Multiplexed Assay for Point-of-Care UTI Diagnosis (ID/AMR)

PROJECT SUMMARY
Nanopath proposes to develop a point-of-care molecular diagnostic that can identify UTI-causing
pathogens and key genetic markers of antibiotic resistance directly from a patient urine sample in
15 minutes, without the need for nucleic acid amplification. Despite the severity and prevalence
of UTIs, the current diagnostic standard-of-care relies on culture-based methods, which take an
average several days to return species-level and antimicrobial resistance information. This time-
intensive diagnostic workflow leaves many patients in pain and/or at-risk of severe infection before
they are prescribed targeted antibiotic therapy. Critically, empiric treatment of UTIs is one of the
largest contributors to the growing problem of antibiotic resistance. Nanopath’s product is a single-
use assay cartridge coupled to a low-cost readout instrument. The assay cartridge integrates
sample preparation with our proprietary molecular nanosensor. Our multiplexed molecular
nanosensor is functionalized with an array of probes complementary to 1) species-specific genetic
sequences and 2) genetic markers of antimicrobial resistance. In our preliminary work, we
designed a 5-target proof-of-concept panel encompassing three bacterial species and two
antimicrobial resistance genes that are commonly observed in UTIs. Our preliminary data
demonstrate highly selective and robust target detection in a variety of sample matrices, including
healthy patient urine. Our Phase II effort will focus on four Specific Aims. First, we will expand our
target panel to encompass >95% of UTI-causing organisms and key markers of antimicrobial
resistance. This will involve rational design and bench-top validation of candidate PNA probes to
inform a finalized panel and probe set. Second, we will optimize the design of the assay cartridge
to integrate sample handling functions, lower limit-of-detection, and enable high throughput
sample processing. This aim will also support low-volume manufacturing of the assay cartridge in
preparation for verification studies. Third, we will perform a series of comprehensive analytical
verification studies on the assay. Finally, we will characterize clinical performance of Nanopath’s
UTI assay in pilot clinical study (n>200) in collaboration with Brigham & Women’s Hospital.
Successful commercialization of this technology will enable point-of-care characterization of UTIs
in <15 minutes, enabling the immediate targeting of antibiotic therapy and alleviating ongoing
contributions to antibiotic resistance. The applications of the proposed platform extend beyond
UTIs and are translatable to other clinical scenarios that currently employ lengthy culture-based
steps and molecular testing workflows, such as respiratory infections, bloodstream infections, and
prosthetic joint infections.

Grant Number: 5R44AI181154-02
NIH Institute/Center: NIH
Principal Investigator: Alison Burklund