M. Van-deuren, P. Brandtzaeg, and J. Van-der-meer, Update on Meningococcal Disease with Emphasis on Pathogenesis and Clinical Management, Clinical Microbiology Reviews, vol.13, issue.1, pp.144-166, 2000.
DOI : 10.1128/CMR.13.1.144-166.2000

A. Jamet, C. Rousseau, J. Monfort, E. Frapy, X. Nassif et al., A two-component system is required for colonization of host cells by meningococcus, Microbiology, vol.155, issue.7, pp.2288-2295, 2009.
DOI : 10.1099/mic.0.027755-0

T. Mendum, J. Newcombe, A. Mannan, A. Kierzek, and J. Mcfadden, Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera, Genome Biology, vol.12, issue.12, 2011.
DOI : 10.1093/nar/28.1.27

J. Laver, S. Hughes, and R. Read, Neisserial Molecular Adaptations to the Nasopharyngeal Niche, Adv Microb Physiol, vol.66, pp.323-355, 2015.
DOI : 10.1016/bs.ampbs.2015.05.001

E. Loh, E. Kugelberg, A. Tracy, Q. Zhang, B. Gollan et al., Temperature triggers immune evasion by Neisseria meningitidis, Nature, vol.110, issue.7470, pp.237-240, 2013.
DOI : 10.1038/nature12616

J. Edwards, L. Cole, J. Green, M. Thomson, A. Wood et al., Binding to DNA Protects Neisseria meningitidis Fumarate and Nitrate Reductase Regulator (FNR) from Oxygen, Journal of Biological Chemistry, vol.285, issue.2, pp.1105-1112, 2010.
DOI : 10.1074/jbc.M109.057810

D. Stephens, L. Hoffman, and Z. Mcgee, Interaction of Neisseria meningitidis with Human Nasopharyngeal Mucosa: Attachment and Entry into Columnar Epithelial Cells, Journal of Infectious Diseases, vol.148, issue.3, pp.369-376, 1983.
DOI : 10.1093/infdis/148.3.369

B. Pron, M. Taha, C. Rambaud, J. Fournet, N. Pattey et al., with the Components of the Blood???Brain Barrier Correlates with an Increased Expression of PilC, The Journal of Infectious Diseases, vol.176, issue.5, pp.1285-1292, 1997.
DOI : 10.1086/514124

K. Trivedi, C. Tang, and R. Exley, Mechanisms of meningococcal colonisation, Trends in Microbiology, vol.19, issue.9, pp.456-463, 2011.
DOI : 10.1016/j.tim.2011.06.006

A. Goodman, N. Mcnulty, Y. Zhao, D. Leip, R. Mitra et al., Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat, Cell Host & Microbe, vol.6, issue.3, pp.279-289, 2009.
DOI : 10.1016/j.chom.2009.08.003

C. Remmele, Y. Xian, M. Albrecht, M. Faulstich, M. Fraunholz et al., Transcriptional landscape and essential genes of Neisseria gonorrhoeae, Nucleic Acids Research, vol.42, issue.16, pp.10579-10595, 2014.
DOI : 10.1093/nar/gku762

A. Jamet, D. Euphrasie, P. Martin, and X. Nassif, Identification of Genes Involved in Neisseria meningitidis Colonization, Infection and Immunity, vol.81, issue.9, pp.3375-3381, 2013.
DOI : 10.1128/IAI.00421-13

A. Zomer, P. Burghout, H. Bootsma, P. Hermans, and S. Van-hijum, ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data, PLoS ONE, vol.7, issue.8, 2012.
DOI : 10.1371/journal.pone.0043012.s003

J. Zilsel, P. Ma, and J. Beatty, Derivation of a mathematical expression useful for the construction of complete genomic libraries, Gene, vol.120, issue.1, pp.89-920378, 1992.
DOI : 10.1016/0378-1119(92)90013-F

