li R, Wei H, Zhang Z, Zhou Y, et al. Cloning and characterization of NAD-dependent protein deacetylase (Rv1151c) from Mycobacterium tuberculosis. Biochemistry (Mosc). 2009; 74 (7):743-748. https://doi.org/10.1134/s0006297909070062 PMID: 19747094

26. Minato Y, Gohl DM, Thiede JM, Chacon JM, Harcombe WR, Maruyama F, et al. Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. mSystems. 2019; 4 (4). https://doi.org/10.1128/mSystems.00070-19 PMID: 31239393
27. Gutierrez MG, Master SS, Singh SB, Taylor GA, Colombo MI, Deretic V. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell. 2004; 119(6):753-766. https://doi.org/10.1016/j.cell.2004.11.038 PMID: 15607973

28. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009; 25(8):1091-1093. https://doi.org/10.1093/bioinformatics/btp101 PMID: 19237447

29. Hood MI, Skaar EP. Nutritional immunity: transition metals at the pathogen-host interface. Nat Rev Microbiol. 2012; 10(8):525-537. https://doi.org/10.1038/nrmicro2836 PMID: 22796883

30. Botella H, Peyron P, Levillain F, Poincloux R, Poquet Y, Brandli I, et al. Mycobacterial p(1)-type ATPases mediate resistance to zinc poisoning in human macrophages. Cell Host Microbe. 2011; 10(3):248-259. https://doi.org/10.1016/j.chom.2011.08.006 PMID: 21925112

31. White C, Lee J, Kambe T, Fritsche K, Petris MJ. A role for the ATP7A copper-transporting ATPase in macrophage bactericidal activity. J Biol Chem. 2009; 284(49):33949-33956. https://doi.org/10.1074/jbc.M109.070201 PMID: 19808669

32. Coyle P, Philcox JC, Carey LC, Rofe AM. Metallothionein: the multipurpose protein. Cell Mol Life Sci. 2002; 59(4):627-647. https://doi.org/10.1007/s00018-002-8454-2 PMID: 12022471

33. Domaille DW, Que EL, Chang CJ. Synthetic fluorescent sensors for studying the cell biology of metals. Nat Chem Biol. 2008; 4(3):168-175. https://doi.org/10.1038/nchembio.69 PMID: 18277978

34. Gee KR, Zhou ZL, Qian WJ, Kennedy R. Detection and imaging of zinc secretion from pancreatic beta-cells using a new fluorescent zinc indicator. J Am Chem Soc. 2002; 124(5):776-778. https://doi.org/10.1021/ja011774y PMID: 11817952

35. Boudehen YM, Faucher M, Marechal X, Miras R, Rech J, Rombouts Y, et al. Mycobacterial resistance to zinc poisoning requires assembly of P-ATPase-containing membrane metal efflux platforms. Nat Commun. 2022; 13(1):4731. https://doi.org/10.1038/s41467-022-32085-7 PMID: 35961955

36. Temml V, Kutil Z. Structure-based molecular modeling in SAR analysis and lead optimization. Comput Struct Biotechnol J. 2021; 19:1431-1444. https://doi.org/10.1016/j.csbj.2021.02.018 PMID: 33777339

37. Queval CJ, Song OR, Delorme V, Iantomasi R, Veyron-Churlet R, Deboosere N, et al. A microscopic phenotypic assay for the quantification of intracellular mycobacteria adapted for high-throughput/high-content screening. J Vis Exp. 2014; 83:e51114. https://doi.org/10.3791/51114 PMID: 24473237

38. Liu Q, Yin X, Languino LR, Altieri DC. Evaluation of drug combination effect using a Bliss independence dose-response surface model. Stat Biopharm Res. 2018; 10(2):112-122. https://doi.org/10.1080/19466315.2018.1437071 PMID: 30881603

39. Christophe T, Jackson M, Jeon HK, Fenistein D, Contreras-Dominguez M, Kim J, et al. High content screening identifies decaprenyl-phosphoribose 2' epimerase as a target for intracellular antimycobacterial inhibitors. PLoS Pathog. 2009; 5(10):e1000645. https://doi.org/10.1371/journal.ppat.1000645 PMID: 19876393

