B. Abela-ridder, R. Sikkema, and R. A. Hartskeerl, Estimating the burden of human leptospirosis, Int J Antimicrob Agents, vol.36, issue.1, pp.5-7, 2010.
DOI : 10.1016/j.ijantimicag.2010.06.012

M. Picardeau, D. M. Bulach, C. Bouchier, R. L. Zuerner, N. Zidane et al., Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis, PLoS One, vol.3, 2008.

B. Adler, History of leptospirosis and Leptospira, Curr Top Microbiol Immunol, vol.387, pp.1-9, 2015.
DOI : 10.1007/978-3-662-45059-8_1

J. S. Lehmann, M. A. Matthias, J. M. Vinetz, and D. E. Fouts, Leptospiral pathogenomics. Pathogens, vol.3, pp.280-308, 2014.

S. Faine, B. Adler, C. Bolin, and P. Perolat, Leptospira and leptospirosis, 1999.

L. Hall-stoodley and P. Stoodley, Biofilm formation and dispersal and the transmission of human pathogens, Trends Microbiol, vol.13, pp.7-10, 2005.

M. Güell, E. Yus, M. Lluch-senar, and L. Serrano, Bacterial transcriptomics: what is beyond the RNA horizome?, Nat Rev Microbiol, vol.9, pp.658-669, 2011.

A. Dötsch, D. Eckweiler, M. Schniederjans, A. Zimmermann, V. Jensen et al., The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing, PLoS One, vol.7, 2012.

S. A. Frese, D. A. Mackenzie, D. A. Peterson, R. Schmaltz, T. Fangman et al., Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont, PLoS Genet, vol.9, 2013.

S. Rumbo-feal, M. J. Gómez, C. Gayoso, L. Álvarez-fraga, M. P. Cabral et al., Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells, PLoS One, vol.8, p.72968, 2013.

P. Ristow, P. Bourhy, S. Kerneis, C. Schmitt, M. C. Prevost et al., Biofilm formation by saprophytic and pathogenic leptospires, Microbiology, vol.154, pp.1309-1317, 2008.

B. Brihuega, L. Samartino, C. Auteri, A. Venzano, and K. Caimi, In vivo cell aggregations of a recent swine biofilm-forming isolate of Leptospira interrogans strain from Argentina, Rev Argent Microbiol, vol.44, pp.138-143, 2012.

B. J. Haas, M. Chin, C. Nusbaum, B. W. Birren, and J. Livny, How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?, BMC Genomics, vol.13, p.734, 2012.

G. Nucifora, L. Chu, S. Silver, and T. K. Misra, Mercury operon regulation by the merR gene of the organomercurial resistance system of plasmid pDU1358, J Bacteriol, vol.171, pp.4241-4247, 1989.

J. L. Hobman, MerR family transcription activators: similar designs, different specificities, Mol Microbiol, vol.63, pp.1275-1278, 2007.

J. U. Kreft, Biofilms promote altruism. Microbiology, vol.150, pp.2751-2760, 2004.

E. Aizenman, H. Engelberg-kulka, and G. Glaser, An Escherichia coli chromosomal "addiction module" regulated by guanosine 3=,5=bispyrophosphate: a model for programmed bacterial cell death, Proc Natl Acad Sci U S A, vol.93, pp.6059-6063, 1996.

K. Pedersen, S. K. Christensen, and K. Gerdes, Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins, Mol Microbiol, vol.45, pp.501-510, 2002.

S. Karlin, J. Mrázek, A. Campbell, and D. Kaiser, Characterizations of highly expressed genes of four fast-growing bacteria, J Bacteriol, vol.183, pp.5025-5040, 2001.

M. D. Bradley, M. B. Beach, A. P. De-koning, T. S. Pratt, and R. Osuna, Effects of Fis on Escherichia coli gene expression during different growth stages, Microbiology, vol.153, pp.2922-2940, 2007.

N. W. Charon, G. R. Daughtry, R. S. Mccuskey, and G. N. Franz, Microcinematographic analysis of tethered Leptospira illini, J Bacteriol, vol.160, pp.1067-1073, 1984.

X. Fang and M. Gomelsky, A post-translational, c-di-GMP-dependent mechanism regulating flagellar motility, Mol Microbiol, vol.76, pp.1295-1305, 2010.

