Sensors (Oct 2024)

Fast and Economic Microarray-Based Detection of Species-, Resistance-, and Virulence-Associated Genes in Clinical Strains of Vancomycin-Resistant Enterococci (VRE)

  • Ibukun Elizabeth Osadare,
  • Stefan Monecke,
  • Abdinasir Abdilahi,
  • Elke Müller,
  • Maximilian Collatz,
  • Sascha Braun,
  • Annett Reissig,
  • Wulf Schneider-Brachert,
  • Bärbel Kieninger,
  • Anja Eichner,
  • Anca Rath,
  • Jürgen Fritsch,
  • Dominik Gary,
  • Katrin Frankenfeld,
  • Thomas Wellhöfer,
  • Ralf Ehricht

DOI
https://doi.org/10.3390/s24196476
Journal volume & issue
Vol. 24, no. 19
p. 6476

Abstract

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Today, there is a continuous worldwide battle against antimicrobial resistance (AMR) and that includes vancomycin-resistant enterococci (VRE). Methods that can adequately and quickly detect transmission chains in outbreaks are needed to trace and manage this problem fast and cost-effectively. In this study, DNA-microarray-based technology was developed for this purpose. It commenced with the bioinformatic design of specific oligonucleotide sequences to obtain amplification primers and hybridization probes. Microarrays were manufactured using these synthesized oligonucleotides. A highly parallel and stringent labeling and hybridization protocol was developed and employed using isolated genomic DNA from previously sequenced (referenced) clinical VRE strains for optimal sensitivity and specificity. Microarray results showed the detection of virulence, resistance, and species-specific genes in the VRE strains. Theoretical predictions of the microarray results were also derived from the sequences of the same VRE strain and were compared to array results while optimizing protocols until the microarray result and theoretical predictions were a match. The study concludes that DNA microarray technology can be used to quickly, accurately, and economically detect specifically and massively parallel target genes in enterococci.

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