%!5&#()1'&%!5, $'$(1M-&! 3&! ',?0#&-%&%! &%"P5&%Q! >&#()1'&%! ,
,#)(&-#%! ,'(! ")#! )1..&-#%! "-0.1$! -'&! #&, 1#! &(! CVQIr! 5O&]! .&%! A1;61)*"0+9! "#1'51").&?&'(! 5O&]! .&%! 0)5($#1&%! N! L#)?! '$2)(18! kiKrlQ! \&%! ".)%?13&%! 5O&]! .&%! A1 ".)%?13&! )! $($! 3$5#1(! 5O&]! !2+1+9! "\:LfK9! -'! ".)%?13&! 3&! #$%1%()'5&! )-! ,
5&!0)5($#1&5&! )-! 81, (&!-'!5, ?(!?$()0,.1M-&!M-1! 3&;#)1(! 5,'3-1#&! N! .&-#! 31%")#1(1,'! ?)1%! 1.! %&?0.&! M-&! .T);)'()2&! %$.&5(18! M-&! "&-;&'(! 52#)(1,'!3&!".)%?13&%!}! ?)1%!5&%!?$5)'1%?&%!%&?0.&'(!?)#21')-WQ!!A#)'5&%!LQ![T7#1&'!&(!%&%!5 #&'3#&! ?,01.1%)0.&! ")#! .T1'(&#?$31)1#&! 3T-'&! )1%?&!&%(!"&-(@p(#&!.)!5.$!M-1!"&#?&(! 3T&W".1M-&#!.)!"&#%1%()'5&!&(!.)!3188-%1,'!3&!(&.%!".)%?13&%Q!>&%!5)($2,#1&%!3&!".)%?13&%)%?13&%!3$5#1(%9!.,1'!3&;)'(!.&%!".)%?13&%! ?,01.1%)0.&%!18%!&(!.&-#!()1..&!%&!%1(-&!.&!".-%!%,-;&'(!)-W!).&'(,-#%!3&!dm0!&, pp.13-14 ,
$!3)'%!.)!3$',?1')(1,'!3&!5&%!3&#'1&#%!?)1%! %&!3$3-1, #2)'1%)1#&Q!\)!()1..&!3T-'!".)%?13&! 'T&%(!")%!%-881%)'(&!",-#!&'!3$3-1#&!%)!5)($2 ,
&! 3$?,'(#&!81'), #&.P;&!&'!8)1(!3T13&!1'($2#)5O)'2&!3&!3$',?1')(1,'Q!F.!%&?0.&! ,
Coagulase-Negative Staphylococcal Infections, Infectious Disease Clinics of North America, vol.23, issue.1, pp.73-98, 2009. ,
DOI : 10.1016/j.idc.2008.10.001
Role of coagulase-negative staphylococci in human disease, Veterinary Microbiology, vol.134, issue.1-2, pp.45-54, 2009. ,
DOI : 10.1016/j.vetmic.2008.09.009
URL : https://hal.archives-ouvertes.fr/hal-00532477
Pathogenesis of infections due to coagulasenegative staphylococci, The Lancet Infectious Diseases, vol.2, issue.11, pp.677-685, 2002. ,
DOI : 10.1016/S1473-3099(02)00438-3
Emergence of Coagulase-Negative Staphylococci as a Cause of Native Valve Endocarditis, Clinical Infectious Diseases, vol.43, issue.9, pp.232-242, 2008. ,
DOI : 10.1128/JCM.43.9.4751-4757.2005
URL : https://hal.archives-ouvertes.fr/hal-00465362
Species identification of coagulase-negative staphylococci: Genotyping is superior to phenotyping, Veterinary Microbiology, vol.134, issue.1-2, pp.20-28, 2009. ,
DOI : 10.1016/j.vetmic.2008.09.012
URL : https://hal.archives-ouvertes.fr/hal-00532480
Comparative Study Using Phenotypic, Genotypic, and Proteomics Methods for Identification of Coagulase-Negative Staphylococci, Journal of Clinical Microbiology, vol.50, issue.4, pp.1437-143906746, 2012. ,
DOI : 10.1128/JCM.06746-11
Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Clinical Microbiology, Clinical Infectious Diseases, vol.49, issue.8, pp.564-572, 2013. ,
DOI : 10.1128/JCM.00431-11
MALDI-TOF Mass Spectrometry: Transformative Proteomics for Clinical Microbiology, Clinical Chemistry, vol.59, issue.2, pp.340-342, 2013. ,
DOI : 10.1373/clinchem.2012.183558
Species by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry, Journal of Clinical Microbiology, vol.48, issue.3, pp.941-94500413, 2010. ,
DOI : 10.1128/JCM.00413-09
Staphylococcus epidermidis ??? the 'accidental' pathogen, Nature Reviews Microbiology, vol.271, issue.8, pp.555-567, 2009. ,
DOI : 10.1099/00221287-146-6-1419
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807625/pdf
Molecular basis of Staphylococcus epidermidis infections, Seminars in Immunopathology, vol.7, issue.12, pp.201-214, 2011. ,
DOI : 10.1038/nrmicro2182
From Clinical Microbiology to Infection Pathogenesis: How Daring To Be Different Works for Staphylococcus lugdunensis, Clinical Microbiology Reviews, vol.21, issue.1, pp.111-13300036, 2008. ,
DOI : 10.1128/CMR.00036-07
URL : http://cmr.asm.org/content/21/1/111.full.pdf
