Clostridioides difficile Strains in the Gut by Next-Generation Shotgun Sequencing: Innocent Bystander or Villain?

Abstract

Background: Pathogenic Clostridioides difficile is the most common cause of nosocomial infections in the United States. However, the prevalence of C. difficile colonization in the general population is poorly understood. Objective: In this study, we sought to determine the presence and nature of various strains of Clostridioides difficile colonizing a representative sample of 121 asymptomatic adult volunteers from around the globe, consisting of 110 healthy and 11 stable Crohn’s patients. Methods: Next-generation sequencing was performed on fecal samples from 121 study participants. Stool samples were collected by patients utilizing a Zymo collection kit, which preserves bacterial DNA and RNA. Following collection, DNA was extracted, quantitated, and then normalized for downstream library fabrication utilizing shotgun methodology. Prepared and indexed libraries were subsequently pooled and sequenced on the Illumina NextSeq 550 System. Results: All 121 of 121 subjects (100%) were found to possess the bacterium Clostridioides difficile as identified by the NGS bioinformatics metagenomic pipeline. To visualize comparative abundances of Clostridioides difficile present in study participants, normalized read counts were highlighted (Fig. 1). Conclusions: NGS provides a unique opportunity to increase the resolution and identification of Clostridioides difficile compared to traditional categorizations, such as PCR ribotypes (ie, RT027), restriction endonuclease groups (BI), and North American pulsotypes (ie, NAP1). This is accomplished by its ability to differentiate species based on a nucleotides, while targeting entire bacterial genomes. Our approach for this study was to utilize a bioinformatics pipeline that would provide Clostridioides difficile strain-specific resolution when aligning to genomes in the NCBI (National Center for Biotechnology Information) database. In our representative sample of 121 volunteers, all (100%) possessed at least 1 Clostridioides difficile strain in their gut. Although it is recognized that some Clostridioides difficile strains are pathogenic, our findings suggest that nonpathogenic Clostridioides difficile strains make up an important component of the commensal gut microbiome and may perhaps play a protective role. Although symptomatic toxigenic CDI is a clear indication for therapy, Clostridioides difficile colonization with nontoxigenic strains is not believed to be a direct precursor for CDI. These findings demonstrate the need to be aware of the existence of numerous strains of Clostridioides difficile, and the relevance of sequencing prior to hospitalization or antibiotic treatment to help predict those at risk of CDI, and after treatment to be aware of any loss of what appear to be protective components of our microbiome.

Funding: None

Disclosures: Dr. Sabine Hazan reports that she is the founder and CEO of Ventura Clinical Trials and that she and her spouse receive salaries from the company. She also receives a salary from ProgenaBiome.