1437. Whole Genomic Analysis of the Phylogenetic Diversity of Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli causing bacteremia in Oxfordshire, UK, 2008-2010
Session: Poster Abstract Session: Epidemiology of Multiple Drug-Resistant Gram Negative Rods
Saturday, October 20, 2012
Room: SDCC Poster Hall F-H
  • IDSA_ecol_phylo_08102012.pdf (3.0 MB)
  • Background:

    Antibiotic resistance in extra-intestinal pathogenic Escherichia coli (ExPEC) is of major concern, and features relevant to its spread not fully understood. Extended-spectrum beta-lactamase (ESBL) production, mediating resistance to 3rd generation cephalosporins, is often a marker of multi-drug resistance.

    Partial sequencing schemes, such as multi-locus sequence typing (MLST), have suggested that successful spread is due to specific resistant clones, such as ST-131. High-throughput, short-read sequencing may provide greater insight into diversity and clonal expansion.


    32 E. coli bacteremia isolates with an ESBL phenotype isolated at the John Radcliffe Hospital in Oxford, UK, Jun 2008-Nov 2010, and 42 non-ESBL bacteremia control isolates (matched by calendar year), were whole genome sequenced (Illumina HiSeq 2000), generating 108bp paired-end reads. Reads were de novo assembled using Velvet, and MLST and phylogroup predicted in silico.

    5589 genes from E. coli CFT073 (NC_004431) were used as a reference sequence. Contigs for each clinical isolate, and 10 other reference strains, were compared against this set of genes using BLASTn, and the results concatenated (4667157 bases (b) in total; 2509125 complete in all 74 isolates, of which 284429 [11.3%] were variable). FastML was used to construct a maximum likelihood tree of the data.


    Oxfordshire E. coli bacteremia isolates were distributed throughout all phylogroups except D2/F, although they were predominantly group B2 (Figure).

    We found 25/32 (78%) ESBL isolates but only 2/42 (5%) non-ESBL isolates were ST-131 (p <0.001). Within the ST-131 group, there were 14598 variable sites in the 3894896b sequence common to these isolates. Two distinct ESBL clusters were observed (Figure; inset box; separated by ~1800 single nucleotide variants [SNVs]), with several ESBL and non-ESBL singletons.


    E. coli isolates causing bacteremia in Oxfordshire, 2008-2010, were diverse, although the majority of ESBL-producers were ST-131. However, within the ST-131 group, there were several clusters of ESBL-producers, suggesting clonal expansion of at least two ST-131 variants. This was not discernible by commonly used multi-locus typing methods.

    Figure. Maximum-likelihood phylogeny based on WGS of Oxfordshire E. coli bacteremia isolates, 2008-2010.

    Nicole Stoesser, BA MBBS1,2, Mohamad Azim Ansari3, Tanya Golubchik3, Elizabeth Batty, PhD4, Richard Everitt1, Rory Bowden, PhD4, Peter Donnelly5, A. Sarah Walker, PhD6, Tim Peto, MB BS, DPhil6, David Wyllie, PhD2, Xavier Didelot3 and Derrick Crook, MB, BCh6, (1)Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom, (2)NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom, (3)Department of Statistics, University of Oxford, Oxford, United Kingdom, (4)Statistics, University of Oxford, Oxford, United Kingdom, (5)University of Oxford, Oxford, United Kingdom, (6)NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom


    N. Stoesser, None

    M. A. Ansari, None

    T. Golubchik, None

    E. Batty, None

    R. Everitt, None

    R. Bowden, None

    P. Donnelly, None

    A. S. Walker, None

    T. Peto, None

    D. Wyllie, None

    X. Didelot, None

    D. Crook, Optimer: Investigator, Grant recipient and Speaker honorarium

    Findings in the abstracts are embargoed until 12:01 a.m. PST, Oct. 17th with the exception of research findings presented at the IDWeek press conferences.