40. Ollinger J, Kumar A, Roberts DM, Bailey MA, Casey A, Parish T. A high-throughput whole cell screen to identify inhibitors of Mycobacterium tuberculosis. PLoS ONE. 2019; 14(1):e0205479. https://doi.org/10.1371/journal.pone.0205479 PMID: 30650074

41. Shapira T, Rankine-Wilson L, Chao JD, Pichler V, Rens C, Pfeifer T, et al. High-Content Screening of Eukaryotic Kinase Inhibitors Identify CHK2 Inhibitor Activity Against Mycobacterium tuberculosis. Front Microbiol. 2020; 11:553962. https://doi.org/10.3389/fmicb.2020.553962 PMID: 33042061

42. Ahmed S, Zhou Z, Zhou J, Chen SQ. Pharmacogenomics of Drug Metabolizing Enzymes and Transporters: Relevance to Precision Medicine. Genomics Proteomics Bioinformatics. 2016; 14(5):298-313. https://doi.org/10.1016/j.gpb.2016.03.008 PMID: 27729266

43. Biernacki K, Dasko M, Ciupak O, Kubinski K, Rachon J, Demkowicz S. Novel 1,2,4-Oxadiazole Derivatives in Drug Discovery. Pharmaceuticals (Basel). 2020; 13(6):111. https://doi.org/10.3390/ph13060111 PMID: 32485996

44. Flipo M, Desroses M, Lecat-Guillet N, Dirie B, Carette X, Leroux F, et al. Ethionamide boosters: synthesis, biological activity, and structure-activity relationships of a series of 1,2,4-oxadiazole EthR inhibitors. J Med Chem. 2011; 54(8):2994-3010. https://doi.org/10.1021/jm200076a PMID: 21417236

45. Melo de Oliveira VN, do Amaral Moura CF, Dos Santos Peixoto A, Pinheiro Gonçalves Ferreira V, Mendes Araújo H, Montenegro Pimentel LML, et al. Synthesis of alkynylated 1,2,4-oxadiazole/1,2,3-1H-triazole glycoconjugates: Discovering new compounds for use in chemotherapy against lung carcinoma and Mycobacterium tuberculosis. Eur J Med Chem. 2021; 220:113472. https://doi.org/10.1016/j.ejmech.2021.113472 PMID: 33940463

46. Kimura T, Kambe T. The Functions of Metallothionein and ZIP and ZnT Transporters: An Overview and Perspective. Int J Mol Sci. 2016; 17(3):336. https://doi.org/10.3390/ijms17030336 PMID: 26959009
27. Gutierrez MG, Master SS, Singh SB, Taylor GA, Colombo MI, Deretic V. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell. 2004; 119(6):753-766. https://doi.org/10.1016/j.cell.2004.11.038 PMID: 15607973

28. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009; 25(8):1091-1093. https://doi.org/10.1093/bioinformatics/btp101 PMID: 19237447

29. Hood MI, Skaar EP. Nutritional immunity: transition metals at the pathogen-host interface. Nat Rev Microbiol. 2012; 10(8):525-537. https://doi.org/10.1038/nrmicro2836 PMID: 22796883

30. Botella H, Peyron P, Levillain F, Poincloux R, Poquet Y, Brandli I, et al. Mycobacterial p(1)-type ATPases mediate resistance to zinc poisoning in human macrophages. Cell Host Microbe. 2011; 10(3):248-259. https://doi.org/10.1016/j.chom.2011.08.006 PMID: 21925112

31. White C, Lee J, Kambe T, Fritsche K, Petris MJ. A role for the ATP7A copper-transporting ATPase in macrophage bactericidal activity. J Biol Chem. 2009; 284(49):33949-33956. https://doi.org/10.1074/jbc.M109.070201 PMID: 19808669

32. Coyle P, Philcox JC, Carey LC, Rofe AM. Metallothionein: the multipurpose protein. Cell Mol Life Sci. 2002; 59(4):627-647. https://doi.org/10.1007/s00018-002-8454-2 PMID: 12022471

33. Domaille DW, Que EL, Chang CJ. Synthetic fluorescent sensors for studying the cell biology of metals. Nat Chem Biol. 2008; 4(3):168-175. https://doi.org/10.1038/nchembio.69 PMID: 18277978

34. Gee KR, Zhou ZL, Qian WJ, Kennedy R. Detection and imaging of zinc secretion from pancreatic beta-cells using a new fluorescent zinc indicator. J Am Chem Soc. 2002; 124(5):776-778. https://doi.org/10.1021/ja011774y PMID: 11817952

