Institut Pasteur Unit\351 de G\351n\351tique Mol\351culaire

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Research articles, reviews and commentaries


Brosch, R., Gordon, S.V., Garnier, T., Eiglmeier, K., Frigui, W., Valenti, P., Dos Santos, S., Duthoy, S., Lacroix, C., Garcia-Pelayo, C., Inwald, J.K., Golby, P., Nunez Garcia, J., Hewinson, R.G., Behr, M.A., Quail, M.A., Churcher, C., Barrell, B.G., Parkhill, J., and Cole, S.T. (2007) Genome plasticity of BCG and impact on vaccine efficacy.
Proc Natl Acad Sci U S A. 104: 5596-5601, (news1, news2, news3, news4).

Brosch, R., and Vincent, V. (2007) Cutting-edge science and the future of tuberculosis control. Bull World Health Organ. 85:410-412, (pdf).

Chesne-Seck, M.L., Barilone, N., Boudou, F., Asensio, J.G., Kolattukudy, P.E., Martin, C., Cole, S.T., Gicquel, B., Gopaul, D.N., and Jackson, M. (2007) A point mutation in the two-component regulator PhoP-PhoR accounts for the absence of polyketide-derived acyltrehaloses but not that of phthiocerol dimycocerosates in Mycobacterium tuberculosis H37Ra. J. Bacteriol., [Epub ahead of print].

Coutanceau, E., Decalf, J., Martino, A., Babon, A., Winter, N., Cole, S.T., Albert, M.L., and Demangel, C.(2007) Selective suppression of dendritic cell functions by Mycobacterium ulcerans toxin mycolactone. J Exp Med. [Epub ahead of print] , (JEM highlight-commentary).

de Jonge, M.I., Pehau-Arnaudet, G., Fretz, M.M., Romain, F., Bottai, D., Brodin, P., Honore, N., Marchal, G., Jiskoot, W., England, P., Cole, S.T., and Brosch, R. (2007) ESAT-6 from Mycobacterium tuberculosis dissociates from its putative chaperone CFP-10 under acidic conditions and exhibits membrane-lysing activity. J Bacteriol. [Epub ahead of print]

Grana, M., Haouz, A., Buschiazzo, A., Miras, I., Wehenkel, A., Bondet, V., Shepard, W., Schaeffer, F., Cole, S.T., and Alzari, P.M. (2007) The crystal structure of M. leprae ML2640c defines a large family of putative S-adenosylmethionine-dependent methyltransferases in mycobacteria. Protein Sci. 16:1896-904.

Hong, H., Stinear, T., Porter, J., Demangel, C., and Leadlay, P.F. (2007) A novel mycolactone toxin obtained by biosynthetic engineering. Chembiochem. 8: 2043-2047.

Marsollier, L., Brodin, P., Jackson, M., Kordulakova, J., Tafelmeyer, P., Carbonnelle, E., Aubry, J., Milon, G., Legras, P., Andre, J.P., Leroy, C., Cottin, J., Guillou, M.L., Reysset, G., and Cole, S.T. (2007) Impact of Mycobacterium ulcerans Biofilm on Transmissibility to Ecological Niches and Buruli Ulcer Pathogenesis. PLoS Pathog. 3:e62.

Marsollier, L., Deniaux, E., Brodin, P., Marot, A., Wondje, C.M., Saint-Andre, J.P., Chauty, A., Johnson, C., Tekaia, F., Yeramian, E., Legras, P., Carbonnelle, B., Reysset, G., Eyangoh, S., Milon, G., Cole, S.T., and Aubry, J. (2007) Protection against Mycobacterium ulcerans Lesion Development by Exposure to Aquatic Insect Saliva. PLoS Med. 4:e64 .

Matamouros, S., England, P., and Dupuy, B. (2007) Clostridium difficile toxin expression is inhibited by the novel regulator TcdC. Mol Microbiol. 64:1274-88.

Prado, S., Janin, Y. L., Saint-Joanis, B., Brodin, P., Michel, S., Koch, M., Cole, S. T., Tillequin, F., and Bost, P. E. (2007) Synthesis and antimycobacterial evaluation of benzofurobenzopyran analogues.Bioorg Med Chem. 15:2177-86 .

Prado, S., Toum, V., Saint-Joanis, B., Michel, S., Koch, M., Cole, S.T., Tillequin, F., and Janin, Y.L. (2007) Antimycobacterial Benzofuro[3,2-f]chromenes from a 5-bromochrome-6-ol. Synthesis 10: 1566-1570.

Shepard, W., Haouz, A., Grana, M., Buschiazzo, A., Betton, J.M., Cole, S.T ., and Alzari, P.M. (2007) The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of FABP-like proteins in bacteria. J Bacteriol. 189: 1899-1904 .

Stinear, T. P., Seemann, T., Pidot, S., Frigui, W., Reysset, G., Garnier, T., Me urice, G., Simon, D., Bouchier, C., Ma, L., Tichit, M., Porter, J. L., Ryan, J., Johnson, P. D., Davies, J. K., Jenkin, G. A., Small, P. L., Jones, L. M., Tekai a, F., Laval, F., Daffe, M., Parkhill, J., and Cole, S. T. (2007) Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulce rans, the causative agent of Buruli ulcer. Genome Res. 7:192-200.

Teutschbein, J., Schumann, G., Mollmann, U., Grabley, S., Cole, S.T., Munder, T. (2007) A protein linkage map of the ESAT-6 secretion system 1 (ESX-1) of Mycobacterium tuberculosis. Microbiol Res.

Wehenkel, A., Bellinzoni, M., Grana, M., Duran, R., Villarino, A., Fernandez, P., Andre-Leroux, G., England, P., Takiff, H., Cervenansky, C., Cole, S.T., Alzari, P.M. (2007) Mycobacterial Ser/Thr protein kinases and phosphatases: Physiological roles and therapeutic potential. Biochim Biophys Acta


Araoz, R., Honore, N., Banu, S., Demangel, C., Cissoko, Y., Arama, C., Mafij Uddin, M.K., Abdul Hadi, S.K., Monot, M., Cho, S.N., Ji, B., Brennan, P.J., Sow, S., and Cole, S.T.(2006) Towards an immunodiagnostic test for leprosy. Microbes Infect. 8:2270-2276 .

