Clonotyping Technology for Prediction of Antibiotic Resistance

DESCRIPTION provided by applicant The primary goal of this Phase I STTR proposal is to develop a prototype of a rapid molecular diagnostics test to improve prediction of the antibiotic resistance of uropathogenic Escherichia coli by determining their clonal identity clonotype The clonotype determination will be done by detection of the presence absence of a limited number d of single nucleotide polymorphisms SNPs that will be selected from genetic loci used for the clonal typing of E coli seven loci from the standard multi locus sequence typing MLST scheme for E coli and fast evolving gene for the type fimbrial adhesin fimH The SNPs binary interrogation could be performed in either thermocycler or isothermal DNA amplification protocols using a simple single plex configuration adapted to the standard tube PCR strips and common instrumentation platforms These tests will be designed to perform in near patient settings such as clinical laboratories in emergency rooms urgent care clinics and or hospitals The test will be done using patientsandapos urine in a cost effective and timely manner andlt min with the goal to improve the empirical pre antibiogram choice of antibiotic treatment reducing potential andapos drug bugandapos mismatch and overuse of last line broad spectrum antimicrobials To achieve the goals we will determine MLST fimH and antibiogram profiles of a comprehensive number of clinical isolates and establish the association between resistance to commonly used antibiotics and the clonal identity of pathogens Phylogenetically unlinked homoplasic SNPs that are distributed across the clonotypes in a relatively random and even fashion will be identified Alternate combinations of to SNPs will be analyzed for the ability to discriminate up to of the most critical size and resistance wise clonotypes of E coli Oligonucleotide primers capable of robust interrogation of the SNP combinations will be designed and validated for different amplification protocols The proposed studies will be performed as collaboration between ID Genomics Inc the University of Washingtonandapos s start up company specializing in sequence based typing of microbial pathogens and the University of Washington Seattle laboratory of Evgeni Sokurenko the lead PI PUBLIC HEALTH RELEVANCE We are proposing to develop a molecular diagnostic technology for a test kit to predict antibiotic resistance of bacteria causing urinary tract infectons in humans based on the genetic family clonal type they belong to The kits will be designed for use in emergency or urgent care clinics and hospitals to perform directly on urine and in a timely andlt min manner