M. Achtman, G. Morelli, P. Zhu, T. Wirth, I. Diehl et al., Microevolution and history of the plague bacillus, Yersinia pestis, Proc. Natl. Acad. Sci. U.S.A, vol.101, pp.17837-17842, 2004.

J. Z. Adjemian, M. K. Adjemian, P. Foley, B. B. Chomel, R. W. Kasten et al., Evidence of multiple zoonotic agents in a wild rodent community in the eastern Sierra Nevada, J. Wildl. Dis, vol.44, pp.737-742, 2008.

M. Aepfelbacher, C. Trasak, and K. Ruckdeschel, Effector functions of pathogenic Yersinia species, Thromb. Haemost, vol.98, pp.521-529, 2007.

N. F. Alikhan, N. K. Petty, N. L. Ben-zakour, and S. A. Beatson, BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, vol.12, p.402, 2011.

D. A. Benson, M. Cavanaugh, K. Clark, I. Karsch-mizrachi, D. J. Lipman et al., GenBank. Nucleic Acids Res, vol.41, 2013.

R. Ber, E. Mamroud, M. Aftalion, A. Tidhar, D. Gur et al., Development of an improved selective agar medium for isolation of Yersinia pestis, Appl. Environ. Microbiol, vol.69, pp.5787-5792, 2003.

S. Bergmann and S. Hammerschmidt, Fibrinolysis and host response in bacterial infections, Thromb. Haemost, vol.98, 2007.

E. Bertherat, S. Bekhoucha, S. Chougrani, F. Razik, J. B. Duchemin et al., Plague reappearance in Algeria after 50 years, Emerging Infect. Dis, vol.13, pp.1459-1462, 2003.

G. Blanc and M. Baltazard, Documents sur la peste, Arch. Inst. Pasteur Maroc, vol.3, pp.463-475, 1945.

K. A. Bliven and A. T. Maurelli, Antivirulence genes: insights into pathogen evolution through gene loss, Infect. Immun, vol.80, pp.4061-4070, 2012.

M. Boetzer, P. , and W. , Toward almost closed genomes with GapFiller, Genome Biol, vol.13, p.56, 2012.

S. Capella-gutierrez, J. M. Silla-martinez, and T. Gabaldon, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009.

E. Carniel, The Yersinia high-pathogenicity island: an iron-uptake island, Microbes Infect, vol.3, pp.561-569, 2001.

P. S. Chain, E. Carniel, F. W. Larimer, J. Lamerdin, P. O. Stoutland et al., Insights into the evolution of Yersinia pestis through wholegenome comparison with Yersinia pseudotuberculosis, Proc. Natl. Acad. Sci. U.S.A, vol.101, pp.13826-13831, 2004.

R. N. Charrel, S. B. La, R. , and D. , Multi-pathogens sequence containing plasmids as positive controls for universal detection of potential agents of bioterrorism, BMC Microbiol, vol.4, p.21, 2004.

B. Chevreux, T. Pfisterer, B. Drescher, A. J. Driesel, W. E. Muller et al., Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs, Genome Res, vol.14, pp.1147-1159, 2004.

B. Contreras-moreira and P. Vinuesa, GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis, Appl. Environ. Microbiol, vol.79, pp.7696-7701, 2013.

A. C. Darling, B. Mau, F. R. Blattner, and N. T. Perna, Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res, vol.14, pp.1394-1403, 2004.

C. Egile, H. Hauteville, C. Parsot, and P. J. Sansonetti, SopA, the outer membrane protease responsible for polar localization of IcsA in Shigella flexneri, Mol. Microbiol, vol.23, pp.1063-1073, 1997.

E. Eren, M. Murphy, J. Goguen, . Van-den, and B. Berg, An active site water network in the plasminogen activator pla from Yersinia pestis, Structure, vol.18, pp.809-818, 2010.

D. M. Ferber and R. R. Brubaker, Plasmids in Yersinia pestis, Infect. Immun, vol.31, pp.839-841, 1981.

S. Gao, W. K. Sung, and N. Nagarajan, Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences, J. Comput. Biol, vol.18, pp.1681-1691, 2011.

S. N. Gardner, T. Slezak, and B. G. Hall, kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome, Bioinformatics, vol.31, pp.2877-2878, 2015.

T. Guina, E. C. Yi, H. Wang, M. Hackett, and S. I. Miller, A PhoP-regulated outer membrane protease of Salmonella enterica serovar typhimurium promotes resistance to alpha-helical antimicrobial peptides, J. Bacteriol, vol.182, pp.4077-4086, 2000.

S. Guindon and O. Gascuel, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol, vol.52, pp.696-704, 2003.

F. Guinet, P. Ave, S. Filali, C. Huon, C. Savin et al., Dissociation of Tissue destruction and bacterial expansion during bubonic plague, PLoS Pathog, vol.11, p.1005222, 2015.

