Isolation and identification of bacteria found in the aquatic environment

La résistance aux antibiotiques est une préoccupation mondiale et elle est associée à une mortalité élevée. Cette résistance peut être transmissible entre l'homme, l'animal et l'environnement, sous l'égide du concept de « One Health ». Les gènes de résistance aux antibiotiques sont considérés comme des facteurs majeurs de transmission de cette résistance. En particulier, le milieu aquatique est considéré comme un réservoir de résistance aux antibiotiques, et il peut contribuer à la propagation et à la circulation des gènes de résistance aux antibiotiques. Cet environnement peut jouer un rôle dans l'augmentation des niveaux de ces gènes et peut stimuler leur transfert dans d'autres organismes. En plus d'être un moyen de diffusion de la résistance aux antibiotiques chez les animaux et les humains, l'environnement aquatique est considéré comme une voie par laquelle l'introduction de gènes de résistance aux antibiotiques apparaîtra dans les écosystèmes bactériens naturels. Dans notre travail, nous nous sommes intéressés à la propagation et à la circulation des gènes de résistance aux antibiotiques chez les bactéries Gram-négatives présentes dans le milieu aquatique à Marseille, France.Les objectifs de ma thèse étaient divisés en deux parties principales : (1) donner un aperçu de la propagation de la résistance aux antibiotiques dans les eaux usées, en se concentrant sur les pays méditerranéens ; et (2) réaliser une enquête épidémiologique sur le milieu aquatique à Marseille, en commençant par la détection des bactéries productrices de BLSE, des bactéries résistantes aux carbapénèmes et des bactéries résistantes à la colistine dans l'eau de mer, l'eau douce et les eaux usées.Antibiotic resistance is a worldwide concern and it is associated with high mortality. This resistance can be transmissible between humans, animals and the environment, under the umbrella of “One Health”. Antibiotic resistance genes are considered as major factors in transmitting this resistance. Particularly, the aquatic environment is considered as a reservoir for antibiotic resistance, and it can help in the spread and the circulation of the antibiotic resistance genes (ARGs). This environment, including rivers, lakes, seawater and wastewater, may play a role in increasing the levels of ARGs and may stimulate the transfer of these genes into other organisms. Other than being a way of antibiotic resistance dissemination among animals and humans, the water environment is considered as a route by which the introductionof antibiotic resistance genes will appear in natural bacterial ecosystems. In our work, we were interested in the spread and the circulation of antibiotic resistance genes in Gram-negative bacteria present in the aquatic environment in Marseille, France.The objectives of my thesis were divided into two main parts: (1) to show an overview of the factors enhancing the development of antibiotic resistance in the environment, and the circulation of the antibiotic resistance in the wastewater, focusing on the Mediterranean countries; and (2) to do an epidemiological survey on the aquatic environment in Marseille, starting with the detection of ESBL-producing bacteria, carbapenem-resistant bacteria and colistin-resistant bacteria in seawater, freshwater and wastewater

Draft Genome Sequence of an NDM-1-Producing Sequence Type 101 (ST101) Klebsiella pneumoniae Strain, Marseille-Q1949

International audienceA pan-drug-resistant Klebsiella pneumoniae strain was isolated from the blood of a 70-year-old critically ill patient in April 2019. Interestingly, the patient recovered and was discharged home a month later. The genome of strain Marseille-Q1949 is 5,607,584-bp long and has a 57.1% G+C content and 5,467 protein-coding genes

Draft Genome Sequences of Two Multidrug-Resistant Sequence Type 405 Escherichia coli Isolates without Clinical Infection

International audienceWe present the genome sequences of two carbapenemase-producing sequence type 405 Escherichia coli clinical isolates, strains Marseille-Q1950 and Marseille-Q1951. The isolates were obtained 1 month apart during the patient’s hospitalization in Lebanon, in May (Marseille-Q1950) and June (Marseille-Q1951) 2019. The genome sizes of strains Marseille-Q1950 and Marseille-Q1951 were 5,181,515 bp and 5,213,451 bp, respectively

Trends of Multidrug-Resistant Pathogens, Difficult to Treat Bloodstream Infections, and Antimicrobial Consumption at a Tertiary Care Center in Lebanon from 2015–2020: COVID-19 Aftermath

International audienceIntroduction: We studied the trend of antimicrobial resistance and consumption at Saint George Hospital University Medical Center (SGHUMC), a tertiary care center in Beirut, Lebanon, with a focus on the SARS-CoV-2 pandemic. Materials and Methods: We calculated the isolation density/1000 patient-days (PD) of the most isolated organisms from 1 January 2015–31 December 2020 that included: E. coli (Eco), K. pneumoniae (Kp), P. aeruginosa (Pae), A. baumannii (Ab), S. aureus (Sau), and E. faecium (Efm). We considered March–December 2020 a surrogate of COVID-19. We considered one culture/patient for each antimicrobial susceptibility and excluded Staphylococcus epidermidis, Staphylococcus coagulase-negative, and Corynebacterium species. We analyzed the trends of the overall isolates, the antimicrobial susceptibilities of blood isolates (BSI), difficult-to-treat (DTR) BSI, carbapenem-resistant Enterobacteriaceae (CRE) BSI, and restricted antimicrobial consumption as daily-defined-dose/1000 PD. DTR implies resistance to carbapenems, beta-lactams, fluoroquinolones, and additional antimicrobials where applicable. Results and Discussion: After applying exclusion criteria, we analyzed 1614 blood cultures out of 8314 cultures. We isolated 85 species, most commonly Eco, at 52%. The isolation density of total BSI in 2020 decreased by 16%: 82 patients were spared from bacteremia, with 13 being DTR. The isolation density of CRE BSI/1000 PD decreased by 64% from 2019 to 2020, while VREfm BSI decreased by 34%. There was a significant decrease of 80% in Ab isolates (p-value < 0.0001). During COVID-19, restricted antimicrobial consumption decreased to 175 DDD/1000 PD (p-value < 0.0001). Total carbapenem consumption persistently decreased by 71.2% from 108DDD/1000 PD in 2015–2019 to 31 DDD/1000 PD in 2020. At SGHUMC, existing epidemics were not worsened by the pandemic. We attribute this to our unique and dynamic collaboration of antimicrobial stewardship, infection prevention and control, and infectious disease consultation