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

• US 6,322,985 B1
• Filed: 12/27/1999
• Issued: 11/27/2001
• Est. Priority Date: 12/27/1999
• Status: Expired due to Term

• Current Assignee: TECHNION RESEARCH AND DEVELOPMENT FOUNDATION, LTD. (Technion-Israel Institute Of Technology)
• Original Assignee: TECHNION RESEARCH AND DEVELOPMENT FOUNDATION, LTD. (Technion-Israel Institute Of Technology)
• Inventors: Cohen, Cyril, Shelef, Leora, Hallerman, Eric, Kashi, Yechezkel, Gur-Arie, Riva, Eitan, Yuval
• Primary Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US09/472,035
• Time in Patent Office: 701 Days
• Field of Search: 435/6, 435/91.2, 531/23.1, 531/24.3
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

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.

Claims

1. A method of classifying or typing a prokaryote to a class or a type, the method comprising the step of characterizing a plurality of polymorphic mono or dinucleotide simple sequence repeat loci, each including at least four nucleotides in at least one of its polymorphs, in a genome of said prokaryote, morph combinations of said plurality of polymorphic mono or dinucleotide simple sequence repeat loci being class or type characteristic, and, based on a characterization of said plurality of polymorphic simple sequence repeat loci, classifying or typing said prokaryote to a class or a type.

2. The method of claim 1, wherein said plurality of polymorphic simple sequence repeat loci are in non-coding regions 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 plurality of polymorphic simple sequence repeat loci in said genome of said prokaryote is effected by allele specific oligonucleotide hybridizations.

10. The method of claim 9, wherein said allele specific oligonucleotide hybridizations is effected over a surface of DNA chip.

11. The method of claim 1, wherein characterizing said plurality of polymorphic simple sequence repeat loci in said genome of said prokaryote is effected by polymerase chain reactions.

12. The method of claim 1, wherein characterizing said plurality of polymorphic simple sequence repeat loci in said genome of said prokaryote is effected by sequencing reactions.

13. The method of claim 1, wherein characterizing said plurality of polymorphic simple sequence repeat loci in said genome of said prokaryote is effected by heteroduplex hybridization reactions.

14. The method of claim 1, wherein characterizing said plurality of polymorphic simple sequence repeat loci in said genome of said prokaryote is effected by single strand conformational polymorphisms.

15. The method of claim 1, wherein characterizing said plurality of polymorphic simple sequence repeat loci in said genome of said prokaryote is effected by restriction fragment length polymorphisms.

16. A method of classifying or typing a prokaryote of the genus Escherichia, the method comprising the step of characterizing a plurality of polymorphic simple sequence repeat loci in a genome of said prokaryote of the genus Escherichia, morph combinations of said plurality of polymorphic mono or dinucleotide simple sequence repeat loci being class or type characteristic, and, based on a characterization of said plurality of polymorphic simple sequence repeat loci, classifying or typing said prokaryote of the genus Escherichia to a class or a type.

17. A method of classifying or typing a prokaryote of interest, the method comprising the steps of:

(a) reacting a plurality of allele specific oligonucleotide probes with a genome of said prokaryote of interest, said plurality of allele specific oligonucleotide probes being complementary to a plurality of polymorphic simple sequence repeat loci of a genome of a preclassified or pretyped prokaryote, morph combinations of said plurality of polymorphic mono or dinucleotide simple sequence repeat loci being class or type characteristic;

(b) detecting a presence or an absence of hybridizations between said plurality of allele specific oligonucleotide probes and said genome of said prokaryote; and

(c) according to results of said hybridizations, classifying or typing said prokaryote of interest as belonging to said preclassified or pretyped prokaryote.