Differential determinants of virulence in two Mycobacterium tuberculosis Colombian clinical isolates of the LAM09 family

References

• WHO. Global Tuberculosis Report 2018. Geneva, Switzerland; 2018.
   Google Scholar
• (INS) INdSdC. Boletín Epidemiológico semanal (BES). 2018 [ Cited 2018 Sept 16–22]. Available from: https://wwwinsgovco/buscador-eventos/BoletinEpidemiologico/2018%20Bolet%C3%ADn%20epidemiol%C3%B3gico%20semana%2038pdf.
   Google Scholar
• Hernandez Sarmiento JM, Correa N, Correa M, et al. Tuberculosis among homeless population from Medellin, Colombia: associated mental disorders and socio-demographic characteristics. J Immigr Minor Health. 2013;15(4):693–699. PubMed PMID: 23340806.
   PubMed Web of Science ®Google Scholar
• Rueda ZV, Lopez L, Velez LA, et al. High incidence of tuberculosis, low sensitivity of current diagnostic scheme and prolonged culture positivity in four colombian prisons. A cohort study. PLoS One. 2013;8(11):e80592. PubMed PMID: 24278293; PubMed Central PMCID: PMCPMC3836852.
   PubMed Web of Science ®Google Scholar
• Cadena AM, Fortune SM, Flynn JL. Heterogeneity in tuberculosis. Nat Rev Immunol. 2017;17(11):691–702. PubMed PMID: 28736436.
   PubMed Web of Science ®Google Scholar
• Comas I, Coscolla M, Luo T, et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet. 2013;45(10):1176–1182. PubMed PMID: 23995134; PubMed Central PMCID: PMCPMC3800747.
   PubMed Web of Science ®Google Scholar
• Stucki D, Brites D, Jeljeli L, et al. Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nat Genet. 2016;48(12):1535–1543. PubMed PMID: 27798628; PubMed Central PMCID: PMCPMC5238942.
   PubMed Web of Science ®Google Scholar
• Gagneux S. Ecology and evolution of Mycobacterium tuberculosis. Nat Rev Microbiol. 2018;16(4):202–213. PubMed PMID: 29456241.
   PubMed Web of Science ®Google Scholar
• Lenaerts A, Barry CE 3rd, Dartois V. Heterogeneity in tuberculosis pathology, microenvironments and therapeutic responses. Immunol Rev. 2015;264(1):288–307. PubMed PMID: 25703567; PubMed Central PMCID: PMCPMC4368385.
   PubMed Web of Science ®Google Scholar
• Realpe T, Correa N, Rozo JC, et al. Population structure among mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Colombia. PLoS One. 2014;9(4):e93848. PubMed PMID: 24747767; PubMed Central PMCID: PMCPMC3991582.
   PubMed Web of Science ®Google Scholar
• Lazzarini LC, Spindola SM, Bang H, et al. RDRio Mycobacterium tuberculosis infection is associated with a higher frequency of cavitary pulmonary disease. J Clin Microbiol. 2008;46(7):2175–2183. PubMed PMID: 18463217; PubMed Central PMCID: PMCPMC2446940.
   PubMed Web of Science ®Google Scholar
• Duque C, Arroyo L, Ortega H, et al. Different responses of human mononuclear phagocyte populations to Mycobacterium tuberculosis. Tuberculosis (Edinb). 2014;94(2):111–122. PubMed PMID: 24360327.
   PubMed Web of Science ®Google Scholar
• Del Corral H, Paris SC, Marin ND, et al. IFNgamma response to Mycobacterium tuberculosis, risk of infection and disease in household contacts of tuberculosis patients in Colombia. PLoS One. 2009;4(12):e8257. PubMed PMID: 20011589; PubMed Central PMCID: PMCPMC2788133.
   PubMed Web of Science ®Google Scholar
• Yam KC, D’Angelo I, Kalscheuer R, et al. Studies of a ring-cleaving dioxygenase illuminate the role of cholesterol metabolism in the pathogenesis of Mycobacterium tuberculosis. PLoS Pathog. 2009;5(3):e1000344. PubMed PMID: 19300498; PubMed Central PMCID: PMCPMC2652662.
   PubMed Web of Science ®Google Scholar
• Coll F, McNerney R, Guerra-Assuncao JA, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat Commun. 2014;5:4812. PubMed PMID: 25176035; PubMed Central PMCID: PMCPMC4166679.
