# Exclusive liquid repellency enables next-generation phenotypic antimicrobial susceptibility testing

> **NIH NIH R01** · UNIVERSITY OF WISCONSIN-MADISON · 2024 · $764,423

## Abstract

Project Summary/Abstract
Rapid identification and antimicrobial susceptibility testing (AST) of clinical isolates are crucial to ensure early
appropriate treatment and prevent misuse of broad-spectrum antimicrobials. Both phenotypic (i.e., growth,
inhibition, or killing event-based) and molecular (i.e., resistant gene or molecule-based) ASTs are routinely used in
the hospital clinical microbiology laboratory. The limitations of molecular methods (e.g., qPCR, MALDI-TOF MS)
include their narrow scope (i.e., select resistance genes/molecules), or in some cases the inability to predict
antimicrobial susceptibility, while phenotypic methods involve time-consuming, multi-step expansion culture resulting
in prolonged time to result, which can delay appropriate treatment decisions. This proposal leverages an exclusive
liquid repellency (ELR) based under-oil open microfluidic system for a transformative approach to next-generation
phenotypic ASTs. With a multidisciplinary team including clinicians, microbiologists/pharmacologists, surface
scientists, and bioengineers, we outline three aims for the development of this next-generation, phenotypic AST
system. The ELR-based AST system aims to meet the following criteria: i) direct AST using the original clinical
isolates (e.g., from blood, sputum, urine, abscess) to eliminate time-consuming expansion culture and passage-
associated selection bias ex vivo, ii) comprehensive test coverage including anaerobes, multispecies communities,
heteroresistance (i.e., resistant mutants within the wild-type population), and iii) rapid AST with the goal of sample
to report in less than 4 hours. In Aim 1 we propose to develop ELR-centrifugation and small-volume (
μ
l scale)
lossless sample processing for isolation, enrichment, and preparation of sparse (i.e., 1-100 cfu/ml) bacteria from
whole blood. The goal is to directly isolate and enrich bacteria from whole blood without expansion culture. We will
combine the lossless sample processing enabled by ELR with lysis-centrifugation to maximize the recovery yield of
bacteria (> 90%) from whole blood. In Aim 2 we will demonstrate compatibility of ELR AST with intrinsic fluorescence
label free imaging modalities and deep learning-based identification. The goal is to develop and apply proof-of-
concept advanced label-free, single-cell resolution, live-cell imaging, and deep learning algorithms to integrate
bacterial detection, species identification, and antimicrobial screening thereby eliminating isolate passage
expansion. In Aim 3 we propose to develop label-free, direct detection of heteroresistance in priority human
pathogens in clinical isolates. The goal is to detect heteroresistance [i.e., a small/rare subpopulation (e.g., <1%) of
resistant mutants in clinical isolates], which cannot be identified by standard clinical methods. We will utilize sweep
distribution to array small numbers of bacteria directly from clinical isolates, thus enabling the detection of
these heterore...

## Key facts

- **NIH application ID:** 10941317
- **Project number:** 1R01AI184593-01
- **Recipient organization:** UNIVERSITY OF WISCONSIN-MADISON
- **Principal Investigator:** David J Beebe
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $764,423
- **Award type:** 1
- **Project period:** 2024-06-03 → 2029-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10941317

## Citation

> US National Institutes of Health, RePORTER application 10941317, Exclusive liquid repellency enables next-generation phenotypic antimicrobial susceptibility testing (1R01AI184593-01). Retrieved via AI Analytics 2026-06-02 from https://api.ai-analytics.org/grant/nih/10941317. Licensed CC0.

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