# Pathogenic potential and phylogenomic analysis of stx2-carrying O26:H11 Shiga toxin-producing Escherichia coli isolated from dairy products in France (2014–2024)

## TL;DR

This study examines the pathogenic potential and evolution of stx2-carrying O26:H11 E. coli in French dairy products, linking them to human infections.

## Contribution

The study identifies a predominant clonal lineage, ST21-cl5, in raw milk products and links it to human HUS cases through genomic analysis.

## Key findings

- ST21-cl5 is the predominant stx2-carrying O26:H11 lineage in French raw milk products.
- ST21-cl5 isolates from dairy products show high pathogenic potential and cluster with human HUS isolates.
- Evolutionary rates of ST21-cl5 are consistent with known STEC rates, suggesting shared ecological pressures.

## Abstract

Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens causing sporadic enteric disease and paediatric haemolytic uraemic syndrome (HUS) cases globally. In France, STEC O26:H11 strains carrying the stx2 gene have become the leading cause of paediatric HUS over the last decade. Concurrently, data from the French National Reference Laboratory show an increased proportion of stx2-carrying O26:H11 strains isolated from food, including raw milk products (RMPs). The consumption of RMP contaminated by this specific genotype has been linked to three out of four nationwide outbreaks between 2015 and 2024, confirming its emergence in France with RMPs as a potential source of infections. This study aimed to investigate the population structure, pathogenic potential and evolutionary dynamics of stx2-carrying O26:H11 STEC strains found in RMP in France. Using Illumina whole-genome sequencing, we (i) conducted a comparative analysis of human clinical strains and RMP isolates based on a set of accessory genes to assess pathogenic potential, (ii) performed phylogenomic analysis and (iii) explored evolutionary dynamics of major stx2-carrying STEC clonal lineages identified in RMPs using Bayesian evolutionary analysis sampling trees. Our results identified a predominant stx2-carrying O26:H11 clonal lineage, ST21-cl5, which became predominant in the raw milk production sector across multiple French regions and showed moderate diversification with evolutionary rates consistent with previously reported rates for STEC (i.e. 4.496×10−7 substitution/site/year). ST21-cl5 isolates from RMP displayed a high pathogenic potential, clustering closely with HUS-associated human isolates in both accessory genetic feature-based and core genome-based analyses. These findings suggest that clinical and RMP ST21-cl5 isolates evolved under similar selective pressures and shared a common ecological niche. Conversely, stx2d-carrying O26:H11 isolates also responsible for human infections in France might stem from a different source, as no stx2d-carrying strain was found among RMP isolates.