Ribosomal Ribonucleic Acid Hybridization for Organism Identification

Abstract

The present disclosure relates to method of distinguishing between two or more species of one or more organisms in a sample, by contacting a biological sample comprising ribosomal ribonucleic acid (rRNA) with a set of antisense probes, wherein the set of probes contains at least one detectable probe that is specific for a target rRNA sequence of each species to be tested, and wherein the individual probes specific for each species comprises less than about 85% sequence identity; and, detecting hybridization between one or more of the probes and the rRNA, thereby distinguishing between two or more species in a sample.

Description

CROSS-REFERENCE TO RELATED APPLICATION[0001]This application claims the priority benefit of the earlier filing date of U.S. Provisional Application No. 61 / 794,544, filed Mar. 15, 2013, which is hereby specifically incorporated herein by reference in its entirety.FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT[0002]This invention was made with Government support under Grant number HHSN272200900018C awarded by the National Institutes of Health. The Government has certain rights in the invention.FIELD OF THE INVENTION[0003]The present disclosure relates generally to a hybridization-based method of rapidly detecting and identifying infectious disease pathogens, the probes for detecting one or more types of pathogens, as well as kits including the probes.BACKGROUND OF THE INVENTION[0004]Identification of bacterial pathogens that cause infection is a key first step in devising an informed, effective treatment strategy. To effectively treat bacterial pathogen infection, it is necessary to begi...

AI Technical Summary

Benefits of technology

This patent describes a method for detecting the presence of specific bacteria in a sample. The method involves using a special technique called hybridization-based detection, which involves annealing to the ribosomal RNA present in the sample. The method can be applied to a variety of samples, such as clinical specimens or environmental samples. The technique uses a commercial RNA recognition technology, called Nanostring, which has previously been used to characterize messenger RNA transcripts. The method targets conserved regions of bacterial genomes that are significantly different between different species to ensure selective detection. Overall, the patent provides a reliable and sensitive technique for detecting specific bacteria in various samples.

Problems solved by technology

The reliance on slow culture methods is particularly problematic in view of the current crisis of antibiotic resistance of many pathogens.

However, polymerases used in PCR are relatively intolerant to the biochemical milieu of many clinical samples, requiring processing steps that introduce delays and the possibility of false negative results.

Further, the extrinsic amplification step introduces the possibility of false positives as well.

Mass spectrometry is limited in recognition by the need to unambiguously recognize peptide signatures that have less inherent distinction from human or environmental material that may be present in a sample.

One challenge to rRNA-based diagnosis (as opposed to rDNA, or mRNA) has been that these rRNA molecules have tight secondary structural elements that limit their ability to be recognized by hybridization.

The high degree of sequence conservation poses a second challenge in using rRNA recognition to discriminate between species: the method of choice must recognize all members of a given species to be fully sensitive in a clinical setting, but must not cross-react against other species for optimal specificity.

This approach typically requires PCR amplification of the gene in question and therefore suffers the same limitations as other PCR-based clinical diagnostics, discussed above.

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