35. Boudehen YM, Faucher M, Marechal X, Miras R, Rech J, Rombouts Y, et al. Mycobacterial resistance to zinc poisoning requires assembly of P-ATPase-containing membrane metal efflux platforms. Nat Commun. 2022; 13(1):4731. https://doi.org/10.1038/s41467-022-32085-7 PMID: 35961955

36. Temml V, Kutil Z. Structure-based molecular modeling in SAR analysis and lead optimization. Comput Struct Biotechnol J. 2021; 19:1431-1444. https://doi.org/10.1016/j.csbj.2021.02.018 PMID: 33777339

37. Queval CJ, Song OR, Delorme V, Iantomasi R, Veyron-Churlet R, Deboosere N, et al. A microscopic phenotypic assay for the quantification of intracellular mycobacteria adapted for high-throughput/high-content screening. J Vis Exp. 2014; 83:e51114. https://doi.org/10.3791/51114 PMID: 24473237

38. Liu Q, Yin X, Languino LR, Altieri DC. Evaluation of drug combination effect using a Bliss independence dose-response surface model. Stat Biopharm Res. 2018; 10(2):112-122. https://doi.org/10.1080/19466315.2018.1437071 PMID: 30881603

39. Christophe T, Jackson M, Jeon HK, Fenistein D, Contreras-Dominguez M, Kim J, et al. High content screening identifies decaprenyl-phosphoribose 2' epimerase as a target for intracellular antimycobacterial inhibitors. PLoS Pathog. 2009; 5(10):e1000645. https://doi.org/10.1371/journal.ppat.1000645 PMID: 19876393

40. Ollinger J, Kumar A, Roberts DM, Bailey MA, Casey A, Parish T. A high-throughput whole cell screen to identify inhibitors of Mycobacterium tuberculosis. PLoS ONE. 2019; 14(1):e0205479. https://doi.org/10.1371/journal.pone.0205479 PMID: 30650074

41. Shapira T, Rankine-Wilson L, Chao JD, Pichler V, Rens C, Pfeifer T, et al. High-Content Screening of Eukaryotic Kinase Inhibitors Identify CHK2 Inhibitor Activity Against Mycobacterium tuberculosis. Front Microbiol. 2020; 11:553962. https://doi.org/10.3389/fmicb.2020.553962 PMID: 33042061

42. Ahmed S, Zhou Z, Zhou J, Chen SQ. Pharmacogenomics of Drug Metabolizing Enzymes and Transporters: Relevance to Precision Medicine. Genomics Proteomics Bioinformatics. 2016; 14(5):298-313. https://doi.org/10.1016/j.gpb.2016.03.008 PMID: 27729266

43. Biernacki K, Dasko M, Ciupak O, Kubinski K, Rachon J, Demkowicz S. Novel 1,2,4-Oxadiazole Derivatives in Drug Discovery. Pharmaceuticals (Basel). 2020; 13(6):111. https://doi.org/10.3390/ph13060111 PMID: 32485996

44. Flipo M, Desroses M, Lecat-Guillet N, Dirie B, Carette X, Leroux F, et al. Ethionamide boosters: synthesis, biological activity, and structure-activity relationships of a series of 1,2,4-oxadiazole EthR inhibitors. J Med Chem. 2011; 54(8):2994-3010. https://doi.org/10.1021/jm200076a PMID: 21417236

45. Melo de Oliveira VN, do Amaral Moura CF, Dos Santos Peixoto A, Pinheiro Gonçalves Ferreira V, Mendes Araújo H, Montenegro Pimentel LML, et al. Synthesis of alkynylated 1,2,4-oxadiazole/1,2,3-1H-triazole glycoconjugates: Discovering new compounds for use in chemotherapy against lung carcinoma and Mycobacterium tuberculosis. Eur J Med Chem. 2021; 220:113472. https://doi.org/10.1016/j.ejmech.2021.113472 PMID: 33940463

46. Kimura T, Kambe T. The Functions of Metallothionein and ZIP and ZnT Transporters: An Overview and Perspective. Int J Mol Sci. 2016; 17(3):336. https://doi.org/10.3390/ijms17030336 PMID: 26959009
47. Ghoshal K, Majumder S, Li Z, Dong X, Jacob ST. Suppression of metallothionein gene expression in a rat hepatoma because of promoter-specific DNA methylation. J Biol Chem. 2000; 275(1):539-547.
https://doi.org/10.1074/jbc.275.1.539 PMID: 10617649