   PubMed Web of Science ®Google Scholar
• Prados-Rosales R, Baena A, Martinez LR, et al. Mycobacteria release active membrane vesicles that modulate immune responses in a TLR2-dependent manner in mice. J Clin Invest. 2011;121(4):1471–1483. PubMed PMID: 21364279; PubMed Central PMCID: PMCPMC3069770.
   PubMed Web of Science ®Google Scholar
• Silva GG, Dutilh BE, Matthews TD, et al. Combining de novo and reference-guided assembly with scaffold_builder. Source Code Biol Med. 2013;8(1):23. PubMed PMID: 24267787; PubMed Central PMCID: PMCPMC4177539.
   PubMedGoogle Scholar
• Assefa S, Keane TM, Otto TD, et al. ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics. 2009;25(15):1968–1969. PubMed PMID: 19497936; PubMed Central PMCID: PMCPMC2712343.
   PubMed Web of Science ®Google Scholar
• Otto TD, Dillon GP, Degrave WS, et al. RATT: rapid annotation transfer tool. Nucleic Acids Res. 2011;39(9):e57. PubMed PMID: 21306991; PubMed Central PMCID: PMCPMC3089447.
   PubMed Web of Science ®Google Scholar
• Rutherford K, Parkhill J, Crook J, et al. Artemis: sequence visualization and annotation. Bioinformatics. 2000;16(10):944–945. PubMed PMID: 11120685.
   PubMed Web of Science ®Google Scholar
• Vaser R, Adusumalli S, Leng SN, et al. SIFT missense predictions for genomes. Nat Protoc. 2016;11(1):1–9. PubMed PMID: 26633127.
   PubMed Web of Science ®Google Scholar
• Nattestad M, Schatz MC. Assemblytics: a web analytics tool for the detection of variants from an assembly. Bioinformatics. 2016;32(19):3021–3023. PubMed PMID: 27318204; PubMed Central PMCID: PMCPMC6191160.
   PubMed Web of Science ®Google Scholar
• Isaza JP, Duque C, Gomez V, et al. Whole genome shotgun sequencing of one Colombian clinical isolate of Mycobacterium tuberculosis reveals DosR regulon gene deletions. FEMS Microbiol Lett. 2012;330(2):113–120. PubMed PMID: 22404577.
   PubMed Web of Science ®Google Scholar
• Caws M, Thwaites G, Dunstan S, et al. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. PLoS Pathog. 2008;4(3):e1000034. PubMed PMID: 18369480; PubMed Central PMCID: PMCPMC2268004.
   PubMed Web of Science ®Google Scholar
• Fleischmann RD, Alland D, Eisen JA, et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol. 2002;184(19):5479–5490. PubMed PMID: 12218036; PubMed Central PMCID: PMCPMC135346.
   PubMed Web of Science ®Google Scholar
• Gutacker MM, Smoot JC, Migliaccio CA, et al. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics. 2002;162(4):1533–1543. PubMed PMID: 12524330; PubMed Central PMCID: PMCPMC1462380.
   PubMed Web of Science ®Google Scholar
• Tsolaki AG, Hirsh AE, DeRiemer K, et al. Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc Natl Acad Sci U S A. 2004;101(14):4865–4870. PubMed PMID: 15024109; PubMed Central PMCID: PMCPMC387340.
   PubMed Web of Science ®Google Scholar
• Filliol I, Motiwala AS, Cavatore M, et al. Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol. 2006;188(2):759–772. PubMed PMID: 16385065; PubMed Central PMCID: PMCPMC1347298.
   PubMed Web of Science ®Google Scholar
• Hershberg R, Lipatov M, Small PM, et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 2008;6(12):e311. PubMed PMID: 19090620; PubMed Central PMCID: PMCPMC2602723.
   PubMed Web of Science ®Google Scholar
• Athman JJ, Wang Y, McDonald DJ, et al. Bacterial membrane vesicles mediate the release of Mycobacterium tuberculosis lipoglycans and lipoproteins from infected macrophages. J Immunol. 2015;195(3):1044–1053. PubMed PMID: 26109643; PubMed Central PMCID: PMCPMC4506856.
   PubMed Web of Science ®Google Scholar
• Merker M, Blin C, Mona S, et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet. 2015;47(3):242–249. PubMed PMID: 25599400.
