N. Alikhan, N. K. Petty, N. L. Ben-zakour, and S. A. Beatson, BLAST ring image generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, vol.12, p.402, 2011.

C. C. Almeida, C. V. Romão, P. F. Lindley, M. Teixeira, and L. M. Saraiva, The role of the hybrid cluster protein in oxidative stress defense, J. Biol. Chem, vol.281, pp.32445-32450, 2006.

S. C. Andrews, A. K. Robinson, and F. Rodríguez-quiñones, Bacterial iron homeostasis, FEMS Microbiol. Rev, vol.27, pp.215-237, 2003.

L. Aravind, V. Anantharaman, S. Balaji, M. M. Babu, and L. M. Iyer, The many faces of the helix-turn-helix domain: transcription regulation and beyond, FEMS Microbiol. Rev, vol.29, pp.231-262, 2005.

Y. Asakura and I. Kobayashi, From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene complex, Nucleic Acids Res, vol.37, pp.3021-3031, 2009.

A. Baraniak, A. Grabowska, R. Izdebski, J. Fiett, M. Herda et al., Molecular characteristics of KPC-producing Enterobacteriaceae at the early stage of their dissemination in Poland, Antimicrob. Agents Chemother, vol.55, pp.5493-5499, 2008.

P. Belenky, J. D. Ye, C. B. Porter, N. R. Cohen, M. A. Lobritz et al., Bactericidal antibiotics induce toxic metabolic perturbations that lead to cellular damage, Cell Rep, vol.13, pp.968-980, 2015.

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. Ser. B Stat. Methodol, vol.57, pp.289-300, 1995.

J. L. Blanchard, W. Wholey, E. M. Conlon, and P. J. Pomposiello, Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks, PLOS ONE, vol.2, p.1186, 2007.

K. Bondarczuk and Z. Piotrowska-seget, Molecular basis of active copper resistance mechanisms in Gram-negative bacteria, Cell Biol. Toxicol, vol.29, pp.397-405, 2013.

R. A. Bonomo, E. M. Burd, J. Conly, B. M. Limbago, L. Poirel et al., Carbapenemase-producing organisms: a global scourge, Clin. Infect. Dis, vol.66, pp.1290-1297, 2017.

M. M. Buckner, H. T. Saw, R. N. Osagie, A. Mcnally, V. Ricci et al., Clinically relevant plasmid-host interactions indicate that transcriptional and not genomic modifications ameliorate fitness costs of Klebsiella pneumoniae carbapenemase-carrying plasmids, MBio, vol.9, pp.2303-2320, 2018.

A. Carattoli, E. Zankari, A. García-fernández, M. Voldby-larsen, O. Lund et al., In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing, Antimicrob. Agents Chemother, vol.58, pp.3895-3903, 2014.

T. Carver, M. Berriman, A. Tivey, C. Patel, U. Böhme et al., Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database, Bioinformatics, vol.24, pp.2672-2676, 2008.

L. Chen, K. D. Chavda, R. G. Melano, M. R. Jacobs, B. Koll et al., Comparative genomic analysis of KPC-encoding pKpQILlike plasmids and their distribution in New Jersey and New York Hospitals, Antimicrob. Agents Chemother, vol.58, pp.2871-2877, 2014.

L. Chen, K. D. Chavda, R. G. Melano, M. R. Jacobs, M. H. Levi et al., Complete sequence of a bla(KPC-2)-harboring IncFII(K1) plasmid from a Klebsiella pneumoniae sequence type 258 strain, Antimicrob. Agents Chemother, vol.57, pp.1542-1545, 2013.

L. Chen, B. Mathema, K. D. Chavda, F. R. Deleo, R. A. Bonomo et al., Carbapenemase-producing Klebsiella pneumoniae: molecular and genetic decoding, Trends Microbiol, vol.22, pp.686-696, 2014.

