A. C. Gales, K. A. Gordon, and W. W. Wilke, Occurrence of single-point gyrA mutations among ciprofloxacin-susceptible Escherichia coli isolates causing urinary tract infections in Latin America, Diagn Microbiol Infect Dis, vol.36, pp.61-65, 2000.

A. C. Gales, D. J. Biedenbach, and P. Winokur, Carbapenem-resistant Serratia marcescens isolates producing Bush group 2f beta-lactamase (SME-1) in the United States: results from the MYSTIC Programme, Diagn Microbiol Infect Dis, vol.39, pp.125-132, 2001.

K. C. Kugler, G. A. Denys, M. L. Wilson, and R. N. Jones, Serious streptococcal infections produced by isolates resistant to streptogramins (quinupristin/dalfopristin): case reports from the SENTRY antimicrobial surveillance program, Diagn Microbiol Infect Dis, vol.36, pp.269-72, 2000.

R. N. Jones, L. Deshpande, T. R. Fritsche, and H. S. Sader, Determination of epidemic clonality among multidrug-resistant strains of Acinetobacter spp. and Pseudomonas aeruginosa in the MYSTIC Programme (USA, 1999-2003), Diagn Microbiol Infect Dis, vol.49, pp.211-217, 2004.

L. M. Deshpande, P. R. Rhomberg, H. S. Sader, and R. N. Jones, Emergence of serine carbapenemases (KPC and SME) among clinical strains of Enterobacteriaceae isolated in the United States medical centers: report from the MYSTIC Program, 1999.

, Diagn Microbiol Infect Dis, vol.56, pp.367-72, 2006.

R. V. Goering, Pulsed field gel electrophoresis: a review of application and interpretation in the molecular epidemiology of infectious disease, Infect Genet Evol, vol.10, pp.866-75, 2010.

H. S. Sader, R. J. Hollis, and M. A. Pfaller, The use of molecular techniques in the epidemiology and control of infectious diseases, Clin Lab Med, vol.15, pp.407-438, 1995.

K. Miernyk, C. Debyle, and M. Harker-jones, Serotyping of Streptococcus pneumoniae isolates from nasopharyngeal samples: use of an algorithm combining microbiologic, serologic, and sequential multiplex PCR techniques, J Clin Microbiol, vol.49, pp.3209-3223, 2011.

R. Pai, R. E. Gertz, and B. Beall, Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus pneumoniae isolates, J Clin Microbiol, vol.44, pp.124-155, 2006.

W. W. Wilke, S. A. Marshall, and S. L. Coffman, Vancomycin-resistant Enterococcus raffinosus: molecular epidemiology, species identification error, and frequency of occurrence in a national resistance surveillance program, Diagn Microbiol Infect Dis, vol.29, pp.43-52, 1997.

S. A. Marshall, W. W. Wilke, M. A. Pfaller, and R. N. Jones, Staphylococcus aureus and coagulase-negative staphylococci from blood stream infections: frequency of occurrence, antimicrobial susceptibility, and molecular (mecA) characterization of oxacillin resistance in the SCOPE program, Diagn Microbiol Infect Dis, vol.30, pp.205-219, 1998.

G. E. Nelson, T. Pondo, and K. A. Toews, Epidemiology of invasive group A streptococcal infections in the United States, Clin Infect Dis, vol.63, pp.478-86, 2005.

B. Limbago, G. E. Fosheim, and V. Schoonover, Active Bacterial Core surveillance MRSA Investigators. Characterization of methicillin-resistant Staphylococcus aureus isolates collected in 2005 and 2006 from patients with invasive disease: a population-based analysis, J Clin Microbiol, vol.47, pp.1344-51, 2009.

R. E. Mendes, J. M. Bell, and J. D. Turnidge, Emergence and widespread dissemination of OXA-23, -24/40 and -58 carbapenemases among Acinetobacter spp. in AsiaPacific nations: report from the SENTRY surveillance program, J Antimicrob Chemother, vol.63, pp.55-64, 2009.

R. E. Mendes, K. A. Kiyota, and J. Monteiro, Rapid detection and identification of metallo-beta-lactamase-encoding genes by multiplex real-time PCR assay and melt curve analysis, J Clin Microbiol, vol.45, pp.544-551, 2007.

M. A. Pfaller, J. Acar, and R. N. Jones, Integration of molecular characterization of microorganisms in a global antimicrobial resistance surveillance program, Clin Infect Dis, vol.32, issue.2, pp.156-67, 2001.

