Open Collections

Abstract

Shiga toxin (Stx)-producing Escherichia coli (STEC) are major zoonotic pathogens, with cattle as their primary reservoir. The O157:H7 strains containing the stx2a gene are especially concerning due to their strong association with severe human disease. Phage-based interventions are a promising strategy for reducing STEC burden in livestock; however, the efficacy of this approach is challenged by the presence of bacterial antiviral defence systems (ADSs) that block phage replication, and the risk of prophage induction leading to Stx release. Non-coding RNAs (ncRNAs) are key regulators of stress response gene expression, mobile elements, and phage–host interactions, yet their potential role in modulating ADSs in bovine STEC remains unknown. This thesis characterized the landscape of ncRNAs and ADSs in 76 bovine-derived STEC genomes, including stx2a-positive (n=45) and stx2a-negative (n=21) O157:H7, and non-O157 (n=10) strains. A bioinformatic pipeline was developed to integrate covariance model-based ncRNA detection (Infernal + Rfam), homology searches (BLAST + RNAcentral), and ADS annotation (DefenseFinder). Predicted ncRNAs were filtered and classified by family, structure, and frequency of occurrence in the genomes. Potential regulatory associations between ncRNAs and predicted antiviral gene sequences were inferred based on BLAST-based homology. The analysis revealed distinct ncRNA and ADS profiles across bovine STEC genomes. The stx2a-positive O157:H7 strains were predicted to harbour the most diverse ADSs and prevalent ncRNAs associated with phage regulation and stress adaptation compared to stx2a-negative O157:H7, and non-O157 strains. Several ncRNAs were predicted to co-occur with genes encoding restriction enzymes, signalling domains, and toxin-antitoxin elements, suggesting potential ncRNA-mediated regulation of bacterial immune activity. The findings from this study provides the first comprehensive assessment of ncRNA and ADS profiles in bovine-derived STEC. This work offers a foundation for developing phage-based control strategies that bypass or exploit host regulatory mechanisms by predicting candidate ncRNAs that may suppress STEC antiviral defence pathways. These insights may help reduce prophage activation and Stx release, providing knowledge on future intervention strategies in reducing STEC shedding in cattle on farm.