J. Amemura-maekawa, F. Kura, B. Chang, and H. Watanabe, Legionella pneumophila serogroup 1 isolates from cooling towers in Japan form a distinct genetic cluster, Microbiol. Immunol, vol.49, pp.1027-1033, 2005.

H. Aurell, P. Farge, H. Meugnier, M. Gouy, F. Forey et al., Clinical and environmental isolates of Legionella pneumophila serogroup 1 cannot be distinguished by sequence analysis of two surface protein genes and three housekeeping genes, Appl. Environ. Microbiol, vol.71, pp.282-289, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00427706

Y. M. Bukhari, K. Koivu, and P. M. Tigerstedt, Phylogenetic analysis of Acacia (Mimosaceae) as revealed from chloroplast RFLP data, Theor. Appl. Genet, vol.98, pp.291-298, 1999.

C. Cazalet, S. Jarraud, Y. Ghavi-helm, F. Kunst, P. Glaser et al., Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species, Genome Res, vol.18, pp.431-441, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02348965

C. Cazalet, C. Rusniok, H. Bruggemann, N. Zidane, A. Magnier et al., Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity, Nat. Genet, vol.36, pp.1165-1173, 2004.

D. Chessel, A. Dufour, and J. Thioulouse, The ade4 package -I: one-table methods, R News, vol.4, pp.5-10, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00427558

M. Chien, I. Morozova, S. Shi, H. Sheng, J. Chen et al., The genomic sequence of the accidental pathogen Legionella pneumophila, Science, vol.305, pp.1966-1968, 2004.

W. S. Cleveland, E. Grosse, and W. M. Shyu, Local regression models, pp.309-376, 1992.

V. S. Cooper, D. Schneider, M. Blot, and R. E. Lenski, Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B, J. Bacteriol, vol.183, pp.2834-2841, 2001.

M. Coscollá, M. J. Gosalbes, V. Catalan, and F. Gonzalez-candelas, Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain), Environ. Microbiol, vol.8, pp.1056-1063, 2006.

A. C. Culhane, G. Perrière, E. C. Considine, T. G. Cotter, and D. G. Higgins, Between-group analysis of microarray data, Bioinformatics, vol.18, pp.1600-1608, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00427316

A. Deplano, M. Vaneechoutte, G. Verschraegen, and M. J. Struelens, Typing of Staphylococcus aureus and Staphylococcus epidermidis strains by PCR analysis of inter-IS256 spacer length polymorphisms, J. Clin. Microbiol, vol.35, pp.2580-2587, 1997.

A. Doleans, H. Aurell, M. Reyrolle, G. Lina, J. Freney et al., Clinical and environmental distributions of Legionella strains in France are different, J. Clin. Microbiol, vol.42, pp.458-460, 2004.

S. Dolédec and D. Chessel, Rythmes saisonniers et composantes stationnelles en milieu aquatique. I. Description d'un plan d'observations complet par projection de variables, Acta Oecol, vol.8, pp.403-426, 1987.

R. V. Eck and M. O. Dayhoff, Atlas of protein sequence and structure, National Biomedical Research Foundation, 1966.

A. Edagawa, A. Kimura, H. Doi, H. Tanaka, K. Tomioka et al., Detection of culturable and nonculturable Legionella species from hot water systems of public buildings in Japan, J. Appl. Microbiol, vol.105, pp.2104-2114, 2008.

J. S. Farris, Phylogenetic analysis under Dollo's law, Syst. Zool, vol.26, pp.77-88, 1977.

J. Felsenstein, Confidence limits on phylogenies: an approach using the bootstrap, Evolution, vol.39, pp.783-791, 1985.

J. Felsenstein, PHYLIP-Phylogeny Inference Package (version 3.2), Cladistics, vol.5, pp.164-166, 1989.

A. E. Fica, H. W. Horowitz, H. Lior, and F. C. Cabello, Demonstration of persistence of Salmonella typhimurium in an AIDS patient by molecular methods, J. Clin. Microbiol, vol.32, pp.2327-2330, 1994.