J. Haiko, L. Laakkonen, B. Westerlund-wikstrom, and T. K. Korhonen, Molecular adaptation of a plant-bacterium outer membrane protease towards plague virulence factor Pla, BMC Evol. Biol, vol.11, p.43, 2011.

J. Haiko, M. Suomalainen, T. Ojala, K. Lahteenmaki, and T. K. Korhonen, Invited review: breaking barriers-attack on innate immune defences by omptin surface proteases of enterobacterial pathogens, Innate Immun, vol.15, pp.67-80, 2009.

J. A. Higgins, J. Ezzell, B. J. Hinnebusch, M. Shipley, E. A. Henchal et al., 5 ? nuclease PCR assay to detect Yersinia pestis, J. Clin. Microbiol, vol.36, pp.2284-2288, 1998.

P. Hu, J. Elliott, P. Mccready, E. Skowronski, J. Garnes et al., Structural organization of virulence-associated plasmids of Yersinia pestis, J. Bacteriol, vol.180, pp.5192-5202, 1998.

X. Huang and A. Madan, CAP3: a DNA sequence assembly program, Genome Res, vol.9, pp.868-877, 1999.

D. Hyatt, G. L. Chen, P. F. Locascio, M. L. Land, F. W. Larimer et al., Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, vol.11, p.119, 2010.

I. Janse, R. A. Hamidjaja, J. M. Bok, and B. J. Van-rotterdam, Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification, BMC Microbiol, vol.10, p.314, 2010.

I. Janse, R. A. Hamidjaja, R. , and C. , Yersinia pestis plasminogen activator gene homolog in rat tissues, Emerging Infect. Dis, vol.19, pp.342-344, 2013.

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol, vol.30, pp.772-780, 2013.

D. Kaufman and K. D. Fairchild, Clinical microbiology of bacterial and fungal sepsis in very-low-birth-weight infants, Clin. Microbiol. Rev, vol.17, pp.638-680, 2004.

K. Kowalski and B. Rzebik-kowalska, Mammals of Algeria. Warsaw: Polish Academy of Sciences, 1991.

D. M. Kristensen, L. Kannan, M. K. Coleman, Y. I. Wolf, A. Sorokin et al., A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches, Bioinformatics, vol.26, pp.1481-1487, 2010.

M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne et al., Circos: an information aesthetic for comparative genomics, Genome Res, vol.19, pp.1639-1645, 2009.

V. Kutyrev, R. J. Mehigh, V. L. Motin, M. S. Pokrovskaya, G. B. Smirnov et al., Expression of the plague plasminogen activator in Yersinia pseudotuberculosis and Escherichia coli, Infect. Immun, vol.67, pp.1359-1367, 1999.

K. Lagesen, P. Hallin, E. A. Rodland, H. H. Staerfeldt, T. Rognes et al., RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res, vol.35, pp.3100-3108, 2007.

D. Laslett, C. , and B. , ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences, Nucleic Acids Res, vol.32, pp.11-16, 2004.

I. Lebrun, R. Marques-porto, A. S. Pereira, A. Pereira, and E. A. Perpetuo, Bacterial toxins: an overview on bacterial proteases and their action as virulence factors, Mini Rev. Med. Chem, vol.9, pp.820-828, 2009.

L. Li, C. J. Stoeckert, R. , and D. S. , OrthoMCL: identification of ortholog groups for eukaryotic genomes, Genome Res, vol.13, pp.2178-2189, 2003.

S. H. Lin and Y. C. Liao, CISA: contig integrator for sequence assembly of bacterial genomes, PLoS ONE, vol.8, p.60843, 2013.

S. Y. Lin, M. W. Ho, Y. F. Yang, J. H. Liu, I. K. Wang et al., Abscess caused by Citrobacter koseri infection: three case reports and a literature review, Intern. Med, vol.50, pp.1333-1337, 2011.

C. Loiez, S. Herwegh, F. Wallet, S. Armand, F. Guinet et al., Detection of Yersinia pestis in sputum by real-time PCR, J. Clin. Microbiol, vol.41, pp.4873-4875, 2003.

M. Margulies, M. Egholm, W. E. Altman, S. Attiya, J. S. Bader et al., Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.437, pp.376-380, 2005.

S. W. Montminy, N. Khan, S. Mcgrath, M. J. Walkowicz, F. Sharp et al., Virulence factors of Yersinia pestis are overcome by a strong lipopolysaccharide response, Nat. Immunol, vol.7, pp.1066-1073, 2006.

H. Neubauer, H. Meyer, J. Prior, S. Aleksic, A. Hensel et al., A combination of different polymerase chain reaction (PCR) assays for the presumptive identification of Yersinia pestis, J. Vet. Med. B Infect. Dis. Vet. Public Health, vol.47, pp.573-580, 2000.

