A six-year genomic surveillance of Shiga toxin-producing Escherichia coli infections in Belgium, 2019–2024

Introduction Since the implementation of whole-genome sequencing (WGS) at the Belgian National Reference Center (NRC) for Shiga toxin-producing Escherichia coli (STEC) in 2019, genomic surveillance has enabled detailed characterization of circulating STEC. The increasing availability of genomic data also provided an opportunity to reassess the Belgian hemolytic uremic syndrome (HUS) risk classification introduced in 2018. Methods From 2019 to 2024, the Belgian NRC analyzed 3,212 unduplicated fecal samples voluntarily referred by clinical laboratories. All STEC isolates were confirmed and further characterized using WGS for in silico serotyping, primary virulence gene profiling and cluster detection. In this retrospective study, a binomial generalized additive model was used to evaluate associations between HUS development, age, and stx genes profiles. Results A total of 1,234 STEC isolates were recovered, with a marked increase in number of isolates, non-O157 in particular, in 2023 and 2024. Serogroup O157 (31.3%) was the most prevalent serogroup among all isolates, whereas O26 (34.1%) was most common serogroup among STEC-HUS isolates. The most frequent stx genes profiles in all isolates were stx 1a alone (17.4%) and stx 2a alone (18.9%), while stx 2a alone was present in 59.1% of STEC-HUS isolates. Among 1,161 individuals with known HUS status, 129 (11.1%) developed HUS. Age showed the expected U-shaped association with HUS development. The presence of stx 2a (OR 7.45, 95% CI 3.84–14.43) and stx 2d (OR 3.05, 95% CI 1.02–9.18) was significantly associated with a higher risk of HUS, whereas the presence of stx1a was associated with a reduced risk of HUS (OR 0.32, 95% CI 0.18–0.58). HUS was not identified among individuals carrying stx 2f (10.5%), despite being the fourth most common stx genes profile. Discussion The landscape of STEC in Belgium changed considerably over a six-year period, primarily driven by the increased detection of non-O157 STEC. Our findings support retaining stx 2a and stx 2d in the high-risk category for HUS development and support reclassifying stx 2f as low risk. Furthermore, these data informed evidence based WGS selection criteria, focusing on STEC-HUS isolates, stx 2-positive isolates excluding stx 2f and serogroups O26 and O157. These criteria optimize genomic surveillance while maintaining the capacity to detect outbreaks and monitor highly pathogenic STEC.