First report of a left ventricular assist device infection caused by Staphylococcus schleiferi subspecies coagulans: a coagulase-positive organism, Diagnostic Microbiology and Infectious Disease, vol.74, issue.1, pp.68-69, 2012. ,
DOI : 10.1016/j.diagmicrobio.2012.05.027
Référentiel en microbiologie médicale, 2007. ,
Référentiel en microbiologie médicale, 2010. ,
Quantitative Culture of Intravenous Catheters and Other Intravascular Inserts, Journal of Infectious Diseases, vol.141, issue.6, pp.781-786, 1980. ,
DOI : 10.1093/infdis/141.6.781
Diagnosis of central venous catheter-related sepsis. Critical level of quantitative tip cultures, Archives of Internal Medicine, vol.147, issue.5, pp.873-877, 1987. ,
DOI : 10.1001/archinte.147.5.873
MALDI-TOF-mass spectrometry applications in clinical microbiology, Future Microbiology, vol.391, issue.11, pp.1733-1754, 2010. ,
DOI : 10.1007/s00216-008-2161-2
Species distribution of coagulase-negative staphylococcal isolates at a community hospital and implications for selection of staphylococcal identification procedures, J Clin Microbiol, vol.31, pp.1318-1321, 1993. ,
???Staphylococcus pettenkoferi,??? a novel staphylococcal species isolated from clinical specimens, Diagnostic Microbiology and Infectious Disease, vol.43, issue.3, pp.175-182, 2002. ,
DOI : 10.1016/S0732-8893(02)00399-1
First Case of Osteomyelitis Caused by "Staphylococcus pettenkoferi", Journal of Clinical Microbiology, vol.45, issue.3, pp.1069-1071, 2007. ,
DOI : 10.1128/JCM.02328-06
Human bloodstream infection caused by Staphylococcus pettenkoferi, Journal of Medical Microbiology, vol.58, issue.2, pp.270-272, 2009. ,
DOI : 10.1099/jmm.0.004697-0
URL : http://jmm.microbiologyresearch.org/deliver/fulltext/jmm/58/2/270.pdf?itemId=/content/journal/jmm/10.1099/jmm.0.004697-0&mimeType=pdf&isFastTrackArticle=
Isolation of rare coagulase-negative isolates in immunocompromised patients: Staphylococcus gallinarum, Staphylococcus pettenkoferi and Staphylococcus pasteuri, Ann Clin Lab Sci, vol.42, pp.182-185, 2012. ,
Clinical Significance of Coagulase-Negative Staphylococci Recovered from Nonsterile Sites, Journal of Clinical Microbiology, vol.44, issue.9, pp.3413-341400757, 2006. ,
DOI : 10.1128/JCM.00757-06
Staphylococcus lugdunensis sp. nov. and Staphylococcus schleiferi sp. nov., Two Species from Human Clinical Specimens, International Journal of Systematic Bacteriology, vol.38, issue.2, pp.168-172, 1988. ,
DOI : 10.1099/00207713-38-2-168
Unbiased Species-Level Identification of Clinical Isolates of Coagulase-Negative Staphylococci: Does It Change the Perspective on Staphylococcus lugdunensis?, Journal of Clinical Microbiology, vol.29, issue.1, pp.292-294, 2015. ,
DOI : 10.1086/656280
Staphylococcus lugdunensis Infective Endocarditis: A Literature Review and Analysis of Risk Factors, Journal of Microbiology, Immunology and Infection, vol.43, issue.6, pp.478-484, 2010. ,
DOI : 10.1016/S1684-1182(10)60074-6
Shunt-Related Intracranial Abscess Caused by Staphylococcus lugdunensis in a Hydranencephalic Patient, World Neurosurgery, vol.80, issue.6, pp.387-389, 2013. ,
DOI : 10.1016/j.wneu.2013.01.046
Acute Necrotizing Sinusitis Caused by Staphylococcus lugdunensis: Fig. 1, Journal of Clinical Microbiology, vol.49, issue.7, pp.2740-274200722, 2011. ,
DOI : 10.1128/JCM.00722-11
URL : http://jcm.asm.org/content/49/7/2740.full.pdf
Laboratory and Clinical Characteristics of Staphylococcus lugdunensis Prosthetic Joint Infections, Journal of Clinical Microbiology, vol.48, issue.5, pp.1600-1603, 2010. ,
DOI : 10.1128/JCM.01769-09
Necrotizing fasciitis associated with Staphylococcus lugdunensis. Case Rep Infect Dis 2012: 453685, 2012. ,
DOI : 10.1155/2012/453685