S. Wong and B. Akerley, Identification and Analysis of Essential Genes in Haemophilus influenzae, Methods Mol Biol, vol.416, pp.27-44978, 2008.
DOI : 10.1007/978-1-59745-321-9_3

T. Van-opijnen, K. Bodi, and A. Camilli, Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms, Nature Methods, vol.416, issue.10, pp.767-772, 2009.
DOI : 10.1101/gr.1239303

B. Christen, E. Abeliuk, J. Collier, V. Kalogeraki, B. Passarelli et al., The essential genome of a bacterium, Molecular Systems Biology, vol.7, issue.1, p.528, 2011.
DOI : 10.1038/nmeth.1377

L. Fagnocchi, S. Bottini, G. Golfieri, L. Fantappiè, F. Ferlicca et al., Global Transcriptome Analysis Reveals Small RNAs Affecting Neisseria meningitidis Bacteremia, PLOS ONE, vol.504, issue.5, 2015.
DOI : 10.1371/journal.pone.0126325.s010

J. Parkhill, M. Achtman, K. James, S. Bentley, C. Churcher et al., Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491, Nature, vol.404, issue.6777, pp.502-506, 2000.
DOI : 10.1038/35006655

G. Baart, M. Langenhof, B. Van-de-waterbeemd, H. Hamstra, B. Zomer et al., Expression of phosphofructokinase in Neisseria meningitidis, Microbiology, vol.156, issue.2, pp.530-542, 2010.
DOI : 10.1099/mic.0.031641-0

B. Lundberg, R. Wolf, M. Dinauer, Y. Xu, and F. Fang, Glucose 6-phosphate dehydrogenase is required for Salmonella typhimurium virulence and resistance to reactive oxygen and nitrogen intermediates, Infect Immun, vol.67, pp.436-438, 1999.

J. Rock, M. Mahnane, M. Anjum, J. Shaw, R. Read et al., requires oxygen, but supplements growth by denitrification. Nitrite, nitric oxide and oxygen control respiratory flux at genetic and metabolic levels, Molecular Microbiology, vol.169, issue.3, pp.800-809, 2005.
DOI : 10.1111/j.1365-2958.2005.04866.x

F. Mackinnon, R. Borrow, A. Gorringe, A. Fox, D. Jones et al., Demonstration of lipooligosaccharide immunotype and capsule as virulence factors for Neisseria meningitidis using an infant mouse intranasal infection model, Microbial Pathogenesis, vol.15, issue.5, pp.359-366, 1993.
DOI : 10.1006/mpat.1993.1085

C. Kahler, L. Martin, G. Shih, M. Rahman, R. Carlson et al., The (2¡8)-linked polysialic acid capsule and lipooligosaccharide structure both contribute to the ability of serogroup B Neisseria meningitidis to resist the bactericidal activity of normal human serum, Infect Immun, vol.66, pp.5939-5947, 1998.

J. Hoch, Two-component and phosphorelay signal transduction, Current Opinion in Microbiology, vol.3, issue.2, pp.165-170, 2000.
DOI : 10.1016/S1369-5274(00)00070-9

P. Kumar, S. Sannigrahi, J. Scoullar, C. Kahler, and Y. Tzeng, Characterization of DsbD in Neisseria meningitidis, Molecular Microbiology, vol.78, issue.6, pp.1557-1573, 2011.
DOI : 10.1111/j.1365-2958.2011.07546.x

A. Jamet, A. Jousset, D. Euphrasie, P. Mukorako, A. Boucharlat et al., A New Family of Secreted Toxins in Pathogenic Neisseria Species, PLoS Pathogens, vol.55, issue.(2), 2015.
DOI : 10.1371/journal.ppat.1004592.s010

J. Arenas, V. De-maat, L. Catón, M. Krekorian, J. Herrero et al., Fratricide activity of MafB protein of N. meningitidis strain B16B6, BMC Microbiology, vol.134, issue.1, pp.156-12866, 2015.
DOI : 10.1186/s12866-015-0493-6

