N. S. Akopyants, K. A. Eaton, and D. E. Berg, Adaptive mutation and cocolonization during Helicobacter pylori infection of gnotobiotic piglets, Infect Immun, vol.63, pp.116-121, 1995.

S. G. Andersson and P. M. Sharp, Codon usage and base composition inRickettsia prowazekii, Journal of Molecular Evolution, vol.268, issue.5, pp.525-536, 1996.
DOI : 10.1007/BF02352282

S. G. Andersson and P. M. Sharp, Codon usage in the Mycobacterium tuberculosis complex, Microbiology, vol.142, issue.4, pp.915-925, 1996.
DOI : 10.1099/00221287-142-4-915

A. Beji, P. Vincent, I. Dachis, M. O. Husson, A. Cortol et al., EVIDENCE OF GASTRITIS WITH SEVERAL HELICOBACTER PYLORI STRAINS, The Lancet, vol.334, issue.8676, pp.1402-1405, 1989.
DOI : 10.1016/S0140-6736(89)92020-5

D. E. Berg, R. H. Gilman, and J. Lelwala-guruge, Helicobacter pylori populations in Peruvian patients, & 9 other authors, 1997.

O. G. Berg and C. G. Kurland, Growth rate-optimised tRNA abundance and codon usage, Journal of Molecular Biology, vol.270, issue.4, pp.544-550, 1997.
DOI : 10.1006/jmbi.1997.1142

M. J. Blaser, Helicobacter pylori: Its Role in Disease, Clinical Infectious Diseases, vol.15, issue.3, pp.386-393, 1992.
DOI : 10.1093/clind/15.3.386

M. J. Blaser, Heterogeneity of Helicobacter pylori, European Journal of Gastroenterology & Hepatology, vol.9, pp.3-6, 1997.
DOI : 10.1097/00042737-201204001-00002

M. Borodovsky and J. D. Mcininch, GENMARK: Parallel gene recognition for both DNA strands, Computers & Chemistry, vol.17, issue.2, pp.123-133, 1993.
DOI : 10.1016/0097-8485(93)85004-V

M. Bulmer, Coevolution of codon usage and transfer RNA abundance, Nature, vol.325, issue.6106, pp.728-730, 1987.
DOI : 10.1038/325728a0

M. Bulmer, The effect of context on synonymous codon usage in genes with low codon usage bias, Nucleic Acids Research, vol.18, issue.10, pp.2869-2873, 1990.
DOI : 10.1093/nar/18.10.2869

M. Bulmer, The selection-mutation-drift theory of synonymous codon usage, Genetics, vol.129, pp.897-907, 1991.

P. Cao and T. L. Cover, High-level genetic diversity in the vapD chromosomal region of Helicobacter pylori., Journal of Bacteriology, vol.179, issue.9, pp.2852-2856, 1997.
DOI : 10.1128/jb.179.9.2852-2856.1997

A. Covacci, S. Falkow, D. E. Berg, and R. Rappuoli, Did the inheritance of a pathogenicity island modify the virulence of Helicobacter pylori?, Trends in Microbiology, vol.5, issue.5, pp.205-208, 1997.
DOI : 10.1016/S0966-842X(97)01035-4

A. Eyre-walker and M. Bulmer, Reduced synonymous substitution rate at the start of enterobacterial genes, Nucleic Acids Research, vol.21, issue.19, pp.4599-4603, 1993.
DOI : 10.1093/nar/21.19.4599

R. D. Fleischmann, M. D. Adams, and O. White, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, vol.269, issue.5223, pp.496-512, 1995.
DOI : 10.1126/science.7542800

M. P. Francino and H. Ochman, Strand asymmetries in DNA evolution, Trends in Genetics, vol.13, issue.6, pp.240-245, 1997.
DOI : 10.1016/S0168-9525(97)01118-9

S. Fujimoto, B. Marshall, and M. J. Blaser, PCR-based restriction fragment length polymorphism typing of Helicobacter pylori, J Clin Microbiol, vol.32, pp.331-334, 1994.

$. Go, M. U. Ttke, J. M. Groody, V. Loo, C. A. Fallone et al., Panmyctic population structure due to frequent recombination in Helicobacter pylori, Gut, vol.39, p.121, 1996.

M. Gouy and C. Gautier, Codon usage in bacteria: correlation with gene expressivity, Nucleic Acids Research, vol.10, issue.22, pp.7055-7074, 1982.
DOI : 10.1093/nar/10.22.7055

URL : https://hal.archives-ouvertes.fr/hal-00697906

R. Grantham, C. Gautier, M. Gouy, M. Jacobzone, and R. Mercier, Codon catalog usage is a genome strategy modulated for gene expressivity, Nucleic Acids Research, vol.9, issue.1, pp.43-74, 1981.
DOI : 10.1093/nar/9.1.213-b

URL : https://hal.archives-ouvertes.fr/hal-00697917

M. J. Greenacre, Theory and Applications of Correspondence Analysis, 1984.

S. L. Hazell, R. H. Andrews, H. M. Mitchell, and G. Daskalopoulos, Genetic relationship among isolates of Helicobacter pylori: evidence for the existence of a Helicobacter pylori species-complex, FEMS Microbiology Letters, vol.150, issue.1, pp.27-32, 1997.
DOI : 10.1111/j.1574-6968.1997.tb10345.x

T. Ikemura, Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes, Journal of Molecular Biology, vol.146, issue.1, pp.1-21, 1981.
DOI : 10.1016/0022-2836(81)90363-6