M. Merighi, V. T. Lee, M. Hyodo, Y. Hayakawa, and S. Lory, The second messenger bis-(3=-5=)-cyclic-GMP and its PilZ domain-containing receptor Alg44 are required for alginate biosynthesis in Pseudomonas aerugi, 2007.

, Mol Microbiol, vol.65, pp.876-895

Z. H. Li, K. Dong, J. P. Yuan, B. Y. Hu, J. X. Liu et al., Characterization of the cheY genes from Leptospira interrogans and their effects on the behaviour of Escherichia coli, Biochem Biophys Res Commun, vol.345, pp.858-866, 2006.

M. Picardeau and A. Brenot, First evidence for gene replacement in Leptospira spp. Inactivation of L. biflexa flaB results in non-motile mutants deficient in endoflagella, Mol Microbiol, vol.40, pp.189-199, 2001.

A. Lambert, M. Picardeau, D. A. Haake, R. W. Sermswan, A. Srikram et al., FlaA proteins in Leptospira interrogans are essential for motility and virulence but are not required for formation of the flagellum sheath, Infect Immun, vol.80, pp.2019-2025, 2012.

M. Pinne and D. A. Haake, A comprehensive approach to identification of surface-exposed, outer membrane-spanning proteins of Leptospira interrogans, PLoS One, vol.4, p.6071, 2009.

D. A. Haake, M. K. Mazel, A. M. Mccoy, F. Milward, G. Chao et al., Leptospiral outer membrane proteins OmpL1 and LipL41 exhibit synergistic immunoprotection, Infect Immun, vol.67, pp.6572-6582, 1999.

L. G. Fernandes, M. L. Vieira, K. Kirchgatter, I. J. Alves, Z. M. De-morais et al., OmpL1 is an extracellular matrix-and plasminogen-interacting protein of Leptospira spp, Infect Immun, vol.80, pp.3679-3692, 2012.

R. Orme, C. W. Douglas, S. Rimmer, and M. Webb, Proteomic analysis of Escherichia coli biofilms reveals the overexpression of the outer membrane protein OmpA, Proteomics, vol.6, pp.4269-4277, 2006.

P. A. Cullen, D. A. Haake, D. M. Bulach, R. L. Zuerner, and B. Adler, LipL21 is a novel surface-exposed lipoprotein of pathogenic Leptospira species, Infect Immun, vol.71, pp.2414-2421, 2003.

J. E. Nally, J. P. Whitelegge, S. Bassilian, D. R. Blanco, and M. A. Lovett, Characterization of the outer membrane proteome of Leptospira interrogans expressed during acute lethal infection, Infect Immun, vol.75, pp.766-773, 2007.

C. Robichon, D. Vidal-ingigliardi, and A. P. Pugsley, Depletion of apolipoprotein N-acyltransferase causes mislocalization of outer membrane lipoproteins in Escherichia coli, J Biol Chem, vol.280, pp.974-983, 2005.

M. Moreno-paz, M. J. Gómez, A. Arcas, and V. Parro, Environmental transcriptome analysis reveals physiological differences between biofilm and planktonic modes of life of the iron oxidizing bacteria Leptospirillum spp. in their natural microbial community, BMC Genomics, vol.11, p.404, 2010.

Y. Chai, P. B. Beauregard, H. Vlamakis, R. Losick, and R. Kolter, Galactose metabolism plays a crucial role in biofilm formation by Bacillus subtilis, vol.3, pp.184-196, 2012.

T. Taniyama, Y. Yanagihara, I. Mifuchi, I. Azuma, and Y. Yamamura, Purification of polysaccharide antigen from Leptospira biflexa strain Urawa, Infect Immun, vol.6, pp.414-415, 1972.

D. M. Bulach, T. Kalambaheti, A. De-la-peña-moctezuma, and B. Adler, Functional analysis of genes in the rfb locus of Leptospira borgpetersenii serovar Hardjo subtype Hardjobovis, Infect Immun, vol.68, pp.3793-3798, 2000.

C. Whitfield, Biosynthesis of lipopolysaccharide O antigens, Trends Microbiol, vol.3, pp.88917-88926, 1995.

M. Timke, D. Wolking, N. Q. Wang-lieu, K. Altendorf, and A. Lipski, Microbial composition of biofilms in a brewery investigated by fatty acid analysis, 2004.

