E. coli is the first causative agent among community-acquired bacteraemia and it is also the most abundant species among facultative anaerobic bacteria in human gastro-intestinal tract (Tenaillon et al., Nat. Rev. Microbiol, 2010; Martin et al., N. Engl. J. Med., 2003). To understand the physiopathology of extra-intestinal infections, many traits should be taken into account including host factors, portal of entry, genetic and metabolic factors of each strain. Moreover, the world-wide epidemiology of E. coli infections including E. coli bloodstream infections (BSI) has been profoundly modified since 2000 with the emergence of strains resistant to 3rd generation cephalosporins (3GC), specifically strains producing extended-spectrum ?-lactamases (ESBL), in both hospitals and the community (Courpon-Claudinon et al., Clin Microbiol Infect., 2011).
EVRest team from IAME laboratory (Inserm UMR1137) (http://www.iame-research.center/) started a research project, named “Septicoli”, for which they received funds from French National Research Agency (ANR-15-CE17-0019). The overall aim of this study is to describe prognostic and severity factors associated with BSI by E. coli, in the context of these major epidemiological shifts. Investigators plan to include 500 adults with E. coli BSI hospitalized in one of the 7 hospitals participating in this study, and sequenced each strains isolated from blood culture.
Guilhem Royer, a PHD student in our team who received grant from APHP (Assistance Publique des Hôpitaux de Paris) and CEA (Commissariat à l’énergie atomique et aux énergies alternatives), will achieve bioinformatics analysis of these strains. We plan to study genetic background, focusing on phylogenetic, antimicrobial resistance, virulence traits, and also metabolic pathways using a pangenome-based approach (Koonin et al., Nucleic Acids Res., 2008) in order to identify specific associations between bacterial characters and clinical data such as disease severity or the portal of entry.
References
Courpon-Claudinon A, Lefort A, Panhard X, et al.
Clin Microbiol Infect. 2011 Apr;17(4):557-65.
Koonin EV, Wolf YI.
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.
Nucleic Acids Res. 2008 Dec;36(21):6688-719.
Martin GS, Mannino DM, Eaton S, Moss M.
The epidemiology of sepsis in the United States from 1979 through 2000.
N. Engl. J. Med. 2003; 348:1546–1554.
Tenaillon O, Skurnik D, Picard B, Denamur E.
The population genetics of commensal Escherichia coli.
Nat Rev Microbiol. 2010 Mar;8(3):207-17.
