Bacterial genomic DNA was extracted using the QIAxtractor (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. Library preparation was conducted according to the Illumina protocol and sequenced on an Illumina HiSeq2000 (Illumina, San Diego, CA, USA) with 100-cycle paired-end runs. Sequence data were retrieved for a further 1,517 open access E. coli isolates associated with bloodstream infections (17 (link), 18 (link)). Of these, 424 were isolated between January 2006 and December 2012 at the Cambridge University Hospitals NHS Foundation Trust, and 1,093 were submitted to the British Society for Antimicrobial Chemotherapy Bacteraemia Resistance Surveillance Project by 11 UK hospitals between 2001 and 2011 (for details, see www. bsacsurv.org and Table S1 in the supplemental material) (31 (link)). Previous description and analysis of these genomes (17 (link), 18 (link)) did not include comparisons with isolates from livestock or meat.
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