R. Podschun and U. Ullmann, Klebsiella spp. as nosocomial pathogens: Epidemiology, taxonomy, typing methods, and pathogenicity factors, Clin Microbiol Rev, vol.11, pp.589-603, 1998.

D. Moradigaravand, V. Martin, P. Sharon, and J. Parkhill, ABSTRACT, mBio, vol.8, issue.1, pp.1976-01916, 2017.
DOI : 10.1128/mBio.01976-16

J. Pendleton, S. Gorman, and B. Gilmore, Clinical relevance of the ESKAPE pathogens, Expert Review of Anti-infective Therapy, vol.12, issue.3, pp.297-308, 2013.
DOI : 10.1016/j.coph.2012.07.004

J. Du, Molecular epidemiology of extensively drug-resistant Klebsiella pneumoniae outbreak in Wenzhou, Southern China, Journal of Medical Microbiology, vol.33, issue.10, pp.1111-1118, 2016.
DOI : 10.1016/j.diagmicrobio.2015.03.017

J. Pitout, P. Nordmann, and L. Poirel, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.59, issue.10, pp.5873-5884, 2015.
DOI : 10.1128/AAC.01019-15

A. Wozniak, Porin alterations present in non-carbapenemase-producing Enterobacteriaceae with high and intermediate levels of carbapenem resistance in Chile, Journal of Medical Microbiology, vol.17, issue.12, pp.1270-1279, 2012.
DOI : 10.1111/j.1469-0691.2011.03514.x

Y. K. Tsai, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.4, pp.1485-1493, 2011.
DOI : 10.1128/AAC.01275-10

T. D. Huang, Increasing proportion of carbapenemase-producing Enterobcareriaeae and emergence of MCR-1 producer through a multicentric study among hospital-based and private laboratories in Belgium from, Eurosurveillance, vol.22, 2015.

J. Robert, A. Pantel, A. Merens, J. P. Lavigne, and M. H. Nicolas-chanoine, Incidence rates of carbapenemase-producing Enterobacteriaceae clinical isolates in France: a prospective nationwide study in 2011-12, Journal of Antimicrobial Chemotherapy, vol.20, issue.5, pp.2706-2712, 2014.
DOI : 10.1111/j.1708-8305.2012.00641.x
URL : https://hal.archives-ouvertes.fr/hal-01061610

J. Wang, Carbapenem-Nonsusceptible Enterobacteriaceae in Taiwan, PLOS ONE, vol.64, issue.3, p.121668, 2015.
DOI : 10.1371/journal.pone.0121668.s001
URL : https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0121668&type=printable

Y. Zhang, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.58, issue.2, pp.1214-1217, 2014.
DOI : 10.1128/AAC.02045-12
URL : https://hal.archives-ouvertes.fr/hal-01126336

A. Garcia-fernandez, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.56, issue.4, pp.2143-2145, 2012.
DOI : 10.1128/AAC.05308-11

M. Masi, M. Réfregiers, K. Pos, and J. Pagès, Mechanisms of envelope permeability and antibiotic influx and efflux in Gram-negative bacteria, Nature Microbiology, vol.3, issue.3, p.17001, 2017.
DOI : 10.1073/pnas.0901695106
URL : https://hal.archives-ouvertes.fr/hal-01490432

F. M. Kaczmarek, F. Dib-hajj, W. Shang, and T. D. Gootz, High-Level Carbapenem Resistance in a Klebsiella pneumoniae Clinical Isolate Is Due to the Combination of blaACT-1 ??-Lactamase Production, Porin OmpK35/36 Insertional Inactivation, and Down-Regulation of the Phosphate Transport Porin PhoE, Antimicrobial Agents and Chemotherapy, vol.50, issue.10, pp.3396-3406, 2006.
DOI : 10.1128/AAC.00285-06

V. Jarlier, M. H. Nicolas, G. Fournier, and A. Philippon, Extended Broad-Spectrum ??-Lactamases Conferring Transferable Resistance to Newer ??-Lactam Agents in Enterobacteriaceae: Hospital Prevalence and Susceptibility Patterns, Clinical Infectious Diseases, vol.10, issue.4, pp.867-878, 1988.
DOI : 10.1093/clinids/10.4.867

A. Criscuolo and S. Brisse, AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads, Genomics, vol.102, issue.5-6, pp.500-506, 2013.
DOI : 10.1016/j.ygeno.2013.07.011
URL : https://doi.org/10.1016/j.ygeno.2013.07.011