   PubMed Web of Science ®Google Scholar
• Chernyaeva E, Rotkevich M, Krasheninnikova K, et al. Whole-genome analysis of Mycobacterium tuberculosis from patients with tuberculous spondylitis, Russia. Emerg Infect Dis. 2018;24(3):579–583. PubMed PMID: 29460750; PubMed Central PMCID: PMCPMC5823328.
   PubMed Web of Science ®Google Scholar
• Sheen P, Requena D, Gushiken E, et al. A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. BMC Genomics. 2017;18(1):769. PubMed PMID: 29020922; PubMed Central PMCID: PMCPMC5637355.
   PubMedGoogle Scholar
• Parish T, Smith DA, Kendall S, et al. Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. Infect Immun. 2003;71(3):1134–1140. PubMed PMID: 12595424; PubMed Central PMCID: PMCPMC148821.
   PubMed Web of Science ®Google Scholar
• Freeman ZN, Dorus S. Waterfield NR. The KdpD/KdpE two-component system: integrating K(+) homeostasis and virulence. PLoS Pathog. 2013;9(3):e1003201. PubMed PMID: 23555240; PubMed Central PMCID: PMCPMC3610689.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–D13. PubMed PMID: 30476243; PubMed Central PMCID: PMCPMC6323986.
   PubMed Web of Science ®Google Scholar
• De Voss JJ, Rutter K, Schroeder BG, et al. The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages. Proc Natl Acad Sci U S A. 2000;97(3):1252–1257. PubMed PMID: 10655517; PubMed Central PMCID: PMCPMC15586.
   PubMed Web of Science ®Google Scholar
• Burbaud S, Laval F, Lemassu A, et al. Trehalose polyphleates are produced by a glycolipid biosynthetic pathway conserved across phylogenetically distant mycobacteria. Cell Chem Biol. 2016;23(2):278–289. PubMed PMID: 27028886.
   PubMed Web of Science ®Google Scholar
• Nandy A, Mondal AK, Pandey R, et al. Adipocyte model of Mycobacterium tuberculosis infection reveals differential availability of iron to bacilli in the lipid-rich caseous environment. Infect Immun. 2018;86(6). DOI:10.1128/IAI.00041-18. PubMed PMID: 29632245; PubMed Central PMCID: PMCPMC5964510.
   PubMed Web of Science ®Google Scholar
• Griffin JE, Gawronski JD, Dejesus MA, et al. High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. PLoS Pathog. 2011;7(9):e1002251. PubMed PMID: 21980284; PubMed Central PMCID: PMCPMC3182942.
   PubMed Web of Science ®Google Scholar
• Daniel J, Sirakova T, Kolattukudy P. An acyl-CoA synthetase in Mycobacterium tuberculosis involved in triacylglycerol accumulation during dormancy. PLoS One. 2014;9(12):e114877. PubMed PMID: 25490545; PubMed Central PMCID: PMCPMC4260918.
   PubMed Web of Science ®Google Scholar
• Srivastava S, Chaudhary S, Thukral L, et al. Unsaturated lipid assimilation by mycobacteria requires auxiliary cis-trans enoyl CoA isomerase. Chem Biol. 2015;22(12):1577–1587. PubMed PMID: 26628360.
   PubMedGoogle Scholar
• Broset E, Martin C, Gonzalo-Asensio J. Evolutionary landscape of the Mycobacterium tuberculosis complex from the viewpoint of PhoPR: implications for virulence regulation and application to vaccine development. MBio. 2015;6(5):e01289–15. PubMed PMID: 26489860; PubMed Central PMCID: PMCPMC4620462.
   PubMed Web of Science ®Google Scholar
• Williams M, Mizrahi V, Kana BD. Molybdenum cofactor: a key component of Mycobacterium tuberculosis pathogenesis? Crit Rev Microbiol. 2014;40(1):18–29. PubMed PMID: 23317461.
   PubMed Web of Science ®Google Scholar
• Rosas-Magallanes V, Stadthagen-Gomez G, Rauzier J, et al. Signature-tagged transposon mutagenesis identifies novel Mycobacterium tuberculosis genes involved in the parasitism of human macrophages. Infect Immun. 2007;75(1):504–507. PubMed PMID: 17030567; PubMed Central PMCID: PMCPMC1828433.
   PubMed Web of Science ®Google Scholar
• Homolka S, Niemann S, Russell DG, et al. Functional genetic diversity among Mycobacterium tuberculosis complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival. PLoS Pathog. 2010;6(7):e1000988. PubMed PMID: 20628579; PubMed Central PMCID: PMCPMC2900310.
