Simultaneous detection of marine fish pathogens by using multiplex PCR and a DNA microarray

Abstract

We coupled multiplex PCR and a DNA microarray to construct an assay suitable for the simultaneous detection of five important marine fish pathogens (Vibrio vulnificus, Listonella anguillarum, Photobacterium damselae subsp. damselae, Aeromonas salmonicida subsp. salmonicida, and Vibrio parahaemolyticus). The array was composed of nine short oligonucleotide probes (25-mer) complementary to seven chromosomal loci (cyt, rpoN, gyrB, toxR, ureC, dly, and vapA) and two plasmid-borne loci (fatA and A.sal). Nine primer sets were designed to amplify short fragments of these loci (100 to 177 bp) in a multiplex PCR. PCR products were subsequently labeled by nick translation and hybridized to the microarray. All strains of the five target species (n = 1 to 21) hybridized to at least one species-specific probe. Assay sensitivities ranged from 100% for seven probes to 83 and 67% for the two remaining probes. Multiplex PCR did not produce any nonspecific amplification products when tested against 23 related species of bacteria (n = 40 strains; 100% specificity). Using purified genomic DNA, we were able to detect PCR products with < 20 fg of genomic DNA per reaction (equivalent to four or five cells), and the array was at least fourfold more sensitive than agarose gel electrophoresis for detecting PCR products. In addition, our method allowed the tentative identification of virulent strains of L. anguillarum serotype O1 based on the presence of the fatA gene (67% sensitivity and 100% specificity). This assay is a sensitive and specific tool for the simultaneous detection of multiple pathogenic bacteria that cause disease in fish and humans.

FIG. 1.

Positive control hybridizations. (Upper left panel) Specificity for L. anguillarum with the multiplex PCR and microarray hybridization. Genotypes for R-82 (O1), ATCC 43305 (O1), and ATCC 43306 (O2) match the respective genotypes for rpoN and fatA. (Upper right panel and lower left panel) Hybridization with probes complementary to V. vulnificus (cyt), V. parahaemolyticus (gyrB and toxR), P. damselae (ureC and dly), and A. salmonicida (vapA and A.plas.) in four different PCRs. (Lower right panel) Positions of oligonucleotide probes and the biotin control on the microarray.