M. Anderson, K. A. Aly, Y. Chen, and D. Missiakas, Secretion of atypical protein substrates by the ESAT-6 secretion system of Staphylococcus aureus: ESAT-6 secretion in S. aureus, Mol. Microbiol, vol.90, pp.734-743, 2013.

I. Anguera, Staphylococcus lugdunensis infective endocarditis: description of 10 cases and analysis of native valve, prosthetic valve, and pacemaker lead endocarditis clinical profiles, Heart, vol.91, p.10, 2005.

R. D. Arbeit, W. W. Karakawa, W. F. Vann, and J. B. Robbins, Predominance of two newly described capsular polysaccharide types among clinical isolates of Staphylococcus aureus, Diagn. Microbiol. Infect. Dis, vol.2, pp.90002-90008, 1984.

X. Argemi, S. Dahyot, J. Lebeurre, Y. Hansmann, C. Ronde-oustau et al., Staphylococcus lugdunensis small colony variant conversion resulting in chronic prosthetic joint infection, Méd. Mal. Infect, vol.47, pp.498-501, 2017.

X. Argemi, V. Martin, V. Loux, S. Dahyot, J. Lebeurre et al., Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements, Genome Biol. Evol, vol.9, p.77, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01604276

X. Argemi, D. Matelska, K. Ginalski, P. Riegel, Y. Hansmann et al., Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer, BMC Genom, vol.19, p.621, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02343593

M. Arias, D. Tena, M. Apellániz, M. P. Asensio, P. Caballero et al., Skin and soft tissue infections caused by Staphylococcus lugdunensis: report of 20 cases. Scand, J. Infect. Dis, vol.42, pp.879-884, 2010.

D. Arndt, J. R. Grant, A. Marcu, T. Sajed, A. Pon et al., PHASTER: a better, faster version of the PHAST phage search tool, Nucleic Acids Res, vol.44, pp.16-21, 2016.

C. Arrecubieta, M. Lee, A. Macey, T. J. Foster, and F. D. Lowy, SdrF, a Staphylococcus epidermidis surface protein, binds type I collagen, J. Biol. Chem, vol.282, pp.18767-18776, 2007.

F. C. Beasley, E. D. Vinés, J. C. Grigg, Q. Zheng, S. Liu et al., Characterization of staphyloferrin a biosynthetic and transport mutants in Staphylococcus aureus, Mol. Microbiol, vol.72, pp.947-963, 2009.

L. Bieber and G. Kahlmeter, Staphylococcus lugdunensis in several niches of the normal skin flora, Clin. Microbiol. Infect, vol.16, pp.385-388, 2010.

S. Bocher, B. Tonning, R. L. Skov, and J. Prag, Staphylococcus lugdunensis, a common cause of skin and soft tissue infections in the community, J. Clin. Microbiol, vol.47, pp.946-950, 2009.

M. G. Bowden, W. Chen, J. Singvall, Y. Xu, S. J. Peacock et al., Identification and preliminary characterization of cell-wall-anchored proteins of Staphylococcus epidermidis, Microbiol. Read. Engl, vol.151, pp.1453-1464, 2005.

H. B. Bratcher, J. S. Bennett, and M. C. Maiden, Evolutionary and genomic insights into meningococcal biology, Future Microbiol, vol.7, pp.873-885, 2012.

M. L. Burts, A. C. Dedent, D. M. Missiakas, W. A. Williams, K. Debord et al., EsxA and EsxB are secreted by an ESAT-6-like system that is required for the pathogenesis of Staphylococcus aureus infections, Proc. Natl. Acad. Sci. U. S. A, vol.69, pp.1169-1174, 2005.

Z. Cao, M. G. Casabona, H. Kneuper, J. D. Chalmers, and T. Palmer, The type VII secretion system of Staphylococcus aureus secretes a nuclease toxin that targets competitor bacteria, Nat. Microbiol, vol.2, p.16183, 2016.

