347. Whole Genome Sequencing Enhances Clostridium difficile Outbreak Investigation
Session: Poster Abstract Session: Clostridium difficile - Epidemiology, Diagnosis, Treatment, and Prevention
Friday, October 21, 2011
Room: Poster Hall B1
Handouts
  • Paper_30780_handout_299_0.pdf (4.0 MB)
  • Background: Clostridium difficile (CD) strain typing allows potentially related infections to be identified by outbreak investigators. Whole genome sequencing (WGS) provides much higher resolution genetic data that may confirm or refute whether isolates are part of transmission clusters.

    Methods: Isolates from a complete outbreak of a rare CD multi-locus sequence type, ST63, underwent WGS. Hospital admission and ward movement data were available for each case from an established research database. Seven samples were obtained from 5 patients over 63 days. Extracted DNA was sequenced using the Illumina HiSeq platform and mapped to the CD630 reference genome with STAMPY. Base and variant calls were made using SAMTOOLS, PICARD and bespoke Python scripts. One isolate was sequenced 3 times to ensure outputs were consistent. 

    Results: The 5 CD cases initially tested positive in 4 locations (3 separate hospitals and an outpatient location). However, ward movement data revealed 3 cases shared time on one ward after the earliest case and before the later 2 cases. The other 2 cases also shared time on another ward between positive samples, but in a different hospital. All 5 cases shared the same specialty and clinicians. WGS was used to test if all 5 cases had a recent common source. All sequences from the cluster of 3 cases were identical, including 1 isolate from a relapse 36 days later and 3 technical replicates from the same isolate. Within the cluster of 2 patients, 2 single nucleotide variants (SNVs) was identified between cases, and then not seen in a relapse of the 2nd case 39 days later suggesting the identical and variant lineages may have both been acquired at the point of transmission. The 2 clusters were at least 37 SNVs different, despite their common clinical team. The SNVs were distributed throughout the genome, so cannot be explained by 1 recombination event. Additional data showing the stability of CD genomes in patients over time suggests the 2 clusters seen are very unlikely related by a transmission during the outbreak.

    Conclusion: Considering the location of diagnosis is insufficient for identifying CD transmission events. Combining detailed epidemiological databases and whole genome sequencing provides a powerful and reliable tool for outbreak investigation.



    Subject Category: N. Hospital-acquired and surgical infections, infection control, and health outcomes including general public health and health services research

    David Eyre1, Madeleine Cule1, A. Sarah Walker, PhD1, Rosalind Harding1, David Griffiths1, Mark Wilcox2, Derrick Crook, MB BCh1 and Tim Peto, MB BS, DPhil1, (1)NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom, (2)Leeds Teaching Hospitals & University of Leeds, Leeds, United Kingdom

    Disclosures:

    D. Eyre, None

    M. Cule, None

    A. S. Walker, None

    R. Harding, None

    D. Griffiths, None

    M. Wilcox, bioMerieux: Consultant and Grant Investigator, Consulting fee, Research grant and Support to attend meetings
    Optimer Pharmaceuticals: Consultant and Grant Investigator, Consulting fee, Research grant and Support to attend meetings
    Novacta: Consultant and Grant Investigator, Consulting fee, Research grant and Support to attend meetings
    Pfizer: Consultant and Grant Investigator, Consulting fee, Research grant and Support to attend meetings
    Summit: Consultant and Grant Investigator, Consulting fee, Research grant and Support to attend meetings
    The Medicines Company: Consultant and Grant Investigator, Consulting fee, Research grant and Support to attend meetings
    Viropharma: Consultant and Grant Investigator, Consulting fee, Research grant and Support to attend meetings

    D. Crook, Optimer Pharmaceuticals: Investigator and Scientific Advisor, Consulting fee and Institution received per-case funding to support trial patient expenses

    T. Peto, Optimer Pharmaceuticals: Scientific Advisor, Consulting fee

    Findings in the abstracts are embargoed until 12:01 a.m. EST Thursday, Oct. 20 with the exception of research findings presented at IDSA press conferences.