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Abstract

Antimicrobial resistance (AMR) is an ever-increasing global health concern. One crucial facet in tackling the AMR epidemic is earlier and more accurate AMR diagnosis, particularly in the dangerous and highly multi-drug-resistant ESKAPE pathogen, .

We aimed to develop two SYBR Green-based mismatch amplification mutation assays (SYBR-MAMAs) targeting GyrA T83I (248) and GyrA D87N, D87Y and D87H (259). Together, these variants cause the majority of fluoroquinolone (FQ) AMR in .

Following assay validation, the 248 and 259 SYBR-MAMAs were tested on 84 Australian clinical isolates, 46 of which demonstrated intermediate/full ciprofloxacin resistance according to antimicrobial susceptibility testing.

Our two SYBR-MAMAs correctly predicted an AMR phenotype in the majority (83%) of isolates with intermediate/full FQ resistance. All FQ-sensitive strains were predicted to have a sensitive phenotype. Whole-genome sequencing confirmed 100 % concordance with SYBR-MAMA genotypes.

Our GyrA SYBR-MAMAs provide a rapid and cost-effective method for same-day identification of FQ AMR in . An additional SYBR-MAMA targeting the GyrB S466Y/S466F variants would increase FQ AMR prediction to 91 %. Clinical implementation of our assays will permit more timely treatment alterations in cases where decreased FQ susceptibility is identified, leading to improved patient outcomes and antimicrobial stewardship.

Funding
This study was supported by the:
  • University of the Sunshine Coast
    • Principle Award Recipient: MaddenDanielle E.
  • Wishlist (Award 2019-14)
    • Principle Award Recipient: FraserTamieka A.
  • Wishlist (Award 2019-14)
    • Principle Award Recipient: PriceErin P.
  • Wishlist (Award 2019-14)
    • Principle Award Recipient: SarovichDerek S.
  • Wishlist (Award 2019-14)
    • Principle Award Recipient: BairdTimothy
  • Advance Queensland (Award AQRF13016-17RD2)
    • Principle Award Recipient: SarovichDerek S.
  • Advance Queensland (Award AQIRF0362018)
    • Principle Award Recipient: PriceErin P.
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-10-27
2024-05-02
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