S. Tunio, N. Oldfield, D. Ala-'aldeen, K. Wooldridge, and D. Turner, The role of glyceraldehyde 3-phosphate dehydrogenase (GapA-1) in Neisseria meningitidis adherence to human cells, BMC Microbiology, vol.10, issue.1, p.280, 2010.
DOI : 10.1186/1471-2180-10-280

J. Deutscher, F. Aké, M. Derkaoui, A. Zébré, T. Cao et al., The Bacterial Phosphoenolpyruvate:Carbohydrate Phosphotransferase System: Regulation by Protein Phosphorylation and Phosphorylation-Dependent Protein-Protein Interactions, Microbiology and Molecular Biology Reviews, vol.78, issue.2, pp.231-256, 2014.
DOI : 10.1128/MMBR.00001-14

URL : https://hal.archives-ouvertes.fr/hal-01204432

G. Baart, B. Zomer, A. De-haan, L. Van-der-pol, E. Beuvery et al., Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes, Genome Biology, vol.8, issue.7, 2007.
DOI : 10.1186/gb-2007-8-7-r136

B. Kather, K. Stingl, M. Van-der-rest, K. Altendorf, and D. Molenaar, Another Unusual Type of Citric Acid Cycle Enzyme in Helicobacter pylori: the Malate:Quinone Oxidoreductase, Journal of Bacteriology, vol.182, issue.11, pp.3204-3209, 2000.
DOI : 10.1128/JB.182.11.3204-3209.2000

M. Jennings, P. Van-der-ley, K. Wilks, D. Maskell, J. Poolman et al., Cloning and molecular analysis of the galE gene of Neisseria meningitidis and its role in lipopolysaccharide biosynthesis. Mol M i c r o b i o l 1 0 : 3 6 1 ? 3 6 9, 1993.

W. Veal, R. Nicholas, and W. Shafer, Overexpression of the MtrC-MtrD-MtrE Efflux Pump Due to an mtrR Mutation Is Required for Chromosomally Mediated Penicillin Resistance in Neisseria gonorrhoeae, Journal of Bacteriology, vol.184, issue.20, pp.5619-5624, 2002.
DOI : 10.1128/JB.184.20.5619-5624.2002

W. Shafer, X. Qu, A. Waring, and R. Lehrer, Modulation of Neisseria gonorrhoeae susceptibility to vertebrate antibacterial peptides due to a member of the resistance/nodulation/division efflux pump family, Proceedings of the National Academy of Sciences, vol.95, issue.4, pp.1829-1833, 1998.
DOI : 10.1073/pnas.95.4.1829

R. Mcclure, B. Tjaden, and C. Genco, Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions, Frontiers in Microbiology, vol.31, p.456, 2014.
DOI : 10.1093/nar/gkg595

D. Tordello, E. Bottini, S. Muzzi, A. Serruto, and D. , Analysis of the Regulated Transcriptome of Neisseria meningitidis in Human Blood Using a Tiling Array, Journal of Bacteriology, vol.194, issue.22, pp.6217-623201055, 2012.
DOI : 10.1128/JB.01055-12

D. Perkins-balding, M. Ratliff-griffin, and I. Stojiljkovic, Iron Transport Systems in Neisseria meningitidis, Microbiology and Molecular Biology Reviews, vol.68, issue.1, pp.154-171, 2004.
DOI : 10.1128/MMBR.68.1.154-171.2004

F. Biville, C. Brézillon, D. Giorgini, and M. Taha, Pyrophosphatemediated iron acquisition from transferrin in Neisseria meningitidis does not require TonB activity, PLoS One, vol.9, 2014.

I. Stojiljkovic and N. Srinivasan, Neisseria meningitidis tonB, exbB, and exbD genes: Ton-dependent utilization of protein-bound iron in Neisseriae., Journal of Bacteriology, vol.179, issue.3, pp.805-812, 1997.
DOI : 10.1128/jb.179.3.805-812.1997

Y. Sun, S. Bakshi, R. Chalmers, and C. Tang, Functional genomics of Neisseria meningitidis pathogenesis, Nat Med, vol.6, pp.1269-1273, 2000.