T. J. Carver, K. M. Rutherford, M. Berriman, M. Rajandream, B. G. Barrell et al., ACT: the artemis comparison tool, Bioinform. Oxf. Engl, vol.21, pp.3422-3423, 2005.

B. Chassain, L. Lemee, J. Didi, J. Thiberge, S. Brisse et al., Multilocus sequence typing analysis of staphylococcus lugdunensis implies a clonal population structure, J. Clin. Microbiol, vol.50, pp.3003-3009, 2012.

H. Chen, Y. Chang, J. Tsai, W. Hung, Y. Lin et al., New structure of phage-related islands carrying fusb and a virulence gene in fusidic acid-resistant Staphylococcus epidermidis, Antimicrob. Agents Chemother, vol.57, pp.5737-5739, 2013.

L. Chen, D. Zheng, B. Liu, J. Yang, J. et al., VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on, Nucleic Acids Res, vol.44, pp.694-697, 2016.

J. L. Cocchiaro, M. I. Gomez, A. Risley, R. Solinga, D. O. Sordelli et al., Molecular characterization of the capsule locus from non-typeable Staphylococcus aureus, Mol. Microbiol, vol.59, pp.948-960, 2006.

C. Cucarella, C. Solano, J. Valle, B. Amorena, I. Lasa et al., , 2001.

. Bap, Staphylococcus aureus surface protein involved in biofilm formation, J. Bacteriol, vol.183, pp.2888-2896

J. Dagerhamn, C. Blomberg, S. Browall, K. Sjöström, E. Morfeldt et al., Determination of accessory gene patterns predicts the same relatedness among strains of Streptococcus pneumoniae as sequencing of housekeeping genes does and represents a novel approach in molecular epidemiology, J. Clin. Microbiol, vol.46, pp.863-868, 2008.

S. Dahyot, J. Lebeurre, X. Argemi, P. François, L. Lemée et al., Multiple-locus variable number tandem repeat analysis (MLVA) and tandem repeat sequence typing (TRST), helpful tools for subtyping Staphylococcus lugdunensis, Sci. Rep, vol.8, p.11669, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02344059

S. Dahyot, J. Lebeurre, F. Laumay, X. Argemi, C. Dubos et al., fbl-typing of Staphylococcus lugdunensis: a frontline tool for epidemiological studies, but not predictive of fibrinogen binding ability, Front. Microbiol, vol.10, p.1109, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02343588

Y. Dai, Y. Wang, Q. Liu, Q. Gao, H. Lu et al., A Novel ESAT-6 secretion system-secreted protein esxx of community-associated Staphylococcus aureus lineage ST398 contributes to immune evasion and virulence, Front. Microbiol, vol.8, p.819, 2017.

J. Didi, L. Lemee, L. Gibert, J. Pons, and M. Pestel-caron, Multivirulence-locus sequence typing of Staphylococcus lugdunensis generates results consistent with a clonal population structure and is reliable for epidemiological typing, J. Clin. Microbiol, vol.52, pp.3624-3632, 2014.

N. Douiri, Y. Hansmann, N. Lefebvre, P. Riegel, M. Martin et al., Staphylococcus lugdunensis?: a virulent pathogen causing bone and joint infections, Clin. Microbiol. Infect, vol.22, pp.747-748, 2016.

P. Dufour, S. Jarraud, F. Vandenesch, T. Greenland, R. P. Novick et al., High Genetic Variability of the agr locus in Staphylococcus Species, J. Bacteriol, vol.184, pp.1180-1186, 2002.

J. R. Ebright, N. Penugonda, and W. Brown, Clinical experience with Staphylococcus lugdunensis bacteremia: a retrospective analysis, Diagn. Microbiol. Infect. Dis, vol.48, pp.17-21, 2004.

K. L. Frank, J. L. Del-pozo, P. , and R. , From clinical microbiology to infection pathogenesis: how daring to be different works for Staphylococcus lugdunensis, Clin. Microbiol. Rev, vol.21, pp.111-133, 2008.