Araoz, R., Honore, N., Cho, S., Kim, J.P., Cho, S.N., Monot, M., Demangel, C., Brennan, P.J., and Cole S.T. (2006) Antigen discovery: a postgenomic approach to leprosy diagnosis. Infect Immun. 74:175-82.

Brisse, S., Supply, P., Brosch, R., Vincent, V., and Gutierrez, M.C. (2006) A Re-Evaluation of M. prototuberculosis: Continuing the Debate. PLoS Pathog 2(9): e95.

Brodin, P., Majlessi, L., Marsollier, L., de Jonge, M.I., Bottai, D., Demangel, C., Hinds, J., Neyrolles, O., Butcher, P.D., Leclerc, C., Cole, S.T., and Brosch, R. (2006) Dissection of ESAT-6 system 1 of Mycobacterium tuberculosis and impact on immunogenicity and virulence. Infect Immun. 74:88-98.

Coutanceau, E., Legras, P., Marsollier, L., Reysset, G., Cole, S.T., and Demangel C. (2006) Immunogenicity of Mycobacterium ulcerans Hsp65 and protective efficacy of a Mycobacterium leprae Hsp65-based DNA vaccine against Buruli ulcer. Microbes Infect. 8:2075-81.

Dupuy, B., and Matamouros, S. (2006) Regulation of toxin and bacteriocin synthesis in Clostridium species by a new subgroup of RNA polymerase sigma-factors. Res Microbiol. 157:201-5.

Dupuy, B., Raffestin, S., Matamouros, S., Mani, N., Popoff, M. R., and Sonenshein, A. L. (2006) Regulation of toxin and bacteriocin gene expression in Clostridium by interchangeable RNA polymerase sigma factors. Mol Microbiol. 60:1044-1057.

Fernandez, P., Saint-Joanis, B., Barilone, N., Jackson, M., Gicquel, B., Cole, S.T., and Alzari, P.M.(2006) The Ser/Thr protein kinase PknB is essential to sustain mycobacterial growth. J Bacteriol. 188:7778-84.

Hervas-Stubbs, S., Majlessi, L., Simsova, M., Morova, J., Rojas, M.J., Nouze, C., Brodin, P., Sebo, P., and Leclerc, C. (2006) High frequency of CD4+ T cells specific for the TB10.4 protein correlates with protection against Mycobacterium tuberculosis infection. Infect Immun. 74:3396-407.

Majlessi, L., Simsova, M., Jarvis, Z., Brodin, P., Rojas, M.J., Bauche, C., Nouze, C., Ladant, D., Cole, S.T., Sebo, P., Leclerc, C. (2006) An Increase in Antimycobacterial Th1-Cell Responses by Prime-Boost Protocols of Immunization Does Not Enhance Protection against Tuberculosis. Infect Immun. 74:2128-37.

Mani, N., Dupuy, B., Sonenshein, A.L. (2006) Isolation of RNA polymerase from Clostridium difficile and characterization of glutamate dehydrogenase and rRNA gene promoters in vitro and in vivo. J Bacteriol.188:96-102.

Marsollier, L., Andre, J.P., Frigui, W., Reysset, G., Milon, G., Carbonnelle, B., Aubry, J., and Cole, S.T.(2006) Early trafficking events of Mycobacterium ulcerans within Naucoris cimicoides. Cell Microbiol.9:347-55 .

Rosas-Magallanes, V., Deschavanne, P., Quintana-Murci, L., Brosch, R., Gicquel, B., Neyrolles, O. (2006) Horizontal Transfer of a Virulence Operon to the Ancestor of Mycobacterium tuberculosis. Mol Biol Evol. 23:1129-35

Prado, S., Ledeit, H., Michel, S., Koch, M., Darbord, J.C., Cole, S.T., Tillequin, F., and Brodin, P. (2006) Benzofuro[3,2-f][1]benzopyrans: A new class of antitubercular agents. Bioorg Med Chem 14:5423-8.

Saint-Joanis, B., Demangel, C., Jackson, M., Brodin, P., Marsollier, L., Boshoff, H., and Cole, S.T. (2006). Inactivation of Rv2525c, a Substrate of the Twin Arginine Translocation (Tat) System of Mycobacterium tuberculosis, Increases {beta}-Lactam Susceptibility and Virulence. J Bacteriol. 188:6669-79.

Schumann, G., Schleier, S., Rosenkrands, I., Nehmann, N., Halbich, S., Zipfel, P.F., de Jonge, M.I., Cole, S.T., Munder, T., and Mollmann, U. (2006). Mycobacterium tuberculosis secreted protein ESAT-6 interacts with the human protein syntenin-1. Centr Eur J Biol, 1:183-202.

Sebaihia, M., Wren, B.W., Mullany, P., Fairweather, N.F., Minton, N., Stabler, R., Thomson, N.R., Roberts, A.P., Cerdeno-Tarraga, A.M., Wang, H., Holden, M.T., Wright, A;, Churcher, C., Quail, M.A., Baker, S., Bason, N., Brooks, K., Chillingworth, T., Cronin, A., Davis, P., Dowd, L., Fraser, A., Feltwell, T., Hance, Z., Holroyd, S., Jagels, K., Moule, S., Mungall, K., Price, C., Rabbinowitsch, E., Sharp, S., Simmonds, M., Stevens, K., Unwin, L., Whithead, S., Dupuy, B., Dougan, G., Barrell, B., and Parkhill, J. (2006). The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet.38:779-86.


Brodin, P., de Jonge, M.I., Majlessi, L., Leclerc, C., Nilges, M., Cole, S.T., and Brosch R. (2005) Functional analysis of ESAT-6, the dominant T-cell antigen of Mycobacterium tuberculosis , reveals key residues involved in secretion, complex-formation, virulence and immunogenicity. J Biol Chem. 280: 33953-59, (pdf-v1).

Cole, S.T., and Alzari, P.M. (2005) TB--a new target, a new drug. Science. 307:214-5.

Coutanceau, E., Marsollier, L., Brosch, R., Perret, E., Goossens, P., Tanguy, M., Cole, S. T., Small, P.L., and Demangel, C. (2005) Modulation of the host immune response by a transient intracellular stage of Mycobacterium ulcerans : the contribution of endogenous mycolactone toxin. Cell Microbiol. 7:1187-96.

