Multilocus Sequence-Typing (MLST) is a phylogenetic technique based on the detection of differences in multiple conserved housekeeping genes. Together with powerful evaluation software, MLST provides an extensive classification scheme for highly diverse species. However, despite the increasing use of MLST as a trusted epidemiological tool, the population structure of UPEC has been poorly studied using this technique, as most of the previous studies conducted have been limited either by bias towards certain characteristics, such as antimicrobial resistance and serogroup, or included a limited number of strains. Such studies can give a false impression of the population structure due to overrepresentation of certain Sequence types (STs).In this thesis, MLST was applied to 300 E. coli isolates collected from in the North West of England between June 2007 and June 2009. Firstly, the prevalence, diversity, epidemiological relationships and phylogenetic origins of the identified STs were determined. Secondly, possible associations of key UPEC STs with other genotypic and phenotypic profiles were assessed. Thirdly, as ST131 was recently reported as one of the most successful UPEC clones, an extensive examination of isolates of this clone was carried out involving identification of multiple drug resistant subclones and attempts were made to recognise putative predictor markers for identification of the ST131 clone.MLST analysis of the studied population revealed a consistent profile of STs that occurred repeatedly in the collection. It consisted primarily of ST73 (16%) followed by ST131 (13.3%), ST69 (9%), ST95 (6.3%), ST10 (4.3%), ST127 (3.6%), ST14 (2.6%) and ST405 (1.6%) some of the STs (ST127 and ST80) in the panel have never been reported as remarkable uropathogens.The broad range of virulence factor (VF) genes screened here allowed the recognition of VF patterns significantly associated with different STs. Most notably, ST127, which, based on phylogenetic analysis, appears to be a newly evolved clone, gave the highest virulence score. This virulent genotype may permit survival of ST127 isolates in the population long enough for them to gain antibiotic resistance. In contrast, multidrug resistant isolates of the ST131 clone were defined by a low virulence score and distinctive VF profiles.Metabolic reactions have been conventionally used for the classification of bacteria into families and species. Interestingly, in the assessment of the metabolic activity of different STs, members of the ST131 clone showed a high metabolic capacity compared to those of other STs, which may compensate for the low virulence capacity and explain the virulence reported for members of this ST. In contrast, ST127 showed the lowest metabolic capacity, even though it held the highest VF-score among the commonly detected STs. Multivariate logistic regression analysis demonstrated that ST131 is best described by its fluoroquinolone resistance and possession of PAI, the ibeA gene and expression of DR antigen-specific adhesins, whereas the O25b-CTX-M-15 ST131 sub-clone was only differentiated from the rest of the ST131 clone members by the production of Extended spectrum Beta-lactamase (ESBL) enzymes.

La diffusion des entérobactéries multirésistantes aux antibiotiques (MDR) à l’échelle mondiale constitue une menace de santé publique majeure. Résistantes à au moins trois classes d’antibiotiques, les entérobactéries MDR entrainent des infections échappant aux traitements de première intention. La première partie de ce travail s’intéresse à l’épidémiologie moléculaire des souches d’entérobactéries MDR isolées dans les infections et les colonisations des patients hospitalisés en Languedoc-Roussillon, en France, et dans un pays où cette épidémiologie est encore peu connue, l’Algérie. Nous avons montré, dans notre région et au niveau national, que la résistance aux carbapénèmes était essentiellement liée à des modifications de la perméabilité membranaire (87,4% des entérobactéries résistantes, au niveau national). Dans la deuxième partie de ce travail, nous avons étudié les modulations de la perméabilité membranaire et de l’efflux chez Escherichia coli ST131, l’exemple-type d’un clone MDR. Nous avons montré que ce clone mondial présentait une remarquable adaptabilité à la pression antibiotique. Cette adaptabilité avait un impact significatif sur la virulence et le fitness de E. coli. Les capacités de formation de biofilm et la virulence chez Caenorhabditis elegans étaient augmentées chez les souches de phénotypes « efflux ». Inversement, les souches de phénotypes « imperméabilité » présentaient un faible potentiel de virulence, associé à une diminution significative de la formation de biofilm et de la mobilité par swimming. / The spread of multidrug-resistant (MDR) Enterobacteriaceae is a major public health threat worldwide. Resistant to at least three classes of antibiotics, MDR Enterobacteriaceae cause infections for which first-line treatments are inefficient. The first part of this work focused on the molecular epidemiology of MDR Enterobacteriaceae strains isolated in infections and colonizations of patients hospitalized in Languedoc-Roussillon, in France and in Algeria, a country where few data are currently available. We showed in our region and nationally, that resistance to carbapenems was mainly due to changes in membrane permeability (87.4% of resistant Enterobacteriaceae, nationally).In the second part of this work, we studied the modulation of membrane efflux and permeability in the quintessential example of an international MDR high-risk clone, Escherichia coli ST131. We showed that this global clone had a remarkable adaptability to antibiotic pressure. This adaptability had a significant impact on the virulence and the fitness of E. coli. The biofilm formation and virulence capacities in Caenorhabditis elegans model were increased in strains overexpressing an efflux system. Conversely, the strains with altered porins expression had a low potential virulence, associated with a significant reduction in biofilm formation and swimming mobility.