351. Clostridium difficile Exhibits Genomic Stability in Longitudinally Sampled Patients
Session: Poster Abstract Session: Clostridium difficile - Epidemiology, Diagnosis, Treatment, and Prevention
Friday, October 21, 2011
Room: Poster Hall B1
Background: Whole genome sequences (WGS) of Clostridium difficile (CD) have revealed substantial sequence diversity within strains. How much diversity accumulates within a strain within an individual before the infection is cleared is not known.

Methods: CD toxin enzyme immunoassay positive samples from routine clinical testing underwent culture and multi-locus sequence typing (MLST). Sequential isolates sampled from 42 patients repeatedly positive with the same sequence type (ST) during 2007-10 were sequenced using the Illumina GA-2 and HiSeq platforms. Reads were mapped to the CD630 reference genome with STAMPY. Base and variant calls were made using SAMTOOLS, GATK and bespoke Python scripts.

Results: WGSs were obtained from 121 isolates, from 15 different STs. A mean (SD) 80.6% (5.1%) of the 4.3Mb CD630 genome was successfully called. The median (IQR) time between first and all subsequent samples was 42 (1-84) days (2-8 tests/patient). WGSs from the 72 subsequent samples were compared with the 43 baseline samples (42 patients, 1 with 2 STs). WGSs from pairs of samples taken on the same day from 7 patients were all identical. 31/43 (72%) patients had identical sequences throughout, a median (IQR) 24 (1-72) days apart. 4/43 (9%) developed 1 single nucleotide variant (SNV) over a median 52 days, and 3/43 (7%) patients 2 SNVs, over a median 204 days. 5 exceptions to this pattern occurred; 1 transient SNV occurred in 3 cases (on a background of 0, 1 and 2 SNVs); 1 relapse after 60 days produced a variant with 823 SNVs; and 1 transient switch produced a variant with 101 SNVs after 39 days, returning to the exact initial sequence after 113 days. The 2 divergent examples revealed evidence for multiple recombination and mutation events strongly suggesting infection with another strain. Excluding these 2 events, across the remaining samples, 13 non-transient SNVs occurred over total 2553 days follow up, a crude rate of 1.9 SNVs/year. In contrast the mean SNV difference between different patients with the same ST was 177 and 18663 across STs.

Conclusion: Strains typically accumulate a limited number of SNVs over time of infection within a patient. WGSs obtained against CD630 provide an ideal level of strain resolution for analyzing transmission within outbreaks of strain variants. 


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, Rosalind Harding1, Camila Ip1, A. Sarah Walker, PhD1, 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

R. Harding, None

C. Ip, None

A. S. Walker, 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.