Whole-genome sequencing of clinical Clostridioides difficile isolates reveals molecular epidemiology and discrepancies with conventional laboratory diagnostic testing

K McLean; J-M Balada-Llasat; A Waalkes; P Pancholi; S J Salipante

doi:10.1016/j.jhin.2020.11.014

Whole-genome sequencing of clinical Clostridioides difficile isolates reveals molecular epidemiology and discrepancies with conventional laboratory diagnostic testing

J Hosp Infect. 2021 Feb:108:64-71. doi: 10.1016/j.jhin.2020.11.014. Epub 2020 Nov 20.

Authors

K McLean¹, J-M Balada-Llasat², A Waalkes¹, P Pancholi³, S J Salipante⁴

Affiliations

¹ University of Washington Department of Laboratory Medicine, Seattle, WA, USA.
² Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA.
³ Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA. Electronic address: preeti.pancholi@osumc.edu.
⁴ University of Washington Department of Laboratory Medicine, Seattle, WA, USA. Electronic address: stevesal@uw.edu.

PMID: 33227298
DOI: 10.1016/j.jhin.2020.11.014

Abstract

Background: The high clinical burden of Clostridioides difficile infections merits rapid and sensitive identification of affected individuals. However, effective diagnosis remains challenging. Current best practice guidelines recommend molecular and/or direct toxin detection-based screening for symptomatic individuals, but previous work has called into question the concordance and performance of extant clinical assays.

Aim: To better correlate the genomic and phenotypic properties of clinical C. difficile isolates with laboratory testing outcomes in both C. difficile-infected patients and asymptomatic carriers.

Methods: Whole-genome sequencing of clinical C. difficile isolates collected from an inpatient population at a single healthcare institution was performed, enabling examination of their molecular epidemiology and toxigenic gene content. Genomic findings were compared with clinical testing outcomes, identifying multiple diagnostic discrepancies.

Findings: Toxigenic culture, considered a 'reference standard', provided perfect sensitivity and specificity in predicting toxigenic gene content, whereas reduced performance was observed for Simplexa C. difficile Direct Assay (100% specificity, 88% sensitivity), Gene Xpert CD/Epi Assay (86% specificity, 83% sensitivity), and Quick Check Complete Tox A/B (100% specificity, 30% sensitivity). Genomic analysis additionally revealed variability in toxin gene sequences among C. difficile strains, phylogenomic equivalency between isolates from affected patients and carriers, and patient carriage with uncommon environmentally derived C. difficile lineages, as well as presenting opportunities for tracing pathogen transmission events.

Conclusion: These results highlight the variable performance of clinical stool-based testing approaches as well as the potential diagnostic utility of whole-genome sequencing as an alternative to conventional testing algorithms.

Keywords: Clinical testing; Clostridioides difficile; Diagnosis; Epidemiology; Whole-genome sequencing.

MeSH terms

Clinical Laboratory Techniques / standards*
Clostridioides difficile / genetics*
Clostridium Infections / diagnosis*
Clostridium Infections / microbiology
Diagnostic Tests, Routine
Feces
Genome, Bacterial
Humans
Inpatients
Molecular Epidemiology
Sensitivity and Specificity
Whole Genome Sequencing