A. Cheruvanky, N. Stoesser, A. E. Sheppard, D. W. Crook, P. S. Hoffman et al., Enhanced Klebsiella pneumoniae carbapenemase expression from a novel Tn4401 deletion, Antimicrob. Agents Chemother, vol.61, pp.25-42, 2017.

K. J. Cheung, V. Badarinarayana, D. W. Selinger, D. Janse, and G. M. Church, A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli, Genome Res, vol.13, pp.206-215, 2003.

S. Chillappagari, A. Seubert, H. Trip, O. P. Kuipers, M. A. Marahiel et al., Copper stress affects iron homeostasis by destabilizing iron-sulfur cluster formation in Bacillus subtilis, J. Bacteriol, vol.192, pp.2512-2524, 2010.

G. Cuzon, T. Naas, A. Correa, J. P. Quinn, M. Villegas et al., Dissemination of the KPC-2 carbapenemase in non-Klebsiella pneumoniae enterobacterial isolates from Colombia, Int. J. Antimicrob. Agents, vol.42, pp.59-62, 2013.

G. Cuzon, T. Naas, M. Villegas, A. Correa, J. P. Quinn et al., Wide dissemination of pseudomonas aeruginosa producing lactamase blaKPC-2 gene in Colombia, Antimicrob. Agents Chemother, vol.55, pp.5350-5353, 2011.

G. L. Daikos and A. Markogiannakis, Carbapenemaseproducing Klebsiella pneumoniae: (when) might we still consider treating with carbapenems?, Clin. Microbiol. Infect, vol.17, pp.1135-1141, 2011.

G. L. Daikos, S. Tsaousi, L. S. Tzouvelekis, I. Anyfantis, M. Psichogiou et al., Carbapenemase-producing Klebsiella pneumoniae bloodstream infections: lowering mortality by antibiotic combination schemes and the role of carbapenems, Antimicrob. Agents Chemother, vol.58, pp.2322-2328, 2014.

T. A. Davies, W. Shang, K. Bush, and R. K. Flamm, Affinity of doripenem and comparators to penicillin-binding proteins in Escherichia coli and Pseudomonas aeruginosa, Antimicrob. Agents Chemother, vol.52, pp.1510-1512, 2008.

F. R. Deleo, L. Chen, S. F. Porcella, C. A. Martens, S. D. Kobayashi et al., Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae, Proc. Natl. Acad. Sci. U.S.A, vol.111, pp.4988-4993, 2014.

M. Doumith, J. Findlay, H. Hirani, K. L. Hopkins, D. M. Livermore et al., Major role of pKpQIL-like plasmids in the early dissemination of KPC-type carbapenemases in the UK, J. Antimicrob. Chemother, vol.72, pp.2241-2248, 2017.

M. Dupont, E. Dé, R. Chollet, J. Chevalier, and J. Pagès, Enterobacter aerogenes OmpX, a cation-selective channel mar-and osmo-regulated, FEBS Lett, vol.569, pp.27-30, 2004.

D. J. Dwyer, P. A. Belenky, J. H. Yang, I. C. Macdonald, J. D. Martell et al., Antibiotics induce redox-related physiological alterations as part of their lethality, Proc. Natl. Acad. Sci. U.S.A, vol.111, pp.2100-2109, 2014.

B. Felden and V. Cattoir, Bacterial adaptation to antibiotics through regulatory RNAs, Antimicrob. Agents Chemother, vol.62, pp.2503-2520, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01764887

P. J. Finley, R. Norton, C. Austin, A. Mitchell, S. Zank et al., Unprecedented silver resistance in clinically isolated enterobacteriaceae: major implications for burn and wound management, Antimicrob. Agents Chemother, vol.59, pp.4734-4741, 2015.

