What is it about?

Within our collection of pathogenic E. coli, we selected some that gave different PCR results for detection of Shiga toxins in every assay and some with consistent PCR detection of Shiga toxins. We then compared whole genome sequences for both groups

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Why is it important?

We found that many of the isolates with inconsistent PCR detection had one or more fragments of Shiga toxin genes integrated in their genomes. These large fragments are potentially being detected by the PCR, although a subsequent study found that only E. coli with complete Shiga toxin genes were able to produce Shiga toxin. PCR is then identifying the E. coli with large fragmentary Shiga toxins as pathogens when they are unlikely to be so.


Rapid genetic changes in E. coli include the integration and excision of bacteriophages which carry the Shiga toxin genes. The gain and loss of the bacteriophages increases the difficulty in determining which E. coli are potentially pathogenic. We need to be looking at other markers that are better conserved and developing new assays using these markers to improve food safety.

Kim Stanford
University of Lethbridge

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This page is a summary of: Inconsistent PCR detection of Shiga toxin-producing Escherichia coli: Insights from whole genome sequence analyses, PLoS ONE, September 2021, PLOS, DOI: 10.1371/journal.pone.0257168.
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