URL : https://doi.org/10.1155/2012/453685
Skin and soft tissue infections caused by Staphylococcus lugdunensis: Report of 20 cases, Scandinavian Journal of Infectious Diseases, vol.51, issue.11-12, pp.879-884, 2010. ,
DOI : 10.1128/AAC.00719-06
Genotypic Diversity of Coagulase-Negative Staphylococci Causing Endocarditis: a Global Perspective, CW, International Collaboration on Endocarditis?Microbiology Investigators, pp.1780-178402405, 2008. ,
DOI : 10.1128/JCM.02405-07
URL : https://hal.archives-ouvertes.fr/hal-00464779
Hemolysins and other characteristics that help differentiate and biotype Staphylococcus lugdunensis and Staphylococcus schleiferi, J Clin Microbiol, vol.28, pp.2425-2431, 1990. ,
Characterization of the fibrinogen-binding surface protein Fbl of Staphylococcus lugdunensis, Microbiology, vol.150, issue.11, pp.3831-3841, 2004. ,
DOI : 10.1099/mic.0.27337-0
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 Research Notes, vol.4, issue.1, 2011. ,
DOI : 10.1096/fj.10-175208
Clinical and Microbiological Characteristics of 28 Patients with Staphylococcus schleiferi Infection, European Journal of Clinical Microbiology and Infectious Diseases, vol.20, issue.3, pp.153-158, 2001. ,
DOI : 10.1007/PL00011251
Case of Staphylococcus schleiferi subspecies coagulans endocarditis and metastatic infection in an immune compromised host, Transplant Infectious Disease, vol.29, issue.4, pp.336-338, 2007. ,
DOI : 10.2460/javma.2005.227.928
Infective endocarditis, The Lancet, vol.363, issue.9403, pp.139-149, 2004. ,
DOI : 10.1016/S0140-6736(03)15266-X
URL : https://hal.archives-ouvertes.fr/hal-00465409
When is coagulase-negative Staphylococcus bacteraemia clinically significant? Scand, J Infect Dis, vol.45, pp.664-671, 2013. ,
The significance of coagulase-negative staphylococci bacteremia in a low resource setting, J Infect Dev Ctries, vol.7, pp.448-452, 2013. ,
How to discriminate contamination from bloodstream infection due to coagulase-negative staphylococci: a prospective study with 654 patients, Clinical Microbiology and Infection, vol.18, issue.9, pp.355-361, 2012. ,
DOI : 10.1111/j.1469-0691.2012.03964.x
True bacteremias caused by coagulase negative Staphylococcus are difficult to distinguish from blood culture contaminants, European Journal of Clinical Microbiology & Infectious Diseases, vol.73, issue.10, pp.2639-2644, 2012. ,
DOI : 10.1128/MMBR.00005-09
Methicillin Resistance Alters the Biofilm Phenotype and Attenuates Virulence in Staphylococcus aureus Device-Associated Infections, PLoS Pathogens, vol.151, issue.4, 2012. ,
DOI : 10.1371/journal.ppat.1002626.s005
Clinical microbiology procedures handbook, 2007. ,
Ongoing Revolution in Bacteriology: Routine Identification of Bacteria by Matrix???Assisted Laser Desorption Ionization Time???of???Flight Mass Spectrometry, Clinical Infectious Diseases, vol.49, issue.4, pp.543-551, 2009. ,
DOI : 10.1086/600885
%4A)(! a6)26)342'9(cM!, 394)2!SA(!43A4(0! 24%'(94!63)4(A0(0!@A!+]9(!*0 0%! )2+A/%4'39-! ,%'0! %A00'! @(! 934)(! ,2453@(! @N2&%/A%4'39! @,394)2!A9(!%003<'%4'39!04%4'04'SA(! D3)4(! (94)(! < al. Blood cultures positive for coagulase-negative staphylococci: antisepsis, pseudobacteremia , and therapy of patients, pp.242-248, 1998. ,
Diagnosis of Central Venous Catheter-Related Sepsis, Archives of Internal Medicine, vol.147, issue.5, pp.873-880, 1987. ,
DOI : 10.1001/archinte.1987.00370050069012
biofilms, Pathogens and Disease, vol.28, issue.suppl 1, pp.321-352, 2014. ,
DOI : 10.1016/j.ijantimicag.2006.05.012
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs, Nature Protocols, vol.6577, issue.7, pp.1260-84, 2012. ,