S. Gama-castro, H. Salgado, A. Santos-zavaleta, D. Ledezma-tejeida, L. Muñiz-rascado et al., RegulonDB version 9.0: highlevel integration of gene regulation, coexpression, motif clustering and beyond, Nucleic Acids Res, vol.44, pp.133-143, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01460125

A. García-fernández, L. Villa, C. Carta, C. Venditti, A. Giordano et al., Klebsiella pneumoniae ST258 producing KPC-3 identified in italy carries novel plasmids and OmpK36/OmpK35 porin variants, Antimicrob. Agents Chemother, vol.56, pp.2143-2145, 2012.

K. Gerstle, K. Klätschke, U. Hahn, and N. Piganeau, The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress in E. coli, RNA Biol, vol.9, pp.458-468, 2012.

D. Girlich, R. A. Bonnin, A. Jousset, and T. Naas, Promoter characterization and expression of the blaKPC-2 gene in Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii, J. Antimicrob. Chemother, vol.72, pp.1597-1601, 2017.

S. Gottesman and V. Stout, Regulation of capsular polysaccharide synthesis in Escherichia coli K12, Mol. Microbiol, vol.5, pp.1599-1606, 1991.

M. R. Hemm, B. J. Paul, J. Miranda-ríos, A. Zhang, N. Soltanzad et al., Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies, J. Bacteriol, vol.192, pp.46-58, 2010.

C. Hidalgo-grass, G. Warburg, V. Temper, S. Benenson, A. E. Moses et al., KPC-9, a novel carbapenemase from clinical specimens in Israel, Antimicrob. Agents Chemother, vol.56, pp.6057-6059, 2012.

B. Hwang, N. Varadarajan, H. Li, S. Rodriguez, B. L. Iverson et al., Substrate specificity of the Escherichia coli outer membrane protease OmpP, J. Bacteriol, vol.189, pp.522-530, 2007.

A. B. Jousset, R. A. Bonnin, I. Rosinski-chupin, D. Girlich, G. Cuzon et al., 4.5 years within-patient evolution of a colistin resistant KPC-producing Klebsiella pneumoniae ST258, Clin. Infect. Dis, vol.67, pp.1388-1394, 2018.
URL : https://hal.archives-ouvertes.fr/in2p3-00020670

N. Kaldalu, R. Mei, L. , and K. , Killing by ampicillin and ofloxacin induces overlapping changes in Escherichia coli transcription profile, Antimicrob. Agents Chemother, vol.48, pp.890-896, 2004.

I. M. Keseler, A. Mackie, A. Santos-zavaleta, R. Billington, C. Bonavides-martínez et al., The EcoCyc database: reflecting new knowledge about Escherichia coli K-12, Nucleic Acids Res, vol.45, 2017.

T. Kieser, Factors affecting the isolation of CCC DNA from Streptomyces lividans and Escherichia coli, Plasmid, vol.12, pp.19-36, 1984.

J. Kim, Y. J. Kim, S. Seo, M. Seong, and K. Lee, Functional role of bdm during flagella biogenesis in Escherichia coli, Curr. Microbiol, vol.70, pp.369-373, 2015.

K. Kim, K. Kim, J. Choi, J. Lim, J. Lee et al., Outer membrane proteins A (OmpA) and X (OmpX) are essential for basolateral invasion of Cronobacter sakazakii, Appl. Environ. Microbiol, vol.76, pp.5188-5198, 2010.

M. A. Kohanski, D. J. Dwyer, and J. J. Collins, How antibiotics kill bacteria: from targets to networks, Nat. Rev. Microbiol, vol.8, pp.423-435, 2010.

M. A. Kohanski, D. J. Dwyer, B. Hayete, C. A. Lawrence, and J. J. Collins, A common mechanism of cellular death induced by bactericidal antibiotics, Cell, vol.130, pp.797-810, 2007.

D. Landman, C. Urban, M. Bäcker, P. Kelly, N. Shah et al., Susceptibility profiles, molecular epidemiology, and detection of KPCproducing Escherichia coli isolates from the New York City vicinity, J. Clin. Microbiol, vol.48, pp.4604-4607, 2010.

