# Rapid Identification and Susceptibility Testing Directly From Urine Specimens, Reducing Turnaround Time, a Step Towards Advancing Diagnostic Stewardship

## TL;DR

This study shows how using MALDI-TOF MS and direct AST can significantly reduce the time to diagnose and test antibiotic susceptibility in urinary tract infections.

## Contribution

The novel contribution is a combined protocol that enables rapid identification and AST of uropathogens directly from urine specimens within six to eight hours.

## Key findings

- Direct MALDI-TOF MS correctly identified 88.2% and 90.7% of uropathogens in standardization and validation phases.
- Direct AST achieved over 90% categorical agreement with reference methods within six to eight hours.
- The protocol reduced the turnaround time for results to 39-43 hours, compared to traditional methods.

## Abstract

Background

Urinary tract infections (UTIs) are the most common bacterial infections with a turnaround time (TAT) of 48-72 hours for routine culture and antimicrobial susceptibility testing (AST). Here, we aimed to improve diagnostic stewardship by reducing TAT for the most commonly encountered uropathogens, that is, Escherichia coli and Klebsiella pneumoniae by combining the usage of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the direct identification of pathogens from urine specimen, along with direct AST at different time points.

Methods

Urine specimens were examined by compound microscopy under high power field (HPF). Thirty-six urine specimens and 25 urine specimens were included for the standardization phases of direct MALDI-TOF MS and direct AST, respectively, while 65 and 55 specimens were included for the validation phases, respectively. AST was read at four hours, six hours, eight hours and 16-18/16-20 hours using the Clinical and Laboratory Standards Institute (CLSI) M100, 34th edition, 2024 breakpoints for direct blood cultures and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) version 7.1, 2024 breakpoints for short incubation disc diffusion. Culture-based MALDI-TOF MS identification, culture-based VITEK II (BioMérieux, Marcy-l'Étoile, France) or AST were considered the reference standard. All readings were compared with reference standard values for statistical and agreement analysis.

Results

Using direct MALDI-TOF MS, 88.2% (30/34) and 90.7% (59/65) of uropathogens were correctly identified in the standardization and validation phases, respectively. The results of direct AST showed that most antibiotics had a categorical agreement of greater than 90%, and acceptable error rates by six to eight hours, resulting in a TAT reduction in the range of 39-43 hours.

Conclusion

This proof-of-concept study using a combined protocol is a feasible way to give final identification and AST results within six to eight hours of sample reception, thus providing an impetus to diagnostic stewardship and ensuring timely intervention.