Persistent cross-species transmission systems dominate Shiga toxin-producingEscherichia coliO157:H7 epidemiology in a high incidence region: a genomic epidemiology study

  1. Gillian A.M. Tarr
  2. Linda Chui
  3. Kim Stanford
  4. Emmanuel W. Bumunang
  5. Rahat Zaheer
  6. Vincent Li
  7. Stephen B. Freedman
  8. Chad R. Laing
  9. Tim A. McAllister
4 evaluations Published on
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Abstract

Background

Several areas of the world suffer notably high incidence of Shiga toxin-producingEscherichia coli, among them Alberta, Canada. We assessed the impact of persistent cross-species transmission systems on the epidemiology ofE. coliO157:H7 in Alberta.

Methods

We sequenced and assembled 229E. coliO157:H7 isolates originating from collocated cattle (n=108) and human (n=121) populations from 2007-2015 in Alberta. We constructed a timed phylogeny using BEAST2 using a structured coalescent model. We then extended the tree with human isolates through 2019 (n=430) to assess the long-term disease impact of locally persistent lineages. Shiga toxin gene (stx) profile was determined for all isolates.

Results

During 2007 to 2015, we estimated 108 (95% HPD 104, 112) human lineages arose from cattle lineages, and 14 (95% HPD 5, 23) from other human lineages; i.e., 88.5% of human lineages arose from cattle lineages. We identified 11 persistent lineages local to Alberta, which were associated with 38.0% (95% CI 29.3%, 47.3%) of human isolates. Of 117 isolates in locally persistent lineages, 6.0% carried only the Shiga toxin genestx2aand the rest bothstx1aandstx2a. During the later period, six locally persistent lineages continued to be associated with human illness, including 74.7% (95% CI 68.3%, 80.3%) of reported cases in 2018 and 2019. Thestxprofile of isolates in locally persistent lineages shifted from the earlier period, with 51.2% encoding onlystx2a.

Conclusions

Our study identified multiple locally evolving lineages transmitted between cattle and humans persistently associated withE. coliO157:H7 illnesses for up to 13 years. Of concern, there was a dramatic shift in locally persistent lineages toward strains with the more virulentstx2a-only profile. Locally persistent lineages may be a principal cause of the high incidence ofE. coliO157:H7 in locations such as Alberta and offer opportunities for understanding the disease ecology supportingE. coliO157:H7 persistence, as well as for local prevention efforts.

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