K. S. Lang, J. L. Danzeisen, W. Xu, J. , and T. J. , Transcriptome mapping of pAR060302, a blaCMY-2-positive broad-host-range IncA/C plasmid, Appl. Environ. Microbiol, vol.78, pp.3379-3386, 2012.

B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, 2009.

, Genome Biol, vol.10, p.25

A. F. Lau, H. Wang, R. A. Weingarten, S. K. Drake, A. F. Suffredini et al., A rapid matrix-assisted laser desorption ionization-time of flight mass spectrometry-based method for single-plasmid tracking in an outbreak of carbapenem-resistant Enterobacteriaceae, J. Clin. Microbiol, vol.52, pp.2804-2812, 2014.

M. E. Laubacher and S. E. Ades, The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance, J. Bacteriol, vol.190, pp.2065-2074, 2008.

G. C. Lee and D. S. Burgess, Treatment of Klebsiella Pneumoniae carbapenemase (KPC) infections: a review of published case series and case reports, Ann. Clin. Microbiol. Antimicrob, vol.11, p.32, 2012.

K. J. Livak and T. D. Schmittgen, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method, Methods, vol.25, pp.402-408, 2001.

V. I. Lushchak, Adaptive response to oxidative stress: bacteria, fungi, plants and animals, Comp. Biochem. Physiol. C Toxicol. Pharmacol, vol.153, pp.175-190, 2011.

N. Majdalani and S. Gottesman, The Rcs phosphorelay: a complex signal transduction system, Annu. Rev. Microbiol, vol.59, 2005.

H. Mi, X. Huang, A. Muruganujan, H. Tang, C. Mills et al., PANTHER version 11: expanded annotation data from gene ontology and reactome pathways, and data analysis tool enhancements, Nucleic Acids Res, vol.45, pp.183-189, 2017.

B. Michel, After 30 years of study, the bacterial SOS response still surprises us, PLoS Biol, vol.3, p.255, 2005.

F. Mika and R. Hengge, Small RNAs in the control of RpoS, CsgD, and biofilm architecture of Escherichia coli, RNA Biol, vol.11, pp.494-507, 2014.

C. Miller, SOS response induction by lactams and bacterial defense against antibiotic lethality, Science, vol.305, pp.1629-1631, 2004.

A. Mortazavi, B. A. Williams, K. Mccue, L. Schaeffer, and B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nat. Methods, vol.5, pp.621-628, 2008.

T. Naas, G. Cuzon, A. Babics, N. Fortineau, I. Boytchev et al., Endoscopy-associated transmission of carbapenem-resistant Klebsiella pneumoniae producing KPC-2 ?-lactamase, J. Antimicrob. Chemother, vol.65, pp.1305-1306, 2010.

T. Naas, G. Cuzon, H. Truong, and P. Nordmann, Role of ISKpn7 and deletions in blaKPC gene expression, Antimicrob. Agents Chemother, vol.56, pp.4753-4759, 2012.

Z. Nagy, C. , and M. , Regulation of transposition in bacteria, Res. Microbiol, vol.155, pp.387-398, 2004.

S. Navon-venezia, K. Kondratyeva, and A. Carattoli, Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance, FEMS Microbiol. Rev, vol.41, pp.252-275, 2017.

C. C. Papagiannitsis, V. D. Pilato, T. Giani, P. Giakkoupi, E. Riccobono et al., Characterization of KPC-encoding plasmids from two endemic settings, Greece and Italy, J. Antimicrob. Chemother, vol.71, 2016.

S. R. Partridge, Tn4401 carrying blaKPC is inserted within another insertion in pKpQIL and related plasmids, J. Clin. Microbiol, vol.52, pp.4448-4449, 2014.

