Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data
Open accessAbstract
Accurate and rapid typing of pathogens is essential for effective surveillance and outbreak detection. Conventional serotyping of Escherichia coli is a delicate, laborious, time-consuming, and expensive procedure. With whole-genome sequencing (WGS) becoming cheaper, it has vast potential in routine typing and surveillance. The aim of this study was to establish a valid and publicly available tool for WGS-based in silico serotyping of E. coli applicable for routine typing and surveillance. A FASTA database of specific O-antigen processing system genes for O typing and flagellin genes for H typing was created as a component of the publicly available Web tools hosted by the Center for Genomic Epidemiology (CGE) ( www.genomicepidemiology.org ). All E. coli isolates available with WGS data and conventional serotype information were subjected to WGS-based serotyping employing this specific SerotypeFinder CGE tool. SerotypeFinder was evaluated on 682 E. coli genomes, 108 of which were sequenced for this study, where both the whole genome and the serotype were available. In total, 601 and 509 isolates were included for O and H typing, respectively. The O-antigen genes wzx , wzy , wzm , and wzt and the flagellin genes fliC , flkA , fllA , flmA , and flnA were detected in 569 and 508 genome sequences, respectively. SerotypeFinder for WGS-based O and H typing predicted 560 of 569 O types and 504 of 508 H types, consistent with conventional serotyping. In combination with other available WGS typing tools, E. coli serotyping can be performed solely from WGS data, providing faster and cheaper typing than current routine procedures and making WGS typing a superior alternative to conventional typing strategies.
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Serotyping of E. coli 5C was validated at the Statens Serum Institut according to a previously described method.
“To validate the result obtained, we also made the serotyping determination at the Statens Serum Institut (Copenhagen, Denmark) according to a method previously described [107].”
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 [107]
Phylotypes A and B2 are the most distant from each other phylogenetically among E. coli sensu stricto.
“Recent findings have shown that phylotypes A and B2 are the most distant from each other phylogenetically among E. coli sensu stricto [107]”
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 [107]
The SerotypeFinder H-typing database section compares flagellin-gene variants within and between H types, not the phylogenetic distance between E. coli phylotypes. Searches for phylotypes A and B2 and their phylogenetic distance found no passage in our copy addressing the claim; page numbers were not available. (LLM, conf=0.72)
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“Recent findings have shown that phylotypes A and B2 are the most distant from each other phylogenetically among E. coli sensu stricto [107]; that strains responsible for extra-intestinal infection were far more likely to be members of phylogroups B2 than A [143, 144]; and that the B2 phylotype is…”
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- Authors
- Joensen, K. G., Tetzschner, A. M. M., Iguchi, A., Aarestrup, F. M., & Scheutz, F.
- Affiliations
- Statens Serum Institut (DK)
- University of Miyazaki (JP)
- Technical University of Denmark (DK)
- Venue
- Journal of Clinical Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2015-08
- Volume
- 53
- Issue
- 8
- Pages
- 2410-2426
- ISSN
- 0095-1137 (ISSN-L)
- 1098-660X
- PMC
- PMC4508402
- OpenAlex
- W1961504819
- Cited by
- 915
- References
- 38
- Citations by year
- 2026: 84 · 2025: 93 · 2024: 100 · 2023: 82 · 2022: 109 · 2021: 122 · 2020: 94 · 2019: 70 · 2018: 68 · 2017: 41 · 2016: 47 · 2015: 5
- FWCI
- 41.59
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Clinical Microbiology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Escherichia coli research studies
- Life Sciences › Agricultural and Biological Sciences › Food Science › Salmonella and Campylobacter epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Keywords
- Escherichia coli, whole genome sequencing, flagellin gene, FliC, pathogen surveillance, outbreak detection
- MeSH terms
- Antigens, Bacterial, Computer Simulation, Costs and Cost Analysis, Escherichia coli, Humans, Serotyping, Time Factors, Genome, Bacterial, Sequence Analysis, DNA, O Antigens, Computational Biology
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