We studied 161 well-characterized E. coli isolates from bacteremia; this set of isolates (Additional file 1) has been previously described [30 (link)]. Briefly, isolates were collected between December 2002 and December 2003 and correspond to all consecutive episodes of E. coli bacteremia in two major university hospitals in Paris. Epidemiological (age, sex gender), clinical (community/nosocomial acquired infection, immune status, underlying diseases, primary source of infection, severity sepsis scoring and outcome), and laboratory data for each episode were recorded in an anonymous computer database in accordance with French law. We determined the primary source of bacteremia by clinical and radiological presentation and/or by evidence, based on antibiogram and/or serotyping, of an identical strain isolated from blood and other body sites culture [30 (link)]. When the primary source of infection was not found, the origin of infection was assigned to the digestive tract. All the above 161 isolates are listed in supplementary Table 1. The ECOR collection of 72 reference strains [52 (link)] was included for phylogenetic comparisons; five ECOR strains could not be sequenced at all eight genes (see below) and were removed from the analysis: ECOR5 (A), ECOR6 (A), ECOR9 (A), ECOR13 (A) and ECOR64 (B2). In addition, seven strains for which the complete genome sequence is available (K-12 MG1655, O157:H7-EDL933, 536, CFT073, UTI89, RS218) or underway (ED1a, ColiScope project, ) were used.
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