   PubMed Web of Science ®Google Scholar
• Peters JS, Calder B, Gonnelli G, et al. Identification of quantitative proteomic differences between Mycobacterium tuberculosis lineages with altered virulence. Front Microbiol. 2016;7:813. PubMed PMID: 27303394; PubMed Central PMCID: PMCPMC4885829.
   PubMed Web of Science ®Google Scholar
• Gouzy A, Larrouy-Maumus G, Bottai D, et al. Mycobacterium tuberculosis exploits asparagine to assimilate nitrogen and resist acid stress during infection. PLoS Pathog. 2014;10(2):e1003928. PubMed PMID: 24586151; PubMed Central PMCID: PMCPMC3930563.
   PubMed Web of Science ®Google Scholar
• Gouzy A, Larrouy-Maumus G, Wu TD, et al. Mycobacterium tuberculosis nitrogen assimilation and host colonization require aspartate. Nat Chem Biol. 2013;9(11):674–676. PubMed PMID: 24077180; PubMed Central PMCID: PMCPMC3856356.
   PubMed Web of Science ®Google Scholar
• Kosikowska P, Bochno M, Macegoniuk K, et al. Bisphosphonic acids as effective inhibitors of Mycobacterium tuberculosis glutamine synthetase. J Enzyme Inhib Med Chem. 2016;31(6):931–938. PubMed PMID: 26235917.
   PubMed Web of Science ®Google Scholar
• Ali MK, Li X, Tang Q, et al. Regulation of inducible potassium transporter KdpFABC by the KdpD/KdpE two-component system in Mycobacterium smegmatis. Front Microbiol. 2017;8:570. PubMed PMID: 28484428; PubMed Central PMCID: PMCPMC5401905.
   PubMed Web of Science ®Google Scholar
• Salina EG, Waddell SJ, Hoffmann N, et al. Potassium availability triggers Mycobacterium tuberculosis transition to, and resuscitation from, non-culturable (dormant) states. Open Biol. 2014;4(10). DOI:10.1098/rsob.140106. PubMed PMID: 25320096; PubMed Central PMCID: PMCPMC4221891.
   PubMed Web of Science ®Google Scholar
• Wilburn KM, Fieweger RA, VanderVen BC. Cholesterol and fatty acids grease the wheels of Mycobacterium tuberculosis pathogenesis. Pathog Dis. 2018;76(2). DOI:10.1093/femspd/fty021. PubMed PMID: 29718271.
   PubMed Web of Science ®Google Scholar
• Winder FG, Brennan PJ. Initial steps in the metabolism of glycerol by Mycobacterium tuberculosis. J Bacteriol. 1966;92(6):1846–1847. PubMed PMID: 4959723; PubMed Central PMCID: PMCPMC316274.
   PubMed Web of Science ®Google Scholar
• de Carvalho LP, Fischer SM, Marrero J, et al. Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates. Chem Biol. 2010;17(10):1122–1131. PubMed PMID: 21035735.
   PubMedGoogle Scholar
• Billig S, Schneefeld M, Huber C, et al. Lactate oxidation facilitates growth of Mycobacterium tuberculosis in human macrophages. Sci Rep. 2017;7(1):6484. PubMed PMID: 28744015; PubMed Central PMCID: PMCPMC5526930.
   PubMedGoogle Scholar
• Boradia VM, Malhotra H, Thakkar JS, et al. Mycobacterium tuberculosis acquires iron by cell-surface sequestration and internalization of human holo-transferrin. Nat Commun. 2014;5:4730. PubMed PMID: 25163484.
   PubMed Web of Science ®Google Scholar
• Coppola M, van Meijgaarden KE, Franken KL, et al. New genome-wide algorithm identifies novel in-vivo expressed Mycobacterium tuberculosis antigens inducing human T-cell responses with classical and unconventional cytokine profiles. Sci Rep. 2016;6:37793. PubMed PMID: 27892960; PubMed Central PMCID: PMCPMC5125271.
   PubMedGoogle Scholar
• Brennan MJ. The Enigmatic PE/PPE multigene family of mycobacteria and tuberculosis vaccination. Infect Immun. 2017;85(6). DOI:10.1128/IAI.00969-16. PubMed PMID: 28348055; PubMed Central PMCID: PMCPMC5442627.