N. K. Fry, S. Alexiou-daniel, J. M. Bangsborg, S. Bernander, M. Pastoris et al., A multicenter evaluation of genotypic methods for the epidemiologic typing of Legionella pneumophila serogroup 1: results of a pan-European study, Clin. Microbiol. Infect, vol.5, pp.462-477, 1999.

V. Gaia, N. K. Fry, B. Afshar, P. C. Lück, H. Meugnier et al., Consensus sequence-based scheme for epidemiological typing of clinical and environmental isolates of Legionella pneumophila, J. Clin. Microbiol, vol.43, pp.2047-2052, 2005.

V. Gaia, N. K. Fry, T. G. Harrison, and R. Peduzzi, Sequence-based typing of Legionella pneumophila serogroup 1 offers the potential for true portability in legionellosis outbreak investigation, J. Clin. Microbiol, vol.41, pp.2932-2939, 2003.

C. Ginevra, M. Lopez, F. Forey, M. Reyrolle, H. Meugnier et al., Evaluation of a nested-PCRderived sequence-based typing method applied directly to respiratory samples from patients with Legionnaires' disease, J. Clin. Microbiol, vol.47, pp.981-987, 2009.

G. Glöckner, C. Albert-weissenberger, E. Weinmann, S. Jacobi, E. Schunder et al., Identification and characterization of a new conjugation/type IVA secretion system (trb/tra) of Legionella pneumophila Corby localized on two mobile genomic islands, Int. J. Med. Microbiol, vol.298, pp.411-428, 2008.

T. G. Harrison, B. Afshar, N. Doshi, N. K. Fry, and J. V. Lee, Distribution of Legionella pneumophila serogroups, monoclonal antibody subgroups and DNA sequence types in recent clinical and environmental isolates from England and Wales, Eur. J. Clin. Microbiol. Infect. Dis, vol.28, pp.781-791, 2000.

J. H. Helbig, S. Bernander, M. Pastoris, J. Etienne, V. Gaia et al., IS ELEMENTS AS EPIDEMIOLOGICAL TOOLS IN LEGIONELLA, vol.49, 2011.

D. Lauwers, P. C. Lindsay, T. Lück, S. Marques, M. F. Mentula et al., Pan-European study on culture-proven Legionnaires' disease: distribution of Legionella pneumophila serogroups and monoclonal subgroups, Eur. J. Clin. Microbiol. Infect. Dis, vol.21, pp.710-716, 2002.

J. H. Helbig, E. Fernandez-moreira, E. Jacobs, P. C. Lück, and M. Witt, Lipopolysaccharide architecture of Legionella pneumophila grown in broth and host cells, pp.261-264, 2006.

P. R. Hunter and M. A. Gaston, Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity, J. Clin. Microbiol, vol.26, pp.2465-2466, 1988.

F. Huygens, G. R. Nimmo, J. Schooneveldt, W. J. Munckhof, and P. M. Giffard, Genotyping of methicillin-resistant Staphylococcus aureus by assaying for the presence of variable elements associated with mecA, J. Clin. Microbiol, vol.40, pp.3093-3097, 2002.

K. Ichikawa, T. Yagi, M. Moriyama, T. Inagaki, T. Nakagawa et al., Characterization of Mycobacterium avium clinical isolates in Japan using subspecies-specific insertion sequences, and identification of a new insertion sequence, ISMav6, J. Med. Microbiol, vol.58, pp.945-950, 2009.

J. R. Joly, R. M. Mckinney, J. O. Tobin, W. F. Bibb, I. D. Watkins et al., Development of a standardized subgrouping scheme for Legionella pneumophila serogroup 1 using monoclonal antibodies, J. Clin. Microbiol, vol.23, pp.768-771, 1986.