R. N. Jones, S. A. Marshall, and M. A. Pfaller, Nosocomial enterococcal blood stream infections in the SCOPE Program: antimicrobial resistance, species occurrence, molecular testing results, and laboratory testing accuracy. SCOPE Hospital Study Group, Diagn Microbiol Infect Dis, vol.29, pp.95-102, 1997.

D. J. Diekema, M. A. Pfaller, and J. Turnidge, Sentry Participants Group. Genetic relatedness of multidrug-resistant, methicillin (oxacillin)-resistant Staphylococcus aureus bloodstream isolates from SENTRY antimicrobial resistance surveillance centers worldwide, Microb Drug Resist, vol.6, pp.213-234, 1998.

M. Castanheira, S. E. Farrell, and L. M. Deshpande, Prevalence of ?-lactamase-encoding genes among Enterobacteriaceae bacteremia isolates, p.26

U. S. , hospitals: report from the SENTRY antimicrobial surveillance program, vol.57, pp.3012-3032, 2010.

J. A. Karlowsky, S. H. Lob, and K. M. Kazmierczak, In vitro activity of imipenem against carbapenemase-positive Enterobacteriaceae isolates collected by the SMART global surveillance program from 2008 to, J Clin Microbiol, vol.55, pp.1638-1687, 2014.

H. Nitschke, P. Slickers, and E. Müller, DNA microarray-based typing of Streptococcus agalactiae isolates, J Clin Microbiol, vol.52, pp.3933-3976, 2014.

A. Sanchini, F. Campanile, and M. Monaco, DNA microarray-based characterisation of Panton-Valentine leukocidin-positive community-acquired methicillin-resistant Staphylococcus aureus from Italy, Eur J Clin Microbiol Infect Dis, vol.30, pp.1399-408, 2011.

N. J. Loman and M. J. Pallen, Twenty years of bacterial genome sequencing, Nat Rev Microbiol, vol.13, pp.787-94, 2015.

M. J. Dark, Whole-genome sequencing in bacteriology: state of the art, Infect Drug Resist, vol.6, pp.115-138, 2013.

S. J. Peacock, J. Parkhill, and N. M. Brown, Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens, Microbiology, vol.164, pp.1213-1232, 2018.

L. M. Deshpande, M. Castanheira, R. K. Flamm, and R. E. Mendes, Evolving oxazolidinone resistance mechanisms in a worldwide collection of enterococcal clinical isolates: results from the SENTRY antimicrobial surveillance program, J Antimicrob Chemother, vol.73, pp.2314-2336, 2018.

D. D. Rhoads, Commentary: lowering the barriers to routine whole genome sequencing of bacteria in the clinical microbiology laboratory, J Clin Microbiol, vol.56, pp.813-831, 2018.

Y. Yang, K. E. Niehaus, and T. M. Walker, Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data, Bioinformatics, vol.34, pp.1666-71, 2018.

R. E. Mendes, M. Castanheira, and L. N. Woosley, Molecular ?-lactamase characterization of Gram-negative pathogens recovered from patients enrolled in the ceftazidime-avibactam phase 3 trials (RECAPTURE 1 and 2) for complicated urinary tract infections: efficacies analysed against susceptible and resistant subsets, Int J Antimicrob Agents, vol.52, pp.287-92, 2018.

R. E. Mendes, M. Castanheira, and L. N. Woosley, Molecular ?-lactamase characterization of aerobic gram-negative pathogens recovered from patients enrolled in the ceftazidime-avibactam phase 3 trials for complicated intra-abdominal infections, with efficacies analyzed against susceptible and resistant subsets, Antimicrob Agents Chemother, vol.61, p.2447, 2017.

R. E. Mendes, M. Castanheira, and L. Gasink, ?-Lactamase characterization of gram-negative pathogens recovered from patients enrolled in the phase 2 trials for ceftazidime-avibactam: clinical efficacies analyzed against subsets of molecularly characterized isolates, Antimicrob Agents Chemother, vol.60, pp.1328-1363, 2015.

R. E. Mendes, H. S. Sader, and L. M. Deshpande, Characterization of baseline methicillin-resistant Staphylococcus aureus isolates recovered from phase IV clinical trial for linezolid, J Clin Microbiol, vol.48, pp.568-74, 2010.

