A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens.

Escherichia coli is a major causative agent of acute infections, both gastrointestinal and extraintestinal [1, 2]. Extraintestinal pathogenic E coli (ExPEC), a subset of E coli, is the major cause of urinary tract infections (UTIs), newborn meningitis, and bacterial sepsis. Extraintestinal pathogenic E coli strains are highly clonal, with certain closely related clonal groups associated with characteristic antimicrobial resistance profiles [3–6]. Therefore, subspecies delineation of ExPEC clonal groups has significant potential for improving the diagnostics of antimicrobial resistance, especially if it can be performed directly from the clinical specimen and quickly (eg, <1 hour). The current standard for clonal typing is multilocus sequence typing (MLST) [7], which involves sequencing of approximately 7 housekeeping genes and splitting E coli into sequence types (STs). However, MLST is laborious and time consuming, and thus it is not well suited for clinical or epidemiological applications. We have recently introduced a method for predicting clonal types and associated resistance profiles based on sequencing of only 2 genes: fumC and fimH (ie, CH typing). This scheme was shown to subdivide E coli into a large number of clonal groups or combinations thereof (clonotypes), and it was effective both in predicting and subdividing specific ExPEC STs [3, 8]. We have successfully used CH typing as a proof-of-principle for the use of clonotyping to predict antibiotic resistance among clinical isolates. However, the fumC/fimH clonotyping scheme still involves DNA sequencing, limiting its broader application. In this study, we report a novel method for ExPEC clonotyping that incorporates polymerase chain reaction (PCR) or quantitative PCR (qPCR)-based determination of the presence or absence of just 7 single nucleotide polymorphisms (SNPs) within fumC and fimH. We demonstrate that alternative binary combinations of the 7 SNPs splits ExPEC clinical isolates into several dozen clonal types that exhibit distinct antibiotic susceptibility profiles. We show that the 7-SNP typing test can rapidly identify clonal types of E coli directly from urine specimens, demonstrating the potential to predict antibiotic resistance using a clonal diagnostics approach in the point-of-care setting.