DOI : 10.1186/gb-2008-9-3-r55
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-77, 2012. ,
DOI : 10.1089/cmb.2012.0021
Integrative genomics viewer, Nature Biotechnology, vol.306, issue.1, pp.24-30, 2011. ,
DOI : 10.1093/bioinformatics/btp472
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346182/pdf
Bayesian Modeling Using WinBUGS, 2009. ,
DOI : 10.1002/9780470434567
SignalP 4.0: discriminating signal peptides from transmembrane regions, Nature Methods, vol.6, issue.10, pp.785-791, 2011. ,
DOI : 10.1016/0005-2795(75)90109-9
Clinical and Microbiological Characteristics of Community-Acquired Staphylococcus lugdunensis Infections in Southern Taiwan, Journal of Clinical Microbiology, vol.49, issue.8, pp.3015-3023, 2011. ,
DOI : 10.1128/JCM.01138-11
Culture with BACTEC Peds Plus/F Bottle Compared with Conventional Methods for Detection of Bacteria in Synovial Fluid, Journal of Clinical Microbiology, vol.39, issue.12, pp.4468-71, 2001. ,
DOI : 10.1128/JCM.39.12.4468-4471.2001
2015 Infectious Diseases Society of America (IDSA) Clinical Practice Guidelines for the Diagnosis and Treatment of Native Vertebral Osteomyelitis in Adults, Clinical Infectious Diseases, vol.67, issue.RR-11, pp.26-46, 2015. ,
DOI : 10.1093/rheumatology/kel228
Laboratory and Clinical Characteristics of Staphylococcus lugdunensis Prosthetic Joint Infections, Journal of Clinical Microbiology, vol.48, issue.5, pp.1600-1603, 2010. ,
DOI : 10.1128/JCM.01769-09
Patient-related medical risk factors for periprosthetic joint infection of the hip and knee, Ann Transl Med, vol.3, 2015. ,
Hyperglycemia enhances coagulation and reduces neutrophil degranulation, whereas hyperinsulinemia inhibits fibrinolysis during human endotoxemia, Blood, vol.112, issue.1, pp.82-91, 2008. ,
DOI : 10.1182/blood-2007-11-121723
URL : http://www.bloodjournal.org/content/bloodjournal/112/1/82.full.pdf
The role of microbial biofilms in prosthetic joint infections, Acta Orthopaedica, vol.351, issue.16, pp.147-58, 2015. ,
DOI : 10.1056/NEJMra040181
Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors, FEMS Microbiology Letters, vol.31, issue.1, pp.60-67, 2011. ,
DOI : 10.1016/S0167-7012(97)00090-0
Genetic and biochemical properties of an extracellular neutral metalloprotease from Staphylococcus hyicus subsp. hyicus, MGG Molecular & General Genetics, vol.242, issue.4, pp.421-451, 1994. ,
DOI : 10.1007/BF00281792
: the database of proteolytic enzymes, their substrates and inhibitors, Nucleic Acids Research, vol.42, issue.D1, pp.503-512, 2014. ,
DOI : 10.1016/j.cell.2013.05.014
Matrix metalloproteinases as master regulators of the vicious cycle of bone metastasis, Bone, vol.48, issue.1, pp.44-53, 2011. ,
DOI : 10.1016/j.bone.2010.06.007
Metalloproteinases and their natural inhibitors in inflammation and immunity, Nature Reviews Immunology, vol.300, issue.9, pp.649-65, 2013. ,
DOI : 10.1152/ajpgi.00504.2009
Clinical microbiology procedures handbook, 2010. ,
The Fibrinogen- and Fibronectin-Binding Domains of Staphylococcus aureus Fibronectin-Binding Protein A Synergistically Promote Endothelial Invasion and Experimental Endocarditis, Infection and Immunity, vol.76, issue.8, pp.3824-3855, 2008. ,
DOI : 10.1128/IAI.00405-08
Implementation of MALDI-TOF MS in routine clinical laboratories Q4 improves identification of coagulase-negative staphylococci and reveals the pathogenic role of Staphylococcus lugdunensis, Clinical Microbiology and Infection J Clin Microbiol, vol.23, pp.177-192, 2015. ,
Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors, FEMS Microbiology Letters, vol.31, issue.1, pp.60-67, 2011. ,
DOI : 10.1016/S0167-7012(97)00090-0