48. Majumder S, Ghoshal K, Li Z, Bo Y, Jacob ST. Silencing of metallothionein-1 gene in mouse lymphosarcoma cells by methylation. Oncogene. 1999; 18(46):6287-6295. https://doi.org/10.1038/sj.onc.1203004 PMID: 10597227

49. Neyrolles O, Wolschendorf F, Mitra A, Niederweis M. Mycobacteria, metals, and the macrophage. Immunol Rev. 2015; 264(1):249-263. https://doi.org/10.1111/imr.12265 PMID: 25703564

50. Leseigneur C, Le-Bury P, Pizarro-Cerda J, Dussurget O. Emerging Evasion Mechanisms of Macrophage Defenses by Pathogenic Bacteria. Front Cell Infect Microbiol. 2020; 10:577559. https://doi.org/10.3389/fcimb.2020.577559 PMID: 33102257

51. Vaughn B, Abu K Y. Idiosyncratic Biogenesis of Intracellular Pathogens-Containing Vacuoles. Front Cell Infect Microbiol. 2021; 11:722433. https://doi.org/10.3389/fcimb.2021.722433 PMID: 34858868

52. Liu WJ, Ye L, Huang WF, Guo LJ, Xu ZG, Wu HL, et al. p62 links the autophagy pathway and the ubiquitin-proteasome system upon ubiquitinated protein degradation. Cell Mol Biol Lett. 2016; 21:29. https://doi.org/10.1186/s11658-016-0031-z PMID: 28536631

53. Ramon-Garcia S, Ng C, Anderson H, Chao JD, Zheng X, Pfeifer T, et al. Synergistic drug combinations for tuberculosis therapy identified by a novel high-throughput screen. Antimicrob Agents Chemother. 2011; 55(8):3861-3869. https://doi.org/10.1128/AAC.00474-11 PMID: 21576426

54. Yilancioglu K, Cokol M. Design of high-order antibiotic combinations against M. tuberculosis by ranking and exclusion. Sci Rep. 2019; 9(1):11876. https://doi.org/10.1038/s41598-019-48410-y PMID: 31417151

55. Lee BY, Clemens DL, Silva A, Dillon BJ, Maslesa-Galic S, Nava S, et al. Drug regimens identified and optimized by output-driven platform markedly reduce tuberculosis treatment time. Nat Commun. 2017; 8:14183. https://doi.org/10.1038/ncomms14183 PMID: 28117835

56. Guieu B, Jourdan JP, Dreneau A, Willand N, Rochais C, Dallemagne P. Desirable drug-drug interactions or when a matter of concern becomes a renewed therapeutic strategy. Drug Discov Today. 2021; 26(2):315-328. https://doi.org/10.1016/j.drudis.2020.11.026 PMID: 33253919

57. Flipo M, Desroses M, Lecat-Guillet N, Villemagne B, Blondiaux N, Leroux F, et al. Ethionamide boosters. 2. Combining bioisosteric replacement and structure-based drug design to solve pharmacokinetic issues in a series of potent 1,2,4-oxadiazole EthR inhibitors. J Med Chem. 2012; 55(1):68-83. https://doi.org/10.1021/jm200825u PMID: 22098589

58. Greenwood DJ, Dos Santos MS, Huang S, Russell MRG, Collinson LM, MacRae JI, et al. Subcellular antibiotic visualization reveals a dynamic drug reservoir in infected macrophages. Science. 2019; 364 (6447):1279-1282. https://doi.org/10.1126/science.aat9689 PMID: 31249058

59. Moreira-Teixeira L, Mayer-Barber K, Sher A, O'Garra A. Type I interferons in tuberculosis: Foe and occasionally friend. J Exp Med. 2018; 215(5):1273-1285. https://doi.org/10.1084/jem.20180325 PMID: 29666166

60. Teles RM, Graeber TG, Krutzik SR, Montoya D, Schenk M, Lee DJ, et al. Type I interferon suppresses type II interferon-triggered human anti-mycobacterial responses. Science. 2013; 339(6126):1448-1453. https://doi.org/10.1126/science.1233665 PMID: 23449998

