K. Becker, C. Heilmann, and G. Peters, Coagulase-negative staphylococci, Clin Microbiol Rev, vol.27, pp.870-926, 2014.

R. E. Mendes, L. M. Deshpande, and R. N. Jones, Linezolid update: stable in vitro activity following more than a decade of clinical use and summary of associated resistance mechanisms, Drug Resist Updat, vol.17, pp.1-12, 2014.

D. Shinabarger, Mechanism of action of the oxazolidinone antibacterial agents, Expert Opin Investig Drugs, vol.8, pp.1195-202, 1999.

J. W. Decousser, M. Desroches, and N. Bourgeois-nicolaos, Susceptibility trends including emergence of linezolid resistance among coagulasenegative staphylococci and meticillin-resistant Staphylococcus aureus from invasive infections, Int J Antimicrob Agents, vol.46, pp.622-652, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01911214

R. K. Flamm, R. E. Mendes, and P. A. Hogan, Linezolid surveillance results for the United States (LEADER Surveillance Program, Antimicrob Agents Chemother, vol.60, pp.2273-80, 2014.

B. Gu, T. Kelesidis, and S. Tsiodras, The emerging problem of linezolidresistant Staphylococcus, J Antimicrob Chemother, vol.68, pp.4-11, 2013.

D. J. Diekema and R. N. Jones, Oxazolidinone antibiotics, Lancet, vol.358, pp.1975-82, 2001.

M. H. Kollef, J. Rello, and S. K. Cammarata, Clinical cure and survival in Grampositive ventilator-associated pneumonia: retrospective analysis of two double-blind studies comparing linezolid with vancomycin, Intensive Care Med, vol.30, pp.388-94, 2004.

D. N. Wilson, F. Schluenzen, and J. M. Harms, The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning, Proc Natl Acad Sci, vol.105, pp.13339-13383, 2008.

S. Besier, A. Ludwig, and J. Zander, Linezolid resistance in Staphylococcus aureus: gene dosage effect, stability, fitness costs, and cross-resistances, Antimicrob Agents Chemother, vol.52, pp.1570-1572, 2008.

C. Kehrenberg, S. Schwarz, and L. Jacobsen, A new mechanism for chloramphenicol, florfenicol and clindamycin resistance: methylation of 23S ribosomal RNA at A2503, Mol Microbiol, vol.57, pp.1064-73, 2005.

S. M. Toh, L. Xiong, and C. A. Arias, Acquisition of a natural resistance gene renders a clinical strain of methicillin-resistant Staphylococcus aureus resistant to the synthetic antibiotic linezolid, Mol Microbiol, vol.64, pp.1506-1520, 2007.

T. Candela, J. C. Marvaud, and T. K. Nguyen, A cfr-like gene cfr(C) conferring linezolid resistance is common in Clostridium difficile, Int J Antimicrob Agents, vol.50, pp.496-500, 2017.

L. M. Deshpande, D. S. Ashcraft, and H. P. Kahn, Detection of a new cfr-like gene, cfr(B), in Enterococcus faecium isolates recovered from human specimens in the United States as part of the SENTRY Antimicrobial Surveillance Program, Antimicrob Agents Chemother, vol.59, pp.6256-61, 2015.

Y. Wang, Y. Lv, and J. Cai, A novel gene, optrA, that confers transferable resistance to oxazolidinones and phenicols and its presence in Enterococcus faecalis and Enterococcus faecium of human and animal origin, J Antimicrob Chemother, vol.70, pp.2182-90, 2015.

R. Fan, D. Li, and Y. Wang, Presence of the optrA gene in methicillinresistant Staphylococcus sciuri of porcine origin, Antimicrob Agents Chemother, vol.60, pp.7200-7205, 2016.

D. Li, Y. Wang, and S. Schwarz, Co-location of the oxazolidinone resistance genes optrA and cfr on a multiresistance plasmid from Staphylococcus sciuri, J Antimicrob Chemother, vol.71, pp.1474-1482, 2016.

