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Carbapenemase-producing Escherichia coli (CP-Ec) represents a major public health threat with a risk of dissemination in the community as has occurred for lineages producing extended-spectrum β-lactamases. To characterize the extent of CP-Ec spread in France, isolates from screening and infection samples received at the French National Reference Center (F-NRC) laboratory for carbapenemase-producing Enterobacterales were investigated. A total of 691 CP-Ec isolates collected between 2012 and 2015 and 22 isolates collected before 2012 were fully sequenced. Analysis of their genome sequences revealed some disseminating multidrug-resistant (MDR) lineages frequently acquiring diverse carbapenemase genes mainly belonging to clonal complex 23 (CC23) (sequence type 410 [ST410]) and CC10 (ST10 and ST167) and sporadic isolates, including rare ST131 isolates (n = 17). However, the most represented sequence type (ST) was ST38 (n = 92) with four disseminated lineages carrying blaOXA-48-like genes inserted in the chromosome. Globally, the most frequent carbapenemase gene (n = 457) was blaOXA-48. It was also less frequently associated with MDR isolates being the only resistance gene in 119 isolates. Thus, outside the ST38 clades, its acquisition was frequently sporadic with no sign of dissemination, reflecting the circulation of the IncL plasmid pOXA-48 in France and its high frequency of conjugation. In contrast, blaOXA-181 and blaNDM genes were often associated with the evolution of MDR E. coli lineages characterized by mutations in ftsI and ompC. IMPORTANCE Carbapenemase-producing Escherichia coli (CP-Ec) might be difficult to detect, as MICs can be very low. However, their absolute number and their proportion among carbapenem-resistant Enterobacterales have been increasing, as reported by WHO and national surveillance programs. This suggests a still largely uncharacterized community spread of these isolates. Here, we have characterized the diversity and evolution of CP-Ec isolated in France before 2016. We show that carbapenemase genes are associated with a wide variety of E. coli genomic backgrounds and a small number of dominant phylogenetic lineages. In a significant proportion of CP-Ec, the most frequent carbapenemase gene blaOXA-48, was detected in isolates lacking any other resistance gene, reflecting the dissemination of pOXA-48 plasmids, likely in the absence of any antibiotic pressure. In contrast, carbapenemase gene transfer may also occur in multidrug-resistant E. coli, ultimately giving rise to at-risk lineages encoding carbapenemases with a high potential of dissemination.

Over the last two decades, antimicrobial resistance has become a global health problem. In Gram-negative bacteria, metallo-β-lactamases (MBLs), which inactivate virtually all β-lactams, increasingly contribute to this phenomenon. The aim of this study is to characterize VIM-52, a His224Arg variant of VIM-1, identified in a clinical isolate. VIM-52 conferred lower MICs to cefepime and ceftazidime as compared to VIM-1. These results were confirmed by steady state kinetic measurements, where VIM-52 yielded a lower activity towards ceftazidime and cefepime but not against carbapenems. Residue 224 is part of the L10 loop (residues 221-241), which borders the active site. As Arg 224 and Ser 228 are both playing an important and interrelated role in enzymatic activity, stability and substrate specificity for the MBLs, targeted mutagenesis at both positions were performed and further confirmed their crucial role for substrate specificity.

