ArticleMicrobial genomics2018
ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping.
Article in Microbial genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 416 papers.
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Who cites it
416 citing papers in PubMed.
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- Genomic diversity, antimicrobial resistance, and virulence-associated characteristics of Escherichia coli recovered from poultry hatchery-box material.Poultry science · 2026Article
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- Comprehensive genomic characterization of extraintestinal pathogenic Escherichia coli isolated from neonates: multiple center insights into virulence, resistance, and transmission dynamics.Genome medicine · 2026Article
- Human wastewater contamination drives the emergence of multidrug-resistant bacteria in the Galápagos marine ecosystem.Nature communications · 2026Article
- Detection of an ExPEC-likeBiotech (Basel (Switzerland)) · 2026Article
- Linking land use to the likely origins of third-generation cephalosporin-resistant Enterobacterales in freshwater.Applied and environmental microbiology · 2026Article
- Genomic Insights and Antimicrobial Resistance Profiling of DiarrheagenicMicroorganisms · 2026Article
- Molecular characterization of extended-spectrum β-lactamases-producing Escherichia coli isolated from patients with bacteremia.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Antimicrobial resistance and genomic characteristics of bovine Escherichia coli from five northern provinces of China.BMC genomics · 2026Article
- Genomic analyses of antibiotic-resistant Escherichia coli from extensive beef cattle and sheep farms identifies inter-species and farm-farm sharing as clonal dissemination pathways.The Journal of antimicrobial chemotherapy · 2026Article
- Molecular epidemiology reveals distinct lineages and genomic profiles of avian pathogenic and commensalMicrobial genomics · 2026Article
- Whole genome analysis of a multidrug-resistant blaBMC microbiology · 2026Article
- EcoliTyper: a species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli.BMC bioinformatics · 2026Article
- Tracking Extended-Spectrum β-Lactamase-ProducingAntibiotics (Basel, Switzerland) · 2026Article
- Genomic Characterization of Selected Multidrug-ResistantAnimals : an open access journal from MDPI · 2026Article
356 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genus Escherichia is composed of Escherichia albertii, E. fergusonii, five cryptic Escherichia clades and E. coli sensu stricto. Furthermore, the E. coli species can be divided into seven main phylogroups termed A, B1, B2, C, D, E and F. As specific lifestyles and/or hosts can be attributed to these species/phylogroups, their identification is meaningful for epidemiological studies. Classical phenotypic tests fail to identify non-sensu stricto E. coli as well as phylogroups. Clermont and colleagues have developed PCR assays that allow the identification of most of these species/phylogroups, the triplex/quadruplex PCR for E. coli phylogroup determination being the most popular. With the growing availability of whole genome sequences, we have developed the ClermonTyping method and its associated web-interface, the ClermonTyper, that allows a given strain sequence to be assigned to E. albertii, E. fergusonii, Escherichia clades I-V, E. coli sensu stricto as well as to the seven main E. coli phylogroups. The ClermonTyping is based on the concept of in vitro PCR assays and maintains the principles of ease of use and speed that prevailed during the development of the in vitro assays. This in silico approach shows 99.4 % concordance with the in vitro PCR assays and 98.8 % with the Mash genome-clustering tool. The very few discrepancies result from various errors occurring mainly from horizontal gene transfers or SNPs in the primers. We propose the ClermonTyper as a freely available resource to the scientific community at: http://clermontyping.iame-research.center/.
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