R. Zhang and Y. Lin, DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes, Nucleic Acids Research, vol.37, issue.Database, pp.455-458, 2009.
DOI : 10.1093/nar/gkn858

S. Gerdes, M. Scholle, J. Campbell, G. Balázsi, E. Ravasz et al., Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655, Journal of Bacteriology, vol.185, issue.19, pp.5673-5684, 2003.
DOI : 10.1128/JB.185.19.5673-5684.2003

B. Akerley, E. Rubin, V. Novick, K. Amaya, N. Judson et al., A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae, Proceedings of the National Academy of Sciences, vol.99, issue.2, pp.966-971, 2002.
DOI : 10.1073/pnas.012602299

K. Turner, A. Wessel, G. Palmer, J. Murray, and M. Whiteley, Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum, 2015.

G. Langridge, M. Phan, D. Turner, T. Perkins, L. Parts et al., Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants, Genome Research, vol.19, issue.12, pp.2308-2316, 2009.
DOI : 10.1101/gr.097097.109

C. Rusniok, D. Vallenet, S. Floquet, H. Ewles, C. Mouzé-soulama et al., NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis, Genome Biology, vol.10, issue.10, 2009.
DOI : 10.1186/gb-2009-10-10-r110

URL : https://hal.archives-ouvertes.fr/pasteur-00663857

I. Delany, R. Ieva, C. Alaimo, R. Rappuoli, and V. Scarlato, The Iron-Responsive Regulator Fur Is Transcriptionally Autoregulated and Not Essential in Neisseria meningitidis, Journal of Bacteriology, vol.185, issue.20, pp.6032-6041, 2003.
DOI : 10.1128/JB.185.20.6032-6041.2003

R. Gil, F. Silva, J. Peretó, and A. Moya, Determination of the Core of a Minimal Bacterial Gene Set, Microbiology and Molecular Biology Reviews, vol.68, issue.3, pp.518-537518, 2004.
DOI : 10.1128/MMBR.68.3.518-537.2004

D. Vallenet, L. Labarre, Z. Rouy, V. Barbe, S. Bocs et al., MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Research, vol.34, issue.1, pp.53-65, 2006.
DOI : 10.1093/nar/gkj406

C. Schoen, L. Kischkies, J. Elias, and B. Ampattu, Metabolism and virulence in Neisseria meningitidis, Frontiers in Cellular and Infection Microbiology, vol.68, p.114, 2014.
DOI : 10.1128/MMBR.68.1.154-171.2004

A. Levine and A. Puzio-kuter, The Control of the Metabolic Switch in Cancers by Oncogenes and Tumor Suppressor Genes, Science, vol.330, issue.6009, pp.1340-1344, 2010.
DOI : 10.1126/science.1193494

H. Takahashi, T. Yanagisawa, K. Kim, S. Yokoyama, and M. Ohnishi, Multiple Functions of Glutamate Uptake via Meningococcal GltT-GltM l-Glutamate ABC Transporter in Neisseria meningitidis Internalization into Human Brain Microvascular Endothelial Cells, Infection and Immunity, vol.83, issue.9, pp.3555-3567, 2015.
DOI : 10.1128/IAI.00654-15

X. Nassif, J. Beretti, J. Lowy, P. Stenberg, O. Gaora et al., Roles of pilin and PilC in adhesion of Neisseria meningitidis to human epithelial and endothelial cells., Proceedings of the National Academy of Sciences, vol.91, issue.9, pp.3769-3773, 1994.
DOI : 10.1073/pnas.91.9.3769

P. Morand, E. Bille, S. Morelle, E. Eugène, J. Beretti et al., Type IV pilus retraction in pathogenic Neisseria is regulated by the PilC proteins, The EMBO Journal, vol.23, issue.9, pp.2009-2017, 2004.
DOI : 10.1038/sj.emboj.7600200

