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Abstract
We used whole-genome sequencing to investigate the evolutionary context of an emerging highly pathogenic strain of Shiga toxin–producing Escherichia coli (STEC) O157:H7 in England and Wales. A timed phylogeny of sublineage IIb revealed that the emerging clone evolved from a STEC O157:H7 stx-negative ancestor ≈10 years ago after acquisition of a bacteriophage encoding Shiga toxin (stx) 2a, which in turn had evolved from a stx2c progenitor ≈20 years ago. Infection with the stx2a clone was a significant risk factor for bloody diarrhea (OR 4.61, 95% CI 2.24–9.48; p<0.001), compared with infection with other strains within sublineage IIb. Clinical symptoms of cases infected with sublineage IIb stx2c and stx-negative clones were comparable, despite the loss of stx2c. Our analysis highlighted the highly dynamic nature of STEC O157:H7 Stx-encoding bacteriophages and revealed the evolutionary history of a highly pathogenic clone emerging within sublineage IIb, a sublineage not previously associated with severe clinical symptoms.
Highlights
We used whole-genome sequencing to investigate the evolutionary context of an emerging highly pathogenic strain of Shiga toxin–producing Escherichia coli (STEC) O157:H7 in England and Wales
We defined STEC O157:H7 isolates from patients who were hospitalized as a result of their gastrointestinal symptoms or who reported bloody diarrhea as highly pathogenic or as having increased pathogenic potential compared with isolates from patients who were asymptomatic or reporting nonbloody diarrhea
Since July 2015, when Public Health England implemented the use of Whole-genome sequencing (WGS) for STEC, the number of cases identified within sublineage IIb has remained stable (≈60/y)
Summary
We used whole-genome sequencing to investigate the evolutionary context of an emerging highly pathogenic strain of Shiga toxin–producing Escherichia coli (STEC) O157:H7 in England and Wales. A timed phylogeny of sublineage IIb revealed that the emerging clone evolved from a STEC O157:H7 stx-negative ancestor ≈10 years ago after acquisition of a bacteriophage encoding Shiga toxin (stx) 2a, which in turn had evolved from a stx2c progenitor ≈20 years ago. Our analysis highlighted the highly dynamic nature of STEC O157:H7 Stx-encoding bacteriophages and revealed the evolutionary history of a highly pathogenic clone emerging within sublineage IIb, a sublineage not previously associated with severe clinical symptoms. All STEC O157:H7 isolated at local hospital laboratories from fecal samples from hospitalized patients and all cases in the community are submitted to the Gastrointestinal Bacteria Reference Unit (GBRU) at Public Health England for confirmation of identification and typing. The aim of our analysis was to investigate the evolutionary history of this newly emergent strain of STEC O157:H7 PT8 stx2a and assess the risk to public health
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