Accurate identification of organisms based on individual information content

Abstract

An improved method for specific identification of any organisms by DNA hybridization or amplification is disclosed. Oligonucleotides are designed based on information analysis of sequences from a large number of related species. Oligonucleotide sequences that have the maximal specificity to certain nucleic acids from a particular species (or set of species) or type strain are selected for hybridization or amplification using DNA from the target organism. The presence or absence of a PCR or hybridization product may be used to identify the target organism. The resulting PCR products may also be compared with a DNA sequence database to obtain the identity of the organisms. The methods may prove useful in areas where rapid and accurate identification of an organism is desirable, such as in a hospital where identification of infectious agents may be critical, in the ethanol or beer industry where certain bacteria may be detrimental to the manufacturing process, or in the porcine industry where identification of different type strains of the porcine reproductive and respiratory syndrome virus (PRRV) is important for disease prevention.