A. I. Rissman, Reordering contigs of draft genomes using the Mauve Aligner, Bioinformatics, vol.33, issue.16, pp.2071-2073, 2009.
DOI : 10.1093/nar/gki356
URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2071/16888777/btp356.pdf

, SCientiFiC REPORTS |, vol.7

K. A. Jolley, M. C. Maiden, and . Bigsdb, BIGSdb: Scalable analysis of bacterial genome variation at the population level, BMC Bioinformatics, vol.11, issue.1, p.595, 2010.
DOI : 10.1186/1471-2105-11-595

S. Bialek-davenet, Clonal Groups, Emerging Infectious Diseases, vol.20, issue.11, pp.1812-1820, 2014.
DOI : 10.3201/eid2011.140206
URL : https://hal.archives-ouvertes.fr/pasteur-01118613

E. Zankari, Identification of acquired antimicrobial resistance genes, Journal of Antimicrobial Chemotherapy, vol.3, issue.6, pp.2640-2644, 2012.
DOI : 10.1046/j.1365-2958.2002.02861.x

A. Carattoli, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.58, issue.7, pp.3895-3903, 2014.
DOI : 10.1128/AAC.02412-14

S. Bialek-davenet, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.6, pp.2795-2802, 2011.
DOI : 10.1128/AAC.00156-11

S. Bialek-davenet, Differential contribution of AcrAB and OqxAB efflux pumps to multidrug resistance and virulence in Klebsiella pneumoniae, Journal of Antimicrobial Chemotherapy, vol.30, issue.1, pp.81-88, 2015.
DOI : 10.1099/00207713-30-1-225
URL : https://hal.archives-ouvertes.fr/hal-01939541

E. Escmid, Determination of minimum inhibitory concentrations (MICs) of antibacterial agents by broth dilution, Clin Microbiol Infect, vol.9, pp.1-7, 2003.

S. Gayet, R. Chollet, G. Molle, J. M. Pagès, and J. Chevalier, Modification of Outer Membrane Protein Profile and Evidence Suggesting an Active Drug Pump in Enterobacter aerogenes Clinical Strains, Antimicrobial Agents and Chemotherapy, vol.47, issue.5, pp.1555-1559, 2003.
DOI : 10.1128/AAC.47.5.1555-1559.2003

V. Simonet, M. Mallea, D. Fourel, J. M. Bolla, and J. M. Pages, Crucial domains are conserved in Enterobacteriaceae porins, FEMS Microbiology Letters, vol.7, issue.1, pp.91-97, 1996.
DOI : 10.1128/jb.170.8.3611-3617.1988

U. O. Hasdemir, J. Chevalier, P. Nordmann, and J. M. Pages, Detection and Prevalence of Active Drug Efflux Mechanism in Various Multidrug-Resistant Klebsiella pneumoniae Strains from Turkey, Journal of Clinical Microbiology, vol.42, issue.6, pp.2701-2706, 2004.
DOI : 10.1128/JCM.42.6.2701-2706.2004

N. Philippe, In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem, PLOS ONE, vol.287, issue.9, p.138828, 2015.
DOI : 10.1371/journal.pone.0138828.s009
URL : https://hal.archives-ouvertes.fr/hal-01237665

L. Villa, C. Feudi, D. Fortini, A. García-fernández, and A. Carattoli, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.58, issue.3, pp.1707-1712, 2014.
DOI : 10.1128/AAC.01803-13

M. G. Lamarche, B. L. Wanner, S. Crepin, and J. Harel, The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis, FEMS Microbiology Reviews, vol.2, issue.3, pp.461-473, 2008.
DOI : 10.1128/JB.187.23.8088-8103.2005

S. Gardner, K. Johns, R. Tanner, and W. Mccleary, The PhoU Protein from Escherichia coli Interacts with PhoR, PstB, and Metals To Form a Phosphate-Signaling Complex at the Membrane, Journal of Bacteriology, vol.196, issue.9, pp.1741-1752, 2014.
DOI : 10.1128/JB.00029-14

M. Veleba, P. G. Higgins, G. Gonzalez, H. Seifert, and T. Schneidersa, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.56, issue.8, pp.4450-4458, 2012.
DOI : 10.1128/AAC.00456-12

E. H. Lee, Association of two resistance mechanisms in a clinical isolate of Enterobacter cloacae with high-level resistance to imipenem., Antimicrobial Agents and Chemotherapy, vol.35, issue.6, pp.1093-1098, 1991.
DOI : 10.1128/AAC.35.6.1093