Demangel, C., Garnier, T., Rosenkrands, I., and Cole S.T. (2005) Differential effects of prior exposure to environmental mycobacteria on vaccination with Mycobacterium bovis BCG or a recombinant BCG Strain expressing RD1 antigens. Infect. Immun. 73: 2190 - 2196.

Dupuy, B., Mani, N., Katayama, S., and Sonenshein, A.L.(2005) Transcription activation of a UV-inducible Clostridium perfringens bacteriocin gene by a novel sigma factor. Mol Microbiol. 55:1196-206.

Duran, R., Villarino, A., Bellinzoni, M., Wehenkel, A., Fernandez, P., Boitel, B., Cole, S.T., Alzari, P.M., and Cervenansky, C. (2005) Conserved autophosphorylation pattern in activation loops and juxtamembrane regions of Mycobacterium tuberculosis Ser/Thr protein kinases. Biochem Biophys Res Commun. 333:858-67.

Guimaraes, B.G., Souchon, H., Honore, N., Saint-Joanis, B., Brosch, R., Shepard, W., Cole, S. T., and Alzari, P. M. (2005) Structure and mechanism of the alkyl hydroperoxidase AhpC, a key element of the Mycobacterium tuberculosis defense system against oxidative stress. J Biol Chem. 280:25735-42, (pdf-v1).

Gutierrez, M.C., Brisse, S., Brosch, R., Fabre, M., Omais, B., Marmiesse, M., Supply, P., and Vincent V. (2005) Ancient Origin and Gene Mosaicism of the Progenitor of Mycobacterium tuberculosis . PLoS Pathog 1:e5 (News-Commentary).

de Jonge, M.I., Brosch, R., Brodin, P., Demangel, C., and Cole, S.T. (2005) Tuberculosis: from genome to vaccine. Expert Rev Vaccines 4:541-51.

Kaufmann, S.H., Cole, S.T., Mizrahi, V., Rubin, E., and Nathan C. (2005) Mycobacterium tuberculosis and the host response. J Exp Med. 201:1693-7.

Majlessi, L., Brodin, P., Brosch, R., Rojas, M.J., Khun, H., Huerre, M., Cole, S.T., and Leclerc, C. (2005) Influence of ESAT-6 secretion system 1 (RD1) of Mycobacterium tuberculosis on the interaction between mycobacteria and the host immune system. J Immunol. 174:3570-9.

Marsollier, L., Aubry, J., Coutanceau, E., Andre, J.P., Small, P.L., Milon, G., Legras, P., Guadagnini, S., Carbonnelle, B., and Cole, S.T. (2005) Colonization of the salivary glands of Naucoris cimicoides by Mycobacterium ulcerans requires host plasmatocytes and a macrolide toxin, mycolactone. Cell Microbiol.7:935-43.

Monot, M., Honore, N., Garnier, T., Araoz, R., Coppee, J. Y., Lacroix, C., Sow, S., Spencer, J. S., Truman, R. W, Williams, D. L., Gelber, R., Virmond, M., Flageul, B., Cho, S. N., Ji, B., Paniz-Mondolfi, A., Convit, J., Young, S., Fine, P.E., Rasolofo, V., Brennan, P. J., and Cole, S. T. (2005) On the origin of leprosy. Science. 308:1040-2.

Raffestin, S. Dupuy, B., Marvaud, J.C., and Popoff, M.R.  (2005). BotR/A and TetR are alternative RNA polymerase sigma factors controlling the expression of the neurotoxin and associated protein genes in Clostridium botulinum type A and Clostridium tetani. Mol. Microbiol. 55, 235-249 .

Rupnik, M., Dupuy, B., Fairweather, N.F., Gerding, D.N., Johnson, S., Just, I., Lyerly, D.M., Popoff, M.R., Rood, J.I., Sonenshein, A.L., Thelestam, M., Wren, B.W., Wilkins, T.D. and von Eichel-Streiber C. (2005) Revised nomenclature of Clostridium difficile toxins and associated genes. J Med Microbiol 54: 113-117.

Sinha, S., Kosalai, K., Arora, S., Namane, A., Sharma, P., Gaikwad, A.N., Brodin, P., and Cole, S.T. (2005) Immunogenic membrane-associated proteins of Mycobacterium tuberculosis revealed by proteomics. Microbiology. 151:2411-9.

Spencer, J.S., Dockrell, H.M., Kim, H.J., Marques, M.A., Williams, D.L., Martins, M.V., Martins, M.L., Lima, M.C., Sarno, E.N., Pereira, G.M., Matos, H., Fonseca, L.S., Sampaio, E.P., Ottenhoff, T.H., Geluk, A., Cho, S.N., Stoker, N.G., Cole, S.T., Brennan, P.J., and Pessolani, M.C. (2005) Identification of specific proteins and peptides in Mycobacterium leprae suitable for the selective diagnosis of leprosy. J Immunol. 175:7930-8.

Stinear, T.P., Hong, H., Frigui, W., Pryor, M.J., Brosch, R., Garnier, T., Leadlay, P.F., and Cole, S.T (2005) Common evolutionary origin for the unstable virulence plasmid pMUM found in geographically diverse strains of Mycobacterium ulcerans. J Bact 187 :1668-1676

Stinear, T.P., Pryor, M.J., Porter, J.L., and Cole, S.T. (2005) Functional analysis and annotation of the virulence plasmid pMUM001 from Mycobacterium ulcerans. Microbiology. 151:683-92.

Villarino, A., Duran, R., Wehenkel, A., Fernandez, P., England, P., Brodin, P., Cole, S.T., Zimny-Arndt, U., Jungblut, P.R., Cervenansky, C., and Alzari P.M.(2005) Proteomic identification of M. tuberculosis protein kinase substrates: PknB recruits GarA, a FHA domain-containing protein, through activation loop-mediated interactions. J Mol Biol. 350:953-63.