A. G. Kluge and J. S. Farris, Quantitative phyletics and the evolution of anurans, Syst. Zool, vol.18, pp.1-32, 1969.

K. S. Ko, H. Miyamoto, H. K. Lee, M. Y. Park, K. Fukuda et al., Genetic diversity of Legionella pneumophila inferred from rpoB and dotA sequences, Clin. Microbiol. Infect, vol.12, pp.254-261, 2006.

N. A. Kozak, R. F. Benson, E. Brown, N. T. Alexander, T. H. Taylor et al., Distribution of lag-1 alleles and sequence-based types among Legionella pneumophila serogroup 1 clinical and environmental isolates in the United States, J. Clin. Microbiol, vol.47, pp.2525-2535, 2009.

J. D. Lebreton, R. Sabatier, G. Banco, and A. M. Bacou, Principal component and correspondence analyses with respect to instrumental variables: an overview of their role in studies of structure-activity and speciesenvironment relationships, pp.85-114, 1991.

H. K. Lee, J. I. Shim, H. E. Kim, J. Y. Yu, and Y. H. Kang, Distribution of Legionella species from environmental water sources of public facilities and genetic diversity of L. pneumophila serogroup 1 in South Korea, Appl. Environ. Microbiol, vol.76, pp.6547-6554, 2010.

V. A. Luna, D. B. Jernigan, A. Tice, J. D. Kellner, and M. C. Roberts, A novel multiresistant Streptococcus pneumoniae serogroup 19 clone from Washington State identified by pulsed-field gel electrophoresis and restriction fragment length patterns, J. Clin. Microbiol, vol.38, pp.1575-1580, 2000.

J. Mahillon and M. Chandler, Insertion sequences. Microbiol, Mol. Biol. Rev, vol.62, pp.725-774, 1998.
URL : https://hal.archives-ouvertes.fr/hal-00021179

T. Margush and F. R. Mcmorris, Consensus n-trees, Bull. Math. Biol, vol.43, pp.239-244, 1981.

V. Mouchtouri, E. Velonakis, and C. Hadjichristodoulou, Thermal disinfection of hotels, hospitals, and athletic venues hot water distribution systems contaminated by Legionella species, Am. J. Infect. Control, vol.35, pp.623-627, 2007.

M. Nei and W. H. Li, Mathematical model for studying genetic variation in terms of restriction endonucleases, Proc. Natl. Acad. Sci. U. S. A, vol.76, pp.5269-5273, 1979.

H. J. Newton, D. K. Ang, I. R. Van-driel, and E. L. Hartland, Molecular pathogenesis of infections caused by Legionella pneumophila, Clin. Microbiol. Rev, vol.23, pp.274-298, 2010.

D. Papadopoulos, D. Schneider, J. Meier-eiss, W. Arber, R. E. Lenski et al., Genomic evolution during a 10,000-generation experiment with bacteria, Proc. Natl. Acad. Sci. U. S. A, vol.96, pp.3807-3812, 1999.

C. R. Rao, The use and interpretation of principal component analysis in applied research, Sankhya, vol.26, pp.329-359, 1964.

S. Ratzow, V. Gaia, J. H. Helbig, N. K. Fry, and P. C. Lück, Addition of neuA, the gene encoding N-acylneuraminate cytidylyl transferase, increases the discriminatory ability of the consensus sequence-based scheme for typing Legionella pneumophila serogroup 1 strains, J. Clin. Microbiol, vol.45, pp.1965-1968, 2007.

R. Development-core and . Team, R: a language and environment for statistical computing. R Foundation for Statistical Computing, 2007.

K. Reichardt, E. Jacobs, I. Röske, and J. H. Helbig, Legionella pneumophila carrying the virulence-associated lipopolysaccharide epitope possesses two functionally different LPS components, Microbiology, vol.156, pp.2953-2961, 2010.

A. R. Reimer, S. Au, S. Schindle, and K. A. Bernard, Legionella pneumophila monoclonal antibody subgroups and DNA sequence types isolated in Canada between 1981 and 2009: laboratory component of national surveillance, Eur. J. Clin. Microbiol. Infect. Dis, vol.29, pp.191-205, 2010.