P. Bidet, In Vivo Transfer of Plasmid-Encoded ACC-1 AmpC from Klebsiella pneumoniae to Escherichia coli in an Infant and Selection of Impermeability to Imipenem in K. pneumoniae, Antimicrobial Agents and Chemotherapy, vol.49, issue.8, pp.3562-3565, 2005.
DOI : 10.1128/AAC.49.8.3562-3565.2005

D. Skurnik, Development of ertapenem resistance in a patient with mediastinitis caused by Klebsiella pneumoniae producing an extended-spectrum ??-lactamase, Journal of Medical Microbiology, vol.194, issue.3, pp.115-119, 2010.
DOI : 10.1016/j.amjsurg.2007.01.023

A. Leavitt, Ertapenem Resistance among Extended-Spectrum-??-Lactamase-Producing Klebsiella pneumoniae Isolates, Journal of Clinical Microbiology, vol.47, issue.4, pp.969-974, 2009.
DOI : 10.1128/JCM.00651-08
URL : http://jcm.asm.org/content/47/4/969.full.pdf

M. Doumith, M. J. Ellington, D. M. Livermore, and N. Woodford, Molecular mechanisms disrupting porin expression in ertapenem-resistant Klebsiella and Enterobacter spp. clinical isolates from the UK, Journal of Antimicrobial Chemotherapy, vol.17, issue.1, pp.659-667, 2009.
DOI : 10.1093/clinids/17.1.120
URL : https://academic.oup.com/jac/article-pdf/63/4/659/2107098/dkp029.pdf

G. A. Jacoby, D. M. Mills, and N. Chow, Role of ??-Lactamases and Porins in Resistance to Ertapenem and Other ??-Lactams in Klebsiella pneumoniae, Antimicrobial Agents and Chemotherapy, vol.48, issue.8, pp.3203-3206, 2004.
DOI : 10.1128/AAC.48.8.3203-3206.2004
URL : http://aac.asm.org/content/48/8/3203.full.pdf

L. Cerdeira, Draft genome sequence of a CTX-M-15-producing Klebsiella pneumoniae sequence type 340 (clonal complex 258) isolate from a food-producing animal, Journal of Global Antimicrobial Resistance, vol.7, pp.67-68, 2016.
DOI : 10.1016/j.jgar.2016.07.012

G. Horna, J. Velasquez, N. Fernandez, J. Tamariz, and J. Ruiz, Characterisation of the first KPC-2-producing Klebsiella pneumoniae ST340 from Peru, Journal of Global Antimicrobial Resistance, vol.9, pp.36-40, 2017.
DOI : 10.1016/j.jgar.2016.12.011

W. M. Martin, Coproduction of KPC-2 and QnrB19 in Klebsiella pneumoniae ST340 isolate in Brazil, Diagnostic Microbiology and Infectious Disease, vol.83, issue.4, pp.375-376, 2015.
DOI : 10.1016/j.diagmicrobio.2015.09.003

G. Peirano, The importance of clonal complex 258 and IncFK2-like plasmids among a global collection of Klebsiella pneumoniae with bla KPCs, Antimicrob Agents Chemother, vol.61, pp.2610-2616, 2017.

S. G. Gardner, Genetic analysis, structural modeling, and direct coupling analysis suggest a mechanism for phosphate signaling in Escherichia coli, BMC Genetics, vol.16, issue.Suppl 2, p.2, 2015.
DOI : 10.1128/JB.185.3.1112-1115.2003
URL : https://bmcgenet.biomedcentral.com/track/pdf/10.1186/1471-2156-16-S2-S2?site=bmcgenet.biomedcentral.com

F. Santos-beneit, The Pho regulon: a huge regulatory network in bacteria, Frontiers in Microbiology, vol.6, pp.1-13, 2015.
DOI : 10.3389/fmicb.2015.00402
URL : http://journal.frontiersin.org/article/10.3389/fmicb.2015.00402/pdf

A. Brauner, O. Fridman, O. Gefen, and N. Balaban, Distinguishing between resistance, tolerance and persistence to antibiotic treatment, Nature Reviews Microbiology, vol.37, issue.5, pp.320-330, 2016.
DOI : 10.1007/s00284-009-9395-x

H. Van-acker and T. Coenye, The Role of Efflux and Physiological Adaptation in Biofilm Tolerance and Resistance, Journal of Biological Chemistry, vol.6, issue.24, pp.12565-12572, 2016.
DOI : 10.1128/mBio.00731-15

B. Van-den-bergh, Frequency of antibiotic application drives rapid evolutionary adaptation of Escherichia coli persistence, Nature Microbiology, vol.501, issue.5, p.16020, 2016.
DOI : 10.1046/j.1472-765X.2003.01340.x