R. E. Mendes, L. M. Deshpande, and D. S. Smyth, Characterization of methicillin-resistant Staphylococcus aureus strains recovered from a phase IV clinical trial for linezolid versus vancomycin for treatment of nosocomial pneumonia, J Clin Microbiol, vol.50, pp.3694-702, 2012.

S. J. Campbell, H. S. Deshmukh, and C. L. Nelson, Genotypic characteristics of Staphylococcus aureus isolates from a multinational trial of complicated skin and skin structure infections, J Clin Microbiol, vol.46, pp.678-84, 2008.

P. Harris, P. A. Tambyah, and D. C. Lye, Effect of piperacillin-tazobactam vs meropenem on 30-day mortality for patients with E coli or Klebsiella pneumoniae bloodstream infection and ceftriaxone resistance: a randomized clinical trial, MERINO Trial Investigators and the Australasian Society for Infectious Disease Clinical Research Network (ASID-CRN), vol.320, pp.984-94, 2018.

R. E. Mendes, D. Shortridge, and L. N. Woosley, Molecular characterization of clinical trial isolates exhibiting increased MIC results during fosfomycin (ZTI-01) treatment in a phase 2/3 clinical trial for complicated urinary tract infections (ZEUS), ASM Microbe, pp.7-11, 2018.

G. A. Atlanta,

J. D. Forbes, N. C. Knox, C. L. Peterson, and A. R. Reimer, Highlighting clinical metagenomics for enhanced diagnostic decision-making: a step towards wider implementation, Comput Struct Biotechnol J, vol.16, pp.108-128, 2018.

K. Wu, H. O'grady, and M. Workentine, Impact of ascending dosages of cadazolid or vancomycin on the intestinal microbiome during treatment of Clostridium difficile infection, Open Forum Infect Dis, vol.2, issue.1, p.149, 2015.

K. Cannon, B. Byrne, and J. Happe, Enteric microbiome profiles during a randomized phase 2 clinical trial of surotomycin versus vancomycin for the treatment of Clostridium difficile infection, J Antimicrob Chemother, vol.72, pp.3453-61, 2017.

A. J. Sabat, E. Van-zanten, and V. Akkerboom, Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identificationincreased discrimination of closely related species, Sci Rep, vol.7, p.3434, 2017.

E. Lesho, R. Clifford, and F. Onmus-leone, The challenges of implementing next generation sequencing across a large healthcare system, and the molecular epidemiology and antibiotic susceptibilities of carbapenemase-producing bacteria in the healthcare system of the U.S. Department of Defense, Plos One, vol.11, p.155770, 2016.

R. H. Deurenberg, E. Bathoorn, and M. A. Chlebowicz, The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies, Angers-Loustau A, vol.243, p.459, 2017.

E. Zankari, H. Hasman, and R. S. Kaas, Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing, J Antimicrob Chemother, vol.68, pp.771-778, 2013.

S. M. Lakin, C. Dean, and N. R. Noyes, MEGARes: an antimicrobial resistance database for high throughput sequencing, Nucleic Acids Res, vol.45, pp.574-80, 2017.

S. K. Gupta, B. R. Padmanabhan, and S. M. Diene, ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes, Antimicrob Agents Chemother, vol.58, pp.212-232, 2014.

T. J. De-man and B. M. Limbago, SSTAR, a stand-alone easy-to-use antimicrobial resistance gene predictor, mSphere, vol.1, p.50, 2016.

L. B. Rice, L. L. Carias, and A. M. Hujer, High-level expression of chromosomally encoded SHV-1 beta-lactamase and an outer membrane protein change confer resistance to ceftazidime and piperacillin-tazobactam in a clinical isolate of Klebsiella pneumoniae, Antimicrob Agents Chemother, vol.44, pp.362-369, 2000.

C. Héritier, L. Poirel, and P. E. Fournier, Characterization of the naturally occurring oxacillinase of Acinetobacter baumannii, Antimicrob Agents Chemother, vol.49, pp.4174-4183, 2005.

S. Figueiredo, L. Poirel, and A. Papa, Overexpression of the naturally occurring blaOXA-51 gene in Acinetobacter baumannii mediated by novel insertion sequence ISAba9, Antimicrob Agents Chemother, vol.53, pp.4045-4052, 2009.

L. Poirel, S. Figueiredo, and V. Cattoir, Acinetobacter radioresistens as a silent source of carbapenem resistance for Acinetobacter spp, Antimicrob Agents Chemother, vol.52, pp.1252-1258, 2008.

