Bacterial diagnostic probe

A method for determining the presence or absence of Escherichia coli or Salmonella species nucleic acid in a sample comprising enterobacterial species nucleic acid, wherein said method comprises:

• (a) providing single-stranded nucleic acid from said sample comprising enterobacterial species to be tested for said E. coli or Salmonella species;
• (b) hybridizing any E. coli or Salmonella single-stranded nucleic acid in said sample to at least a portion of a nucleic acid probe, under hybridization conditions;
• (c) removing any unhybridized nucleic acid probe;
• and
• (d) determining the presence or absence of said E. coli or Salmonella nucleic acid by detecting the presence or absence of hybridized nucleic acid probe,
• wherein said portion of said nucleic acid probe contains one or more of the nucleotide sequences selected from the group consisting of:
• ' ANT GCCMGAT GC GPCGY (0, 5) PCGYC TT ATCEGGC CTACP 3';
• 5' GCCMGAT GGC GPCGY (0, 5) PCGYC TT ATCEGGC CTACP 3';
• 5' YGTAG GCCMGAT AA GPCGY (0, 5) PCGYC GC ATCEGGC ANT 3';
• 5' YGTAG GCCMGAT AA GPCGY (0, 5) PCGYC GCC ATCEGGC ANT 3';
• and
• 5' GCCGGATG (0, 5) CATCCGGC 3',
• wherein N is T or A, M is T or G, P is A or G, Y is T or C, E is A or C, and (0, 5) represents a region of 0 to 5 nucleotides that is A-T rich, and
• wherein said nucleic acid probe is not an entire E. coli or Salmonella species genome.

A method for determining the presence or absence of Bordetella pertussis in a sample, wherein said method comprises:

• (a) providing single-stranded nucleic acid from said sample to be tested for said Bordetella pertussis;
• (b) hybridizing any Bordetella pertussis single-stranded nucleic acid in said sample to at least a portion of a nucleic acid probe, under hybridization conditions;
• (c) removing any unhybridized nucleic acid probe;
• and
• (d) determining the presence or absence of any said Bordetella pertussis by detecting the presence or absence of hybridized nucleic acid probe,
• wherein said nucleic acid probe contains one or more of the nucleotide sequences selected from the group consisting of
• CTGGGACGTATCCAGCGCCCTGGCCACCGGGTCACGGGCAACCGACGCGATACCGTTGAGGGGG CCGGCTGGGACTTCGTCTTCGTGGCCATCGATGACCACGCCCGCGTGGCCTTCACCGACATCCA CCCCGACGAGCGCTTCCCCAGCGCCGTCCAGTTCCTCAAGGACGCAGTGGCCTACTACCAGCGC CTGGGCGTGACCATCCAGCGCTTGCTCACCGACAATGGCTCGGCCTTTCGCAGCCGGCCTTCGC CGCGCTGTGCCATGAG;
• and
• CTGGGCATCAAGCACCGCTT TACCCGACCTTACCGCCCAC AGACCAATGGCAAGGCCGAA CGCTTCATCCAGTCGGCCTT GCGTGAGTGGGCTTACGCTC ACACCTACCAGAACTCCCAA CACCGAGCCGATGCCATGAA ATCCTGGCTACACCACTACA ACTGGCATCGACCCCACCAAG GCATCGGGCGCGCTGTACCC ATCTCCAGACTCAACCTGGA CGAATACAACCTATTGACAG TTCACAG
• or a fragment thereof having about 240 nucleotides.

A method for determining the presence or absence of Bordetella pertussis nucleic acid in a sample, wherein said method comprises:

• (a) providing single-stranded nucleic acid from said sample to be tested for said Bordetella pertussis;
• (b) hybridizing any Bordetella pertussis single-stranded nucleic acid in said sample to at least a portion of a nucleic acid probe, under hybridization conditions;
• (c) removing any unhybridized nucleic acid probe;
• and
• (d) determining the presence or absence of any said Bordetella pertussis nucleic acid by detecting the presence or absence of hybridized nucleic acid probe,
• wherein said nucleic acid probe contains one or more of the nucleotide sequences selected from the group consisting of
• CTGGGACGTATCCAGCGCCCTGGCCACCGGGTCACGGGCAACCGACGCGATACCGTTGAGGGGG CCGGCTGGGACTTCGTCTTCGTGGCCATCGATGACCACGCCCGCGTGGCCTTCACCGACATCCA CCCCGACGAGCGCTTCCCCAGCGCCGTCCAGTTCCTCAAGGACGCAGTGGCCTACTACCAGCGC CTGGGCGTGACCATCCAGCGCTTGCTCACCGACAATGGCTCGGCCTTTCGCAGCCGGCCTTCGC CGCGCTGTGCCATGAG;
• and
• CTGGGCATCAAGCACCGCTT TACCCGACCTTACCGCCCAC AGACCAATGGCAAGGCCGAA CGCTTCATCCAGTCGGCCTT GCGTGAGTGGGCTTACGCTC ACACCTACCAGAACTCCCAA CACCGAGCCGATGCCATGAA ATCCTGGCTACACCACTACA ACTGGCATCGACCCCACCAAG GCATCGGGCGCGCTGTACCC ATCTCCAGACTCAACCTGGA CGAATACAACCTATTGACAG TTCACAG
• or a fragment thereof having about 240 nucleotides.