Laboratory and Clinical Characteristics of Staphylococcus lugdunensis Prosthetic Joint Infections, Journal of Clinical Microbiology, vol.48, issue.5, pp.1600-1603, 2010. ,
DOI : 10.1128/JCM.01769-09
Pacemaker-related Infection, Emerging Infectious Diseases, vol.11, issue.8, pp.1283-1289, 2005. ,
DOI : 10.3201/eid1108.041177
Multi-virulence locus sequence typing of Staphylococcus lugdunensis is consistent with clonal structure and reliable for epidemiological typing, J Clin Microbiol, 2014. ,
Clinical Characteristics and Outcomes of Prosthetic Joint Infection Caused by Small Colony Variant Staphylococci, mBio, vol.5, issue.5, pp.1910-191401910, 2014. ,
DOI : 10.1128/mBio.01910-14
Phenotypic Variants of Staphylococci and Their Underlying Population Distributions Following Exposure to Stress, PLoS ONE, vol.18, issue.10, p.77614, 2013. ,
DOI : 10.1371/journal.pone.0077614.s002
Staphylococcus lugdunensis : a virulent pathogen causing bone and joint infections, Clinical Microbiology and Infection, vol.22, issue.8, 2016. ,
DOI : 10.1016/j.cmi.2016.05.031
URL : https://doi.org/10.1016/j.cmi.2016.05.031
5I!:%1I!6%!6'55&%5'01!:(I!+/10,(I-!6(I!31I!F%)!)%FF0)5!%38!%35)(I-!,%'I! %3II'! F%)! )%FF0)5! %38! X! +/10,(I! B0,F6(5I! :'IF01'?6(I! :%1I! 6%! 6'55, %5'23(I! :/B)'5I! :%1I!6(!F%)%+)%F<(!:(I!,%5/)'(6I!(5!,/5<0:(IM!! ?.:0(%3%:*,!103I!%&01I!F3!)/%6'I()!31!%II(,?6%+(!A'1%6!I03I!6%!A0),(!:N31!B<)0,0I0,(! 31'23(! F03)! 6(I! R! +/10,(I! %'1I'! 23N31(! %1105%5'01! B0,F5(! :(I! '1I()5'01I-! :/6/5'01I! (5! B<%1+(,(15I! :(! 13B6/05':(I! F01B53(6IWM! 7N%1105%5'01! )(5)03&(! :(!1B(I! B0:%15(I-! :015! (5! %&(B! 31! B015(13! (1! @[! :(! ##M]! S! #`MY\M! b1&')01! "c#! :(I! I/23(1B(I! B0:%15(I! ':(15'A'(I! B0))(IF01:(15! S! :(I! F)05')01! #a\! :(I! I 6%!F)/I(1B(!:(!Y!F0II'?6(I!I:'23(IM![(I!Y!F6%I,':(I!015!31(!601+3(3)!:(! #""a!S!"XYR_!F?-!31!B015(13!(1!@[!:(!X]MR\!S!##MZ\!(5!:(!#!S!"#!I, pp.5-6011 ,
! 0?I()&%5'01! 1(! B01I5'53(! F%I! 6%! F)(3&(! :N31! 5)%1IA()5! F6%I, %35)(I! F6%I 31! F6%I,':(! :/B)'5! B<(e!'(#1*0"*,M!I3)(!0h!6(!5)%1IA()5!:! 6%! &')36(1B(! :(! '(# 1*0"*,M! b1A'1-! 103I! 1N%&01I!F%I!,'I!(1!/&':(1B(!:NV605I!:(!F%5<0+ ,
VISLISI trial, a prospective clinical study allowing identification of a new metalloprotease and putative virulence factor from Staphylococcus lugdunensis, Clinical Microbiology and Infection, vol.23, issue.5, 2016. ,
DOI : 10.1016/j.cmi.2016.12.018
URL : https://hal.archives-ouvertes.fr/hal-01703142
PHASTER: a better, faster version of the PHAST phage search tool, Nucleic Acids Research, vol.6, issue.W1, pp.16-21, 2016. ,
DOI : 10.1093/bioinformatics/bts565
ABACAS: algorithm-based automatic contiguation of assembled sequences, Bioinformatics, vol.33, issue.suppl_2, pp.1968-1969, 2009. ,
DOI : 10.1093/nar/gki356
: the coagulase-negative staphylococcus you don???t want to ignore, Expert Review of Anti-infective Therapy, vol.111, issue.10, pp.901-907, 2011. ,
DOI : 10.1161/CIRCULATIONAHA.105.165564
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-477, 2012. ,
DOI : 10.1089/cmb.2012.0021
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/pdf
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system, Nucleic Acids Research, vol.34, issue.12, pp.3533-3545, 2006. ,
DOI : 10.1093/nar/gkl471
ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.58, issue.7, pp.3895-3903, 2014. ,
DOI : 10.1128/AAC.02412-14
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database, Bioinformatics, vol.16, issue.23, pp.2672-2676, 2008. ,
DOI : 10.1093/bioinformatics/16.10.944
Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches, Pathogens, vol.4, issue.4, pp.36-56, 2014. ,
