Clonotyping Technology for Prediction of Antibiotic Resistance

DESCRIPTIONprovided by applicantThe primary goal of this proposal is to develop and finalize configuration of a rapid molecular diagnostics test to predict antibiotic resistance of th major human uropathogensEscherichia coliKlebsiella pneumoniaeEnterobacter spp and Pmirabilisby determining the sub species clonal identityclonotypeof the infecting bacteria directly from urine samplesCurrentlythe empiricalpreantibiogramchoice of antibiotic treatment is guided by an educated guess about the suspected species of pathogen and its cumulative antibiogram from data compiled locally every yearWe have shownin the Phase Istudies that a significant improvement in antibiotic choice against uropathogenic Ecoli could be achieved if the antibiotic treatment choice would be guided by cumulative antibiogram of the clonotype to which the infecting Ecoli strain belongsWe also have shown that the clonal identity of Ecoli can be determined directly in urine using qPCRThe basic idea for the Phase II studies is to refine the Ecoli clonotyping test and add to the test clonal and or species markers for nonEcoli uropathogenswith a goal of coveringof pathogensand reduce the potential drug bug mismatch for common antibiotics at leastfolgClonotype determination is done by detection of the presence absence of a limited numbere gsix to tenof polymorphic gene markersmosaicallydistributed genes and or nucleotide polymorphismsthat will be selected genome wideInterrogation of the markers will be performed by qPCR using a simpleadaptable configuration of standard PCR tube strips and existing FDA cleared instrumentation platformsTo achieve these goalswe will determine genome sequences and cumulative antibiograms of a comprehensive number of Ecoli and non Ecoli clinical isolatesand establish the association between the resistance to common antibiotics and clonal identity of the pathogensPolymorphic clonal markersthat are suitable for binary differentiationwill be identified across the genome of each speciesOligonucleotide primerscapable of robust interrogation of the binary lociwill be designed and validated using clinical isolates from different geographic regions of the USA overyearsThe proposed studies will be performed as a collaboration between ID GenomicsInca Seattle based start up companyspecializing in sequence based typing of microbial pathogensand the University of WashingtonSeattlethe laboratory of Evgeni Sokurenkoand a consortium of eight different clinical microbiology laboratories