A. Deghmane, D. Giorgini, M. Larribe, J. Alonso, and M. Taha, Down-regulation of pili and capsule of Neisseria meningitidis upon contact with epithelial cells is mediated by CrgA regulatory protein, Molecular Microbiology, vol.43, issue.6, 2002.
DOI : 10.1128/IAI.69.4.2502-2511.2001

J. Sarkari, N. Pandit, E. Moxon, and M. Achtman, Variable expression of the Opc outer membrane protein in Neisseria meningitidis is caused by size variation of a promoter containing poly-cytidine, Molecular Microbiology, vol.10, issue.2, pp.207-217, 1994.
DOI : 10.1016/0092-8674(89)90011-1

H. Omer, G. Rose, K. Jolley, E. Frapy, J. Zahar et al., Genotypic and Phenotypic Modifications of Neisseria meningitidis after an Accidental Human Passage, PLoS ONE, vol.23, issue.5, 2011.
DOI : 10.1371/journal.pone.0017145.s002

URL : https://hal.archives-ouvertes.fr/hal-01190490

D. Kellogg, I. Cohen, L. Norins, A. Schroeter, and G. Reising, Neisseria gonorrhoeae. II. Colonial variation and pathogenicity during 35 months in vitro, J Bacteriol, vol.96, pp.596-605, 1968.

B. Weksler, E. Subileau, N. Perrière, P. Charneau, K. Holloway et al., Blood-brain barrier-specific properties of a human adult brain endothelial cell line, The FASEB Journal, vol.19, pp.1872-187404, 2005.
DOI : 10.1096/fj.04-3458fje

M. Coureuil, G. Mikaty, F. Miller, H. Lécuyer, C. Bernard et al., Meningococcal Type IV Pili Recruit the Polarity Complex to Cross the Brain Endothelium, Science, vol.325, issue.5936, pp.83-87, 2009.
DOI : 10.1126/science.1173196

X. Nassif, D. Puaoi, and M. So, Transposition of Tn1545-delta 3 in the pathogenic Neisseriae: a genetic tool for mutagenesis., Journal of Bacteriology, vol.173, issue.7, pp.2147-2154, 1991.
DOI : 10.1128/jb.173.7.2147-2154.1991

J. Dillard, Genetic manipulation of Neisseria gonorrhoeae, Curr Protoc Microbiol Chapter, 2011.

D. Depledge, A. Palser, S. Watson, I. Lai, E. Gray et al., Specific capture and wholegenome sequencing of viruses from clinical samples, PLoS One, vol.6, 2011.

M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, and M. Tanabe, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Research, vol.40, issue.D1, pp.109-114, 2012.
DOI : 10.1093/nar/gkr988

E. Kopylova, L. Noé, and H. Touzet, SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinformatics, vol.28, issue.24, pp.3211-3217, 2012.
DOI : 10.1093/bioinformatics/bts611

URL : https://hal.archives-ouvertes.fr/hal-00748990

A. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, issue.15, pp.2114-2120, 2014.
DOI : 10.1093/bioinformatics/btu170

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 1923.
DOI : 10.1093/bioinformatics/btp352

S. Anders, P. Pyl, and W. Huber, HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, issue.2, pp.166-169, 2015.
DOI : 10.1093/bioinformatics/btu638

L. Peña-castillo, M. Grüell, M. Mulligan, and A. Lang, DETECTION OF BACTERIAL SMALL TRANSCRIPTS FROM RNA-SEQ DATA: A COMPARATIVE ASSESSMENT, Biocomputing 2016, pp.456-467, 2016.
DOI : 10.1142/9789814749411_0042

A. Quinlan and I. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-842, 2010.
DOI : 10.1093/bioinformatics/btq033

V. Rangannan and M. Bansal, PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes, BMC Research Notes, vol.4, issue.1, pp.2571756-0500, 2011.
DOI : 10.1093/bioinformatics/btg041