, Appl Microbiol Biotechnol, vol.66, pp.100-107

C. Theilacker, P. Sanchez-carballo, T. I. Fabretti, F. Sava, I. Kropec et al., Glycolipids are involved in biofilm accumulation and prolonged bacteraemia in Enterococcus faecalis, Mol Microbiol, vol.71, pp.1055-1069, 2009.

L. Bruno, D. Pippo, F. Antonaroli, S. Gismondi, A. Valentini et al., Characterization of biofilm-forming cyanobacteria for biomass and lipid production, J Appl Microbiol, vol.113, pp.1052-1064, 2012.

L. M. Purish, L. G. Asaulenko, D. R. Abdulina, V. N. Vasil'ev, and G. A. Iutinskaia, Role of polymer complexes in the formation of biofilms by corrosive bacteria on steel surfaces, Prikl Biokhim Mikrobiol, vol.48, pp.294-301, 2012.

H. Louvel, S. Bommezzadri, N. Zidane, C. Boursaux-eude, S. Creno et al., Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp, J Bacteriol, vol.188, pp.7893-7904, 2006.

C. L. Stallings, N. C. Stephanou, L. Chu, A. Hochschild, B. E. Nickels et al., CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence, Cell, vol.138, pp.146-159, 2009.

F. H. Yildiz and G. K. Schoolnik, Role of rpoS in stress survival and virulence of Vibrio cholerae, J Bacteriol, vol.180, pp.773-784, 1998.

K. Yamanaka and M. Inouye, Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli, J Bacteriol, vol.183, pp.2808-2816, 2001.

M. Ochs, S. Veitinger, I. Kim, D. Welz, A. Angerer et al., Regulation of citrate-dependent iron transport of Escherichia coli: fecR is required for transcription activation by FecI, Mol Microbiol, vol.15, pp.119-132, 1995.

S. Gottesman and G. Storz, Bacterial small RNA regulators: versatile roles and rapidly evolving variations, Cold Spring Harb Perspect Biol, vol.3, 2011.

M. J. Caimano, S. K. Sivasankaran, A. Allard, D. Hurley, K. Hokamp et al., A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by Leptospira interrogans serovar Copenhageni, PLoS Pathog, vol.10, 2014.

. R-core-team, R: a language and environment for statistical computing. R Foundation for Statistical Computing, 2014.

Y. Liao, G. K. Smyth, and W. Shi, The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote, Nucleic Acids Res, vol.41, 2013.

M. D. Robinson, D. J. Mccarthy, and G. K. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, pp.139-140, 2010.

M. J. Cros, A. De-monte, J. Mariette, P. Bardou, B. Grenier-boley et al., RNAspace.org: an integrated environment for the prediction, annotation, and analysis of ncRNA, RNA, vol.17, pp.1947-1956, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00642716

P. R. Kulkarni, X. Cui, J. W. Williams, A. M. Stevens, and R. V. Kulkarni, Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri, Nucleic Acids Res, vol.34, pp.3361-3369, 2006.

J. Söding, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, pp.951-960, 2005.

M. Remmert, A. Biegert, A. Hauser, and J. Söding, HHblits: lightningfast iterative protein sequence searching by HMM-HMM alignment, Nat Methods, vol.9, pp.173-175, 2012.
DOI : 10.1038/nmeth.1818
URL : http://pubman.mpdl.mpg.de/pubman/item/escidoc:1944218/component/escidoc:1945401/1944218.pdf

G. Csardi and T. Nepusz, The igraph software package for complex network research. InterJournal Complex Systems 1695, 2006.

A. J. Baümler and K. Hantke, Ferrioxamine uptake in Yersinia enterocolitica: characterization of the receptor protein FoxA, Mol Microbiol, vol.6, pp.1309-1321, 1992.

S. F. Rouf, I. Ahmad, N. Anwar, S. K. Vodnala, A. Kader et al., Opposing contributions of polynucleotide phosphorylase and the membrane protein NlpI to biofilm formation by Salmonella enterica serovar Typhimurium, J Bacteriol, vol.193, pp.580-582, 2011.