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Detection assay of polymyxin resistance coding mcr-1 gene based on CRISPR/Cas13a system

Yingjie Song1, Qiang Hu1, Yao Han1

  • 1State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China.

Frontiers in Cellular and Infection Microbiology
|June 20, 2025
PubMed
Abstract

Insights

A new CRISPR/Cas13a assay with lateral flow strips can detect the polymyxin resistance gene mcr-1. This portable method is suitable for primary healthcare and field surveillance of multidrug-resistant bacteria.

Area of Science:

  • Microbiology
  • Molecular Biology
  • Antimicrobial Resistance

Background:

  • Polymyxins are crucial for treating multidrug-resistant Gram-negative bacterial infections.
  • The emergence of the mcr-1 gene confers polymyxin resistance, posing a significant threat to public health.
  • Accurate and rapid detection of mcr-1 is essential for guiding treatment and controlling resistance spread.

Purpose of the Study:

  • To develop a sensitive and portable method for detecting the mcr-1 gene.
  • To evaluate the performance of the developed assay compared to quantitative real-time PCR (qPCR).

Main Methods:

  • CRISPR/Cas13a system combined with lateral flow strips was utilized for mcr-1 gene detection.
  • Assay optimization and validation were performed using clinical isolates of Escherichia coli.
  • Comparison with qPCR was conducted to assess accuracy and concordance.

Main Results:

  • A detection limit of 100 copies/mL was achieved for the mcr-1 gene.
  • The assay demonstrated high analytical specificity, with no cross-reactivity observed.
  • 100% concordance with qPCR results was observed for 36 clinical isolates, correctly identifying 31 mcr-1 positive strains.

Conclusions:

  • A novel CRISPR/Cas13a-based detection method for the mcr-1 gene was successfully established.
  • The assay provides visual readouts without requiring specialized equipment, enhancing portability.
  • This method holds potential for application in primary healthcare settings and field surveillance of polymyxin resistance.
Keywords:
CRISPR/Cas13aantibiotic resistancelateral flow stripmcr-1polymyxin

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