Williams, A., Hatch, G.J., Clark, S.O., Gooch, K.E., Hatch, K.A., Hall, G.A., Huygen, K., Ottenhoff, T.H., Franken, K.L., Andersen, P., Doherty, T.M., Kaufmann, S.H., Grode, L., Seiler, P., Martin, C., Gicquel, B., Cole, S.T., Brodin, P., Pym, A.S., Dalemans, W., Cohen, J., Lobet, Y., Goonetilleke, N., McShane, H., Hill, A., Parish, T., Smith, D., Stoker, N.G., Lowrie, D.B., Kallenius, G., Svenson, S., Pawlowski, A., Blake, K., and Marsh, P.D. (2005) Evaluation of vaccines in the EU TB Vaccine Cluster using a guinea pig aerosol infection model of tuberculosis. Tuberculosis (Edinb).85:29-38.


Banu, S., Gordon, S.V., Palmer, S., Islam, R., Ahmed, S., Alam, K.M., Cole, S.T. and Brosch, R.(2004) Genotypic analysis of Mycobacterium tuberculosis in Bangladesh and prevalence of the Beijing strain. J. Clin. Microbiol. 42: 674-682, (pdf).

Brodin, P., Majlessi, L., Brosch, R., Smith, D., Bancroft, G., Clark, S., Williams, A., Leclerc, C., and Cole, S.T. (2004) Enhanced protection against tuberculosis by vaccination with recombinant Mycobacterium microti vaccine that induces T cell immunity against region of difference 1 antigens. J. Infect. Dis. 190: 115-122.

Brodin, P., Rosenkrands, I., Andersen, P., Cole, S.T. , and Brosch, R. (2004) ESAT-6 proteins: protective antigens and virulence factors? Trends Microbiol.12:500-508.

Cheung, J.K., Dupuy, B., Deveson, D.S, and Rood, J.I.(2004) The spatial organization of the VirR boxes is critical for VirR-mediated expression of the perfringolysin O gene, pfoA, from Clostridium perfringens. J. Bacteriol. 186: 3321-30.

Demangel, C., Brodin, P., Cockle, P.J., Brosch, R., Majlessi, L., Leclerc, C., and Cole S.T. (2004) Cell envelope protein PPE68 contributes to Mycobacterium tuberculosis RD1 immunogenicity independently of a 10-Kilodalton culture filtrate protein and ESAT-6. Infect Immun. 72:2170-6.

Demangel C, Brosch R, Marmiesse M, Cole ST. (2004) [Use of the mycobacteria genome to develop new vaccines and therapeutic targets] Med Trop 2004;64(3):221-3.

Jean, D., Briolat, V., and Reysset, G. (2004) Oxidative stress response in Clostridium perfringens. Microbiology 150: 1649-1659.

Hong H, Gates PJ, Staunton J, Stinear T, Cole ST, Leadlay PF, and Spencer JB. (2004). Identification using LC-MSn of co-metabolites in the biosynthesis of the polyketide toxin mycolactone by a clinical isolate of Mycobacterium ulcerans. Chem Comm . 22:2822-3.

Marmiesse, M., Brodin, P., Buchrieser, C., Gutierrez, C., Simoes, N., Vincent, V., Glaser, P., Cole, ST and Brosch, R. (2004) Macro-array and bioinformatic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex. Microbiology 150: 483 - 496., (pdf).

Marsollier, L., Severin, T., Aubry, J., Merritt, R.W., Saint Andre, J.P., Legras, P., Manceau, A.L, Chauty, A., Carbonnelle, B.,and Cole, S.T. (2004) Aquatic Snails, Passive Hosts of Mycobacterium ulcerans. Appl Environ Microbiol. 70: 6296-6298.

Marsollier, L., Stinear, T., Aubry, J., Saint Andre, J.P., Robert, R., Legras, P., Manceau, A.L., Audrain, C., Bourdon, S., Kouakou, H., and Carbonnelle, B. (2004) Aquatic plants stimulate the growth of and biofilm formation by Mycobacterium ulcerans in axenic culture and harbor these bacteria in the environment. Appl Environ Microbiol. 70: 1097-1103.

Raffestin, S., Marvaud, J.C., Cerrato, R., Dupuy, B. and Popoff, M .R. (2004).Organization and regulation of the neurotoxin genes in Clostridium botulinum and Clostridium tetani. Anaerobe 10: 93-100.

Spencer, J.S., Kim, H.J., Marques, A.M., Gonzalez-Juarerro, M., Lima, M.C., Vissa, V.D., Truman, R.W., Gennaro, M.L., Cho, S.N., Cole, S.T. and Brennan, P.J. (2004). Comparative analysis of B- and T-cell epitopes of Mycobacterium leprae and Mycobacterium tuberculosis culture filtrate protein 10. Infect Immun. 72: 3161-3170.

Stinear, T.P., Mve-Obiang, A., Small, P.L.C., Frigui, W., Pryor, M.J., Brosch, R., Jenkin, G.A., Johnson, P.D.R, Davies, J.K., Lee, R.E., Adusumilli, S., Garnier, T., Haydock, S.F., Leadlay, P.F., and Cole, S.T. (2004) Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans. Proc Natl Acad Sci U S A. 101: 1345-1349, (pdf).


Boitel, B., Ortiz-Lombardia, M., Duran, R., Pompeo, F., Cole, S.T., Cervenansky, C., and Alzari, P.M. (2003) PknB kinase activity is regulated by phosphorylation in two Thr residues and dephosphorylation by PstP, the cognate phospho-Ser/Thr phosphatase, in Mycobacterium tuberculosis. Mol Microbiol. 49:1493-1508.

Brosch, R., Marmiesse, M., and Cole, S.T.(2003) La genomique et le developpement de nouvelles strategies therapeutiques et preventives dans la lutte contre la tuberculose Medecine et Maladies Infectieuses 33, Suppl. 3, 141-146.

Garnier, T., Eiglmeier, K., Camus, J.C., Medina, N., Mansoor, H., Pryor, M., Duthoy, S., Grondin, S., Lacroix, C., Monsempe, C., Simon, S., Harris, B., Atkin, R., Doggett, J., Mayes, R., Keating, L., Wheeler, P.R., Parkhill, J., Barrell, B.G., Cole, S.T., Gordon, S.V., and Hewinson, R.G. (2003) The complete genome sequence of Mycobacterium bovis. Proc. Natl. Acad. Sci. U S A. 100: 7877-82, (fulltext).

