title: A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens.
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.
authors.affiliation: Departments of Microbiology.
authors.forename: Veronika
authors.initials: V
authors.lastname: Tchesnokova
authors.affiliation: Departments of Microbiology.
authors.forename: Hovhannes
authors.initials: H
authors.lastname: Avagyan
authors.affiliation: Departments of Microbiology.
authors.forename: Mariya
authors.initials: M
authors.lastname: Billig
authors.affiliation: Departments of Microbiology.
authors.forename: Sujay
authors.initials: S
authors.lastname: Chattopadhyay
authors.affiliation: ID Genomics, Inc. , Seattle, Washington.
authors.forename: Pavel
authors.initials: P
authors.lastname: Aprikian
authors.affiliation: Departments of Microbiology.
authors.forename: Diana
authors.initials: D
authors.lastname: Chan
authors.affiliation: Gemotest , Moscow , Russia.
authors.forename: Julietta
authors.initials: J
authors.lastname: Pseunova
authors.affiliation: ID Genomics, Inc. , Seattle, Washington.
authors.forename: Elena
authors.initials: E
authors.lastname: Rechkina
authors.affiliation: GroupHealth Cooperative, Seattle, Washington.
authors.forename: Kim
authors.initials: K
authors.lastname: Riddell
authors.affiliation: GroupHealth Cooperative, Seattle, Washington.
authors.forename: Delia
authors.initials: D
authors.lastname: Scholes
authors.affiliation: Departments ofMicrobiology; Laboratory Medicine, University of Washington School of Medicine, Seattle.
authors.forename: Ferric C
authors.initials: FC
authors.lastname: Fang
authors.affiliation: VA Medical Center and University of Minnesota , Minneapolis.
authors.forename: James R
authors.initials: JR
authors.lastname: Johnson
authors.affiliation: Departments of Microbiology.
authors.forename: Evgeni V
authors.initials: EV
authors.lastname: Sokurenko
keywords: Escherichia coli; antibiotic resistance; clonal typing; personal therapy; point-of-care testing