Abundant, well distributed and hyperpolymorphic simple sequence repeats in prokaryote genomes and use of same for prokaryote classification and typing

Abstract

A method is provided for classifying or typing a prokaryote to a class or a type. The method is effected by characterizing at least one polymorphic simple sequence repeat locus in a genome of the prokaryote and, based on a characterization of the polymorphic simple sequence repeat, classifying or typing the prokaryote to a class or a type. Compounds and articles of manufacture are provided for effecting the method.

What is claimed is:  
     
         1 . A method of classifying or typing a prokaryote to a class or a type, the method comprising the step of characterizing at least one polymorphic simple sequence repeat locus in a genome of said prokaryote and, based on a characterization of said polymorphic simple sequence repeat, classifying or typing said prokaryote to a class or a type.  
     
     
         2 . The method of  claim 1 , wherein said at least one polymorphic simple sequence repeat locus is in a non-coding region of said genome.  
     
     
         3 . The method of  claim 1 , wherein said prokaryote is of the genus Escherichia.  
     
     
         4 . The method of  claim 3 , wherein said prokaryote is  Escherichia coli.    
     
     
         5 . The method of  claim 1 , wherein said prokaryote is of a genus selected from the group consisting of Aquifex, Treponema, Bacillus, Listeria and Mycobacterium.  
     
     
         6 . The method of  claim 5 , wherein said prokaryote is selected from the group consisting of  Aquifex aeolicus, Treponema pallidum, Bacillus subtilis, Listeria monocytogenes  and  Mycobacterium tuberculosis.    
     
     
         7 . The method of  claim 1 , wherein said prokaryote is of a genus selected from the group consisting of Haemophilius, Mycoplasma, Helicobacter, Methanococcus, Archaeoglobus and Synechocystis.  
     
     
         8 . The method of  claim 7 , wherein said prokaryote is selected from the group consisting of  Haemophilius influenzae, Mycoplasma pneumoniae, Helicobacter pylori, Methanococcus jannaschii, Archaeoglobus fulgidus  and Synechocystis sp PCC6803.  
     
     
         9 . The method of  claim 1 , wherein characterizing said at least one polymorphic simple sequence repeat locus in said genome of said prokaryote is effected by an allele specific oligonucleotide hybridization.  
     
     
         10 . The method of  claim 9 , wherein said allele specific oligonucleotide hybridization is effected over a surface of DNA chip.  
     
     
         11 . The method of  claim 1 , wherein characterizing said at least one polymorphic simple sequence repeat locus in said genome of said prokaryote is effected by a polymerase chain reaction.  
     
     
         12 . The method of  claim 1 , wherein characterizing said at least one polymorphic simple sequence repeat locus in said genome of said prokaryote is effected by a sequencing reaction.  
     
     
         13 . The method of  claim 1 , wherein characterizing said at least one polymorphic simple sequence repeat locus in said genome of said prokaryote is effected by a heteroduplex hybridization reaction.  
     
     
         14 . The method of  claim 1 , wherein characterizing said at least one polymorphic simple sequence repeat locus in said genome of said prokaryote is effected by single strand conformational polymorphism.  
     
     
         15 . The method of  claim 1 , wherein characterizing said at least one polymorphic simple sequence repeat locus in said genome of said prokaryote is effected by restriction fragment length polymorphism.  
     
     
         16 . A pair of polymerase chain reaction primers having a sequence adapted for exponential amplification of a polymorphic simple sequence repeat locus in a genome of a prokaryote.  
     
     
         17 . A polymerase chain reaction product derived by amplifying a portion of said genome using the pair of polymerase chain reaction primers of  claim 16 .  
     
     
         18 . The pair of polymerase chain reaction primers of  claim 16 , wherein said polymorphic simple sequence locus is in a non-coding region of said genome.  
     
     
         19 . The pair of polymerase chain reaction primers of  claim 16 , wherein said prokaryote is of the genus Escherichia.  
     
     
         20 . The pair of polymerase chain reaction primers of  claim 19 , wherein said prokaryote is  Escherichia coli.    
     
     
         21 . The pair of polymerase chain reaction primers of  claim 16 , wherein said prokaryote is of a genus selected from the group consisting of Aquifex, Treponema, Bacillus, Listeria and Mycobacterium.  
     
     
         22 . The pair of polymerase chain reaction primers of  claim 21 , wherein said prokaryote is selected from the group consisting of  Aquifex aeolicus, Treponema pallidum, Bacillus subtilis, Listeria monocytogenes  and  Mycobacterium tuberculosis.    
     
     
         23 . The pair of polymerase chain reaction primers of  claim 16 , wherein said prokaryote is of a genus selected from the group consisting of Haemophilius, Mycoplasma, Helicobacter, Methanococcus, Archaeoglobus and Synechocystis.  
     
     
         24 . The pair of polymerase chain reaction primers of  claim 23 , wherein said prokaryote is selected from the group consisting of  Haemophilius influenzae, Mycoplasma pneumoniae, Helicobacter pylori, Methanococcus jannaschii, Archaeoglobus fulgidus  and Synechocystis sp. PCC6803.  
     
     
         25 . An allele specific oligonucleotide comprising a sequence of nucleotides adapted for effectively hybridizing only with a specific simple sequence repeat of a polymorphic simple sequence repeat locus in a genome of a prokaryote, under stringent allele specific oligonucleotide hybridization sequence repeat of a polymorphic simple sequence repeat locus in a genome of a prokaryote, under stringent allele specific oligonucleotide hybridization conditions of (i) a hybridization solution of 2×standard sodium citrate (SSC) and 0.1% sodium dodecyl sulfate (SDS); (ii) a hybridization temperature of from 42° C. to Tm −5° C. for 30 minutes to overnight, wherein Tm is estimated as 2×(the number of A plus T residues)+4×(the number of G plus C residues)l and (iii) post hybridization washes with 0.75×SSC and 0.1% SDS at a temperature from 42° C. to Tm −5° C.  
     