Hong, H., Gates, P.J., Staunton, J., Stinear, T., Cole, S.T., Leadlay, P.F. and Spencer, J.B. (2003) Identification using LC-MSn of co-metabolites in the biosynthesis of the polyketide toxin mycolactone by a clinical isolate of Mycobacterium ulcerans. Chem Commun (Camb) 2822-3.

Karlsson, S., Dupuy, B., Mukherjee, K., Norin, E., Burman, L.G., and Akerlund, T. (2003) Expression of Clostridium difficile toxins A and B and their sigma factor TcdD is controlled by temperature. Infect Immun. 71:1784-93.

Kremer L, Dover LG, Morbidoni HR, Vilcheze C, Maughan WN, Baulard A, Tu SC, Honore N, Deretic V, Sacchettini JC, Locht C, Jacobs WR, Besra GS. (2003) Inhibition of InhA activity, but not KasA activity, induces formation of a KasA-containing complex in mycobacteria. J Biol Chem. 278:20547-54

Krutzik SR, Ochoa MT, Sieling PA, Uematsu S, Ng YW, Legaspi A, Liu PT, Cole ST, Godowski PJ, Maeda Y, Sarno EN, Norgard MV, Brennan PJ, Akira S, Rea TH, Modlin RL. (2003) Activation and regulation of Toll-like receptors 2 and 1 in human leprosy. Nat Med. 9:525-532

Majlessi L, Rojas MJ, Brodin P, Leclerc C. CD8+-T-cell responses of Mycobacterium-infected mice to a newly identified major histocompatibility complex class I-restricted epitope shared by proteins of the ESAT-6 family. Infect Immun.71:7173-7.

Marsollier, L., Honore, N., Legras, P., Manceau, A.L., Kouakou, H., Carbonnelle, B., and Cole ST.(2003) Isolation of three Mycobacterium ulcerans strains resistant to rifampin after experimental chemotherapy of mice. Antimicrob Agents Chemother. 47:1228-32.

Marsollier, L., Prevot, G., Honore, N., Legras, P., Manceau, A.L., Payan, C., Kouakou, H. and Carbonnelle, B. (2003) Susceptibility of Mycobacterium ulcerans to a combination of amikacin/rifampicin. Int J Antimicrob Agents 22: 562-6.

Pym, A.S., Brodin, P., Majlessi, L., Brosch, R., Demangel, C., Williams, A., Griffiths, K.E., Marchal, G., Leclerc, C., and S. T. Cole (2003) Recombinant BCG exporting ESAT-6 confers enhanced protection against tuberculosis Nat. Med. 9:533-539,(pdf), (related news and views-pdf).

Sola, C., Rastogi, N., Gutierrez, M.C., Vincent, V., Brosch, R., and Parsons, L.(2003) Is Mycobacterium africanum subtype II (Uganda I and Uganda II) a genetically well-defined subspecies of the Mycobacterium tuberculosis complex? J Clin Microbiol. 41:1345-6


Banu, S., Honore, N., Saint-Joanis, B., Philpott, D., Prevost, M.C, and Cole S.T. (2002) Are the PE-PGRS proteins of Mycobacterium tuberculosisvariable surface antigens? Mol Microbiol 44:9-19, (full-text).

Briolat, V, and Reysset, G.(2002)Identification of the Clostridium perfringensgenes involved in the adaptive response to oxidative stress.
J Bacteriol. 184:2333-2343 (full-text).

Brodin, P., Eiglmeier, K., Marmiesse, M., Billault, A., Garnier, T., Niemann, S., Cole, S.T., and Brosch, R. (2002) Bacterial Artificial Chromosome-Based Comparative Genomic Analysis Identifies Mycobacterium microtias a Natural ESAT-6 Deletion Mutant.
Infect Immun. 70:5568-5578. (fulltext), (pdf).

Brosch, R., Gordon, S.V., Marmiesse, M., Brodin, P., Buchrieser, C., Eiglmeier, K., Garnier, T., Gutierrez, C, Hewinson, G., Kremer, K., Parsons, L.M., Pym, A.S., Samper, S., van Soolingen, D., and Cole, S.T. (2002) A new evolutionary scenario for the Mycobacterium tuberculosiscomplex.
Proc Natl Acad Sci USA 99: 3684-3689.(pdf), (Supporting Table 1, Supporting Table 2).(Science-Editor's choice commentary).

Cole S. T. (2002). Comparative mycobacterial genomics as a tool for drug target and antigen discovery. Eur Resp J 20: 78-86, suppl..

Cole S. T. (2002). Comparative and functional genomics of the Mycobacterium tuberculosiscomplex. Microbiology 148: 2919-2928. (pdf).

Camus, J.C., Pryor M.J., Midigue C., and Cole, S.T. (2002). Re-annotation of the genome sequence of Mycobacterium tuberculosisH37Rv. Microbiology 148: 2967-2973. (pdf).

Domenech, P., Pym, A.S., Cellier, M., Barry, C.E. and Cole, S.T. (2002) Inactivation of the Mycobacterium tuberculosisNramp orthologue (mntH) does not affect virulence in a mouse model of tuberculosis. FEMS Microbiol Lett 207: 81-6 (pdf).

Gordon, S. V, Brosch, R., Eiglmeier, K., Garnier, T., Hewinson, R. G., Cole, S. T. (2002) Royal Society of Tropical Medicine and Hygiene Meeting at Manson House, London, 18th January 2001. Pathogen genomes and human health. Mycobacterial genomics.
Trans R Soc Trop Med Hyg. 96:1-6.

Honore N. (2002) [The Mycobacterium leprae genome: from sequence analysis to therapeutic implications] Med Trop 62:473-9.

Mani, N., Lyras, D., Barroso, L., Howarth, P., Wilkins, T., Rood, J. I., Sonenshein, A. L., and Dupuy, B. (2002) Environmental response and autoregulation of Clostridium difficileTxeR, a sigma factor for toxin gene expression. J Bacteriol. 184:5971-8, (pdf).