61. Berry MP, Graham CM, McNab FW, Xu Z, Bloch SA, Oni T, et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature. 2010; 466(7309):973-977. https://doi.org/10.1038/nature09247 PMID: 20725040

62. Mayer-Barber KD, Andrade BB, Oland SD, Amaral EP, Barber DL, Gonzales J, et al. Host-directed therapy of tuberculosis based on interleukin-1 and type I interferon crosstalk. Nature. 2014; 511(7507):99-103. https://doi.org/10.1038/nature13489 PMID: 24990750

63. Giraud-Gatineau A, Coya JM, Maure A, Biton A, Thomson M, Bernard EM, et al. The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection. eLife 2020: 9. https://doi.org/10.7554/eLife.55692 PMID: 32369020

64. van Kessel JC, Hatfull GF. Recombineering in Mycobacterium tuberculosis. Nat Methods. 2007; 4 (2):147-152. https://doi.org/10.1038/nmeth996 PMID: 17179933

65. Boudehen YM, Wallat M, Rousseau P, Neyrolles O, Gutierrez C. An improved Xer-cise technology for the generation of multiple unmarked mutants in Mycobacteria. BioTechniques. 2020; 68(2):106-110. https://doi.org/10.2144/btn-2019-0119 PMID: 31937110

66. Gram AM, Wright JA, Pickering RJ, Lam NL, Booty LM, Webster SJ, et al. Salmonella Flagellates NAIP/NLRC4 and Canonical NLRP3 Inflammasomes in Human Macrophages. J Immunol. 2021; 206(3):631-640. https://doi.org/10.4049/jimmunol.2000382 PMID: 33380493
47. Ghoshal K, Majumder S, Li Z, Dong X, Jacob ST. Suppression of metallothionein gene expression in a rat hepatoma because of promoter-specific DNA methylation. J Biol Chem. 2000; 275(1):539-547.
https://doi.org/10.1074/jbc.275.1.539 PMID: 10617649

48. Majumder S, Ghoshal K, Li Z, Bo Y, Jacob ST. Silencing of metallothionein-1 gene in mouse lymphosarcoma cells by methylation. Oncogene. 1999; 18(46):6287-6295. https://doi.org/10.1038/sj.onc.1203004 PMID: 10597227

49. Neyrolles O, Wolschendorf F, Mitra A, Niederweis M. Mycobacteria, metals, and the macrophage. Immunol Rev. 2015; 264(1):249-263. https://doi.org/10.1111/imr.12265 PMID: 25703564

50. Leseigneur C, Le-Bury P, Pizarro-Cerda J, Dussurget O. Emerging Evasion Mechanisms of Macrophage Defenses by Pathogenic Bacteria. Front Cell Infect Microbiol. 2020; 10:577559. https://doi.org/10.3389/fcimb.2020.577559 PMID: 33102257

51. Vaughn B, Abu K Y. Idiosyncratic Biogenesis of Intracellular Pathogens-Containing Vacuoles. Front Cell Infect Microbiol. 2021; 11:722433. https://doi.org/10.3389/fcimb.2021.722433 PMID: 34858868

52. Liu WJ, Ye L, Huang WF, Guo LJ, Xu ZG, Wu HL, et al. p62 links the autophagy pathway and the ubiquitin-proteasome system upon ubiquitinated protein degradation. Cell Mol Biol Lett. 2016; 21:29. https://doi.org/10.1186/s11658-016-0031-z PMID: 28536631

53. Ramon-Garcia S, Ng C, Anderson H, Chao JD, Zheng X, Pfeifer T, et al. Synergistic drug combinations for tuberculosis therapy identified by a novel high-throughput screen. Antimicrob Agents Chemother. 2011; 55(8):3861-3869. https://doi.org/10.1128/AAC.00474-11 PMID: 21576426

54. Yilancioglu K, Cokol M. Design of high-order antibiotic combinations against M. tuberculosis by ranking and exclusion. Sci Rep. 2019; 9(1):11876. https://doi.org/10.1038/s41598-019-48410-y PMID: 31417151

55. Lee BY, Clemens DL, Silva A, Dillon BJ, Maslesa-Galic S, Nava S, et al. Drug regimens identified and optimized by output-driven platform markedly reduce tuberculosis treatment time. Nat Commun. 2017; 8:14183. https://doi.org/10.1038/ncomms14183 PMID: 28117835

