Genome sequences of 15 Escherichia coli O77g strains related to an emerging STEC lineage

In January 2025, the French surveillance system implemented by Sante publique France (SpF) detected several cases of Haemolytic Uremic Syndrome (HUS) in adults caused by a rare serotype of Shiga toxin-producing Escherichia coli, STEC O17:H18. Investigations by health authorities identified convergent epidemiological and traceability elements, linking the consumption of raw-milk cheese to these clustered cases of HUS. The outbreak strain belonged to sequence type (ST) 69 and harboured a Shiga toxin (stx) subtype stx2d located on a unique prophage in the stx-encoding bacteriophage databases. Putative virulence genes cdt-VB, hlyE, fimH and lpfA were detected, however, the established STEC virulence genes involved in attachment to the gut mucosa (eae and aggR) were absent. Phylogenetic analysis of E. coli O17 strains sampled from public databases (Enterobase and NCBI) showed that the epidemic strain is located within a cluster of clinical strains of E. coli O17:H18, ST69, stx2d, all isolated between 2012-2025 and related to one HUS that occurred in France (2012), and three HUS reported in Australia (2014, 2019, 2020). Hence, this strain has already been associated with a HUS in 2012 in France and this is not a new recombination. The closest cluster to the outbreak strain contains eight stx-negative strains all isolated from poultry between 1990 and 2024 in Europe and North America. Differences in virulence gene composition for iha, iss, iucC, iutA and sitA between the "outbreak cluster" and the "poultry cluster" suggest a common ancestor that has likely diverged over time. The "outbreak cluster" is characterized by strains carrying a plasmid encoding a heat-labile enterotoxin gene, which is not found in any other E. coli strain tested in GeneBank database. We have developed qPCR assays specific for the heat-labile enterotoxin and O17 O-group. Combined with a PCR for stx2, these assays allow rapid screening of suspect unpasteurized cheese for the outbreak strain.