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
Affiliations
Ibukun Elizabeth Osadare
Leibniz Institute of Photonic Technology (IPHT), Research Alliance Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
Stefan Monecke
Leibniz Institute of Photonic Technology (IPHT), Research Alliance Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
Abdinasir Abdilahi
Leibniz Institute of Photonic Technology (IPHT), Research Alliance Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
Elke Müller
Leibniz Institute of Photonic Technology (IPHT), Research Alliance Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
Maximilian Collatz
Leibniz Institute of Photonic Technology (IPHT), Research Alliance Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
Sascha Braun
Leibniz Institute of Photonic Technology (IPHT), Research Alliance Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
Annett Reissig
Leibniz Institute of Photonic Technology (IPHT), Research Alliance Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
Wulf Schneider-Brachert
Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
Bärbel Kieninger
Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
Anja Eichner
Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
Anca Rath
Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
Jürgen Fritsch
Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
Dominik Gary
fzmb GmbH, Forschungszentrum für Medizintechnik und Biotechnologie, 99947 Bad Langensalza, Germany
Katrin Frankenfeld
fzmb GmbH, Forschungszentrum für Medizintechnik und Biotechnologie, 99947 Bad Langensalza, Germany
Thomas Wellhöfer
fzmb GmbH, Forschungszentrum für Medizintechnik und Biotechnologie, 99947 Bad Langensalza, Germany
Ralf Ehricht
Leibniz Institute of Photonic Technology (IPHT), Research Alliance Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
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.