Peptide nucleic acid probes for analysis of certain staphylococcus species

Abstract

The present invention relates to peptide nucleic acid (PNA) probes, PNA probe sets and methods for the analysis of certain Staphylococcus species optionally present in a sample. The invention further relates to diagnostic kits comprising such PNA probes or PNA probe sets.

We claim: 
     
         1 . A PNA probe comprising a nucleobase sequence suitable for the analysis of one or more  Staphylococcus  species other than  S. aureus.    
     
     
         2 . A PNA probe comprising a nucleobase sequence suitable for the analysis of two or more  Staphylococcus  species other than  S. aureus.    
     
     
         3 . The PNA probe of  claims 1 - 2 , wherein a target sequence of the  Staphylococcus  species comprises rRNA, rDNA or a complement of rRNA or rDNA. 
     
     
         4 . The PNA probe of  claim 1 - 2 , wherein the nucleobase sequence suitable for the analysis of  Staphylococcus epidermidis, simulans, haemolyticus, lugdunensis,  or  saprophyticus,  comprises one or more of a PNA probe complementary to a target sequence of the  Staphylococcus epidermidis simulans, haemolyticus, lugdunensis,  or  saprophyticus  rRNA or rDNA or a complement thereof. 
     
     
         5 . The PNA probe of  claim 1 , wherein the nucleobase sequence suitable for the analysis of  Staphylococcus epidermidis, simulans, haemolyticus, lugdunensis,  or  saprophyticus  and one or more other  Staphylococcus  species other than  Staphylococcus aureus,  comprises a PNA probe complementary to a target sequence of  Staphylococcus epidermidis, simulans, haemolyticus, lugdunensis,  or  saprophyticus  rRNA or rDNA or a complement thereof. 
     
     
         6 . The PNA probe of  claim 1 ,  2  or  5 , wherein at least a portion of the probe is at least about 86% identical to the nucleobase sequence or complement thereof selected from the following sequences: AGA-CGT-GCA-TAG-T (Seq. Id. No.1), GCT-AAT-ACG-GCG (Seq. Id. No.2), GCT-AAT-ACG-CCG-C (Seq. Id. No.3). 
     
     
         7 . The PNA probe of  claim 1 ,  2  or  5 , wherein at least a portion of the probe is selected from the following sequences: AGA-CGT-GCA-TAG-T (Seq. Id. No.1), GCT-AAT-ACG-GCG (Seq. Id. No.2), GCT-AAT-ACG-CCG-C (Seq. Id. No.3). 
     
     
         8 . The PNA probe of  claim 1 ,  2 , or  5 , wherein the probe sequence is between about 8 and about 17 subunits in length. 
     
     
         9 . The PNA probe of  claim 1 ,  2 , or  5 , wherein the probe is labeled with at least one detectable moiety. 
     
     
         10 . A PNA probe set comprising one or more PNA probes of  claim 1  or  2 , and at least one PNA probe for the analysis of S. aureus. 
     
     
         11 . A PNA probe set comprising one or more PNA probes of  claim 1  or  2 , and at least one PNA blocking probe for the analysis of one or more  Staphylococcus  species other than  S. aureus.    
     
     
         12 . A method for the analysis of  Staphylococcus  species other than  S. aureus  in a sample, comprising:
 a) contacting at least one of the PNA probes of  claims 1 - 9  to the sample,   b) hybridizing the PNA probe to a target sequence of  Staphylococcus  species other than  S. aureus  in the sample; and   c) detecting the hybridization, wherein the detection of hybridization is indicative of the presence, identity and/or amount of  Staphylococcus  species other than  S. aureus  in the sample.   
     
     
         13 . A method for the analysis of two or more  Staphylococcus  species, said method comprising:
 a) contacting a PNA probe set to the sample,   b) hybridizing the PNA probes to a target sequence of  Staphylococcus  species in the sample; and   c) detecting the hybridization, wherein the detection of hybridization is indicative of the presence, identity and/or amount of  Staphylococcus  species in the sample.   
     
     
         14 . The method of  claim 12  or  13 , wherein the probes are independently detectable non-independently detectable, or a combination of independently and non-independently detectable, wherein the probes differ from one another by as little as a single base, and are complementary or substantially complementary to partially conserved target regions of phylogenetically related organisms. 
     
     
         15 . The method of  claim 12  or  13 , wherein  S. aureus  and one or more  Staphylococcus  species other than  S. aureus  are simultaneously and independently detected. 
     
     
         16 . A kit suitable for performing an assay for analysis of one or more  Staphylococcus  species other than  S. aureus  in a sample, wherein said kit comprises: a) a PNA probe according to  claims 1  to  9  and b) other reagents or compositions necessary to perform the assay.