56. Guieu B, Jourdan JP, Dreneau A, Willand N, Rochais C, Dallemagne P. Desirable drug-drug interactions or when a matter of concern becomes a renewed therapeutic strategy. Drug Discov Today. 2021; 26(2):315-328. https://doi.org/10.1016/j.drudis.2020.11.026 PMID: 33253919

57. Flipo M, Desroses M, Lecat-Guillet N, Villemagne B, Blondiaux N, Leroux F, et al. Ethionamide boosters. 2. Combining bioisosteric replacement and structure-based drug design to solve pharmacokinetic issues in a series of potent 1,2,4-oxadiazole EthR inhibitors. J Med Chem. 2012; 55(1):68-83. https://doi.org/10.1021/jm200825u PMID: 22098589

58. Greenwood DJ, Dos Santos MS, Huang S, Russell MRG, Collinson LM, MacRae JI, et al. Subcellular antibiotic visualization reveals a dynamic drug reservoir in infected macrophages. Science. 2019; 364 (6447):1279-1282. https://doi.org/10.1126/science.aat9689 PMID: 31249058

59. Moreira-Teixeira L, Mayer-Barber K, Sher A, O'Garra A. Type I interferons in tuberculosis: Foe and occasionally friend. J Exp Med. 2018; 215(5):1273-1285. https://doi.org/10.1084/jem.20180325 PMID: 29666166

60. Teles RM, Graeber TG, Krutzik SR, Montoya D, Schenk M, Lee DJ, et al. Type I interferon suppresses type II interferon-triggered human anti-mycobacterial responses. Science. 2013; 339(6126):1448-1453. https://doi.org/10.1126/science.1233665 PMID: 23449998

61. Berry MP, Graham CM, McNab FW, Xu Z, Bloch SA, Oni T, et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature. 2010; 466(7309):973-977. https://doi.org/10.1038/nature09247 PMID: 20725040

62. Mayer-Barber KD, Andrade BB, Oland SD, Amaral EP, Barber DL, Gonzales J, et al. Host-directed therapy of tuberculosis based on interleukin-1 and type I interferon crosstalk. Nature. 2014; 511(7507):99-103. https://doi.org/10.1038/nature13489 PMID: 24990750

63. Giraud-Gatineau A, Coya JM, Maure A, Biton A, Thomson M, Bernard EM, et al. The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection. eLife 2020: 9. https://doi.org/10.7554/eLife.55692 PMID: 32369020

64. van Kessel JC, Hatfull GF. Recombineering in Mycobacterium tuberculosis. Nat Methods. 2007; 4 (2):147-152. https://doi.org/10.1038/nmeth996 PMID: 17179933

65. Boudehen YM, Wallat M, Rousseau P, Neyrolles O, Gutierrez C. An improved Xer-cise technology for the generation of multiple unmarked mutants in Mycobacteria. BioTechniques. 2020; 68(2):106-110. https://doi.org/10.2144/btn-2019-0119 PMID: 31937110

66. Gram AM, Wright JA, Pickering RJ, Lam NL, Booty LM, Webster SJ, et al. Salmonella Flagellates NAIP/NLRC4 and Canonical NLRP3 Inflammasomes in Human Macrophages. J Immunol. 2021; 206(3):631-640. https://doi.org/10.4049/jimmunol.2000382 PMID: 33380493
67. Lebreton A, Lakisic G, Job V, Fritsch L, Tham TN, Camejo A, et al. A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response. Science. 2011; 331(6022):1319-1321. https://doi.org/10.1126/science.1200120 PMID: 21252314

68. Pereira JM, Chevalier C, Chaze T, Gianetto Q, Impens F, Matondo M, et al. Infection Reveals a Modification of SIRT2 Critical for Chromatin Association. Cell Rep. 2018; 23(4):1124-1137. https://doi.org/10.1016/j CELREP.2018.03.116 PMID: 29694890

69. Selkrig J, Li N, Hausmann A, Mangan MSJ, Zietek M, Mateus A, et al. Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection. Nat Microbiol. 2020; 5(9):1119-1133. https://doi.org/10.1038/s41564-020-0736-7 PMID: 32514074

