Escherichia coli Variome - Analysis of Clonality of Pathogenic Escherichia coli

The goal of this study was to investigate cross-sectional variability of clonal structure of extraintestinal E. coli populations obtained at various clinical centers in US and Europe. Participating institutions provided random E. coli isolated at their clinical laboratories to Prof. Sokurenko's laboratory at the University of Washington (UW), Seattle WA. The strains were tested for resistance to a standard set of antibiotics using disk diffusion method according to CLSI guidelines. The strains were also typed using Actman's MLST scheme and fumC-fimH (CH) typing scheme (Ref Weisman 2012 AEM). A subset of strains was chosen to do whole genome sequencing using Illumina MiSeq instrument. Isolates were chosen as matched ST-CH types with different antibiotic resistance profiles. The collections are described in more detail in Tchesnokova et al, 2013 JCM; Tchesnokova et al. 2018 CID.