Characterization of the gut microbiome of patients with Clostridioides difficile infection, patients with non- C. difficile diarrhea, and C. difficile-colonized patients

Front Cell Infect Microbiol. 2023 Apr 12:13:1130701. doi: 10.3389/fcimb.2023.1130701. eCollection 2023.

Abstract

Introduction: Clostridioides difficile infection (CDI) is the main cause of nosocomial diarrhea in developed countries. A key challenge in CDI is the lack of objective methods to ensure more accurate diagnosis, especially when differentiating between true infection and colonization/diarrhea of other causes. The main objective of this study was to explore the role of the microbiome as a predictive biomarker of CDI.

Methods: Between 2018 and 2021, we prospectively included patients with CDI, recurrent CDI (R-CDI), non-CDI diarrhea (NO-CDI), colonization by C. difficile, and healthy individuals. Clinical data and fecal samples were collected. The microbiome was analyzed by sequencing the hypervariable V4 region of the 16S rRNA gene on an Illumina Miseq platform. The mothur bioinformatic pipeline was followed for pre-processing of raw data, and mothur and R were used for data analysis.

Results: During the study period, 753 samples from 657 patients were analyzed. Of these, 247 were from patients with CDI, 43 were from patients colonized with C. difficile, 63 were from healthy individuals, 324 were from NOCDI, and 76 were from R-CDI. We found significant differences across the groups in alpha and beta diversity and in taxonomic abundance. We identified various genera as the most significant biomarkers for CDI (Bacteroides, Proteus, Paraprevotella, Robinsoniella), R-CDI (Veillonella, Fusobacterium, Lactobacillus, Clostridium sensu stricto I), and colonization by C. difficile (Parabacteroides, Faecalicoccus, Flavonifractor, Clostridium XVIII).

Discussion: We observed differences in microbiome patterns between healthy individuals, colonized patients, CDI, R-CDI, and NOCDI diarrhea. We identified possible microbiome biomarkers that could prove useful in the diagnosis of true CDI infections. Further studies are warranted.

Keywords: 16S rRNA; C. difficile; CDI; R-CDI; microbiome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Clostridioides difficile* / genetics
  • Clostridium Infections* / diagnosis
  • Clostridium Infections* / microbiology
  • Diarrhea / microbiology
  • Feces / microbiology
  • Gastrointestinal Microbiome*
  • Humans
  • RNA, Ribosomal, 16S / genetics

Substances

  • RNA, Ribosomal, 16S

Grants and funding

This study was funded by Fondo de Investigaciones Sanitarias (FIS), Research Project number PI16/00490 and PI20/01381, PFIS grant number FI21/00310, and by the European Regional Development Fund (FEDER) “A way of making Europe”. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication”. This study was funded by Fondo de Investigaciones Sanitarias (FIS), Research Project number PI16/00490 and PI20/01381, PFIS grant number FI21/00310, and by the European Regional Development Fund (FEDER) “A way of making Europe”.