S. Figueiredo, R. A. Bonnin, and L. Poirel, Identification of the naturally occurring genes encoding carbapenem-hydrolysing oxacillinases from Acinetobacter haemolyticus, Acinetobacter johnsonii, and Acinetobacter calcoaceticus, Clin Microbiol Infect, vol.18, pp.907-920, 2012.

K. Shannon, H. Williams, A. King, and I. Phillips, Hyperproduction of TEM-1 beta-lactamase in clinical isolates of Escherichia coli serotype O15, FEMS Microbiol Lett, vol.55, pp.319-342, 1990.

N. D. Hanson and C. C. Sanders, Regulation of inducible AmpC beta-lactamase expression among Enterobacteriaceae, Curr Pharm Des, vol.5, pp.881-94, 1999.

G. Bou and J. Martínez-beltrán, Cloning, nucleotide sequencing, and analysis of the gene encoding an AmpC beta-lactamase in Acinetobacter baumannii, Antimicrob Agents Chemother, vol.44, pp.428-460, 2000.

M. Hamidian and R. M. Hall, Tn6168, a transposon carrying an ISAba1-activated ampC gene and conferring cephalosporin resistance in Acinetobacter baumannii, J Antimicrob Chemother, vol.69, pp.77-80, 2014.

C. Hot, N. Berthet, and O. Chesneau, Characterization of sal(A), a novel gene responsible for lincosamide and streptogramin A resistance in Staphylococcus sciuri, Antimicrob Agents Chemother, vol.58, pp.3335-3376, 2014.

H. Chalhoub, Y. Saenz, and W. W. Nichols, Loss of activity of ceftazidime-avibactam due to Mex-AB-OprM efflux and overproduction of AmpC cephalosporinase in Pseudomonas aeruginosa isolated from patients suffering from cystic fibrosis, Int J Antimicrob Agents, vol.52, pp.697-701, 2018.

B. Housseini, G. Phan, and I. Broutin, Functional mechanism of the efflux pumps transcription regulators from Pseudomonas aeruginosa based on 3D structures, Front Mol Biosci, vol.5, p.57, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02150022

P. Blanco, S. Hernando-amado, and J. A. Reales-calderon, Bacterial multidrug efflux pumps: much more than antibiotic resistance determinants, Microorganisms, vol.4, p.14, 2016.

X. Z. Li, P. Plésiat, and H. Nikaido, The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria, Clin Microbiol Rev, vol.28, pp.337-418, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01695304

B. D. Schindler and G. W. Kaatz, Multidrug efflux pumps of Gram-positive bacteria, Drug Resist Updat, vol.27, pp.1-13, 2016.

L. Martínez-martínez, Extended-spectrum beta-lactamases and the permeability barrier, Clin Microbiol Infect, vol.14, issue.1, pp.82-91, 2008.

R. A. Alm, M. R. Johnstone, and S. D. Lahiri, Characterization of Escherichia coli NDM isolates with decreased susceptibility to aztreonam/avibactam: role of a novel insertion in PBP3, J Antimicrob Chemother, vol.70, pp.1420-1428, 2015.

A. Zapun, C. Contreras-martel, and T. Vernet, Penicillin-binding proteins and beta-lactam resistance, FEMS Microbiol Rev, vol.32, pp.361-85, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01158934

C. R. Cannavino, R. E. Mendes, and H. S. Sader, Evolution of ceftaroline-resistant mrsa in a child with cystic fibrosis following repeated antibiotic exposure, Pediatr Infect Dis J, vol.35, pp.813-818, 2016.

E. H. Sanchez, R. E. Mendes, H. S. Sader, and G. M. Allison, In vivo emergence of ceftaroline resistance during therapy for MRSA vertebral osteomyelitis, J Antimicrob Chemother, vol.71, pp.1736-1744, 2016.

R. E. Mendes, A. Tsakris, and H. S. Sader, Characterization of methicillin-resistant Staphylococcus aureus displaying increased MICs of ceftaroline, J Antimicrob Chemother, vol.67, pp.1321-1325, 2012.

. S78-?-ofid-;-?-mendes, , 2019.

M. Pringle, J. Poehlsgaard, B. Vester, and K. S. Long, Mutations in ribosomal protein L3 and 23S ribosomal RNA at the peptidyl transferase centre are associated with reduced susceptibility to tiamulin in Brachyspira spp. isolates, Mol Microbiol, vol.54, pp.1295-306, 2004.

