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. 2023 May 16;11(5):1298.
doi: 10.3390/microorganisms11051298.

Whole-Genome Sequencing of Shiga Toxin-Producing Escherichia coli for Characterization and Outbreak Investigation

Heather M Blankenship  1   2 , Stephen E Dietrich  1 , Elizabeth Burgess  1 , Jason Wholehan  1 , Marty Soehnlen  1 , Shannon D Manning  2
Affiliations

Whole-Genome Sequencing of Shiga Toxin-Producing Escherichia coli for Characterization and Outbreak Investigation

Heather M Blankenship et al. Microorganisms. .

Abstract

Shiga toxin-producing Escherichia coli (STEC) causes high frequencies of foodborne infections worldwide and has been linked to numerous outbreaks each year. Pulsed-field gel electrophoresis (PFGE) has been the gold standard for surveillance until the recent transition to whole-genome sequencing (WGS). To further understand the genetic diversity and relatedness of outbreak isolates, a retrospective analysis of 510 clinical STEC isolates was conducted. Among the 34 STEC serogroups represented, most (59.6%) belonged to the predominant six non-O157 serogroups. Core genome single nucleotide polymorphism (SNP) analysis differentiated clusters of isolates with similar PFGE patterns and multilocus sequence types (STs). One serogroup O26 outbreak strain and another non-typeable (NT) strain, for instance, were identical by PFGE and clustered together by MLST; however, both were distantly related in the SNP analysis. In contrast, six outbreak-associated serogroup O5 strains clustered with five ST-175 serogroup O5 isolates, which were not part of the same outbreak as determined by PFGE. The use of high-quality SNP analyses enhanced the discrimination of these O5 outbreak strains into a single cluster. In all, this study demonstrates how public health laboratories can more rapidly use WGS and phylogenetics to identify related strains during outbreak investigations while simultaneously uncovering important genetic attributes that can inform treatment practices.

Keywords: Escherichia coli; Shiga toxin; genome sequencing; outbreak; phylogenetics.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Frequency of Shiga toxin-producing Escherichia coli (STEC) isolates (n = 510) that were subjected to whole-genome sequencing in Michigan per year (black line) and the overall frequency (%) of non-O157 and O157 serogroups identified for each of the four years.
Figure 2
Figure 2
Neighbor-joining tree based on seven multilocus sequence typing loci for 509 Shiga toxin-producing Escherichia coli (STEC) isolates constructed with 1000 bootstrap replicates. Sequence types (STs) are indicated after each serotype along with the number (n) of strains examined, and bootstrap percentages (>80%) are shown at the nodes. Serogroup O157 strains are noted in blue font. Black stars indicate the STs and serogroups containing outbreak-associated isolates that were previously identified using pulsed-field gel electrophoresis.
Figure 3
Figure 3
Dendrogram based on high-quality (hq) SNP analysis of 60 sequence type (ST)-119 Shiga toxin-producing Escherichia coli (STEC) strains that clustered with known outbreak strains in the cgSNP analysis. PFGE patterns (XbaI) are shown for all STEC isolates included in the hqSNP analysis and outbreak-associated isolates are denoted with stars. Brackets indicate the number of SNP differences between the specified group of strains.
Figure 4
Figure 4
High-quality (hq) SNP phylogeny and XbaI PFGE patterns for 15 isolates of STEC O157:H7 linked to an outbreak. The six outbreak isolates (ST-66-01, black stars) were compared to nine related O157:H7 isolates, as determined by the cgSNP analysis. Brackets show the number of SNP differences between the specified cluster.
Figure 5
Figure 5
High-quality (hq) SNP phylogeny of 13 STEC O157:H7 isolates recovered from two outbreaks. Isolates from outbreaks ST-66-O2 (colored stars) and ST-66-O3 (open triangles) were included in the analysis as well as four non-outbreak isolates that clustered together in the cgSNP phylogeny. XbaI PFGE patterns are indicated for all but one isolate with missing data, while the brackets denote the number of SNP differences between the specified group of strains.
Figure 6
Figure 6
Phylogeny constructed using high-quality (hq) SNPs extracted from six STEC O5:H9 outbreak strain genomes, which are indicated with black stars. For comparison, nine other strains identified to be closely related in the core genome (cg) SNP analysis (Figure S4) were included. PFGE patterns were derived following digestion with XbaI; brackets indicate the number of SNP differences between a group of strains.
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