70. Xiong L, Wang S, Dean JW, Oliff KN, Jobin C, Curtiss R 3rd, et al. Group 3 innate lymphoid cell pyroptosis represents a host defence mechanism against Salmonella infection. Nat Microbiol. 2022; 7(7):1087-1099. https://doi.org/10.1038/s41564-022-01142-8 PMID: 35668113

71. Palomino JC, Martin A, Camacho M, Guerra H, Swings J, Portaels F. Resazurin microtiter assay plate: simple and inexpensive method for detection of drug resistance in Mycobacterium tuberculosis. Antimycrob Agents Chemother. 2002; 46(8):2720-2722. https://doi.org/10.1128/AAC.46.8.2720-2722.2002 PMID: 12121966

72. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-2120. https://doi.org/10.1093/bioinformatics/btu170 PMID: 24695404

73. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29(1):15-21. https://doi.org/10.1093/bioinformatics/bts635 PMID: 23104886

74. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3):290-295. https://doi.org/10.1038/nbt.3122 PMID: 25690850

75. Bourgey M, Dali R, Eveleigh R, Chen KC, Letourneau L, Fillon J, et al. GenPipes: an open-source framework for distributed and scalable genomic analyses. GigaScience. 2019; 8(6). https://doi.org/10.1093/gigascience/giz037 PMID: 31185495

76. Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015; 12(2):115-121. https://doi.org/10.1038/nmeth.3252 PMID: 25633503

77. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26(1):139-140. https://doi.org/10.1093/bioinformatics/btp616 PMID: 19910308

78. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015; 43(7):e47. https://doi.org/10.1093/nar/gkv007 PMID: 25605792

79. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001; 29(9):e45. https://doi.org/10.1093/nar/29.9.e45 PMID: 11328886
67. Lebreton A, Lakisic G, Job V, Fritsch L, Tham TN, Camejo A, et al. A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response. Science. 2011; 331(6022):1319-1321. https://doi.org/10.1126/science.1200120 PMID: 21252314

68. Pereira JM, Chevalier C, Chaze T, Gianetto Q, Impens F, Matondo M, et al. Infection Reveals a Modification of SIRT2 Critical for Chromatin Association. Cell Rep. 2018; 23(4):1124-1137. https://doi.org/10.1016/j CELREP.2018.03.116 PMID: 29694890

69. Selkrig J, Li N, Hausmann A, Mangan MSJ, Zietek M, Mateus A, et al. Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection. Nat Microbiol. 2020; 5(9):1119-1133. https://doi.org/10.1038/s41564-020-0736-7 PMID: 32514074

70. Xiong L, Wang S, Dean JW, Oliff KN, Jobin C, Curtiss R 3rd, et al. Group 3 innate lymphoid cell pyroptosis represents a host defence mechanism against Salmonella infection. Nat Microbiol. 2022; 7(7):1087-1099. https://doi.org/10.1038/s41564-022-01142-8 PMID: 35668113

71. Palomino JC, Martin A, Camacho M, Guerra H, Swings J, Portaels F. Resazurin microtiter assay plate: simple and inexpensive method for detection of drug resistance in Mycobacterium tuberculosis. Antimycrob Agents Chemother. 2002; 46(8):2720-2722. https://doi.org/10.1128/AAC.46.8.2720-2722.2002 PMID: 12121966

72. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-2120. https://doi.org/10.1093/bioinformatics/btu170 PMID: 24695404

73. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29(1):15-21. https://doi.org/10.1093/bioinformatics/bts635 PMID: 23104886

74. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3):290-295. https://doi.org/10.1038/nbt.3122 PMID: 25690850

75. Bourgey M, Dali R, Eveleigh R, Chen KC, Letourneau L, Fillon J, et al. GenPipes: an open-source framework for distributed and scalable genomic analyses. GigaScience. 2019; 8(6). https://doi.org/10.1093/gigascience/giz037 PMID: 31185495

76. Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015; 12(2):115-121. https://doi.org/10.1038/nmeth.3252 PMID: 25633503

77. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26(1):139-140. https://doi.org/10.1093/bioinformatics/btp616 PMID: 19910308

78. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015; 43(7):e47. https://doi.org/10.1093/nar/gkv007 PMID: 25605792

79. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001; 29(9):e45. https://doi.org/10.1093/nar/29.9.e45 PMID: 11328886