Compositions and methods for detecting group a streptococci

Abstract

Compositions, methods and kits for detecting Group A streptococci. Particularly described are oligonucleotides that are useful as amplification primers and hybridization probes for detecting very low levels of Group A streptococci nucleic acids.

1 . A hybridization assay probe for detecting a  Streptococcus pyogenes  nucleic acid comprising: 
 a probe sequence that comprises 
 a target-complementary sequence of bases, and optionally one or more base sequences that are not complementary to said nucleic acid that is to be detected, 
 wherein said target-complementary sequence of bases consists of 13-22 contiguous bases contained within the sequence of SEQ ID NO:3, or the complement thereof, allowing for the presence of RNA and DNA equivalents and nucleotide analogs, and  
 
   wherein said hybridization assay probe has a length of up to 30 bases and does not comprise any other base sequences that hybridize to nucleic acid derived from  Streptococcus pyogenes.      
     
     
         2 . The hybridization assay probe of  claim 1 , wherein said probe sequence comprises said optional one or more base sequences that are not complementary to said nucleic acid that is to be detected.  
     
     
         3 . The hybridization assay probe of  claim 2 , further comprising a detectable label.  
     
     
         4 . The hybridization assay probe of  claim 2 , further comprising a fluorophore moiety and a quencher moiety, said hybridization assay probe being a molecular beacon.  
     
     
         5 . The hybridization assay probe of  claim 4 , wherein said target-complementary sequence of bases is selected from the group consisting of SEQ ID NO:23, SEQ ID NO:24 and SEQ ID NO:25.  
     
     
         6 . The hybridization assay probe of  claim 1 , wherein said probe sequence does not comprise said optional one or more base sequences that are not complementary to said nucleic acid that is to be detected.  
     
     
         7 . The hybridization assay probe of  claim 6 , further comprising a detectable label.  
     
     
         8 . The hybridization assay probe of  claim 7 , wherein said detectable is selected from the group consisting of a chemiluminescent label and a fluorescent label.  
     
     
         9 . The hybridization assay probe of  claim 8 , wherein said target-complementary sequence of bases is selected from the group consisting of SEQ ID NO:19, SEQ ID NO:20 and SEQ ID NO:21.  
     
     
         10 . A kit for amplifying a  Streptococcus pyogenes  nucleic acid sequence that may be present in a biological sample comprising: 
 a first primer that comprises a 3′ terminal target-complementary sequence and optionally a first primer upstream sequence that is not complementary to said  Streptococcus pyogenes  nucleic acid sequence that is to be amplified, said 3′ terminal target-complementary sequence of said first primer comprising 20 contiguous bases contained within SEQ ID NO:2, allowing for the presence of RNA and DNA equivalents and nucleotide analogs; and    a second primer that comprises a 3′ terminal target-complementary sequence and optionally a second primer upstream sequence that is not complementary to said  Streptococcus pyogenes  nucleic acid sequence that is to be amplified, said 3′ terminal target-complementary sequence of said second primer comprising 26 contiguous bases contained within SEQ ID NO:1, allowing for the presence of RNA and DNA equivalents and nucleotide analogs.    
     
     
         11 . The kit of  claim 10 , wherein said first primer and said second primer are each up to 60 bases in length.  
     
     
         12 . The kit of  claim 10 , wherein said 3′ terminal target-complementary sequence of said first primer and said 3′ terminal target-complementary sequence of said second primer are each up to 33 bases in length.  
     
     
         13 . The kit of  claim 12 , wherein said 3′ terminal target-complementary sequence of said second primer is up to 28 bases in length.  
     
     
         14 . The kit of  claim 13 , wherein said first primer comprises said first primer upstream sequence.  
     
     
         15 . The kit of  claim 14 , wherein said first primer upstream sequence comprises a promoter sequence for T7 RNA polymerase.  
     
     
         16 . The kit of  claim 13 , wherein said 3′ terminal target-complementary sequence of said first primer is selected from the group consisting of SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 and SEQ ID NO:13, and wherein said 3′ terminal target-complementary sequence of said second primer is selected from the group consisting of SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, and SEQ ID NO:7.