P. K. Gupta, Single-molecule DNA sequencing technologies for future genomics research, Trends Biotechnol, vol.26, pp.602-611, 2008.

L. G. Harris, E. Dudley, H. Rohde, L. Frommelt, N. Siemssen et al., Limitations in the use of PSM?, agr, RNAIII, and biofilm formation as biomarkers to define invasive Staphylococcus epidermidis from chronic biomedical device-associated infections, Int. J. Med. Microbiol. IJMM, vol.307, pp.382-387, 2017.

A. Hatoum-aslan, I. Maniv, P. Samai, and L. A. Marraffini, Genetic characterization of antiplasmid immunity through a type III-A CRISPR-Cas system, J. Bacteriol, vol.196, pp.310-317, 2014.

S. Heilbronner, F. Hanses, I. R. Monk, P. Speziale, and T. J. Foster, Sortase a promotes virulence in experimental staphylococcus lugdunensis endocarditis, Microbiology, vol.159, pp.2141-2152, 2013.

S. Heilbronner, M. T. Holden, A. Van-tonder, J. A. Geoghegan, T. J. Foster et al., Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors, FEMS Microbiol. Lett, vol.322, pp.60-67, 2011.

B. Hellmark, B. Söderquist, M. Unemo, and Å. Nilsdotter-augustinsson, Comparison of Staphylococcus epidermidis isolated from prosthetic joint infections and commensal isolates in regard to antibiotic susceptibility, agr type, biofilm production, and epidemiology, Int. J. Med. Microbiol. IJMM, vol.303, pp.32-39, 2013.

S. Higaki, T. Kitagawa, M. Morohashi, Y. , and T. , Distribution and antimicrobial susceptibility of coagulase-negative staphylococci from skin lesions, J. Int. Med. Res, vol.27, pp.191-195, 1999.

M. T. Holden, L. Hsu, K. Kurt, L. A. Weinert, A. E. Mather et al., A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic, Genome Res, vol.23, pp.653-664, 2013.

S. Holtfreter, D. Grumann, M. Schmudde, H. T. Nguyen, P. Eichler et al., Clonal distribution of superantigen genes in clinical Staphylococcus aureus isolates, J. Clin. Microbiol, vol.45, pp.2669-2680, 2007.

S. Jarraud, G. J. Lyon, A. M. Figueiredo, L. G. Rard, F. Vandenesch et al., Exfoliatin-producing strains de?ne a fourth agr speci?city group in Staphylococcus aureus, J. Bacteriol, vol.182, p.6, 2000.

W. Jiang, P. Samai, and L. A. Marraffini, Degradation of phage transcripts by CRISPR-associated rnases enables type III CRISPR-Cas immunity, Cell, vol.164, pp.710-721, 2016.

K. Kavanagh and E. P. Reeves, Exploiting the potential of insects for in vivo pathogenicity testing of microbial pathogens, FEMS Microbiol. Rev, vol.28, pp.101-112, 2004.

S. J. Labrie, J. E. Samson, and S. Moineau, Bacteriophage resistance mechanisms, Nat. Rev. Microbiol, vol.8, pp.317-327, 2010.

D. W. Lambe, C. Jeffery, K. P. Ferguson, and M. D. Cooper, Examination of the glycocalyx of four species of Staphylococcus by transmission electron microscopy and image analysis, Microbios, vol.78, pp.133-143, 1994.

J. Lourtet-hascoët, A. Bicart-see, M. P. Félicé, G. Giordano, and E. Bonnet, Staphylococcus lugdunensis, a serious pathogen in periprosthetic joint infections: comparison to Staphylococcus aureus and Staphylococcus epidermidis, Int. J. Infect. Dis, vol.51, pp.56-61, 2016.