   Web of Science ®Google Scholar
• Abdallah AM, Bestebroer J, Savage ND, et al. Mycobacterial secretion systems ESX-1 and ESX-5 play distinct roles in host cell death and inflammasome activation. J Immunol. 2011;187(9):4744–4753. PubMed PMID: 21957139.
   PubMed Web of Science ®Google Scholar
• Shah S, Cannon JR, Fenselau C, et al. A duplicated ESAT-6 region of ESX-5 is involved in protein export and virulence of mycobacteria. Infect Immun. 2015;83(11):4349–4361. PubMed PMID: 26303392; PubMed Central PMCID: PMCPMC4598393.
   PubMed Web of Science ®Google Scholar
• Converse SE, Cox JS. A protein secretion pathway critical for Mycobacterium tuberculosis virulence is conserved and functional in Mycobacterium smegmatis. J Bacteriol. 2005;187(4):1238–1245. PubMed PMID: 15687187; PubMed Central PMCID: PMCPMC545616.
   PubMed Web of Science ®Google Scholar
• Champion PA. Disconnecting in vitro ESX-1 secretion from mycobacterial virulence. J Bacteriol. 2013;195(24):5418–5420. PubMed PMID: 24123823; PubMed Central PMCID: PMCPMC3889606.
   PubMed Web of Science ®Google Scholar
• Stanley SA, Raghavan S, Hwang WW, et al. Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system. Proc Natl Acad Sci U S A. 2003;100(22):13001–13006. PubMed PMID: 14557536; PubMed Central PMCID: PMCPMC240734.
   PubMed Web of Science ®Google Scholar
• Forrellad MA, Klepp LI, Gioffre A, et al. Virulence factors of the Mycobacterium tuberculosis complex. Virulence. 2013;4(1):3–66. PubMed PMID: 23076359; PubMed Central PMCID: PMCPMC3544749.
   PubMed Web of Science ®Google Scholar
• Pathak SK, Basu S, Basu KK, et al. Direct extracellular interaction between the early secreted antigen ESAT-6 of Mycobacterium tuberculosis and TLR2 inhibits TLR signaling in macrophages. Nat Immunol. 2007;8(6):610–618. PubMed PMID: 17486091.
   PubMed Web of Science ®Google Scholar
• McLaughlin B, Chon JS, MacGurn JA, et al. A mycobacterium ESX-1-secreted virulence factor with unique requirements for export. PLoS Pathog. 2007;3(8):e105. PubMed PMID: 17676952; PubMed Central PMCID: PMCPMC1937011.
   PubMed Web of Science ®Google Scholar
• Singh PK, Saxena R, Tiwari S, et al. RD-1 encoded EspJ protein gets phosphorylated prior to affect the growth and intracellular survival of mycobacteria. Sci Rep. 2015;5:12717. PubMed PMID: 26228622; PubMed Central PMCID: PMCPMC4521147.
   PubMed Web of Science ®Google Scholar
• Haning K, Cho SH, Contreras LM. Small RNAs in mycobacteria: an unfolding story. Front Cell Infect Microbiol. 2014;4:96. PubMed PMID: 25105095; PubMed Central PMCID: PMCPMC4109619.
   PubMed Web of Science ®Google Scholar
• Cantaloube S, Veyron-Churlet R, Haddache N, et al. The Mycobacterium tuberculosis FAS-II dehydratases and methyltransferases define the specificity of the mycolic acid elongation complexes. PLoS One. 2011;6(12):e29564. PubMed PMID: 22216317; PubMed Central PMCID: PMCPMC3245277.
   PubMed Web of Science ®Google Scholar
• Delogu G, Provvedi R, Sali M, et al. Mycobacterium tuberculosis virulence: insights and impact on vaccine development. Future Microbiol. 2015;10(7):1177–1194. PubMed PMID: 26119086.
   PubMed Web of Science ®Google Scholar
• Gerrick ER, Barbier T, Chase MR, et al. Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response. Proc Natl Acad Sci U S A. 2018;115(25):6464–6469. PubMed PMID: 29871950; PubMed Central PMCID: PMCPMC6016810.
   PubMed Web of Science ®Google Scholar
• Zaborina O, Li X, Cheng G, et al. Secretion of ATP-utilizing enzymes, nucleoside diphosphate kinase and ATPase, by Mycobacterium bovis BCG: sequestration of ATP from macrophage P2Z receptors? Mol Microbiol. 1999;31(5):1333–1343. PubMed PMID: 10200955.
