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

B<sc>ackground</sc>

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

M<sc>ethods</sc>

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=432) to assess the long-term disease impact of local persistent lineages. Shiga toxin gene (stx) profile was determined for all isolates.

R<sc>esults</sc>

During 2007 to 2015, we estimated 107 (95% HPD 101, 111) human lineages arose from cattle lineages, and 31 (95% HPD 22, 43) from other human lineages; i.e., 77.5% of human lineages arose from cattle lineages. We identified 11 persistent lineages local to Alberta, which were associated with 36.4% (95% CI 27.8%, 45.6%) of human isolates. Of 115 isolates in local persistent lineages, 6.1% carried onlystx2aand the reststx1a/stx2a. During the later period, six local 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 local persistent lineages shifted from the earlier period, with 51.2% encoding onlystx2a.

C<sc>onclusions</sc>

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 the local persistent lineages toward strains with the more virulentstx2a-only profile. We hypothesize that the large proportion of disease associated with local transmission systems is a principal cause of Alberta’s highE. coliO157:H7 incidence.

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