J. Huang, L. Chen, and Z. Wu, Retrospective analysis of genome sequences revealed the wide dissemination of optrA in Gram-positive bacteria, J Antimicrob Chemother, vol.72, pp.614-620, 2017.

K. A. Ruggero, L. K. Schroeder, and P. C. Schreckenberger, Nosocomial superinfections due to linezolid-resistant Enterococcus faecalis: evidence for a gene dosage effect on linezolid MICs, Diagn Microbiol Infect Dis, vol.47, pp.511-514, 2003.

S. Rahim, S. K. Pillai, and H. S. Gold, Linezolid-resistant, vancomycin-resistant Enterococcus faecium infection in patients without prior exposure to linezolid, Clin Infect Dis, vol.36, pp.146-154, 2003.

G. Morales, J. J. Picazo, and E. Baos, Resistance to linezolid is mediated by the cfr gene in the first report of an outbreak of linezolid-resistant Staphylococcus aureus, Clin Infect Dis, vol.50, pp.821-826, 2010.

G. M. Sanchez, M. A. De-la-torre, and G. Morales, Clinical outbreak of linezolidresistant Staphylococcus aureus in an intensive care unit, JAMA, vol.303, pp.2260-2264, 2010.

J. Bender, B. Strommenger, and M. Steglich, Linezolid resistance in clinical isolates of Staphylococcus epidermidis from German hospitals and characterization of two cfr-carrying plasmids, J Antimicrob Chemother, vol.70, pp.1630-1638, 2015.

H. Bonilla, M. D. Huband, and J. Seidel, Multicity outbreak of linezolidresistant Staphylococcus epidermidis associated with clonal spread of a cfrcontaining strain, Clin Infect Dis, vol.51, pp.796-800, 2010.

V. Karavasilis, O. Zarkotou, and M. Panopoulou, Wide dissemination of linezolid-resistant Staphylococcus epidermidis in Greece is associated with a linezolid-dependent ST22 clone, J Antimicrob Chemother, vol.70, pp.1625-1634, 2015.

S. Kelly, J. Collins, and M. Maguire, An outbreak of colonization with linezolid-resistant Staphylococcus epidermidis in an intensive therapy unit, J Antimicrob Chemother, vol.61, pp.901-908, 2008.

L. Mihaila, G. Defrance, and E. Levesque, A dual outbreak of bloodstream infections with linezolid-resistant Staphylococcus epidermidis and Staphylococcus pettenkoferi in a liver intensive care unit, Int J Antimicrob Agents, vol.40, pp.472-476, 2012.

G. Morroni, A. Brenciani, and C. Vincenzi, A clone of linezolid-resistant Staphylococcus epidermidis bearing the G2576T mutation is endemic in an Italian hospital, J Hosp Infect, vol.94, pp.203-209, 2016.

C. O'connor, J. Powell, and C. Finnegan, Incidence, management and outcomes of the first cfr-mediated linezolid-resistant Staphylococcus epidermidis outbreak in a tertiary referral centre in the Republic of Ireland, J Hosp Infect, vol.90, pp.316-337, 2015.

C. Seral, Y. Saenz, and S. Algarate, Nosocomial outbreak of methicillinand linezolid-resistant Staphylococcus epidermidis associated with catheter-related infections in intensive care unit patients, Int J Med Microbiol, vol.301, pp.354-362, 2011.

M. Trevino, L. Martinez-lamas, R. , and P. A. , Endemic linezolidresistant Staphylococcus epidermidis in a critical care unit, Eur J Clin Microbiol Infect Dis, vol.28, pp.527-560, 2009.

B. Babouee, R. Frei, and E. Schultheiss, Comparison of the DiversiLab repetitive element PCR system with spa typing and pulsed-field gel electrophoresis for clonal characterization of methicillin-resistant Staphylococcus aureus, J Clin Microbiol, vol.49, pp.1549-55, 2011.