K. S. Long, J. Poehlsgaard, and L. H. Hansen, Single 23S rRNA mutations at the ribosomal peptidyl transferase centre confer resistance to valnemulin and other antibiotics in Mycobacterium smegmatis by perturbation of the drug binding pocket, Mol Microbiol, vol.71, pp.1218-1245, 2009.

J. B. Locke, M. Hilgers, and K. J. Shaw, Mutations in ribosomal protein L3 are associated with oxazolidinone resistance in staphylococci of clinical origin, Antimicrob Agents Chemother, vol.53, pp.5275-5283, 2009.

R. N. Klitgaard, E. Ntokou, and K. Nørgaard, Mutations in the bacterial ribosomal protein l3 and their association with antibiotic resistance, Antimicrob Agents Chemother, vol.59, pp.3518-3546, 2015.

J. B. Locke, M. Hilgers, and K. J. Shaw, Novel ribosomal mutations in Staphylococcus aureus strains identified through selection with the oxazolidinones linezolid and torezolid (TR-700), Antimicrob Agents Chemother, vol.53, pp.5265-74, 2009.

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.

S. T. Gregory and A. E. Dahlberg, Erythromycin resistance mutations in ribosomal proteins L22 and L4 perturb the higher order structure of 23 S ribosomal RNA, J Mol Biol, vol.289, pp.827-861, 1999.

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.

. Clsi.-m07ed11e, Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically; Approved Standard, 2018.

. Clsi.-m100ed28e, Performance Standards for Antimicrobial Susceptibility Testing: 28th Informational Supplement, 2018.

J. R. Johnson, S. Porter, P. Thuras, and M. Castanheira, Epidemic emergence in the United States of Escherichia coli sequence type 131-H30 (ST131-H30, Antimicrob Agents Chemother, vol.61, p.732, 2000.

P. Harris, B. Zakour, N. L. Roberts, and L. W. , Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27, vol.73, pp.634-676, 2017.

J. R. Bowers, B. Kitchel, and E. M. Driebe, Genomic analysis of the emergence and rapid global dissemination of the clonal group 258 Klebsiella pneumoniae pandemic, Plos One, vol.10, p.133727, 2015.

G. Peirano, P. A. Bradford, and K. M. Kazmierczak, Importance of clonal complex 258 and IncFK2-like plasmids among a global collection of Klebsiella pneumoniae with blaKPC, Antimicrob Agents Chemother, vol.61, p.2610, 2017.

B. Kitchel, J. K. Rasheed, and J. B. Patel, Molecular epidemiology of KPC-producing Klebsiella pneumoniae isolates in the United States: clonal expansion of multilocus sequence type 258, Antimicrob Agents Chemother, vol.53, pp.3365-70, 2009.

G. Cuzon, T. Naas, and H. Truong, Worldwide diversity of Klebsiella pneumoniae that produce beta-lactamase bla KPC-2 gene, Emerg Infect Dis, vol.16, pp.1349-56, 2010.

D. Mathai, R. N. Jones, and M. A. Pfaller, Epidemiology and frequency of resistance among pathogens causing urinary tract infections in 1,510 hospitalized patients: a report from the SENTRY Antimicrobial Surveillance Program (North America), Diagn Microbiol Infect Dis, vol.40, pp.129-165, 2001.

D. J. Biedenbach, G. J. Moet, and R. N. Jones, Occurrence and antimicrobial resistance pattern comparisons among bloodstream infection isolates from the SENTRY Antimicrobial Surveillance Program, Diagn Microbiol Infect Dis, vol.50, pp.59-69, 1997.

P. L. Winokur, R. Canton, J. M. Casellas, and N. Legakis, Variations in the prevalence of strains expressing an extended-spectrum beta-lactamase phenotype and characterization of isolates from Europe, the Americas, and the Western Pacific region, Clin Infect Dis, vol.32, issue.2, pp.94-103, 2001.

R. E. Mendes, L. M. Deshpande, and H. F. Bonilla, Dissemination of a pSCFS3-like cfr-carrying plasmid in Staphylococcus aureus and Staphylococcus epidermidis clinical isolates recovered from hospitals in Ohio, Antimicrob Agents Chemother, vol.57, pp.2923-2931, 2013.