Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study

Area of Science:

• Microbiology
• Genetics
• Infectious Diseases

Background:

• Clostridium difficile infections (CDI) represent a significant and growing public health concern due to rising incidence and severity.
• Understanding the genetic diversity of C. difficile strains and their correlation with host factors is crucial for effective management.

Purpose of the Study:

• To investigate the genetic diversity of Clostridium difficile strains in a tertiary care setting.
• To correlate pathogen genotypes with host clinical characteristics and disease severity.
• To evaluate the utility of Multilocus Sequence Typing (MLST) and Whole-Genome Sequencing (WGS) for strain characterization.

Main Methods:

• Collected 46 C. difficile isolates from a tertiary care medical center.
• Employed Multilocus Sequence Typing (MLST) to determine sequence types (STs).
• Utilized Whole-Genome Sequencing (WGS) for detailed genomic analysis, including identifying resistance loci and core genome single nucleotide polymorphisms (SNPs).

Main Results:

• Identified 21 known and 2 novel STs, indicating significant genetic diversity.
• ST-1, corresponding to NAP1/ribotype 027, was the most prevalent (32.6%).
• Binary toxin genes were present in 43.5% of isolates, predominantly within ST-1.
• Observed resistance to ciprofloxacin, clindamycin, and tetracycline, with WGS identifying resistance mechanisms.
• Disease severity was highest in patients infected with ST-1 and/or binary toxin gene-positive strains.

Conclusions:

• MLST and core genome SNP typing provide consistent phylogenetic grouping of C. difficile strains.
• WGS offers enhanced strain differentiation within STs and detailed gene-level analysis.
• ST-1 and binary toxin gene presence are associated with increased CDI severity.