N. Malachowa and F. R. Deleo, Mobile genetic elements of Staphylococcus aureus, Cell. Mol. Life Sci, vol.67, pp.3057-3071, 2010.

N. Malachowa, A. R. Whitney, S. D. Kobayashi, D. E. Sturdevant, A. D. Kennedy et al., Global changes in Staphylococcus aureus gene expression in human blood, PLoS One, vol.6, p.18617, 2011.

L. Marlinghaus, K. Becker, M. Korte, S. Neumann, S. G. Gatermann et al., Construction and characterization of three knockout mutants of the fbl gene in Staphylococcus lugdunensis: characterization of isogenic mutants of fbl, APMIS, vol.120, pp.108-116, 2012.

I. H. Mchardy, J. Veltman, J. Hindler, K. Bruxvoort, M. M. Carvalho et al., Clinical and microbiological aspects of ?-lactam resistance in Staphylococcus lugdunensis, J. Clin. Microbiol, vol.55, pp.585-595, 2017.

C. Michaux, M. Sanguinetti, F. Reffuveille, Y. Auffray, B. Posteraro et al., SlyA is a transcriptional regulator involved in the virulence of Enterococcus faecalis, Infect. Immun, vol.79, pp.2638-2645, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02180937

L. R. Non and C. A. Santos, The occurrence of infective endocarditis with Staphylococcus lugdunensis bacteremia: a retrospective cohort study and systematic review, J. Infect, vol.74, pp.179-186, 2017.

R. P. Novick, G. E. Christie, and J. R. Penadés, The phage-related chromosomal islands of gram-positive bacteria, Nat. Rev. Microbiol, vol.8, pp.541-551, 2010.

R. P. Novick, R. , and G. , Staphylococcal pathogenicity islands -movers and shakers in the genomic firmament, Curr. Opin. Microbiol, vol.38, pp.197-204, 2017.

R. P. Novick and A. Subedi, The SaPIs: mobile pathogenicity islands of Staphylococcus, Chemical Immunology and Allergy, pp.42-57, 2007.

K. O'riordan and J. C. Lee, Staphylococcus aureus capsular polysaccharides, Clin. Microbiol. Rev, vol.17, pp.218-234, 2004.

F. Poitevin-later, F. Vandenesch, K. Dyke, J. Fleurette, E. et al., , 1992.

, Cadmium-resistance plasmid in Staphylococcus lugdunensis, FEMS Microbiol. Lett, vol.78, pp.59-63

V. Post, L. G. Harris, M. Morgenstern, L. Mageiros, M. D. Hitchings et al., Comparative genomics study of Staphylococcus epidermidis isolates from orthopedic-device-related infections correlated with patient outcome, J. Clin. Microbiol, vol.55, pp.3089-3103, 2017.

C. Poulsen, S. Panjikar, S. J. Holton, M. Wilmanns, and Y. Song, WXG100 protein superfamily consists of three subfamilies and exhibits an a-helical c-terminal conserved residue pattern, PLoS One, vol.9, p.12, 2014.

N. Ramarao, C. Nielsen-leroux, and D. Lereclus, The insect Galleria mellonella as a powerful infection model to investigate bacterial pathogenesis, J. Vis. Exp, vol.70, p.4392, 2012.

R. J. Roberts, M. O. Carneiro, and M. C. Schatz, The advantages of SMRT sequencing, Genome Biol, vol.14, p.405, 2013.

M. Roghmann, K. L. Taylor, A. Gupte, M. Zhan, J. A. Johnson et al., Epidemiology of capsular and surface polysaccharide in Staphylococcus aureus infections complicated by bacteraemia, J. Hosp. Infect, vol.59, pp.27-32, 2005.

C. C. Rossi, T. Souza-silva, A. V. Araújo-alves, and M. Giambiagi-demarval, CRISPR-cas systems features and the gene-reservoir role of coagulasenegative staphylococci, Front. Microbiol, vol.8, p.1545, 2017.

