Detection and Genomic Characterisation of Clostridioides difficile from Spinach Fields

Area of Science:

• Environmental microbiology
• Food safety
• Infectious disease epidemiology

Background:

• Clostridioides difficile infections (CDI) are increasing globally.
• Limited data exists on C. difficile reservoirs and dissemination routes.
• Understanding environmental sources is crucial for preventing CDI.

Purpose of the Study:

• To investigate the prevalence and characteristics of C. difficile in spinach agricultural fields.
• To identify potential reservoirs and transmission pathways of C. difficile in the food chain.

Main Methods:

• Culture-based detection of C. difficile in spinach and soil samples.
• Whole genome sequencing (WGS) for isolate characterization (clade, ST, RT).
• Detection of toxin genes (A, B, CDT) and antimicrobial resistance profiling (E test, WGS).

Main Results:

• C. difficile detected in 3.3% of spinach and 10% of soil samples.
• Spinach isolates were hypervirulent clade 5, ST11 (RT078, RT126), carrying toxin genes.
• Soil isolates included various toxigenic and one non-toxigenic clade 1 strains with antimicrobial resistance.
• WGS revealed a broader range of resistance genes than phenotypic testing.

Conclusions:

• Horticultural environments, specifically spinach fields, can harbor C. difficile.
• Multiple sources and dissemination routes for C. difficile exist, including agricultural settings.
• Findings contribute to understanding the environmental ecology of C. difficile and CDI prevention strategies.