A diagnostic kit for the detection of the presence or absence of Escherichia coli or Salmonella species in a sample comprising enterobacterial species, comprising

• a nucleic acid probe which comprises a nucleic acid, wherein at least a portion of said nucleic acid is hybridizable to a nucleic acid present in said E. coli or Salmonella species,
• wherein said portion of said nucleic acid probe contains one or more of the nucleotide sequences selected from the group consisting of:
• 5' ANT GCCMGAT GC GPCGY (0, 5) PCGYC TT ATCEGGC CTACP 3';
• 5' GCCMGAT GGC GPCGY (0, 5) PCGYC TT ATCEGGC CTACP 3';
• 5' YGTAG GCCMGAT AA GPCGY (0, 5) PCGYC GC ATCEGGC ANT 3';
• 5' YGTAG GCCMGAT AA GPCGY (0, 5) PCGYC GCC ATCEGGC ANT 3';
• and
• 5' GCCGGATG (0, 5) CATCCGGC 3',
• wherein N is T or A, M is T or G, P is A or G, Y is T or C, E is A or C, and (0, 5) represents a region of 0 to 5 nucleotides that is A-T rich, and
• wherein said nucleic acid probe is not an entire E. coli or Salmonella species genome.

A diagnostic kit for the detection of the presence or absence of Bordetella pertussis in a sample, comprising

• a nucleic acid probe which comprises a nucleic acid, wherein at least a portion of said nucleic acid is hybridizable to a nucleic acid present in said Bordetella pertussis,
• wherein said hybridizable portion of said nucleic acid probe contains one or more of the nucleotide sequences selected from the group consisting of
• CTGGGACGTATCCAGCGCCCTGGCCACCGGGTCACGGGCAACCGACGCGATACCGTTGAGGGGG CCGGCTGGGACTTCGTCTTCGTGGCCATCGATGACCACGCCCGCGTGGCCTTCACCGACATCCA CCCCGACGAGCGCTTCCCCAGCGCCGTCCAGTTCCTCAAGGACGCAGTGGCCTACTACCAGCGC CTGGGCGTGACCATCCAGCGCTTGCTCACCGACAATGGCTCGGCCTTTCGCAGCCGGCCTTCGC CGCGCTGTGCCATGAG;
• and
• CTGGGCATCAAGCACCGCTT TACCCGACCTTACCGCCCAC AGACCAATGGCAAGGCCGAA CGCTTCATCCAGTCGGCCTT GCGTGAGTGGGCTTACGCTC ACACCTACCAGAACTCCCAA CACCGAGCCGATGCCATGAA ATCCTGGCTACACCACTACA ACTGGCATCGACCCCACCAAG GCATCGGGCGCGCTGTACCC ATCTCCAGACTCAACCTGGA CGAATACAACCTATTGACAG TTCACAG
• or a fragment thereof having about 240 nucleotides.

An isolated single- or double-stranded DNA containing one or more of the nucleotide sequences selected from the group consisting of:

• 5' ANT GCCMGAT GC GPCGY (0, 5) PCGYC TT ATCEGGC CTACP 3';
• 5' GCCMGAT GGC GPCGY (0, 5) PCGYC TT ATCEGGC CTACP 3';
• 5' YGTAG GCCMGAT AA GPCGY (0, 5) PCGYC GC ATCEGGC ANT 3';
• 5' YGTAG GCCMGAT AA GPCGY (0, 5) PCGYC GCC ATCEGGC ANT 3';
• and
• 5' GCCGGATG (0, 5) CATCCGGC 3',
• wherein N is T or A, M is T or G, P is A or G, Y is T or C, E is A or C, and (0, 5) represents a region of 0 to 5 nucleotides that is A-T rich.