B. Py and F. Barras, Building Fe-S proteins: bacterial strategies, Nat. Rev. Microbiol, vol.8, pp.436-446, 2010.

C. Rademacher and B. Masepohl, Copper-responsive gene regulation in bacteria, Microbiology, vol.158, pp.2451-2464, 2012.

M. H. Rau, K. Bojanovi?, A. T. Nielsen, and K. S. Long, Differential expression of small RNAs under chemical stress and fed-batch fermentation in E. coli, BMC Genomics, vol.16, p.1051, 2015.

S. Ren, Q. Li, L. Xie, and J. Xie, Molecular mechanisms underlying the function diversity of ArsR family metalloregulator, Crit. Rev. Eukaryot. Gene Expr, vol.27, pp.19-35, 2017.

J. T. Robinson, H. Thorvaldsdóttir, W. Winckler, M. Guttman, E. S. Lander et al., Integrative genomics viewer, Nat. Biotechnol, vol.29, pp.24-26, 2011.

L. J. Rojas, M. Salim, E. Cober, S. S. Richter, F. Perez et al., Colistin resistance in carbapenem-resistant Klebsiella pneumoniae: laboratory detection and impact on mortality, Clin. Infect. Dis, vol.64, pp.711-718, 2017.

L. J. Rojas, G. M. Weinstock, E. De-la-cadena, L. Diaz, R. Rios et al., An analysis of the epidemic of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae: convergence of two evolutionary mechanisms creates the "Perfect Storm, J. Infect. Dis, vol.217, pp.82-92, 2018.

I. Rosinski-chupin, E. Sauvage, O. Sismeiro, A. Villain, V. Da-cunha et al., Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae, BMC Genomics, vol.16, p.419, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01169621

A. L. Roth, P. M. Kurpiel, P. D. Lister, and N. D. Hanson, bla KPC RNA expression correlates with two transcriptional start sites but not always with gene copy number in four genera of gram-negative pathogens, Antimicrob. Agents Chemother, vol.55, pp.3936-3938, 2011.

I. Ruiz-de-los-mozos, M. Vergara-irigaray, V. Segura, M. Villanueva, N. Bitarte et al., Base pairing interaction between 5 ? -and 3 ? -UTRs controls icaR mRNA translation in Staphylococcus aureus, PLoS Genet, vol.9, p.1004001, 2013.

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

S. W. Seo, D. Kim, R. Szubin, and B. O. Palsson, , 2015.

, Genome-wide reconstruction of OxyR and SoxRS transcriptional regulatory networks under oxidative stress in Escherichia coli K-12 MG1655, Cell Rep, vol.12, pp.1289-1299

S. A. Signs, J. S. Tan, S. J. Salstrom, and T. M. File, Pharmacokinetics of imipenem in serum and skin window fluid in healthy adults after intramuscular or intravenous administration, Antimicrob. Agents Chemother, vol.36, pp.1400-1403, 1992.

P. Siguier, J. Perochon, L. Lestrade, J. Mahillon, C. et al., ISfinder: the reference centre for bacterial insertion sequences, Nucleic Acids Res, vol.34, pp.32-36, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00021179

S. Sim, J. Yeom, C. Shin, W. Song, E. Shin et al., Escherichia coli ribonuclease III activity is downregulated by osmotic stress: consequences for the degradation of bdm mRNA in biofilm formation, Mol. Microbiol, vol.75, pp.413-425, 2010.

E. Singlas, Clinical pharmacokinetics of an imipenem-cilastatin combination, Presse Med, vol.19, pp.598-605, 1990.

F. Supek, M. Bo?njak, N. ?kunca, and T. ?muc, REVIGO summarizes and visualizes long lists of gene ontology terms, PLoS ONE, vol.6, p.21800, 2011.

M. Tumbarello, P. Viale, C. Viscoli, E. M. Trecarichi, F. Tumietto et al., Predictors of mortality in bloodstream infections caused by Klebsiella pneumoniae carbapenemase-producing K. pneumoniae: importance of combination therapy, Clin. Infect. Dis, vol.55, pp.943-950, 2012.

