D. Smet, B. Mayo, M. Peeters, C. Zlosnik, J. Spilker et al., Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources, Int J Syst Evol Microbiol, vol.65, p.25872960, 2015.

K. S. Ong, Y. K. Aw, L. H. Lee, C. M. Yule, Y. L. Cheow et al., Burkholderia paludis sp. nov., an antibioticsiderophore producing novel Burkholderia cepacia complex species, isolated from malaysian tropical peat swamp soil, Front Microbiol. Frontiers Media SA, vol.7, p.28066367, 2016.

P. Drevinek and E. Mahenthiralingam, Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence, Clin Microbiol Infect, vol.16, p.20880411, 2010.

S. A. Sousa, C. G. Ramos, and J. H. Leitão, Burkholderia cepacia complex: Emerging multihost pathogens equipped with a wide range of virulence factors and determinants, Int J Microbiol, vol.607575, p.20811541, 2011.

A. Holmes, R. Nolan, R. Taylor, R. Finley, M. Riley et al., An epidemic of Burkholderia cepacia transmitted between patients with and without cystic fibrosis, J Infect Dis. NIH Public Access, vol.179, p.10191223, 1999.

J. J. Lipuma, T. Spilker, T. Coenye, and C. F. Gonzalez, An epidemic Burkholderia cepacia complex strain identified in soil, Lancet, vol.359, p.12076559, 2002.

I. C. Akinboyo, A. C. Sick-samuels, E. Singeltary, J. Fackler, J. Ascenzi et al., Multistate outbreak of an emerging Burkholderia cepacia complex strain associated with contaminated oral liquid docusate sodium, Infect Control Hosp Epidemiol, vol.39, p.29417919, 2018.

J. Zlosnik, G. Zhou, R. Brant, D. A. Henry, T. J. Hird et al., Burkholderia species infections in patients with cystic fibrosis in British Columbia, Canada: 30 years' experience, Ann Am Thorac Soc, vol.12, p.25474359, 2015.

A. Isles, I. Maclusky, M. Corey, R. Gold, C. Prober et al., Pseudomonas cepacia infection in cystic fibrosis: An emerging problem, J Pediatr, vol.104, issue.84, p.6420530, 1984.

L. Blackburn, K. Brownlee, S. Conway, and M. Denton, Cepacia syndrome' with Burkholderia multivorans, 9 years after initial colonization, J Cyst Fibros, vol.3, p.15463897, 2004.

T. Coenye and P. Vandamme, Diversity and significance of Burkholderia species occupying diverse ecological niches, Environ Microbiol, vol.5, p.12919407, 2003.

S. D. Aaron, W. Ferris, D. A. Henry, D. P. Speert, and N. E. Macdonald, Multiple combination bactericidal antibiotic testing for patients with cystic fibrosis infected with Burkholderia cepacia, Am J Respir Crit Care Med, vol.161, p.10764313, 2000.

S. Nzula, P. Vandamme, and J. Govan, Influence of taxonomic status on the in vitro antimicrobial susceptibility of the Burkholderia cepacia complex, J Antimicrob Chemother, vol.50, p.12161410, 2002.

S. Meyer, S. I. Massoud, D. J. Chitwood, and D. P. Roberts, Evaluation of Trichoderma virens and Burkholderia cepacia for antagonistic activity against root-knot nematode, Meloidogyne incognita, Nematology, vol.2, pp.871-879, 2000.

J. Lamothe, S. Thyssen, and M. A. Valvano, Burkholderia cepacia complex isolates survive intracellularly without replication within acidic vacuoles of Acanthamoeba polyphaga, Cell Microbiol. Blackwell Science Ltd, vol.6, p.15527493, 2004.

N. Stopnisek, D. Zuhlke, A. Carlier, A. Barberan, N. Fierer et al., Molecular mechanisms underlying the close association between soil Burkholderia and fungi, ISME J, vol.10, p.25989372, 2016.

M. Lardi, S. B. De-campos, G. Purtschert, L. Eberl, and G. Pessi, Competition experiments for legume infection identify Burkholderia phymatum as a highly competitive ?-rhizobium. Front Microbiol, vol.8, p.28861050, 2017.

V. B. Weaver and R. Kolter, Burkholderia spp. alter Pseudomonas aeruginosa physiology through iron sequestration, J Bacteriol. American Society for Microbiology, vol.186, pp.2376-2384, 2004.

I. Ventre, A. L. Goodman, I. Vallet-gely, P. Vasseur, C. Soscia et al., Multiple sensors control reciprocal expression of Pseudomonas aeruginosa regulatory RNA and virulence genes, Proc Natl Acad Sci, vol.103, p.16373506, 2006.