DOI : 10.1093/bib/bbn019
First Complete Genome Sequence of Two Staphylococcus epidermidis Bacteriophages, Journal of Bacteriology, vol.189, issue.5, pp.2086-2100, 2007. ,
DOI : 10.1128/JB.01637-06
URL : http://jb.asm.org/content/189/5/2086.full.pdf
Characterization of Novel Phages Isolated in Coagulase-Negative Staphylococci Reveals Evolutionary Relationships with Staphylococcus aureus Phages, Journal of Bacteriology, vol.194, issue.21, pp.5829-5839, 2012. ,
DOI : 10.1128/JB.01085-12
The Staphylococci Phages Family: An Overview, Viruses, vol.4, issue.12, pp.3316-3335, 2012. ,
DOI : 10.1371/journal.pone.0004944
URL : http://www.mdpi.com/1999-4915/4/12/3316/pdf
Fasciites n??crosantes ?? Staphylococcus lugdunensis apr??s dermolipectomie abdominale??: ?? propos de deux cas et revue de la litt??rature, Annales de Chirurgie Plastique Esth??tique, vol.59, issue.2, pp.136-139 ,
DOI : 10.1016/j.anplas.2013.12.002
IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1., Nucleic Acids Research, vol.43, issue.W1, pp.104-108, 2015. ,
DOI : 10.1093/bioinformatics/bts273
URL : https://academic.oup.com/nar/article-pdf/43/W1/W104/7476190/gkv401.pdf
Staphylococcus lugdunensis : a virulent pathogen causing bone and joint infections, Clinical Microbiology and Infection, vol.22, issue.8, pp.747-748, 2016. ,
DOI : 10.1016/j.cmi.2016.05.031
URL : https://doi.org/10.1016/j.cmi.2016.05.031
The phage integrase vector pIPI03 allows RecA -independent, site-specific labelling of Staphylococcus lugdunensis strains, Plasmid, vol.70, issue.3, pp.377-384, 2013. ,
DOI : 10.1016/j.plasmid.2013.09.001
Necrotizing fasciitis associated with Staphylococcus lugdunensis. Case Rep Infect Dis, p.453685, 2012. ,
DOI : 10.1155/2012/453685
URL : https://doi.org/10.1155/2012/453685
InterProScan 5: genome-scale protein function classification, Bioinformatics, vol.32, issue.90001, pp.1236-1240, 2014. ,
DOI : 10.1093/nar/gkh097
URL : https://academic.oup.com/bioinformatics/article-pdf/30/9/1236/653449/btu031.pdf
Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms, PLoS ONE, vol.52, issue.8, p.104984, 2014. ,
DOI : 10.1371/journal.pone.0104984.s011
The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages, Proceedings of the National Academy of Sciences, vol.167, issue.1-2, pp.5174-5179, 2005. ,
DOI : 10.1016/0378-1119(95)00714-8
Evaluation of genomic island predictors using a comparative genomics approach, BMC Bioinformatics, vol.9, issue.1, p.329, 2008. ,
DOI : 10.1186/1471-2105-9-329
Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012. ,
DOI : 10.1093/bioinformatics/btp352
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381/pdf
An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis, Journal of Bacteriology, vol.193, issue.8, pp.1854-1862, 2011. ,
DOI : 10.1128/JB.00162-10
URL : http://jb.asm.org/content/193/8/1854.full.pdf
Mobile genetic elements of Staphylococcus aureus, Cellular and Molecular Life Sciences, vol.29, issue.18, pp.3057-3071, 2010. ,
DOI : 10.1093/clinids/11.Supplement_1.S75
The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated, BMC Microbiology, vol.12, issue.1, p.104, 2012. ,
DOI : 10.1128/AEM.71.11.7504-7514.2005
Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis, Genome Biology and Evolution, vol.18, issue.5, pp.1313-1328, 2015. ,
DOI : 10.1101/gr.074492.107
Pathogenic features of clinically significant coagulase-negative staphylococci in hospital and community infections in Benin, International Journal of Medical Microbiology, vol.307, issue.1, pp.75-82, 2016. ,
DOI : 10.1016/j.ijmm.2016.11.001
Available from: https, 2016. ,