T. Uehara, T. Dinh, and T. G. Bernhardt, LytM-domain factors are required for daughter cell separation and rapid ampicillin-induced lysis in Escherichia coli, J. Bacteriol, vol.191, pp.5094-5107, 2009.

D. Van-duin, J. J. Lok, M. Earley, E. Cober, S. S. Richter et al., Colistin vs. Ceftazidime-avibactam in the treatment of infections due to carbapenem-resistant enterobacteriaceae, Clin. Infect. Dis, vol.66, pp.163-171, 2017.

H. Varet, L. Brillet-guéguen, J. Coppée, and M. Dillies, SARTools: a DESeq2-and EdgeR-based R pipeline for comprehensive differential analysis of RNA-SEQ data, PLOS ONE, vol.11, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01344179

L. Villa, A. García-fernández, D. Fortini, and A. Carattoli, Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants, J. Antimicrob. Chemother, vol.65, pp.2518-2529, 2010.

G. R. Visweswaran, A. Steen, K. Leenhouts, M. Szeliga, B. Ruban et al., AcmD, a homolog of the major autolysin AcmA of Lactococcus lactis, binds to the cell wall and contributes to cell separation and autolysis, PLoS ONE, vol.8, p.72167, 2013.

J. Vogel and K. Papenfort, Small non-coding RNAs and the bacterial outer membrane, Curr. Opin. Microbiol, vol.9, pp.605-611, 2006.

H. Weber, T. Polen, J. Heuveling, V. F. Wendisch, and R. Hengge, Genome-wide analysis of the general stress response network in Escherichia coli: ?S-dependent genes, promoters, and sigma factor selectivity, J. Bacteriol, vol.187, pp.1591-1603, 2005.

T. Weilbacher, K. Suzuki, A. K. Dubey, X. Wang, S. Gudapaty et al., A novel sRNA component of the carbon storage regulatory system of Escherichia coli, Mol. Microbiol, vol.48, pp.657-670, 2003.

S. A. Weisenberg, D. J. Morgan, R. Espinal-witter, and D. H. Larone, Clinical outcomes of patients with Klebsiella pneumoniae carbapenemase-producing K. pneumoniae after treatment with imipenem or meropenem, Diagn. Microbiol. Infect. Dis, vol.64, pp.233-235, 2009.

M. T. Wolfe, J. Heo, J. S. Garavelli, and P. W. Ludden, Hydroxylamine reductase activity of the hybrid cluster protein from Escherichia coli, J. Bacteriol, vol.184, pp.5898-5902, 2002.

M. S. Wright, F. Perez, L. Brinkac, M. R. Jacobs, K. Kaye et al., Population structure of KPC-producing Klebsiella pneumoniae isolates from midwestern U.S. Hospitals, Antimicrob. Agents Chemother, vol.58, pp.4961-4965, 2014.

M. Xiao, Y. Lai, J. Sun, G. Chen, Y. et al., Transcriptional regulation of the outer membrane porin gene ompW reveals its physiological role during the transition from the aerobic to the anaerobic lifestyle of Escherichia coli, Front. Microbiol, vol.7, p.799, 2016.

M. Xiao, X. Zhu, F. Fan, H. Xu, J. Tang et al., Osmotolerance in Escherichia coli is improved by activation of copper efflux genes or supplementation with sulfur-containing amino acids, Appl. Environ. Microbiol, vol.83, pp.3050-3066, 2017.

M. Zheng, X. Wang, L. J. Templeton, D. R. Smulski, R. A. Larossa et al., DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide, J. Bacteriol, vol.183, pp.4562-4570, 2001.

K. Zhou, L. Zhou, Q. Lim, . En, R. Zou et al., Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR, BMC Mol. Biol, vol.12, p.18, 2011.