An isolated DNA containing:

• a first strand containing one or more of the nucleotide sequences selected from the group consisting of:
• 5' ANT GCCMGAT GC GPCGY (0, 5) PCGYC TT ATCEGGC CTACP 3';
• 5' GCCMGAT GGC GPCGY (0, 5) PCGYC TT ATCEGGC CTACP 3';
• 5' YGTAG GCCMGAT AA GPCGY (0, 5) PCGYC GC ATCEGGC ANT 3';
• 5' YGTAG GCCMGAT AA GPCGY (0, 5) PCGYC GCC ATCEGGC ANT 3';
• and
• 5' GCCGGATG (0, 5) CATCCGGC 3',
• wherein N is T or A, M is T or G, P is A or G, Y is T or C, E is A or C, and (0, 5) represents a region of 0 to 5 nucleotides that is A-T rich;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCTGATGGCGCTGTGCGTGTCAGGCCTACG;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCGGATGGCGGCTGTGCCTTGCCCGGCCTACG;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCGGATGGCGCTGCGCTTATCAGGCCTACG;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCCGGTGGCACTGCGTTTACCGGGCCTACG;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCGGATGGCGACATAATGCCTTATTCGGCCTACA;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCGGATGGCGCTTCGCTTATCCGGCCTACG;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCGGGTGGCGCTTGCGCTTATCCGGCTTGTA;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCTGATGGCGCGCAACCTTAAGGCCTACG;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCGGATAGCGGCGCTTTCGCCTTATCCGGCCTACA;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated DNA containing:

• a first strand containing the following nucleotide sequence:
• GCCTGATGGCGCTACGCTTATCAGGCCTACA;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.

An isolated single- or double-stranded DNA containing one or more of the nucleotide sequences selected from the group consisting of:

• CTGGGACGTATCCAGCGCCCTGGCCACCGGGTCACGGGCAACCGACGCGATACCGTTGAGGGGG CCGGCTGGGACTTCGTCTTCGTGGCCATCGATGACCACGCCCGCGTGGCCTTCACCGACATCCA CCCCGACGAGCGCTTCCCCAGCGCCGTCCAGTTCCTCAAGGACGCAGTGGCCTACTACCAGCGC CTGGGCGTGACCATCCAGCGCTTGCTCACCGACAATGGCTCGGCCTTTCGCAGCCGGCCTTCGC CGCGCTGTGCCATGAG;
• and
• CTGGGCATCAAGCACCGCTT TACCCGACCTTACCGCCCAC AGACCAATGGCAAGGCCGAA CGCTTCATCCAGTCGGCCTT GCGTGAGTGGGCTTACGCTC ACACCTACCAGAACTCCCAA CACCGAGCCGATGCCATGAA ATCCTGGCTACACCACTACA ACTGGCATCGACCCCACCAAG GCATCGGGCGCGCTGTACCC ATCTCCAGACTCAACCTGGA CGAATACAACCTATTGACAG TTCACAG
• or a fragment thereof having about 240 nucleotides.

An isolated DNA containing:

• a first strand containing one or more of the nucleotide sequences selected from the group consisting of:
• CTGGGACGTATCCAGCGCCCTGGCCACCGGGTCACGGGCAACCGACGCGATACCGTTGAGGGGG CCGGCTGGGACTTCGTCTTCGTGGCCATCGATGACCACGCCCGCGTGGCCTTCACCGACATCCA CCCCGACGAGCGCTTCCCCAGCGCCGTCCAGTTCCTCAAGGACGCAGTGGCCTACTACCAGCGC CTGGGCGTGACCATCCAGCGCTTGCTCACCGACAATGGCTCGGCCTTTCGCAGCCGGCCTTCGC CGCGCTGTGCCATGAG;
• and
• CTGGGCATCAAGCACCGCTT TACCCGACCTTACCGCCCAC AGACCAATGGCAAGGCCGAA CGCTTCATCCAGTCGGCCTT GCGTGAGTGGGCTTACGCTC ACACCTACCAGAACTCCCAA CACCGAGCCGATGCCATGAA ATCCTGGCTACACCACTACA ACTGGCATCGACCCCACCAAG GCATCGGGCGCGCTGTACCC ATCTCCAGACTCAACCTGGA CGAATACAACCTATTGACAG TTCACAG
• and a fragment thereof containing about 240 nucleotides;
• and
• a second strand containing other isolated DNA, which hybridizes, under stringent hybridization conditions, with said first strand.