G. Chambonnier, L. Roux, D. Redelberger, F. Fadel, A. Filloux et al., The Hybrid Histidine Kinase LadS Forms a Multicomponent Signal Transduction System with the GacS/GacA Two-Component System in Pseudomonas aeruginosa, PLoS Genet, vol.12, p.27176226, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01770245

P. A. Sokol, U. Sajjan, M. B. Visser, S. Gingues, J. Forstner et al., The CepIR quorum-sensing system contributes to the virulence of Burkholderia cenocepacia respiratory infections, Microbiology, vol.149, p.14663096, 2003.

R. J. Malott, A. Baldwin, E. Mahenthiralingam, and P. A. Sokol, Characterization of the cciIR quorum-sensing system in Burkholderia cenocepacia, Infect Immun, vol.73, p.16041013, 2005.

D. F. Aubert, E. P. O'grady, M. A. Hamad, P. A. Sokol, and M. A. Valvano, The Burkholderia cenocepacia sensor kinase hybrid AtsR is a global regulator modulating quorum-sensing signalling, Environ Microbiol, vol.15, p.22830644, 2013.

S. P. Bernier, D. T. Nguyen, and P. A. Sokol, A LysR-type transcriptional regulator in Burkholderia cenocepacia influences colony morphology and virulence, Infect Immun, vol.76, p.17967860, 2008.

E. P. O'grady, D. T. Nguyen, L. Weisskopf, L. Eberl, and P. A. Sokol, The Burkholderia cenocepacia LysR-Type transcriptional regulator ShvR influences expression of quorum-sensing, protease, type II secretion, and afc genes, J Bacteriol, vol.193, p.20971902, 2011.

Y. Kang, R. Carlson, W. Tharpe, and M. A. Schell, Characterization of genes involved in biosynthesis of a novel antibiotic from Burkholderia cepacia BC11 and their role in biological control of Rhizoctonia solani, Appl Environ Microbiol, vol.64, p.9758823, 1998.

S. Subramoni, K. Agnoli, L. Eberl, S. Lewenza, and P. A. Sokol, Role of Burkholderia cenocepacia afcE and afcF genes in determining lipid-metabolism-associated phenotypes, Microbiol, vol.159, pp.603-614, 2013.

S. Subramoni, D. T. Nguyen, and P. A. Sokol, Burkholderia cenocepacia ShvR-regulated genes that influence colony morphology, biofilm formation, and virulence, Infect Immun, vol.79, p.21690240, 2011.

J. Mesureur, J. R. Feliciano, N. Wagner, M. C. Gomes, L. Zhang et al., but not neutrophils, are critical for proliferation of Burkholderia cenocepacia and ensuing host-damaging inflammation, PLoS Pathog, vol.13, p.28651010, 2017.

A. C. Vergunst, A. H. Meijer, S. A. Renshaw, O. 'callaghan, and D. , Burkholderia cenocepacia creates an intramacrophage replication niche in zebrafish embryos, followed by bacterial dissemination and establishment of systemic infection, Infect Immun, vol.78, pp.1495-1508, 2010.

S. T. Cardona and M. A. Valvano, An expression vector containing a rhamnose-inducible promoter provides tightly regulated gene expression in Burkholderia cenocepacia, Plasmid, vol.54, p.15925406, 2005.

E. Depoorter, M. J. Bull, C. Peeters, T. Coenye, P. Vandamme et al., Burkholderia: an update on taxonomy and biotechnological potential as antibiotic producers, Appl Microbiol Biotechnol. Applied Microbiology and Biotechnology, vol.100, p.27115756, 2016.

P. Vandamme and P. Dawyndt, Classification and identification of the Burkholderia cepacia complex: Past, present and future, Syst Appl Microbiol, vol.34, p.21257278, 2011.

T. Spilker, A. Baldwin, A. Bumford, C. G. Dowson, E. Mahenthiralingam et al., Expanded multilocus sequence typing for Burkholderia species, J Clin Microbiol, vol.47, pp.2607-2610, 2009.

S. Uehlinger, S. Schwager, S. P. Bernier, K. Riedel, D. T. Nguyen et al., Identification of specific and universal virulence factors in Burkholderia cenocepacia strains by using multiple infection hosts, Infect Immun, vol.77, p.19528212, 2009.

S. Schwager, K. Agnoli, M. Köthe, F. Feldmann, M. Givskov et al., Identification of Burkholderia cenocepacia strain H111 virulence factors using nonmammalian infection hosts, Infect Immun, vol.81, p.23090963, 2013.

K. Agnoli, R. Freitag, M. C. Gomes, C. Jenul, A. Suppiger et al., The use of synthetic hybrid strains to determine the role of replicon 3 in virulence of the Burkholderia cepacia complex, Appl Environ Microbiol, vol.83, p.28432094, 2017.

O. Caille, D. Zincke, M. Merighi, D. Balasubramanian, H. Kumari et al., Structural and functional characterization of Pseudomonas aeruginosa global regulator AmpR, J Bacteriol, vol.196, p.25182487, 2014.

M. A. Laskowski and B. I. Kazmierczak, Mutational analysis of RetS, an unusual sensor kinase-response regulator hybrid required for Pseudomonas aeruginosa virulence, Infect Immun, vol.74, p.16861632, 2006.