D. A. Robinson, S. K. Hollingshead, J. M. Musser, A. J. Parkinson, D. E. Briles et al., The IS1167 insertion sequence is a phylogenetically informative marker among isolates of serotype 6B Streptococcus pneumoniae, J. Mol. Evol, vol.47, pp.222-229, 1998.

T. J. Rowbotham, Preliminary report on the pathogenicity of Legionella pneumophila for freshwater and soil amoebae, J. Clin. Pathol, vol.33, pp.1179-1183, 1980.

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol, vol.4, pp.406-425, 1987.

E. E. Schilling, Phylogenetic analysis of Helianthus (Asteraceae) based on chloroplast DNA restriction site data, Theor. Appl. Genet, vol.94, pp.925-933, 1997.

J. E. Stout and V. L. Yu, Legionellosis. N. Engl. J. Med, vol.337, pp.682-687, 1997.

H. Suzuki, Y. Kawamoto, O. Takenaka, I. Munechika, H. Hori et al., Phylogenetic relationships among Homo sapiens and related species based on restriction site variations in rDNA spacers, Biochem. Genet, vol.32, pp.257-269, 1994.

G. S. Tamura, M. Herndon, J. Przekwas, C. E. Rubens, P. Ferrieri et al., Analysis of restriction fragment length polymorphisms of the insertion sequence IS1381 in group B streptococci, J. Infect. Dis, vol.181, pp.364-368, 2000.

J. Thioulouse and S. Dray, Interactive multivariate data analysis in R with the ade4 and ade4TkGUI packages, J. Stat. Softw, vol.22, pp.1-14, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00434618

N. Tijet, P. Tang, M. Romilowych, C. Duncan, V. Ng et al., New endemic Legionella pneumophila serogroup 1 clones, Canada. Emerg. Infect. Dis, vol.16, pp.447-454, 2010.

G. Torrea, V. Chenal-francisque, A. Leclercq, and E. Carniel, Efficient tracing of global isolates of Yersinia pestis by restriction fragment length polymorphism analysis using three insertion sequences as probes, J. Clin. Microbiol, vol.44, pp.2084-2092, 2006.

V. M. Vaidya, S. V. Malik, S. Kaur, S. Kumar, and S. B. Barbuddhe, Comparison of PCR, immunofluorescence assay, and pathogen isolation for diagnosis of Q fever in humans with spontaneous abortions, J. Clin. Microbiol, vol.46, pp.2038-2044, 2008.

R. M. Warren, T. C. Victor, E. M. Streicher, M. Richardson, G. D. Van-der-spuy et al., Clonal expansion of a globally disseminated lineage of Mycobacterium tuberculosis with low IS6110 copy numbers, J. Clin. Microbiol, vol.42, pp.5774-5782, 2004.

N. Wellinghausen, C. Frost, and R. Marre, Detection of legionellae in hospital water samples by quantitative real-time LightCycler PCR, Appl. Environ. Microbiol, vol.67, pp.3985-3993, 2001.

M. A. Yáñez, C. Carrasco-serrano, V. M. Barberá, and V. Catalán, Quantitative detection of Legionella pneumophila in water samples by immunomagnetic purification and real-time PCR amplification of the dotA gene, Appl. Environ. Microbiol, vol.71, pp.3433-3441, 2005.

T. Yoshida, N. Kondo, Y. A. Hanifah, and K. Hiramatsu, Combined use of ribotyping, PFGE typing and IS431 typing in the discrimination of nosocomial strains of methicillin-resistant Staphylococcus aureus, Microbiol. Immunol, vol.41, pp.687-695, 1997.

R. L. Zuerner and C. A. Bolin, Differentiation of Leptospira interrogans isolates by IS1500 hybridization and PCR assays, J. Clin. Microbiol, vol.35, pp.2612-2617, 1997.