Antibiotics, and particularly ß- lactams, have long been considered the ultimate weapon for the treatment of bacterial infections, because of their effectiveness, good tolerance and low cost. However, bacteria have developed mechanisms of resistance, including against β- lactams with the broadest spectrum of activity, carbapenems. The latter are considered as last resort antibiotics for the treatment of severe infections due to Gram negative bacilli in hospital. This emerging resistance to carbapenems in Enterobacteriaceae is mainly due to the expression of enzymes called carbapenemases capable of inactivating carbapenems. The worldwide exponential spread of these carbapenemase-producing enterobacteria (CPE) represents a major public health issue. Currently, the most common carbapenemases in the world are KPC (Klebsiella pneumoniae carbapenemase), NDM-1 (New Delhi metallo-β-lactamase) and OXA-48 (Oxacillinase). The first KPC was identified in 1996 in the United States, NDM-1 in 2009 in Sweden in a patient from India and OXA-48 in 2003 in Turkey. In France, OXA-48- type are the most abundant carbapenemases with nearly 70% of the EPCs. Thus, the repercussion of their dissemination and the development of new inhibitors capable of inactivating carbapenemases is becoming more and more urgent.The aims of this thesis were to better understand the mode of action of the 3 main carbapenemases from a molecular and biochemical point of view, in order to identify the structural elements necessary for their functioning, but also to lay the basis for the development of "pan-inhibitors" and noveldiagnostic tools. For this purpose, the biochemical characterization of carbapenemases of the KPC, NDM and OXA-48 type, their natural variants and mutants generated in vitro has been undertaken.We could highlight the involvement of specific residues and structural elements necessary for the hydrolysis of carbapenems. The crystallographic and NMR study as well as the in silico (modeling) studies of these enzymes and their respective mutants, allowed us to better understand the enzyme-substrate interaction mode. We could thus understand the basis of the impressive capacity of these carbapenemases to adapt and therefore to evolve according to the selection pressures exerted.In collaboration with several chemists we participated in the development of different series of "pan-inhibitors" that were able to inhibit the 3 classes of carbapenemases. Thus we could show the inhibitory properties of some compounds of the family of flavonoids including myricetin, the most active molecule. We have also been able to identify a series of compounds, imidazolines, possessing a pan- inhibitory effect with sub-micromolar IC50 values and therefore compatible with in vivo use. Finally, we participated in the development (in collaboration with the CEA) of a rapid diagnostic tool based on theimmunochromatographic, allowing the detection of EPCs in less than 15 minutes.; Les antibiotiques, et plus particulièrement les β-lactamines, furent pendant longtemps considérés comme l’arme absolue pour le traitement des infections bactériennes, du fait de leur efficacité, leur bonne tolérance et de leur faible coût. Cependant, les bactéries ont développé des mécanismes de résistance, y compris vis-à-vis des β-lactamines possédant le spectre d’activité le plus large, les carbapénèmes. Ces derniers sont considérés comme les antibiotiques de derniers recours pour le traitement des infections sévères à bacilles à Gram négatif en milieu hospitalier. Chez les entérobactéries, cette résistance émergente aux carbapénèmes est principalement due à l’expression d’enzymes appelées les carbapénèmases capables d’inactiver les carbapénèmes. L’émergence exponentielle à l’échelle mondiale de ces entérobactéries productrices de carbapénèmases (EPC) constitue un problème majeur de santé publique. Actuellement, les carbapénémases les plus répandues dans le monde sont les KPC (Klebsiella pneumoniae carbapenemase), NDM-1 (New Delhi metallo- β- lactamase) et OXA-48 (Oxacillinase). La première KPC a été identifiée en 1996 aux Etats- Unis, NDM-1 en 2009 en Suède chez une patiente en provenance d’Inde et OXA-48 en 2003 en Turquie. En France, les carbapénèmases de type OXA-48 sont largement majoritaires et représentent près de 70% des EPC. Ainsi, le retentissement de leur dissémination et le besoin de développer de nouveaux inhibiteurs capables d’inactiver les carbapénèmases se fait de plus en plus pressante.Cette thèse a pour objectif de mieux comprendre le mode d’ action de ces 3 carbapénèmases d’un point de vue moléculaire et biochimique, afin d’ identifier les éléments structuraux nécessaires à leur fonctionnement, mais aussi de poser les bases du développement de « pan-inhibiteurs » et de nouveaux outils de diagnostics. Pour cela, la caractérisation biochimique des carbapénèmases de type KPC, NDM et OXA-48, de leurs variants naturels et de mutants générés in vitro a été entreprise. Il a pu être mis en exergue l’implication de résidus spécifiques et d’éléments structuraux nécessaires à l’ hydrolyse des carbapénèmes. L ’ étude cristallographique et RMN ainsi que l’étude in silico (modélisation) de ces enzymes et de leurs mutants respectifs, nous a permis de mieux comprendre le mode d’ interaction enzyme- substrat. Nous avons ainsi pu comprendre les bases de la capacité impressionnante de ces carbapénèmases à s’adapter et à évoluer en fonction des pressions de sélections exercées.En collaborations avec différentes équipes de chimistes nous avons développés différentes séries de molécules « pan-inhibiteurs » capables d’inhiber les 3 classes de carbapénèmases. Ainsi nous avons montré un effet inhibiteur de certains composés de la famille des flavonoïdes dont la myrécétine, molécule la plus active. Nous avons également identifié une série de composés, les imidazolines, possédant un effet pan-inhibiteur avec des valeurs de CI50 sub-micromolaires et donc compatible avec une utilisation in vivo.Enfin, nous avons participé au développement (en collaboration avec le CEA) d’ un outil de diagnostic rapide basé sur l’immunochromatographie, permettant détection des EPC en moins de 15 minutes.