T. Ikemura, Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system, Journal of Molecular Biology, vol.151, issue.3, pp.389-409, 1981.
DOI : 10.1016/0022-2836(81)90003-6

N. Kitamoto, H. Nakamoto, A. Katai, N. Takahara, H. Nakata et al., Heterogeneity of Protein Profiles of Helicobacter pylori Isolated from Individual Patients, Helicobacter, vol.29, issue.3, pp.152-162, 1998.
DOI : 10.1016/S0140-6736(89)92020-5

C. G. Kurland, Major codon preference: theme and variations, Biochemical Society Transactions, vol.21, issue.4, pp.841-846, 1993.
DOI : 10.1042/bst0210841

&. Wolfe and K. H. , Proteome composition and codon usage in spirochaetes : species-specific and DNA strand-specific mutational biases, Nucleic Acids Res, vol.27, pp.1642-1649, 1999.
URL : https://hal.archives-ouvertes.fr/hal-00412912

J. G. Lawrence and H. Ochman, Amelioration of Bacterial Genomes: Rates of Change and Exchange, Journal of Molecular Evolution, vol.44, issue.4, pp.383-397, 1997.
DOI : 10.1007/PL00006158

J. R. Lobry and C. Gautier, Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999, 1994.
URL : https://hal.archives-ouvertes.fr/hal-00698020

A. T. Lloyd and P. M. Sharp, CODONS: A Microcomputer Program for Codon Usage Analysis, Journal of Heredity, vol.83, issue.3, pp.239-240, 1992.
DOI : 10.1093/oxfordjournals.jhered.a111205

J. O. Mcinerney, Prokaryotic Genome Evolution as Assessed by Multivariate Analysis of Codon Usage Patterns, Microbial & Comparative Genomics, vol.2, issue.1, pp.1-10, 1997.
DOI : 10.1089/omi.1.1997.2.89

J. O. Mcinerney, Replicational and transcriptional selection on codon usage in Borrelia burgdorferi, Proceedings of the National Academy of Sciences, vol.95, issue.18, pp.10698-10703, 1998.
DOI : 10.1073/pnas.95.18.10698

M. J. Mclean, K. H. Wolfe, and K. M. Devine, Base Composition Skews, Replication Orientation, and Gene Orientation in 12 Prokaryote Genomes, Journal of Molecular Evolution, vol.47, issue.6, pp.691-696, 1998.
DOI : 10.1007/PL00006428

M. Smith, M. Smith, and N. H. , Detecting recombination from gene trees, Molecular Biology and Evolution, vol.15, issue.5, pp.590-599, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025960

T. Ohama, A. Muto, and S. Osawa, a bacterium with a high genomic GC-content, Nucleic Acids Research, vol.18, issue.6, pp.1565-1569, 1990.
DOI : 10.1093/nar/18.6.1565

G. J. Olsen, C. R. Woese, and R. Overbeek, The winds of (evolutionary) change : breathing new life into microbiology, 1994.

M. Russi and R. A. Musmanno, Comparisons between degree of histological gastritis and DNA fingerprints, cytotoxicity and adhesivity of Helicobacter pylori from different gastric sites, 1993.

G. Perrie-'re, J. R. Lobry, and J. Thioulouse, Correspondence discriminant analysis : a multivariate method for comparing classes of protein and nucleic acid sequences, Comput Appl Biosci, vol.12, pp.519-524, 1996.

L. E. Post and M. Nomura, DNA sequences from the str operon of Escherichia coli, J Biol Chem, vol.255, pp.4660-4666, 1980.

L. Salau-$-n, C. Audibert, L. Gay, G. Burucoa, C. Fauche-'re et al., demonstrated by the comparative study of six genetic markers, FEMS Microbiology Letters, vol.161, issue.2, pp.231-239, 1998.
DOI : 10.1111/j.1574-6968.1998.tb12953.x

P. M. Sharp and W. Li, does not reflect selection for ???rare??? codons, Nucleic Acids Research, vol.14, issue.19, pp.7737-7749, 1986.
DOI : 10.1093/nar/14.19.7737

P. M. Sharp and W. Li, An evolutionary perspective on synonymous codon usage in unicellular organisms, Journal of Molecular Evolution, vol.120, issue.1-2, pp.28-38, 1986.
DOI : 10.1007/BF02099948

D. C. Shields and P. M. Sharp, reflects both translational selection and mutational biases, Nucleic Acids Research, vol.15, issue.19, pp.8023-8040, 1987.
DOI : 10.1093/nar/15.19.8023

URL : http://doi.org/10.1093/nar/15.19.8023

S. Suerbaum, M. Smith, J. Bapumia, K. Morelli, G. Smith et al., Free recombination within Helicobacter pylori, Proceedings of the National Academy of Sciences, vol.95, issue.21, pp.12619-12624, 1998.
DOI : 10.1073/pnas.95.21.12619

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC22880

D. N. Taylor and M. J. Blaser, The Epidemiology of Helicobacter pylori Infection, Epidemiologic Reviews, vol.13, issue.1, pp.42-59, 1991.
DOI : 10.1093/oxfordjournals.epirev.a036078

F. Wright, The ???effective number of codons??? used in a gene, Gene, vol.87, issue.1, pp.23-29, 1990.
DOI : 10.1016/0378-1119(90)90491-9

F. Wright and M. J. Bibb, Codon usage in the G+C-rich Streptomyces genome, Gene, vol.113, issue.1, pp.55-65, 1992.
DOI : 10.1016/0378-1119(92)90669-G