Parsons, L. M., Brosch, R., Cole, S. T., Somoskovi, A., Loder, A., Bretzel, G., Van Soolingen, D., Hale, Y. M., Salfinger, M. (2002) Rapid and Simple Approach for Identification of Mycobacterium tuberculosis Complex Isolates by PCR-Based Genomic Deletion Analysis.
J Clin Microbiol 40:2339-2345, (pdf).

Pym, A. S, Brodin, P., Brosch, R., Huerre, M., Cole, S. T. (2002) Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovisBCG and Mycobacterium microti.
Mol Microbiol 46:709-717, (full-text).

Pym, A.S., Saint-Joanis, B., and Cole S.T. (2002) Effect of katGMutations on the Virulence of Mycobacterium tuberculosisand the Implication for Transmission in Humans. Infect Immun. 70:4955-4960, (pdf).

Sinha, S., Arora, S., Kosalai, K., Namane, A., Pym, A.S., Cole, S.T. (2002) Proteome analysis of the plasma membrane of Mycobacterium tuberculosis Comp Funct Genom 3: 470-483 (pdf).


Brosch, R., Pym, A.S., Gordon, S.V., and Cole S.T. (2001) The evolution of mycobacterial pathogenicity: clues from comparative genomics.
Trends in Microbiology 9: 452-458. (fulltext), (pdf)

Cole, S.T., and Buchrieser, C. (2001) Bacterial genomics. A plague o' both your hosts. Nature 413:467, 469-70.

Cole, S.T., K. Eiglmeier, J. Parkhill, K. D. James, N. R. Thomson, P. R. Wheeler, N. Honore, T. Garnier, C. Churcher, D. Harris, K. Mungall, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. M. Davies, K. Devlin, S. Duthoy, T. Feltwell, A. Fraser, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, C. Lacroix, J. Maclean, S. Moule, L. Murphy, K. Oliver, M. A. Quail, M.-A. Rajandream, K. M. Rutherford, S. Rutter, K. Seeger, S. Simon, M. Simmonds, J. Skelton, R. Squares, S. Squares, K. Stevens, K. Taylor, S. Whitehead, J. R. Woodward & B. G. Barrell. (2001) Massive gene decay in the leprosy bacillus.
Nature, 409: 1007-1011.

Cole, S.T., Supply, P. and Honore. (2001) Repetitive sequences in Mycobacterium leprae and their impact on genome plasticity. Lepr Rev 72: 449-461 (pdf).

Domenech P., Barry C.E., Cole S.T.(2001) Mycobacterium tuberculosis in the post-genomic age. Curr Opin Microbiol. 4:28-34. (pdf)

Domenech, P., Honore, N., Heym, B. and Cole, S.T. (2001) Role of OxyS of Mycobacterium tuberculosis in oxidative stress: overexpression confers increased sensitivity to organic hydroperoxides. Microbes Infect 3: 713-21 (pdf)

Eiglmeier, K., Parkhill, J., Honori, N., Garnier, T., Tekaia, F., Telenti, A., Klatser, P., James, K.D., Thomson, N.R., Wheeler, P.R., Churcher, C., Harris, D., Mungall, K., Barrell, B.G. and Cole, S.T. (2001) The decaying genome of Mycobacterium leprae. Lepr Rev 72: 387-398 (pdf).

Eiglmeier, K., Simon, S., Garnier, T. and Cole, S.T. (2001) The integrated genome map of Mycobacterium leprae. Lepr Rev 72: 462-469 (pdf).

Gordon SV, Eiglmeier K, Garnier T, Brosch R, Parkhill J, Barrell B, Cole ST, and Hewinson RG (2001) Genomics of Mycobacterium bovis. Tuberculosis (Edinb) 2001 81:1-2 157-63

Grosset, J.H. and Cole, S.T. (2001) Genomics and the chemotherapy of leprosy. Lepr Rev 72: 429-440 (pdf).

Honore, N., Roche, P.W., Grosset, J.H. and Cole, S.T. (2001) A method for rapid detection of rifampicin-resistant isolates of Mycobacterium leprae. Lepr Rev 72: 441-448 (pdf).

Jones, L.M., Moszer, I. and Cole, S.T. (2001) Leproma: A Mycobacterium leprae genome browser. Lep Rev 72: 470-477 ( pdf).

Mani N, Dupuy B. (2001) Regulation of toxin synthesis in Clostridium difficile by an alternative RNA polymerase sigma factor. Proc Natl Acad Sci U S A 98:5844-9 .

Pym, A.S., Domenech, P., Honore, N., Song, J., Deretic, V., and Cole, S.T. (2001) Regulation of catalase-peroxidase (KatG) expression, isoniazid sensitivity and virulence by furA of Mycobacterium tuberculosis. Mol Microbiol. 40:879-889(HTML).

Sofia, M., Maniscalco, M., Honore, N., Molino, A., Mormile, M., Heym, B. and Cole, S.T. (2001) Familial outbreak of disseminated multidrug-resistant tuberculosis and meningitis. Int J Tuberc Lung Dis 5: 551-8.


Alape-Giron A, Flores-Diaz M, Guillouard I, Naylor CE, Titball RW, Rucavado A, Lomonte B, Basak AK, Gutierrez JM, Cole ST and M. Thelestam. (2000) Identification of residues critical for toxicity in Clostridium perfringens phospholipase C, the key toxin in gas gangrene. Eur. J. Biochem. 267:5191-97.

Banu S, Ohtani K, Yaguchi H, Swe T, Cole ST, Hayashi H, Shimizu T. (2000) Identification of novel VirR/VirS-regulated genes in Clostridium perfringens. Mol Microbiol. 35:854-64.

Brosch, R., Gordon, S.V., Buchrieser, C., Pym, A.S., Garnier, T., Cole S.T. (2000) Comparative genomics uncovers large tandem chromosomal duplications in Mycobacterium bovis BCG Pasteur. Comparative and Functional Genomics (Yeast) 17:111-123.(PDF).

Brosch, R., Gordon, S.V., Eiglmeier, K., Garnier, T., and Cole, S.T. (2000) Comparative genomics of the leprosy and tubercle bacilli.
Res. Microbiol. 151: 135-142. (pdf)

Brosch,R., Gordon, S.V., Pym, A., Eiglmeier, K., Garnier, T., and Cole S.T. (2000) Comparative genomics of the mycobacteria.
Int. J. Med. Microbiol. 290, 143-152., (PDF)

Cole ST, Honore N, Eiglmeier K (2000)Preliminary analysis of the genome sequence of Mycobacterium leprae. Lepr Rev. 71 Suppl:162-7.