International audience; The global spread of carbapenemase-producing Enterobacteriaceae (CPE) that are often resistant to most, if not all, classes of antibiotics is a major public health concern. The NDM-1 carbapenemase is among the most worrisome carbapenemases given its rapid worldwide spread. We have developed and evaluated a lateral flow immunoassay (LFIA) (called the NDM LFIA) for the rapid and reliable detection of NDM-like carbapenemase-producing Enterobacteriaceae from culture colonies. We evaluated the NDM LFIA using 175 reference enterobacterial isolates with characterized β-lactamase gene content and 74 nonduplicate consecutive carbapenem-resistant clinical isolates referred for expertise to the French National Reference Center (NRC) for Antibiotic Resistance during a 1-week period (in June 2016). The reference collection included 55 non-carbapenemase producers and 120 carbapenemase producers, including 27 NDM producers. All 27 NDM-like carbapenemase producers of the reference collection were correctly detected in less than 15 min by the NDM LFIA, including 22 strains producing NDM-1, 2 producing NDM-4, 1 producing NDM-5, 1 producing NDM-7, and 1 producing NDM-9. All non-NDM-1 producers gave a negative result with the NDM LFIA. No cross-reaction was observed with carbapenemases (VIM, IMP, NDM, KPC, and OXA-48-like), extended-spectrum β-lactamases (ESBLs) (TEM, SHV, and CTX-M), AmpCs (CMY-2, DHA-2, and ACC-1), and oxacillinases (OXA-1, -2, -9, and -10). Similarly, among the 74 referred nonduplicate consecutive clinical isolates, all 7 NDM-like producers were identified. Overall, the sensitivity and specificity of the assay were 100% for NDM-like carbapenemase detection with strains cultured on agar. The NDM LFIA was efficient, rapid, and easy to implement in the routine workflow of a clinical microbiology laboratory for the confirmation of NDM-like carbapenemase-producing Enterobacteriaceae.

The global spread of carbapenemase-producing Enterobacteriaceae (CPE) that are often resistant to most, if not all, classes of antibiotics is a major public health concern. The NDM-1 carbapenemase is among the most worrisome carbapenemases given its rapid worldwide spread. We have developed and evaluated a lateral flow immunoassay (LFIA) (called the NDM LFIA) for the rapid and reliable detection of NDM-like carbapenemase-producing Enterobacteriaceae from culture colonies. We evaluated the NDM LFIA using 175 reference enterobacterial isolates with characterized β-lactamase gene content and 74 nonduplicate consecutive carbapenem-resistant clinical isolates referred for expertise to the French National Reference Center (NRC) for Antibiotic Resistance during a 1-week period (in June 2016). The reference collection included 55 non-carbapenemase producers and 120 carbapenemase producers, including 27 NDM producers. All 27 NDM-like carbapenemase producers of the reference collection were correctly detected in less than 15 min by the NDM LFIA, including 22 strains producing NDM-1, 2 producing NDM-4, 1 producing NDM-5, 1 producing NDM-7, and 1 producing NDM-9. All non-NDM-1 producers gave a negative result with the NDM LFIA. No cross-reaction was observed with carbapenemases (VIM, IMP, NDM, KPC, and OXA-48-like), extended-spectrum β-lactamases (ESBLs) (TEM, SHV, and CTX-M), AmpCs (CMY-2, DHA-2, and ACC-1), and oxacillinases (OXA-1, -2, -9, and -10). Similarly, among the 74 referred nonduplicate consecutive clinical isolates, all 7 NDM-like producers were identified. Overall, the sensitivity and specificity of the assay were 100% for NDM-like carbapenemase detection with strains cultured on agar. The NDM LFIA was efficient, rapid, and easy to implement in the routine workflow of a clinical microbiology laboratory for the confirmation of NDM-like carbapenemase-producing Enterobacteriaceae.