The C lermont E scherichia coli phylo‐typing method revisited: improvement of specificity and detection of new phylo‐groups
Abstract
Summary: There is extensive genetic substructure within the species E scherichia coli . In 2000 a simple triplex PCR method was described by C lermont and colleagues that enables an E . coli isolate to be assigned to one of the phylo‐groups A , B 1, B 2 or D . The growing body of multi‐locus sequence data and genome data for E . coli has refined our understanding of E . coli 's phylo‐group structure and eight phylo‐groups are now recognized: seven ( A , B 1, B 2, C , D , E , F ) belong to E . coli sensu stricto , whereas the eighth is the E scherichia cryptic clade I . Here a new PCR ‐based method is developed that enables an E . coli isolate to be assigned to one of the eight phylo‐groups and which allows isolates that are members of the other cryptic clades ( II to V ) of E scherichia to be identified. The development of the method is described and the method is validated. Over 95% of E . coli isolates can be correctly assigned to a phylo‐group. Two collections of human faecal isolates were screened using the new phylo‐group assignment method demonstrating that about 13% of E . coli isolates belong to the newly described phylo‐groups C , E , F and clade I .
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E. coli 5C belongs to phylogroup A based on matching only the ArpA gene among the five genes considered in the quadruplex method.
“among the five genes considered in the quadruplex method [108], E. coli 5C matches only with the ArpA gene, therefore belonging to the phylogroup A (Online Resource 14).”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [108]
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“As regards phylotyping, among the five genes considered in the quadruplex method [108], E. coli 5C matches only with the ArpA gene, therefore belonging to the phylogroup A (Online Resource 14).”
- Authors
- Clermont, O., Christenson, J. K., Denamur, E., & Gordon, D. M.
- Affiliations
- Inserm (FR)
- Australian National University (AU)
- UMR‐S 722 INSERM Paris F‐75018 France
- Corresponding author
- Clermont, Olivier
- Venue
- Environmental Microbiology Reports
- Publisher
- Wiley
- Published
- 2012-12-24
- Volume
- 5
- Issue
- 1
- Pages
- 58-65
- ISSN
- 1758-2229 (ISSN-L)
- OpenAlex
- W2097005840
- Cited by
- 1,698
- References
- 29
- Citations by year
- 2026: 94 · 2025: 124 · 2024: 158 · 2023: 153 · 2022: 201 · 2021: 194 · 2020: 164 · 2019: 156 · 2018: 126 · 2017: 124 · 2016: 89 · 2015: 65 · 2014: 37 · 2013: 13
- FWCI
- 23.49
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Environmental Microbiology Reports (publishedVersion)
- PubMed (publishedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Escherichia coli research studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Enterobacteriaceae and Cronobacter Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Escherichia coli, triplex PCR, method validation
- MeSH terms
- DNA, Bacterial, Escherichia coli, Feces, Humans, Phylogeny, Sensitivity and Specificity, Reproducibility of Results, Bacterial Typing Techniques, Polymerase Chain Reaction, Sequence Analysis, DNA, Escherichia coli Proteins
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