M. J. Pallen and B. W. Wren, Bacterial pathogenomics, Nature, vol.449, pp.835-842, 2007.

R. D. Perry and J. D. Fetherston, Yersinia pestis-etiologic agent of plague, Clin Microbiol Rev, vol.10, issue.1, pp.35-66, 1997.

R. D. Perry and J. D. Fetherston, Yersiniabactin iron uptake: mechanisms and role in Yersinia pestis pathogenesis, Microbes Infect, vol.13, pp.808-817, 2011.

R. Pollitzer, Plague studies: 10. Control and prevention, Bull. World Health Organ, vol.9, pp.457-551, 1953.

M. Punta, P. C. Coggill, R. Y. Eberhardt, J. Mistry, J. Tate et al., The Pfam protein families database, Nucleic Acids Res, vol.40, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01294685

C. Rajanna, T. Revazishvili, M. H. Rashid, S. Chubinidze, L. Bakanidze et al., Characterization of pPCP1 Plasmids in Yersinia pestis Strains Isolated from the Former Soviet Union, Int. J. Microbiol, p.760819, 2010.

J. M. Riehm, D. Tserennorov, D. Kiefer, I. W. Stuermer, H. Tomaso et al., Yersinia pestis in small rodents, Mongolia. Emerging Infect. Dis, vol.17, pp.1320-1322, 2011.

R. Saito, M. E. Smoot, K. Ono, J. Ruscheinski, P. L. Wang et al., A travel guide to Cytoscape plugins, Nat. Methods, vol.9, pp.1069-1076, 2012.

S. V. Samoilova, L. V. Samoilova, I. N. Yezhov, I. G. Drozdov, and A. P. Anisimov, Virulence of pPst+ and pPst? strains of Yersinia pestis for guinea-pigs, J. Med. Microbiol, vol.45, pp.440-444, 1996.

J. D. Sanders, Y. Tagawa, R. E. Briggs, and L. B. Corbeil, Transformation of a virulence associated gene of Haemophilus somnus into a strain lacking the gene, FEMS Microbiol. Lett, vol.154, pp.251-258, 1997.

S. Simon, C. Demeure, P. Lamourette, S. Filali, M. Plaisance et al., Fast and simple detection of Yersinia pestis applicable to field investigation of plague foci, PLoS ONE, vol.8, p.54947, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-02072553

O. A. Sodeinde and J. D. Goguen, Genetic analysis of the 9.5-kilobase virulence plasmid of Yersinia pestis, Infect. Immun, vol.56, pp.2743-2748, 1988.

O. A. Sodeinde, Y. V. Subrahmanyam, K. Stark, T. Quan, Y. Bao et al., A surface protease and the invasive character of plague, Science, vol.258, pp.1004-1007, 1992.

S. Stumpe, R. Schmid, D. L. Stephens, G. Georgiou, and E. P. Bakker, Identification of OmpT as the protease that hydrolyzes the antimicrobial peptide protamine before it enters growing cells of Escherichia coli, J. Bacteriol, vol.180, pp.4002-4006, 1998.

R. L. Tatusov, D. A. Natale, I. V. Garkavtsev, T. A. Tatusova, U. T. Shankavaram et al., The COG database: new developments in phylogenetic classification of proteins from complete genomes, Nucleic Acids Res, vol.29, pp.22-28, 2001.

S. M. Townsend, H. A. Pollack, I. Gonzalez-gomez, H. Shimada, and J. L. Badger, Citrobacter koseri brain abscess in the neonatal rat: survival and replication within human and rat macrophages, Infect. Immun, vol.71, pp.5871-5880, 2003.

A. Untergasser, I. Cutcutache, T. Koressaar, J. Ye, B. C. Faircloth et al., Primer3-new capabilities and interfaces, Nucleic Acids Res, vol.40, p.115, 2012.

S. L. Welkos, A. M. Friedlander, D. , and K. J. , Studies on the role of plasminogen activator in systemic infection by virulent Yersinia pestis strain C092, Microb. Pathog, vol.23, pp.211-223, 1997.

S. Whelan and N. A. Goldman, General empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach, Mol. Biol. Evol, vol.18, pp.691-699, 2001.

Y. Zhou, Y. Liang, K. H. Lynch, J. J. Dennis, and D. S. Wishart, PHAST: a fast phage search tool, Nucleic Acids Res, vol.39, 2011.

M. H. Ziwa, M. I. Matee, B. S. Kilonzo, and B. M. Hang'ombe, Evidence of Yersinia pestis DNA in rodents in plague outbreak foci in Mbulu and Karatu Districts, northern Tanzania, Tanzan. J. Health Res, vol.15, pp.152-157, 2013.