A. J. Grisold, G. Zarfel, and V. Strenger, Use of automated repetitivesequence-based PCR for rapid laboratory confirmation of nosocomial outbreaks, J Infect, vol.60, pp.44-51, 2010.

S. H. Wang, K. B. Stevenson, and L. Hines, Evaluation of repetitive element polymerase chain reaction for surveillance of methicillin-resistant Staphylococcus aureus at a large academic medical center and community hospitals, Diagn Microbiol Infect Dis, vol.81, pp.13-20, 2015.

D. R. Zerbino and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, pp.821-830, 2008.

D. E. Deatherage and J. E. Barrick, Identification of mutations in laboratoryevolved microbes from next-generation sequencing data using breseq, Methods Mol Biol, vol.1151, pp.165-88, 2014.

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

T. J. Treangen, B. D. Ondov, and S. Koren, The Harvest suite for rapid coregenome alignment and visualization of thousands of intraspecific microbial genomes, Genome Biol, vol.15, p.524, 2014.

K. Tamura, D. Peterson, and N. Peterson, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol, vol.28, pp.2731-2740, 2011.

J. B. Locke, J. Finn, and M. Hilgers, Structure-activity relationships of diverse oxazolidinones for linezolid-resistant Staphylococcus aureus strains possessing the cfr methyltransferase gene or ribosomal mutations, Antimicrob Agents Chemother, vol.54, pp.5337-5380, 2010.

K. S. Long and B. Vester, Resistance to linezolid caused by modifications at its binding site on the ribosome, Antimicrob Agents Chemother, vol.56, pp.603-615, 2012.

A. Wong, S. P. Reddy, and D. S. Smyth, Polyphyletic emergence of linezolidresistant staphylococci in the United States, Antimicrob Agents Chemother, vol.54, pp.742-750, 2010.

A. Liakopoulos, I. Spiliopoulou, and A. Damani, Dissemination of two international linezolid-resistant Staphylococcus epidermidis clones in Greek hospitals, J Antimicrob Chemother, vol.65, pp.1070-1071, 2010.

R. E. Mendes, L. M. Deshpande, and M. Castanheira, First report of cfr-mediated resistance to linezolid in human staphylococcal clinical isolates recovered in the United States, Antimicrob Agents Chemother, vol.52, p.2244, 2008.

H. Chen, W. Wu, and M. Ni, Linezolid-resistant clinical isolates of enterococci and Staphylococcus cohnii from a multicentre study in China: molecular epidemiology and resistance mechanisms, Int J Antimicrob Agents, vol.42, pp.317-338, 2013.

A. Brenciani, G. Morroni, and S. Pollini, Characterization of novel conjugative multiresistance plasmids carrying cfr from linezolid-resistant Staphylococcus epidermidis clinical isolates from Italy, J Antimicrob Chemother, vol.71, pp.307-320, 2016.

M. Miragaia, J. C. Thomas, and I. Couto, Inferring a population structure for Staphylococcus epidermidis from multilocus sequence typing data, J Bacteriol, vol.189, pp.2540-52, 2007.

D. Chessa, G. Ganau, and V. Mazzarello, An overview of Staphylococcus epidermidis and Staphylococcus aureus with a focus on developing countries, J Infect Dev Ctries, vol.9, pp.547-50, 2015.

F. Cafini, T. T. Nguyen-le, and M. Higashide, Horizontal gene transmission of the cfr gene to MRSA and Enterococcus: role of Staphylococcus epidermidis as a reservoir and alternative pathway for the spread of linezolid resistance, J Antimicrob Chemother, vol.71, pp.587-92, 2016.

S. J. Van-hal, T. P. Lodise, and D. L. Paterson, The clinical significance of vancomycin minimum inhibitory concentration in Staphylococcus aureus infections: a systematic review and meta-analysis, Clin Infect Dis, vol.54, pp.755-71, 2012.

, Long-lasting outbreak of linezolid-resistant CoNS