The phage-related chromosomal islands of Gram-positive bacteria, Nature Reviews Microbiology, vol.367, issue.8, pp.541-551 ,
DOI : 10.1093/clinids/11.Supplement_1.S83
Staphylococcus aureus toxins, Current Opinion in Microbiology, vol.17, pp.32-37, 2014. ,
DOI : 10.1016/j.mib.2013.11.004
Staphylococcus epidermidis ??? the 'accidental' pathogen, Nature Reviews Microbiology, vol.271, issue.8, pp.555-567, 2009. ,
DOI : 10.1099/00221287-146-6-1419
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807625/pdf
The Toxic Shock Syndrome and Staphylococcus lugdunensis Bacteremia, Annals of Internal Medicine, vol.128, issue.7, pp.603-604, 1998. ,
DOI : 10.7326/0003-4819-128-7-199804010-00029
Cadmium-resistance plasmid in Staphylococcus lugdunensis, FEMS Microbiol Lett, vol.78, pp.59-63, 1992. ,
DOI : 10.1111/j.1574-6968.1992.tb05542.x
Integrative genomics viewer, Nature Biotechnology, vol.306, issue.1, pp.24-26, 2011. ,
DOI : 10.1093/bioinformatics/btp472
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346182/pdf
: a rare but destructive cause of coagulase-negative staphylococcus infective endocarditis, European Heart Journal: Acute Cardiovascular Care, vol.29, issue.3, pp.275-280, 2014. ,
DOI : 10.1007/s10096-003-0953-z
pathogenicity islands, Microbiology and Immunology, vol.187, issue.13, pp.91-99, 2013. ,
DOI : 10.1128/JB.187.15.5301-5309.2005
Cro's role in the CI Cro bistable switch is critical for ??'s transition from lysogeny to lytic development, Genes & Development, vol.21, issue.19, pp.2461-2472, 2007. ,
DOI : 10.1101/gad.1584907
Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy, Frontiers in Microbiology, vol.6, issue.188, p.242, 2015. ,
DOI : 10.1371/journal.pone.0026041
Mobility of Plasmids, Microbiology and Molecular Biology Reviews, vol.74, issue.3, pp.434-452, 2010. ,
DOI : 10.1128/MMBR.00020-10
URL : https://hal.archives-ouvertes.fr/pasteur-01374958
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs, Nature Protocols, vol.6577, issue.7, pp.1260-1284, 2012. ,
DOI : 10.1186/gb-2008-9-3-r55
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648784/pdf
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps, Genome Biology, vol.11, issue.4, p.41, 2010. ,
DOI : 10.1186/gb-2010-11-4-r41
Fulminant Staphylococcus lugdunensis septicaemia following a pelvic varicella-zoster virus infection in an immune-deficient patient: a case report, Eur J Med Res, vol.15, pp.410-414, 2010. ,
Phages of Staphylococcus aureus and their impact on host evolution, Infection, Genetics and Evolution, vol.21, pp.593-601, 2014. ,
DOI : 10.1016/j.meegid.2013.04.022
PHAST: A Fast Phage Search Tool, Nucleic Acids Research, vol.113, issue.2, pp.347-352, 2011. ,
DOI : 10.1016/S0092-8674(03)00276-9
URL : https://academic.oup.com/nar/article-pdf/39/suppl_2/W347/7631619/gkr485.pdf
B+&(-,3! 0,3?&:,&.&B,2'/!)D,+!;71-):.,?!.)!(,B+,D,3)-,*,-1!0,3?&:,&.&B, !, vol.871793838835788831317561311878, issue.81 312608931313 <7 3 2 61282732232, pp.3-151 ,
&+)'9! 8.'(!B1+1?)'9!3&00, p.98 ,
6!, Q#G!rA)SE!! ! ! C6! O+.#)+3&-:+#, pp.1-13 ,
1)*!(8'81/0)&+! *2&*!71-')1+*!6G-&7 ,
XM!*51!31, IJM! 6G2,7)*H! ,
27'2;2*+! h ,
&U!92-'!6+! O!0)&+*!<2$'3#1&-4565750?H!D.!1805, pp.1-5 ,
A&'81 ,
+*!d!3/51!.]+&'81, 8+! 62&*!.2!.-''812'51+H!! ,
+Q+!31, &+H!! +&7+!6]5&!'+.!*%*') ,
8-&+*! 321'-75.-)1+*!!3, Z2.+&'+*!+&'1+!.2!31s=i!+'!.2!321 ,
2!Z-15.+&7+! ,27'81-+&&+H!! `+*!25'+51*!31+! '(8/1-45+!6]-&'+127'-/&!6+!7+''+! 25, 1+!-.!&]%!2!32*!6]+Q3.-72'-/&*!*51!.+! 1u.+!6+!7+''+!25'/.%*-&+!62&*!.2!9 ,
J4)0)00/4!0, %2!I-0;-(-I!, pp.12-303 ,
0CI!I-dC-30-!/3/4JI1I!e*_EOf!13!6;)Q/;J)(10! (/\)3)HJ&!EJI(&!O664&!*10;)<1)4&!9, \10!I,)0Q!IJ32;)H-!/32!B('.IJ&*0*00%2! &%$,%+-+2)2!<, pp.446-410 ,
