# Rapid multiplex method for direct phenotypic ID/AST of bacterial pathogens

> **NIH NIH R01** · GUILD ASSOCIATES, INC. · 2020 · $1,168,045

## Abstract

Urinary tract infections (UTI) are diseases of the kidneys, ureters, bladder or urethra and are caused by
microbes that live in the bowel. They afflict millions of people every year and are the second most common
type of bacterial infection encountered by humans throughout their life span. Approximately 150 million UTI
occur worldwide annually, accounting for $6 billion in healthcare costs. In the U.S.A., UTI are responsible for 8
million annual visits to healthcare providers. Some infections can lead to serious kidney complications and
septicemia, with 13,000 deaths annually being attributed to nosocomial UTI. Although different microorganisms
(e.g. bacteria, viruses, fungi) can cause these infections, Gram-negative bacteria are the most prevalent. The
standard methods for species diagnosis are culture-based protocols that take up to 48 h. As a result, UTI are
one of the most frequent reasons for antimicrobial prescriptions in healthcare facilities without a confirmed
diagnosis. Therefore, modern rapid diagnostic methods that promote antimicrobial stewardship are crucial.
Moreover, as patient outcomes are directly correlated to length of time to diagnosis and administration of
appropriate therapy, the development of novel diagnostics that can rapidly identify (ID) the pathogen directly in
clinical specimens, and simultaneously provide antibiotic susceptibility testing (AST) is a critical factor for UTI
management.
 The goal of this project is to develop a product called multIDAST UTI that is superior to microbiological
culture-based methods used for ID/AST of UTI. MultIDAST UTI will be developed as a qualitative in vitro
diagnostic (IVD) test for rapid (<3 h) multiplexed identification of Gram-negative pathogens of uncomplicated
UTI directly from urine and simultaneous characterization of their phenotypic responses to commonly
prescribed antimicrobials. The product thereby bypasses the need for bacterial amplification and isolation and
thus overcomes the major time-limiting step of current diagnostics. This will be achieved by uniquely combining
species-specific phages, which have been engineered to produce a signature molecule upon bacterial
infection, and isothermal helicase dependent amplification (HDA), which amplifies the signal ∼108-fold. The
ensuing phenotypic signal is directly correlated to cell fitness; thus, we can rapidly generate information related
to the pathogens sensitivity or resistance to a particular drug by incubation in the absence or presence of
antimicrobials. Signal responses will be measured using Solana, a fluorometer currently used in multiple FDA-
cleared HDA diagnostic assays. The practical purpose of this contemporary system is to identify the pathogen
and determine the antibiotic suitable to cure an infection, thereby promoting antimicrobial stewardship. It will
support the fight against antibiotic resistance by addressing the emergence of carbapenem-resistant
Enterobacteriaceae (CRE), classified by the Centers fo...

## Key facts

- **NIH application ID:** 9921292
- **Project number:** 5R01AI138971-03
- **Recipient organization:** GUILD ASSOCIATES, INC.
- **Principal Investigator:** Ian Fleming
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $1,168,045
- **Award type:** 5
- **Project period:** 2018-05-17 → 2022-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9921292

## Citation

> US National Institutes of Health, RePORTER application 9921292, Rapid multiplex method for direct phenotypic ID/AST of bacterial pathogens (5R01AI138971-03). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9921292. Licensed CC0.

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