M. A. Sabe, N. K. Shrestha, S. Gordon, and V. Menon, Staphylococcus lugdunensis?: a rare but destructive cause of coagulase-negative staphylococcus infective endocarditis, Eur. Heart J. Acute Cardiovasc. Care, vol.3, pp.275-280, 2014.

T. Seemann, Prokka: rapid prokaryotic genome annotation, Bioinforma. Oxf. Engl, vol.30, pp.2068-2069, 2014.

N. B. Shah, D. R. Osmon, H. Fadel, R. Patel, P. C. Kohner et al., Laboratory and clinical characteristics of Staphylococcus lugdunensis prosthetic joint infections, J. Clin. Microbiol, vol.48, pp.1600-1603, 2010.

V. K. Singh, R. P. Ring, V. Aswani, M. E. Stemper, J. Kislow et al., Phylogenetic distribution and expression of a penicillin-binding protein homologue, ear and its significance in virulence of Staphylococcus aureus, J. Med. Microbiol, vol.66, pp.1811-1821, 2017.

F. Szabados, Y. Nowotny, L. Marlinghaus, M. Korte, S. Neumann et al., Occurrence of genes of putative fibrinogen binding proteins and hemolysins, as well as of their phenotypic correlates in isolates of S. lugdunensis of different origins, BMC Res. Notes, vol.4, p.113, 2011.

L. Tan, S. R. Li, B. Jiang, X. M. Hu, L. et al., Therapeutic targeting of the Staphylococcus aureus accessory gene regulator (agr) system, Front. Microbiol, vol.9, p.55, 2018.

S. Tseng, Y. Lin, J. Tsai, W. Hung, H. Chen et al., Genotypes and phenotypes of Staphylococcus lugdunensis isolates recovered from bacteremia, J. Microbiol. Immunol. Infect, vol.48, pp.397-405, 2015.

M. Unnikrishnan, C. Constantinidou, T. Palmer, and M. J. Pallen, The enigmatic esx proteins: looking beyond mycobacteria, Trends Microbiol, vol.25, pp.192-204, 2017.

N. Van-der-mee-marquet, A. Achard, L. Mereghetti, A. Danton, M. Minier et al., Staphylococcus lugdunensis infections: high frequency of inguinal area carriage, J. Clin. Microbiol, vol.41, pp.1404-1409, 2003.

Y. Wang, M. Hu, Q. Liu, J. Qin, Y. Dai et al., Role of the ESAT-6 secretion system in virulence of the emerging community-associated Staphylococcus aureus lineage ST398, Sci. Rep, vol.6, p.25163, 2016.

B. Warne, C. P. Harkins, S. R. Harris, A. Vatsiou, N. Stanley-wall et al., The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity, BMC Genomics, vol.17, p.222, 2016.

J. C. Whitney, S. B. Peterson, J. Kim, M. Pazos, A. J. Verster et al., A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria, vol.6, p.26938, 2017.

B. J. Wilkinson and K. M. Holmes, Staphylococcus aureus cell surface: capsule as a barrier to bacteriophage adsorption, Infect Immun, vol.23, pp.549-552, 1979.

C. Yeh, S. Chang, C. Cheng, J. Lin, T. Liu et al., Clinical features, outcomes, and molecular characteristics of community-and health care-associated Staphylococcus lugdunensis Infections, J. Clin. Microbiol, vol.54, pp.2051-2057, 2016.

E. Zankari, H. Hasman, S. Cosentino, M. Vestergaard, S. Rasmussen et al., Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother, vol.67, pp.2640-2644, 2012.

D. Zhang, L. M. Iyer, A. , and L. , A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems, Nucleic Acids Res, vol.39, pp.4532-4552, 2011.

A. Zipperer, M. C. Konnerth, C. Laux, A. Berscheid, D. Janek et al., Human commensals producing a novel antibiotic impair pathogen colonization, Nature, vol.535, pp.511-516, 2016.