;!DP!X)44/32!a_P![)G4-;!iL&!B('.IJ&*0*00%2, %2! S3F-0(1)3I>!D612-H1)4)7JP!U/(,)6,JI1)4)7JP!Y41310, pp.31-38 ,
C4-30-!a, 6J&!a)\13I!9:<A=! ,
J4)0)00/4!/32!I(;-6()0)00, )()\13I&!Y413&!*10;)<1)4&!9 ,
<-;(I!a`&! EH/44!Y,/37-I!13!D3:1;), )3I!13!O3(1<1)7J!/32!*-H<;/3-![/((J!O012!Y)H6)I1(1)3!13!B('.IJ&*0*00%2!&%$,%+-+2)2&! U_)E!'8D!9:<>=!T=, pp.3-3 ,
0CI!E-dC-30-!aJ6137!O3, IJ&*0*00%2!&%$,%+-+2)2!SH641-I!/!Y4)3/4!U)6C4/(1)3!E(;C0(C;-&!K&!Y413&!*10;)<1)4&! 9:<9=!?M>%MM%@%MM]&!! ,
C4-30-!_)0CI! E-dC-30-!aJ6137!)F!B ,
;1\+ OII1I(-2!_/I-;!B-I, )3pS)31W/(1)3!a1H-!)F![417I-2!aJ6137!)F!D\2C0137!D&!0)41!@!O!8):-4!a))4! F), p.213 ,
)4)71-!-(!l!4, Ea9OK"$N&!O00-II-2!%! ,
+41Q-!-4-H-3(I!)F! 7-3-(10!-\0,;)H)I)H/4!1I4/32I!)F! L, <1)4&!9:<:=!T>I1!DP!*)3Q!K*P!OW1W!9`P![)321!*P!81W-(!iP!U/4II)3!Zw&!Y)H6)H-+ I0/4-!H)2-44137!)F!B('.IJ&*0*00%2!'%/-%2!I(;/13I!12-3(1F1-I!I(;/13+I6-01F10!H, pp.7-37 ,
)3!);!6;)(-13!I-0-44-;!RP!L;),H/33!D&!Y)3gC7/(1:-!(J6-!Si! I-0;-(1)3!IJI(-HI!13!L, )3!IJI10!O012I!9-I&!9:J)(10!(J6-!Si! I-0;-(1)3!IJI(-HI&!*10;)<1)4&!*)4&!Z1))3!)F!64/IH12I!II)01/(-2&!Z*Y!*10;)<1)4&!9:<9=! "$>"MN&!! ""%&!! E/3!*144/3!OP!U-z/+*144-;!9P!a)44+91-;/!*P!-(!/4&!U)I1 ,
J4)0)00/4!0/II-((-! 0,;)H)I)H-!H-0!I(;C0(C;-I!13!0, J4)0)001!/32!, pp.3-16 ,
)3!G1(,! 04CH6137!F/0();!O!/32!F1<;)3-0(13!<132137!6;)(-13!O!()!6;-:-3(!B('.IJ&*0*00%2!'%/-%2! 13F-0(1)3!)F!, EP!iC)37!YP!^/)!^P!-(!/4&!`-J!;)4-!)F!6)4J+7/HH2&!K&!Y413&!S3:-I(&!9::==!)I![P!8)G)!<132137!6;)(-13I!/32!,-H)4JI13IP!/I!G-44!/I!)F!J610!0);;-4/(-I!13! 1I)4/(-I!)F!B4!&%$,%+-+2)2!)F!21FF-;-3(!), pp.3-37 ,
!7-3)H-I!F;)H!0)3(17I&!8, YP!Z, vol.139421, issue.3322 ,
!())4&! 8C04-10!O012I!9-I&!9, 4&!8C04-10!O012I!9-I&!9:<A=!NN>R"A+$"&!! "#T&!!, pp.63-107 ,
40-!Y&!DFF-0(I!)F!H/(;1\!H-(/44)6;)(-13/I-! 13,1<1();I!)3!<)3-!;-I), 32!);(,)2)3(10!())(,!H):-H-3(&!K&!B-3(&!9-I&!9 ,
44/QC;J!ZiE&!U;)73)I(10! E1731F10/30-!)F!*/(;1\!*-(/44)6;)(-13/I-!$!/32!a1IIC-!S3,1<1();!)F!*-(/44)6;)(-13/I-!$! D\6, II1)3!13!U;)I(, pp.4-9 ,
/44)6;)(-13/I-! 13, 21I-/I-I&!8/(&!9-:&!B;C7!B1I0):&! 9::B=!A>NTM@N]T&!!, pp.62-65 ,
)3!13!2-:10-+/II)01, 13I(!<1)F14H!13I1<1)F14H)7;/H?&!U/(,)7&!B1I&!9:<A=!#N&!!, pp.0-6 ,
3I-3!_XP!Ey;-3I-3!EK&!a, )3!<-(G--3! <1)F14H!F), pp.33-33 ,
)3!)F!64, IH12!B8O!<J!H)21F1-2!<)14137!4JI1I&!8/(&!U;)()0&!9::A=!">%MTT@%M]%&!! ,
)3!)F!64, 2I!D3WJH)4&!9 ,
J!6)G-;!)F!*O_BS+ a', %2! 1I)4/(-I&!K&!*10;)<1)4&!*-(,)2I!9:<>=!"MM>?T@A]&!! ,
)3!)F! B('.IJ&*0*00%2!&%$,%+-+2)2!-32)0, (;)310! 2-:10-I&!S3(&!K&!S3F-0(&!B1I&!SKSB!'FF&!UC<4&!S3(&!E)0&!S3F-0(&!B1I&!9:<9=!"A>-NAN+NA#&!! ,
C4-30-!F/0();I!/H)37!B('.IJ&*0*00%2! &%$,%+-+2)2!, II)012&!DC;&!K&!Y413&!*10;)<1)4&! S3F-0(&!B1I&!9:<>=!%NeNf>##%+T&, p.31 ,
J6-I!/32!6,-3)(J6-I!)F!B('.IJ&*0*00%2! &%$,%+-+2)2!1I)4/(-I!;-0):-;-2!F, <1)4&!SHHC3), pp.4-7 ,
37!bP!X))Q!*P![)I(-;!aK&!*), 1W/(1)3!)F!)3!)F!E, pp.6-9 ,
IJ&*0*00%2!&%$,%+-+2)2!X`tM]+M"!U;):12-I!, )3&!U_'E!L-3-(&!9:<A=! "$>, pp.6-7 ,
1F1-;! 6C1I! IkdC-30-;! /F13! 2-! 0/;/0(k;1I-;! I-I! 6;)6;1k(kI! <1)0,1H1dC-I! -(! I)3! -3:1;)33-H-3(! 7k31dC-&! D3F13P! 3)CI! /:)3I!, ! ,-! +*3*! 2-! #! I)C0,-I! 2-! B4! &%$,%+-+2)2!-(!2kH)(I!7k3k(1dC-I!H)<14-I&!, pp.45-46 ,
%+-+2)2! 13F-0(1)3I! /32! 1(I!!:1;C4-30, )CI!13F-0(1)3I!)F!C3CICF13/4!)<g-0(1:-!G/I!()!2-(-;H13-!(,-!I(/(1I(10/4!)3I,16!<-(G--3!(,)I-! (G)!/3213I! 1I)4/(-2! 0/H-! F;)H! 13F-0(-2! 6/(1-3(I! /32! H)I(! )F! (,)I-! 13F-0(1)3I! G-;-! )I)374J!/II)01/(-2!G1(,!)I13F-0(1)3I&!a,1I!I-0;-(-2!6;)(-13!)!)F!(,-!0)2137!I-dC-30-&!R-!/4I)!/0,1-:-2!,-!+*3*!I-dC-30137!)F! #! I(;/13I! )F! B4!&%$,%+-+2)2! /32! F)C32! (,/(! I-:-;/4! H)<14-! 7-3-(10! -4-H-3(I! <-4)37-2! ()! (,-!I-dC-30-I!/I!64, pp.6-07 ,