   PubMed Web of Science ®Google Scholar
• Florio W, Batoni G, Esin S, et al. Influence of culture medium on the resistance and response of Mycobacterium bovis BCG to reactive nitrogen intermediates. Microbes Infect. 2006;8(2):434–441. PubMed PMID: 16298152.
   PubMed Web of Science ®Google Scholar
• Wang XM, Lu C, Soetaert K, et al. Biochemical and immunological characterization of a cpn60.1 knockout mutant of Mycobacterium bovis BCG. Microbiology. 2011;157(Pt 4):1205–1219. PubMed PMID: 21127129.
   PubMedGoogle Scholar
• Venkataswamy MM, Goldberg MF, Baena A, et al. In vitro culture medium influences the vaccine efficacy of Mycobacterium bovis BCG. Vaccine. 2012;30(6):1038–1049. PubMed PMID: 22189700; PubMed Central PMCID: PMCPMC3269512.
   PubMed Web of Science ®Google Scholar
• Dhar N, McKinney J, Manina G. Phenotypic heterogeneity in Mycobacterium tuberculosis. Microbiol Spectr. 2016;4(6). DOI:10.1128/microbiolspec.TBTB2-0021-2016. PubMed PMID: 27837741.
   PubMed Web of Science ®Google Scholar
• Mathema B, Kurepina N, Yang G, et al. Epidemiologic consequences of microvariation in Mycobacterium tuberculosis. J Infect Dis. 2012;205(6):964–974. PubMed PMID: 22315279; PubMed Central PMCID: PMCPMC3415951.
   PubMed Web of Science ®Google Scholar
• Carey AF, Rock JM, Krieger IV, et al. TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathog. 2018;14(3):e1006939. PubMed PMID: 29505613; PubMed Central PMCID: PMCPMC5854444.
   PubMed Web of Science ®Google Scholar
• von Groll A, Martin A, Portaels F, et al. Growth kinetics of Mycobacterium tuberculosis measured by quantitative resazurin reduction assay: a tool for fitness studies. Braz J Microbiol. 2010;41(2):300–303. PubMed PMID: 24031495; PubMed Central PMCID: PMCPMC3768668.
   PubMed Web of Science ®Google Scholar
• Hartkoorn RC, Sala C, Uplekar S, et al. Genome-wide definition of the SigF regulon in Mycobacterium tuberculosis. J Bacteriol. 2012;194(8):2001–2009. PubMed PMID: 22307756; PubMed Central PMCID: PMCPMC3318452.
   PubMed Web of Science ®Google Scholar
• Betts JC, Lukey PT, Robb LC, et al. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol. 2002;43(3):717–731. PubMed PMID: 11929527.
   PubMed Web of Science ®Google Scholar
• Chen P, Ruiz RE, Li Q, et al. Construction and characterization of a Mycobacterium tuberculosis mutant lacking the alternate sigma factor gene, sigF. Infect Immun. 2000;68(10):5575–5580. PubMed PMID: 10992456; PubMed Central PMCID: PMCPMC101508.
   PubMed Web of Science ®Google Scholar
• Geiman DE, Kaushal D, Ko C, et al. Attenuation of late-stage disease in mice infected by the Mycobacterium tuberculosis mutant lacking the SigF alternate sigma factor and identification of SigF-dependent genes by microarray analysis. Infect Immun. 2004;72(3):1733–1745. PubMed PMID: 14977982; PubMed Central PMCID: PMCPMC356042.
   PubMed Web of Science ®Google Scholar
• Prados-Rosales R, Weinrick BC, Pique DG, et al. Role for Mycobacterium tuberculosis membrane vesicles in iron acquisition. J Bacteriol. 2014;196(6):1250–1256. PubMed PMID: 24415729; PubMed Central PMCID: PMCPMC3957709.
   PubMed Web of Science ®Google Scholar
• Clemmensen HS, Knudsen NPH, Rasmussen EM, et al. An attenuated Mycobacterium tuberculosis clinical strain with a defect in ESX-1 secretion induces minimal host immune responses and pathology. Sci Rep. 2017;7:46666. PubMed PMID: 28436493; PubMed Central PMCID: PMCPMC5402389.
   PubMedGoogle Scholar
• Krzywinski M, Schein J, Birol I, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639–1645. PubMed PMID: 19541911; PubMed Central PMCID: PMCPMC2752132.
   PubMed Web of Science ®Google Scholar