Makui, H., Roig, E., Cole, S.T., Helmann, J.D., Gros, P., Cellier, M.F. (2000) Identification of the Escherichia coli K-12 Nramp orthologue (MntH) as a selective divalent metal ion transporter. Mol Microbiol. 35:1065-78., (pdf).

Pym, A.S. and Brosch, R. (2000) Tools for the Population Genomics of the Tubercle Bacilli. Genome Res. 10: 1837-1839.(full-text).

Roche PW, Shrestha N, Thomas A, Honore N, Cole ST (2000) Rapid detection of resistance to rifampicin in Mycobacterium leprae. Lepr Rev. 71, Suppl:96-99.

Trinh, S., Briolat, B. and Reysset, G. (2000) Growth response of Clostridium perfringens to oxidative stress. Anaerobe, 6:233-240.


Brosch, R., Philipp, W.J., Stavropoulos, E., Colston, M.J., Cole, S.T., and Gordon, S.V. (1999) Genomic analysis reveals variation between Mycobacterium tuberculosis H37Rv and the attenuated M. tuberculosis H37Ra strain.Infect. Immun. 67:5768-74 (HTML).

Cole, S.T. (1999) Learning from the genome sequence of Mycobacterium tuberculosis H37Rv. FEBS Letters 452, 7-10.

Gordon, S.V., Brosch, R., Billault, A., Garnier, T., Eiglmeier, K. and Cole, S.T. (1999) Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol. Microbiol. 32: 643-656..(HTML)

Gordon, S.V., Heym, B., Parkhill, J., Barrell, B. and Cole, S.T. (1999) New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv. Microbiology 145: 881-892. (PDF)

Heym B, Saint-Joanis B, Cole ST. (1999) The molecular basis of isoniazid resistance in Mycobacterium tuberculosis. Review. Tuber Lung Dis. 79:267-71.

Lichtinger, T., Heym, B., E., M., Eichner, H., Cole, S.T. and Benz, R. (1999) Evidence for a small anion-selective channel in the cell wall of Mycobacterium bovis BCG besides a wide cation-selective pore. FEBS Letters 454: 349-355.

Pym, A.S. and Cole, S.T. (1999) Post DOTS, post genomics: the next century of tuberculosis control. Lancet 353: 1004-1005.

Saint-Joanis, B., Souchon, H., Wilming, M., Johnsson, K., Alzari, P.M. and Cole, S.T. (1999) Use of site-directed mutagenesis to probe the structure, function and isoniazid activation of the catalase/peroxidase, KatG, from Mycobacterium tuberculosis. Biochem J 338: 753-760 (HTML).

Tekaia, F., Gordon, S.V., Garnier, T., Brosch, R., Barrell, B.G. and Cole, S.T. (1999) Analysis of the proteome of Mycobacterium tuberculosis in silico. Tubercle and Lung Disease 79: 329-342, (pdf).


Brosch, R., Gordon, S.V., Billault, A., Garnier, T., Eiglmeier, K., Soravito, C., Barrell, B.G. and Cole, S.T. (1998) Use of a Mycobacterium tuberculosis H37Rv Bacterial Artificial Chromosome (BAC) library for genome mapping, sequencing and comparative genomics.
Infect. Immun. 66: 2221-2229(PDF).

Buchrieser, C., Brosch, R., Bach, S., Guiyoule, A., Carniel, E. (1998) The high-pathogenicity island of Yersinia pseudotuberculosis can be inserted into any of the three chromosomal asn tRNA genes. Mol Microbiol. 30:965-78(HTML)

Cole, S.T. (1998) Comparative mycobacterial genomics. Curr. Opin. Microbiol. 1: 567-581.

Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S.V., Eiglmeier, K., Gas, S., Barry, C.E., III, Tekaia, F., Badcock, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R., Devlin, K., Feltwell, T., Gentles, S., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K., Krogh, A., McLean, A., Moule, S., Murphy, L., Oliver, K., Osborne, J., Quail, M.A., Rajandream, M.-A., Rogers, J., Rutter, S., Seeger, K., Skelton, J., Squares, R., Squares, S., Sulston, J.E., Taylor, K., Whitehead, S. and Barrell, B.G. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
Nature 393: 537-544. (fulltext), (pdf).

Dupuy, B. and Sonenshein, A.L. (1998) Regulated transcription of Clostridium difficile toxin genes. Mol. Microbiol. 27: 107-20.(HTML)

Flores-Diaz, M., Alape-Giron, A., Titball, R.W., Moos, M., Guillouard, I., Cole, S., Howells, A.M., von Eichel-Streiber, C., Florin, I. and Thelestam, M. (1998) UDP-glucose deficiency causes hypersensitivity to the cytotoxic effect of Clostridium perfringens phospholipase C. J Biol Chem 273: 24433-24438.

Philipp, W., Schwartz, D.C., Telenti, A. and Cole, S.T. (1998) Mycobacterial genome structure. Electrophoresis 19: 573-576.

Silbaq, F.S., Cho, S.N., Cole, S.T. and Brennan, P.J. (1998) Characterization of a 34-kilodalton protein of Mycobacterium leprae that is isologous to the immunodominant 34-kilodalton antigen of Mycobacterium paratuberculosis. Infect Immun 66: 5576-5579..(HTML).

Trinh, S. and Reysset, G. (1998) Mutagenic action of 5-nitroimidazoles: in vivo induction of GC-->CG. Mutation Research 398: 55-65.

Book chapters


de Jonge, M.I., Stinear, T.P., Cole, S.T., and Brosch, R. (2007) The Mycobacteria: a Postgenomic View. In Bacterial Pathogenomics. Pallen, M.J., Nelson, K.E., and Preston, G.M. (eds). . ASM Press, Washington DC, USA, pp. 49-89.


Pym, A.S., Gordon, S.V. and Brosch, R. (2006) Pathogenomics: Insighst in to Tuberculosis and related mycobacterial diseases. In Pathogenomics: Genome analysis of pathogenic microbes. Hacker, J. and Dobrindt, U. (eds). Weinheim: WILEY-VCH, pp. 211-230.

