ArticleApplied and environmental microbiology2005
Single-nucleotide polymorphism phylotyping of Escherichia coli.
Article in Applied and environmental microbiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Annotation-free delineation of prokaryotic homology groups.PLoS computational biology · 2022Article
- Development of Single Nucleotide Polymorphism (SNP)-Based Triplex PCR Marker for Serotype-specificPathogens (Basel, Switzerland) · 2022Article
- Molecular characterisation of Mycobacterium avium subsp. paratuberculosis in Australia.BMC microbiology · 2021Article
- Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life.Scientific reports · 2020Article
- Genomic Characterization of MDRBioMed research international · 2018Article
- A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens.Open forum infectious diseases · 2016Article
- SNaPBcen: a novel and practical tool for genotyping Burkholderia cenocepacia.Journal of clinical microbiology · 2013Article
- Differentiation of Erwinia amylovora and Erwinia pyrifoliae strains with single nucleotide polymorphisms and by synthesis of dihydrophenylalanine.Current microbiology · 2012Article
- Intergenic sequence comparison of Escherichia coli isolates reveals lifestyle adaptations but not host specificity.Applied and environmental microbiology · 2011Article
- Clinical relevance of multiple single-nucleotide polymorphisms in Pneumocystis jirovecii Pneumonia: development of a multiplex PCR-single-base-extension methodology.Journal of clinical microbiology · 2011Article
- Diarrheagenic Escherichia coli in children from Costa Rica.The American journal of tropical medicine and hygiene · 2010Article
- Highly discriminatory single-nucleotide polymorphism interrogation of Escherichia coli by use of allele-specific real-time PCR and eBURST analysis.Applied and environmental microbiology · 2010Article
- Development of a multiplex primer extension assay for rapid detection of Salmonella isolates of diverse serotypes.Journal of clinical microbiology · 2010Article
- Evaluation of single-nucleotide primer extension for detection and typing of phylogenetic markers used for investigation of microbial communities.Applied and environmental microbiology · 2009Article
- Multilocus sequence typing analysis of Shigella flexneri isolates collected in Asian countries.Journal of medical microbiology · 2007Article
- Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting.Applied and environmental microbiology · 2007Article
- Multiplex assay based on single-nucleotide polymorphisms for rapid identification of Brucella isolates at the species level.Applied and environmental microbiology · 2007Article
- Extraintestinal pathogenic Escherichia coli strains of avian and human origin: link between phylogenetic relationships and common virulence patterns.Journal of clinical microbiology · 2007Article
- Probe hybridization array typing: a binary typing method for Escherichia coli.Journal of clinical microbiology · 2007Article
- Staphylococcus aureus genotyping using novel real-time PCR formats.Journal of clinical microbiology · 2006Article
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Authors and funding
5 authors.
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Abstract
We describe a rapid and easily automated phylogenetic grouping technique based on analysis of bacterial genome single-nucleotide polymorphisms (SNPs). We selected 13 SNPs derived from a complete sequence analysis of 11 essential genes previously used for multilocus sequence typing (MLST) of 30 Escherichia coli strains representing the genetic diversity of the species. The 13 SNPs were localized in five genes, trpA, trpB, putP, icdA, and polB, and were selected to allow recovery of the main phylogenetic groups (groups A, B1, E, D, and B2) and subgroups of the species. In the first step, we validated the SNP approach in silico by extracting SNP data from the complete sequences of the five genes for a panel of 65 pathogenic strains belonging to different E. coli pathovars, which were previously analyzed by MLST. In the second step, we determined these SNPs by dideoxy single-base extension of unlabeled oligonucleotide primers for a collection of 183 commensal and extraintestinal clinical E. coli isolates and compared the SNP phylotyping method to previous well-established typing methods. This SNP phylotyping method proved to be consistent with the other methods for assigning phylogenetic groups to the different E. coli strains. In contrast to the other typing methods, such as multilocus enzyme electrophoresis, ribotyping, or PCR phylotyping using the presence/absence of three genomic DNA fragments, the SNP typing method described here is derived from a solid phylogenetic analysis, and the results obtained by this method are more meaningful. Our results indicate that similar approaches may be used for a wide variety of bacterial species.
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