Whole-genome sequencing improves discrimination of relapse from reinfection and identifies transmission events among patients with recurrent Clostridium difficile infections.
BACKGROUND
Recurrent Clostridium difficile infection (CDI) represents a significant healthcare challenge. Patients may suffer multiple episodes of CDI with the index strain (relapse) or become infected by another strain acquired nosocomially (reinfection).


OBJECTIVE
We aimed to characterize C. difficile isolates causing recurrent CDI at a tertiary referral hospital by whole-genome sequencing (WGS) to assess strain similarities at the highest level of genetic resolution and accurately detect relapse, reinfection, and putative strain transmission events.


METHODS
An 18-month prospective study of recurrent CDI was undertaken. Clostridium difficile was cultured from stool samples collected longitudinally from any patients suffering ≥2 clinically defined CDI episodes. Patient demographics and clinical data were recorded, and strain relatedness investigated by both polymerase chain reaction (PCR)-based ribotyping and WGS.


RESULTS
Nineteen patients were identified with ≥2 clinically defined CDI episodes who cumulatively suffered 39 recurring CDI episodes (58 total episodes). Patients had a median length of stay (LOS) of 144 days and experienced between two and seven CDI episodes. Ribotyping indicated 27 apparent same-strain relapses, five reinfections and the predominance of ribotypes 078 (ST-11) and 020 (ST-2). WGS allowed characterization of relapse with increased certainty and identified emergent within-strain single nucleotide variants (SNVs) with potential functional impact on diverse genes. Shared ribotypes among 14 patients with recurrent CDI suggested 10 possible patient-to-patient transmission events. However, WGS revealed greater diversity at the sub-ribotype level, excluding all but four transmission events.


CONCLUSIONS
WGS exhibits several advantages over PCR-based ribotyping in terms of its ability to distinguish relapse from reinfection, to identify patient-to-patient transmission events, and to exact fine structure characterization of recurrent CDI epidemiology. This offers the potential for more focused infection prevention strategies to eliminate strain transmission among patients with recurrent CDI.
Department of Clinical Microbiology, Sir Patrick Dun Translational Research Laboratory, School of Medicine, Trinity College Dublin, St James's Hospital, Dublin, Ireland. Electronic address: m.macaogain@tcd.ie.
M
M
Mac Aogáin
Department of Clinical Microbiology, Sir Patrick Dun Translational Research Laboratory, School of Medicine, Trinity College Dublin, St James's Hospital, Dublin, Ireland.
G
G
Moloney
Department of Clinical Microbiology, Sir Patrick Dun Translational Research Laboratory, School of Medicine, Trinity College Dublin, St James's Hospital, Dublin, Ireland.
S
S
Kilkenny
Department of Microbiology, St James's Hospital, Dublin, Ireland.
M
M
Kelleher
Department of Microbiology, St James's Hospital, Dublin, Ireland.
M
M
Kelleghan
Department of Microbiology, St James's Hospital, Dublin, Ireland.
B
B
Boyle
Department of Clinical Microbiology, Sir Patrick Dun Translational Research Laboratory, School of Medicine, Trinity College Dublin, St James's Hospital, Dublin, Ireland; Department of Microbiology, St James's Hospital, Dublin, Ireland.
T R
TR
Rogers
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D016360:Clostridioides difficile / Q000235:genetics* / Q000302:isolation & purification*; D003015:Clostridium Infections / Q000188:drug therapy* / Q000453:epidemiology / Q000635:transmission*; D005260:Female; D016678:Genome; D006801:Humans; D007494:Ireland; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011446:Prospective Studies; D012008:Recurrence; D021521:Ribotyping
D000900:Anti-Bacterial Agents
Clostridium difficile infection; Recurrent infection; Transmission; Whole-genome sequencing