Open Access Highly Accessed Research article

A novel, multiplex, real-time PCR–based approach for the detection of the commonly occurring pathogenic fungi and bacteria

Ádám Horváth1*, Zoltán Pető2, Edit Urbán3, Csaba Vágvölgyi4 and Ferenc Somogyvári1

Author Affiliations

1 Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Dóm tér 10, Szeged H-6720, Hungary

2 Department of Anaesthesiology and Intensive Therapy, Faculty of Medicine, University of Szeged, Semmelweis u. 6, Szeged, Hungary

3 Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Semmelweis u. 6, Szeged, Hungary

4 Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, Hungary

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BMC Microbiology 2013, 13:300  doi:10.1186/1471-2180-13-300

Published: 23 December 2013



Polymerase chain reaction (PCR)-based techniques are widely used to identify fungal and bacterial infections. There have been numerous reports of different, new, real-time PCR-based pathogen identification methods although the clinical practicability of such techniques is not yet fully clarified.

The present study focuses on a novel, multiplex, real-time PCR-based pathogen identification system developed for rapid differentiation of the commonly occurring bacterial and fungal causative pathogens of bloodstream infections.


A multiplex, real-time PCR approach is introduced for the detection and differentiation of fungi, Gram-positive (G+) and Gram-negative (G-) bacteria. The Gram classification is performed with the specific fluorescence resonance energy transfer (FRET) probes recommended for LightCycler capillary real-time PCR. The novelty of our system is the use of a non-specific SYBR Green dye instead of labelled anchor probes or primers, to excite the acceptor dyes on the FRET probes. In conjunction with this, the use of an intercalating dye allows the detection of fungal amplicons.

With the novel pathogen detection system, fungi, G + and G- bacteria in the same reaction tube can be differentiated within an hour after the DNA preparation via the melting temperatures of the amplicons and probes in the same tube.


This modified FRET technique is specific and more rapid than the gold-standard culture-based methods. The fact that fungi, G + and G- bacteria were successfully identified in the same tube within an hour after the DNA preparation permits rapid and early evidence-based management of bloodstream infections in clinical practice.

Clinically relevant bacteria; Candida; Melting point analysis; Fluorescence resonance energy transfer; Bloodstream infections