Vincent, V., Gutierrez, M.C.,and Brosch, R. (2006). Genomics and evolution of the tubercle bacilli. In Series: Lung Biology in Health and Disease Volume: 219, Reichman and Hershfield's Tuberculosis: A Comprehensive International Approach, Third Edition. M.C. Raviglione (Ed).


Brodin, P., Demangel, C., and Cole, S.T.(2005) Introduction to functional genomics of the Mycobacterium tuberculosis com plex. In Tuberculosis and the Tubercle Bacillus; Cole , S.T. Eisenach, K.D., McMurray, D.N. and Jacobs W.R., Jr. (eds), ASM Press, Washington DC, USA. pp143-153.

Brosch, R. and Behr, M.A. (2005) Comparative genomics and evolution of Mycobacterium bovis BCG. In Tuberculosis and the Tubercle Bacillus; Cole, S. T. Eisenach, K.D., McMurray, D.N. and Jacobs W.R., Jr. (eds), ASM Press, Washington DC, USA. pp 155-164.

Gordon, S.V. and Brosch, R. (2005) Genomics of the Mycobcacterium tuberculo sis complex and Mycobacterium leprae. In Encyclopedia of Genetics, Genomics, Pro teomics and Bioinformatics. Dunn M.J., Jorde L.B., Little P.F.R., and Subramani am S. (eds). Volume 3,Chapter 5 : Bacteria and other pathogens, Wiley.

Sonenshein, A. L., J. D. Haraldsen, and B. Dupuy (2005) RNA polymerase and alternative sigma factors, pp. 607-629. In: P. Duerre (ed.), Handbook on Clostridia, CRC Press, Boca Raton, FL


Bentley, S.D., Brosch, R., Gordon, S.V., Hopwood D.A. and Cole S.T.(2004) Genomics of Actinobacteria, the High G+C of Gram-Postive Bacteria. In Part IV: T he Evolution of Microbial Genomes, Microbial Genomes, Fraser, C.M., Read, T, and Nelson, K.E. (eds). pp. 333-360 Humana Press Inc., pp.

Dupuy, B., Deghmane, A.E., and Taha, M.K. (2004) Type IV prepilin peptidase . In Handbook of Proteolytic Enzymes 2nd edition, Elsevier Ldt.

Expertise collective(2004) Tuberculose : Place de la vaccination dans la mantrise de la maladie. Les editions INSERM. Institut National de la Santi et de la Recherche Midicale. Full Document


Brosch, R., Banu, S. and Cole, S.T. (2003) Comparative genomics of the Mycobacterium tuberculosis complex: Evolutionary insights and applications. In Tuberculosis Second Edition. Rom, W.N. and Garay, S. (eds). Philadelphia: Lippincot Williams & Wilkins, pp. 65-73.

Buchrieser, C. and Brosch, R. (2003) Vergleichende Genomforschung: Neue Einsichten in Biologie, Pathogenitaet und Evolution, am Beispiel von Listerien u nd Mykobakterien. In: Infektiologie-Aktuelle Aspekte. Jahrbuch 2003-2004. Janata , O. and Reisinger, E. (eds). pm-Verlag, Austria, pp. 165-179, 399-403.


Camus, J.-C., Moszer, I., Jones, L.M., Pryor, M.J. and Cole, S.T. (2002) TubercuList: a regularly updated database dedicated to the Mycobacterium tuberculosis genome. In Genomics of GC-rich Gram-positive bacteria. Danchin, A. (eds). Wymondham, UK: Caister Academic Press, pp. 159-176.

Pym, A.S. and Cole, S.T. (2002) Tuberculosis chemotherapy - from concept ion to genomics. In Bacterial Resistance to Antimicrobials: Mechanisms, Genetics , Medical Practice and Public Health. Wax, R., Lewis, K., Salyers, A. and Taber, H. (eds). New York: Marcel Dekker, Inc., pp. 355-403.


Brosch, R., Gordon, S.V., Eiglmeier, K., Garnier, T., Tekaia, F, Yeramian, E. , and Cole, S.T.: (2000) Genomics, Biology, and Evolution of the Mycobac terium tuberculosis Complex. In: Molecular Genetics of Mycobacteria. Hatfull , F., and Jacobs, W.R. Jr., (eds). Washington DC: American Society for Microbiology, pp. 19-36.


Cole, S.T. and Saint-Girons, I. (1999) Bacterial genomes - all shapes an d sizes. In: Organization of the prokaryotic genome. Charlebois, R.L. (eds). Was hington DC: American Society for Microbiology, pp. 35-62.

Gordon, S.V., Eiglmeier, K., Brosch, R., Garnier, T., Honori, N., Barrell, B. G. and Cole, S.T. (1999) Genomics of Mycobacterium tuberculosis and Mycobact erium leprae. In Mycobacteria: Molecular biology and virulence. Ratledge, C. and Dale, J.W. (eds). Oxford: Blackwell Science, pp. 93-109.


Bergh, S. and Cole, S.T. (1998) Using MycDB on the World-Wide Web. In Mycobacteria protocols. Parish, T. and Stoker, N.G. (eds). Totowa, NJ: Humana Press Inc., pp. 109-118.

Cole, S.T. and Barrell, B.G. (1998) Analysis of the genome of Mycobacterium tuberculosis H37Rv. In Genetics and tuberculosis (Novartis Foundation Symposium 217). Chadwick, D.J. and Gardew, G. (eds). Chichester: J. Wiley, pp. 160-172.

Philipp, W.J., Gordon, S., Telenti, A. and Cole, S.T. (1998) Pulsed field gel electrophoresis for mycobacteria. In Mycobacteria protocols. Parish, T. and Stoker, N.G. (eds). Totowa, NJ: Humana Press Inc., pp. 51-63.

Telenti, A., Honoré, N. and Cole, S.T. (1998) Detection of mutations in mycobacteria by PCR-SSCP (Single-strand conformation polymorphism). In Mycobacteria protocols. Parish, T. and Stoker, N.G. (eds). Totowa, NJ: Humana Press Inc., pp. 423-430.

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