Whole-Genome Sequencing of Shiga Toxin-Producing <i>Escherichia coli</i> for Characterization and Outbreak Investigation
Shiga toxin-producing <i>Escherichia coli</i> (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-gen...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-05-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/11/5/1298 |
| _version_ | 1827740576688111616 |
|---|---|
| author | Heather M. Blankenship Stephen E. Dietrich Elizabeth Burgess Jason Wholehan Marty Soehnlen Shannon D. Manning |
| author_facet | Heather M. Blankenship Stephen E. Dietrich Elizabeth Burgess Jason Wholehan Marty Soehnlen Shannon D. Manning |
| author_sort | Heather M. Blankenship |
| collection | DOAJ |
| description | Shiga toxin-producing <i>Escherichia coli</i> (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. |
| first_indexed | 2024-03-11T03:28:48Z |
| format | Article |
| id | doaj.art-d104ac9d290f4f0bae00ecdb179108bf |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T03:28:48Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-d104ac9d290f4f0bae00ecdb179108bf2023-11-18T02:34:41ZengMDPI AGMicroorganisms2076-26072023-05-01115129810.3390/microorganisms11051298Whole-Genome Sequencing of Shiga Toxin-Producing <i>Escherichia coli</i> for Characterization and Outbreak InvestigationHeather M. Blankenship0Stephen E. Dietrich1Elizabeth Burgess2Jason Wholehan3Marty Soehnlen4Shannon D. Manning5Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USABureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USABureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USABureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USABureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USADepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USAShiga toxin-producing <i>Escherichia coli</i> (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.https://www.mdpi.com/2076-2607/11/5/1298Shiga toxin<i>Escherichia coli</i>outbreakgenome sequencingphylogenetics |
| spellingShingle | Heather M. Blankenship Stephen E. Dietrich Elizabeth Burgess Jason Wholehan Marty Soehnlen Shannon D. Manning Whole-Genome Sequencing of Shiga Toxin-Producing <i>Escherichia coli</i> for Characterization and Outbreak Investigation Microorganisms Shiga toxin <i>Escherichia coli</i> outbreak genome sequencing phylogenetics |
| title | Whole-Genome Sequencing of Shiga Toxin-Producing <i>Escherichia coli</i> for Characterization and Outbreak Investigation |
| title_full | Whole-Genome Sequencing of Shiga Toxin-Producing <i>Escherichia coli</i> for Characterization and Outbreak Investigation |
| title_fullStr | Whole-Genome Sequencing of Shiga Toxin-Producing <i>Escherichia coli</i> for Characterization and Outbreak Investigation |
| title_full_unstemmed | Whole-Genome Sequencing of Shiga Toxin-Producing <i>Escherichia coli</i> for Characterization and Outbreak Investigation |
| title_short | Whole-Genome Sequencing of Shiga Toxin-Producing <i>Escherichia coli</i> for Characterization and Outbreak Investigation |
| title_sort | whole genome sequencing of shiga toxin producing i escherichia coli i for characterization and outbreak investigation |
| topic | Shiga toxin <i>Escherichia coli</i> outbreak genome sequencing phylogenetics |
| url | https://www.mdpi.com/2076-2607/11/5/1298 |
| work_keys_str_mv | AT heathermblankenship wholegenomesequencingofshigatoxinproducingiescherichiacoliiforcharacterizationandoutbreakinvestigation AT stephenedietrich wholegenomesequencingofshigatoxinproducingiescherichiacoliiforcharacterizationandoutbreakinvestigation AT elizabethburgess wholegenomesequencingofshigatoxinproducingiescherichiacoliiforcharacterizationandoutbreakinvestigation AT jasonwholehan wholegenomesequencingofshigatoxinproducingiescherichiacoliiforcharacterizationandoutbreakinvestigation AT martysoehnlen wholegenomesequencingofshigatoxinproducingiescherichiacoliiforcharacterizationandoutbreakinvestigation AT shannondmanning wholegenomesequencingofshigatoxinproducingiescherichiacoliiforcharacterizationandoutbreakinvestigation |