     
         26 . The allele specific oligonucleotide of  claim 25 , wherein said sequence of nucleotides is perfectly complementary to said specific simple sequence repeat.  
     
     
         27 . A hybrid of the allele specific oligonucleotide of  claim 25  and said specific simple sequence repeat.  
     
     
         28 . The allele specific oligonucleotide of  claim 25 , wherein said polymorphic simple sequence locus is in a non-coding region of said genome.  
     
     
         29 . The allele specific oligonucleotide of  claim 25 , wherein said prokaryote is of the genus Escherichia.  
     
     
         30 . The allele specific oligonucleotide of  claim 29 , wherein said prokaryote is  Escherichia coli.    
     
     
         31 . The allele specific oligonucleotide of  claim 25 , wherein said prokaryote is of a genus selected from the group consisting of Aquifex, Treponema, Bacillus, Listeria and Mycobacterium.  
     
     
         32 . The allele specific oligonucleotide of  claim 31 , wherein said prokaryote is selected from the group consisting of  Aquifex aeolicus, Treponema pallidum, Bacillus subtilis, Listeria monocytogenes  and  Mycobacterium tuberculosis.    
     
     
         33 . The allele specific oligonucleotide of  claim 25 , wherein said prokaryote is of a genus selected from the group consisting of Haemophilius, Mycoplasma, Helicobacter, Methanococcus, Archaeoglobus and Synechocystis.  
     
     
         34 . The allele specific oligonucleotide of  claim 33 , wherein said prokaryote is selected from the group consisting of  Haemophilius influenzae, Mycoplasma pneumoniae, Helicobacter pylori, Methanococcus jannaschii, Archaeoglobus fulgidus  and Synechocystis sp PCC6803.  
     
     
         35 . A primer having a sequence adapted for amplification of a polymorphic simple sequence repeat locus in a genome of a prokaryote.  
     
     
         36 . The primer of  claim 35 , wherein said polymorphic simple sequence locus is in a non-coding region of said genome.  
     
     
         37 . The primer of  claim 35 , wherein said prokaryote is of the genus Escherichia.  
     
     
         38 . The primer of  claim 37 , wherein said prokaryote is  Escherichia coli.    
     
     
         39 . The primer of  claim 35 , wherein said prokaryote is of a genus selected from the group consisting of Aquifex, Treponema, Bacillus, Listeria and Mycobacterium.  
     
     
         40 . The primer of  claim 39 , wherein said prokaryote is selected from the group consisting of  Aquifex aeolicus, Treponema pallidum, Bacillus subtilis, Listeria monocytogenes  and  Mycobacterium tuberculosis.    
     
     
         41 . The primer of  claim 35 , wherein said prokaryote is of a genus selected from the group consisting of Haemophilius, Mycoplasma, Helicobacter, Methanococcus, Archaeoglobus and Synechocystis.  
     
     
         42 . The primer of  claim 41 , wherein said prokaryote is selected from the group consisting of  Haemophilius influenzae, Mycoplasma pneumoniae, Helicobacter pylori, Methanococcus jannaschii, Archaeoglobus fulgidus  and Synechocystis sp PCC6803.  
     
     
         43 . A DNA chip comprising a surface and a plurality of allele specific oligonucleotides attached thereto, each of said plurality of allele specific oligonucleotides including a sequence of nucleotides adapted for effectively hybridizing only with a specific simple sequence repeat of a polymorphic simple sequence repeat locus in a genome of a prokaryote, under stringent allele specific oligonucleotide hybridization conditions of (i) a hybridization solution of 2×standard sodium citrate (SSC) and 0.1% sodium dodecyl sulfate (SDS); (ii) a hybridization temperature of from 42° C. to Tm −5° C. for 30 minutes to overnight, wherein Tm is estimated as 2×(the number of A plus T residues)+4×(the number of G plus C residues); and (iii) post hybridization washes with 0.75×SSC and 0.1% SDS at a temperature from 42 °C. to Tm −5° C.  
     
     
         44 . The DNA chip of  claim 43 , wherein said sequence of nucleotides is perfectly complementary to said specific simple sequence repeat.  
     
     
         45 . The DNA chip of  claim 43 , wherein said polymorphic simple sequence locus is in a non-coding region of said genome.  
     
     
         46 . The DNA chip of  claim 43 , wherein said prokaryote is of the genus Escherichia.  
     
     
         47 . The DNA chip of  claim 46 , wherein said prokaryote is  Escherichia coli.    
     
     
         48 . The DNA chip of  claim 43 , wherein said prokaryote is of a genus selected from the group consisting of Aquifex, Treponema, Bacillus, Listeria and Mycobacterium.  
     
     
         49 . The DNA chip of  claim 48 , wherein said prokaryote is selected from the group consisting of  Aquifex aeolicus, Treponema pallidum, Bacillus subtilis, Listeria monocytogenes  and  Mycobacterium tuberculosis.    
     
     
         50 . The DNA chip of  claim 43 , wherein said prokaryote is of a genus selected from the group consisting of Haemophilius, Mycoplasma, Helicobacter, Methanococcus, Archaeoglobus and Synechocystis.  
     
     
         51 . The DNA chip of  claim 50 , wherein said prokaryote is selected from the group consisting of  Haemophilius influenzae, Mycoplasma pneumoniae, Helicobacter pylori, Methanococcus jannaschii, Archaeoglobus fulgidus  and Synechocystis sp PCC6803.