A. Brencic, K. A. Mcfarland, H. R. Mcmanus, S. Castang, S. L. Dove et al., The GacS/GacA signal transduction system of Pseudomonas aeruginosa acts exclusively through its control over the transcription of the RsmY and RsmZ regulatory small RNAs, Mol Microbiol, vol.73, p.19602144, 2009.

A. L. Goodman, M. Merighi, M. Hyodo, I. Ventre, A. Filloux et al., Direct interaction between sensor kinase proteins mediates acute and chronic disease phenotypes in a bacterial pathogen, Genes Dev, vol.23, p.19171785, 2009.

D. Balasubramanian, H. Kumari, and K. Mathee, Pseudomonas aeruginosa AmpR: an acute-chronic switch regulator, Pathog Dis, vol.73, p.25066236, 2015.

S. P. Bernier, L. Silo-suh, D. E. Woods, D. E. Ohman, and P. A. Sokol, Comparative analysis of plant and animal models for characterization of Burkholderia cepacia virulence, Infect Immun, vol.71, p.12933878, 2003.

C. Jenul, S. Sieber, C. Daeppen, A. Mathew, M. Lardi et al., Biosynthesis of fragin is controlled by a novel quorum sensing signal, Nat Commun, vol.9, p.29602945, 2018.

B. Huber, F. Feldmann, M. Köthe, P. Vandamme, J. Wopperer et al., Identification of a novel virulence factor in Burkholderia cenocepacia H111 required for efficient slow killing of Caenorhabditis elegans, Infect Immun, vol.72, p.15557647, 2004.

O. Geisenberger, M. Givskov, K. Riedel, N. Høiby, B. Tümmler et al., Production of N-acyl-L-homoserine lactones by P. aeruginosa isolates from chronic lung infections associated with cystic fibrosis, FEMS Microbiol Lett, vol.184, p.10713433, 2000.

S. A. Renshaw, C. A. Loynes, D. Trushell, S. Elworthy, P. W. Ingham et al., A transgenic zebrafish model of neutrophilic inflammation, Blood, vol.108, p.16926288, 2006.

M. Nguyen-chi, Q. T. Phan, C. Gonzalez, J. F. Dubremetz, J. P. Levraud et al., Transient infection of the zebrafish notochord with E. coli induces chronic inflammation, Dis Model Mech, vol.7, p.24973754, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02088301

J. Mesureur and A. C. Vergunst, Zebrafish embryos as a model to study bacterial virulence, Methods Mol Biol, vol.1197, 2014.

K. Agnoli, S. Schwager, S. Uehlinger, A. Vergunst, D. F. Viteri et al., Exposing the third chromosome of Burkholderia cepacia complex strains as a virulence plasmid, Mol Microbiol, vol.83, p.22171913, 2012.

F. Ellett and G. J. Lieschke, Computational quantification of fluorescent leukocyte numbers in zebrafish embryos, Methods Enzymol, vol.506, p.22341237, 2012.

. Ncbi-resource-coordinators, Database Resources of the National Center for Biotechnology Information, Nucleic Acids Res, vol.45, p.27899561, 2017.

A. R. Wattam, J. J. Davis, R. Assaf, S. Boisvert, T. Brettin et al., Improvements to PATRIC, the allbacterial Bioinformatics Database and Analysis Resource Center, Nucleic Acids Res, vol.45, p.27899627, 2017.

G. L. Winsor, B. Khaira, T. Van-rossum, R. Lo, M. D. Whiteside et al., The Burkholderia Genome Database: facilitating flexible queries and comparative analyses, Bioinformatics, vol.24, p.18842600, 2008.

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular evolutionary genetics analysis version 6.0, Mol Biol Evol, vol.30, p.24132122, 2013.

M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. Mcgettigan et al., Clustal W and Clustal X version 2.0. Bioinformatics, vol.23, p.17846036, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00206210

M. Goujon, H. Mcwilliam, W. Li, F. Valentin, S. Squizzato et al., A new bioinformatics analysis tools framework at EMBL-EBI, Nucleic Acids Res, vol.38, p.20439314, 2010.

G. Vaidya, D. J. Lohman, and M. R. Sequencematrix, Concatenation software for the fast assembly of multi-gene datasets with character set and codon information, Cladistics, vol.27, pp.171-180, 2011.

S. Tavaré, Some probabilistic and statistical problems in the analysis of DNA sequences, Lectures on Mathematics in the Life Sciences, pp.57-86, 1986.

A. Darling, B. Mau, F. R. Blattner, and N. T. Perna, Mauve: Multiple alignment of conserved genomic sequence with rearrangements, Genome Res, vol.14, p.15231754, 2004.

P. Deng, X. Wang, S. M. Baird, K. C. Showmaker, L. Smith et al., Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis, vol.5, p.26769582, 2016.