Nucleic acid probe-based diagnostic assays targeting ssra genes of prokaryotic and eukaryotic organisms

Abstract

Use of the ssrA gene or tmRNA, an RNA transcript of the ssrA gene, or fragments thereof as target regions in a nucleic acid probe assay for the detection and identification of prokaryotic and/or eukaryotic organisms is described. Nucleotide sequence alignment of tmRNA sequences from various organisms can be used to identify regions of homology and non-homology within the sequences which in turn can be used to design both genus specific and species specific oligonucleotide probes. These newly identified regions of homology and non-homology provide the basis of identifying and detecting organisms at the molecular level. Oligonucleotide probes identified in this way can be used to detect tmRNA in samples thereby giving an indication of the viability of non-viral organisms present in various sample types.

1 - 29 . (canceled) 
     
     
         30 . An isolated nucleic acid sequence selected from the group consisting of the tmRNA sequence for  Chlamydia trachomatis  set forth in SEQ ID NO:20, a DNA sequence encoding said tmRNA sequence, and a complement of said DNA sequence. 
     
     
         31 . An isolated nucleic acid sequence according to  claim 30 , wherein said DNA sequence is the ssrA gene as set forth in SEQ ID NO:19. 
     
     
         32 . A method for diagnosing a bacterial infectious agent comprising determining the presence of a bacterial nucleic acid sequence selected from the group consisting of the tmRNA sequence for  Chlamydia trachomatis  set forth in SEQ ID NO:20, a DNA sequence encoding said tmRNA sequence, and a complement of said DNA sequence. 
     
     
         33 . A method according to  claim 32 , wherein said DNA sequence is the ssrA gene as set forth in SEQ ID NO:19. 
     
     
         34 . The method of  claim 32 , wherein the determination is made by performing an amplification-based assay. 
     
     
         35 . The isolated nucleic acid sequence of  claim 30 , wherein the nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for  Chlamydia trachomatis  set forth in SEQ ID NO:20. 
     
     
         36 . The method of  claim 32 , wherein the bacterial nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for  Chlamydia trachomatis  set forth in SEQ ID NO:20. 
     
     
         37 . The method of  claim 34 , wherein the bacterial nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for  Chlamydia trachomatis  set forth in SEQ ID NO:20.