ArticleOpen forum infectious diseases2016
A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens.
Article in Open forum infectious diseases, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
- Characterisation of Haemolytic Uropathogenic Escherichia coli Isolated From Dogs and Cats.Veterinary medicine and science · 2026Article
- In Vitro Microevolution and Co-Selection Assessment of Amoxicillin and Cefotaxime Impact onAntibiotics (Basel, Switzerland) · 2024Article
- Clonal and resistance profiles of fluoroquinolone-resistant uropathogenicFrontiers in microbiology · 2024Article
- Occurrence and Genomic Characterization of Clone ST1193 Clonotype 14-64 in Uncomplicated Urinary Tract Infections Caused by Escherichia coli in Spain.Microbiology spectrum · 2022Article
- Molecular Identification ofAnimals : an open access journal from MDPI · 2022Article
- Comparative activity of plazomicin against extended-spectrum cephalosporin-resistant Escherichia coli clinical isolates (2012-2017) in relation to phylogenetic background, sequence type 131 subclones, blaEuropean journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2021Article
- Review
- Activity of Imipenem-Relebactam against Carbapenem-Resistant Escherichia coli Isolates from the United States in Relation to Clonal Background, Resistance Genes, Coresistance, and Region.Antimicrobial agents and chemotherapy · 2020Article
- Escherichia coli Clonobiome: Assessing the Strain Diversity in Feces and Urine by Deep Amplicon Sequencing.Applied and environmental microbiology · 2019Article
- Genotypic analysis of uropathogenic Escherichia coli to understand factors that impact the prevalence of β-lactam-resistant urinary tract infections in a community.Journal of global antimicrobial resistance · 2019Article
- Pandemic fluoroquinolone resistantProceedings of the National Academy of Sciences of the United States of America · 2019Article
- The Uropathogenic Escherichia coli Subclone Sequence Type 131-H30 Is Responsible for Most Antibiotic Prescription Errors at an Urgent Care Clinic.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2019Article
- Rapid and Extensive Expansion in the United States of a New Multidrug-resistant Escherichia coli Clonal Group, Sequence Type 1193.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2019Article
- Molecular Epidemiology of Extraintestinal PathogenicEcoSal Plus · 2018Review
- Rapid and Specific Detection of the Escherichia coli Sequence Type 648 Complex within Phylogroup F.Journal of clinical microbiology · 2017Article
- Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection.PloS one · 2017Observational
- Article
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
Abstract
Background. Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods. We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fumC and fimH). A reference set of 2559 E coli isolates, primarily of urinary origin, was used to predict the resolving power of the 7-SNP-based typing method, and 582 representative strains from this set were used to evaluate test robustness. Results. Fifty-four unique SNP combinations ("septatypes") were identified in the reference strains. These septatypes yielded a clonal group resolution power on par with that of traditional multilocus sequence typing. In 72% of isolates, septatype identity predicted sequence type identity with at least 90% (mean, 97%) accuracy. Most septatypes exhibited highly distinctive antimicrobial susceptibility profiles. The 7-SNP-based test could be performed with high specificity and sensitivity using single or multiplex conventional polymerase chain reaction (PCR) and quantitative PCR. In the latter format, E coli presence and septatype identity were determined directly in urine specimens within 45 minutes with bacterial loads as low as 10(2) colony-forming units/mL and, at clinically significant bacterial loads, with 100% sensitivity and specificity. Conclusions. 7-SNP-based typing of E coli can be used for both epidemiological studies and clinical diagnostics, which could greatly improve the empirical selection of antimicrobial therapy.
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