Species specific and universal DNA probes and amplification primers to rapidly detect and identify common bacterial pathogens and associated antibiotic resistance genes from clinical specimens for routine diagnosis in microbiology laboratories

• US 6,001,564 A
• Filed: 09/11/1995
• Issued: 12/14/1999
• Est. Priority Date: 09/12/1994
• Status: Expired due to Term

• Current Assignee: Geneohm Sciences Canada, Inc. (Becton, Dickinson & Co)
• Original Assignee: Infectio Diagnostic, Inc. (Becton, Dickinson & Co)
• Inventors: Bergeron, Michel G., Roy, Paul H., Ouellette, Marc
• Primary Examiner(s): Campbell, Eggerton A.
• Application Number:
  US08/526,840
• Time in Patent Office: 1,555 Days
• Field of Search: 435/6, 435/91.2, 536/22.1
• US Class Current: 435/6.15
• CPC Class Codes: C07K 14/195 from bacteria
• CPC Class Codes: C07K 14/21 from Pseudomonadaceae (F)
• CPC Class Codes: C07K 14/212 Moraxellaceae, e.g. Acinetobacter, Moraxella, Oligella, Psychrobacter
• CPC Class Codes: C07K 14/245 Escherichia (G)
• CPC Class Codes: C07K 14/26 Klebsiella (G)
• CPC Class Codes: C07K 14/285 from Pasteurellaceae (F), e.g. Haemophilus influenza
• CPC Class Codes: C07K 14/31 from Staphylococcus (G)
• CPC Class Codes: C07K 14/315 from Streptococcus (G), e.g. Enterococci
• CPC Class Codes: C07K 14/3156 from Streptococcus pneumoniae (Pneumococcus) Streptokinase C07K14/3153
• CPC Class Codes: C12N 15/65 using markers enzymes used as markers C12N15/52
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

The present invention relates to DNA-based methods for universal bacterial detection, for specific detection of the common bacterial pathogens Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis, Streptococcus pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Staphylococcus saprophyticus, Streptococcus pyogenes, Haemophilus influenzae and Moraxella catarrhalis as well as for specific detection of commonly encountered and clinically relevant bacterial antibiotic resistance genes directly from clinical specimens or, alternatively, from a bacterial colony. The above bacterial species can account for as much as 80% of bacterial pathogens isolated in routine microbiology laboratories.

Claims

1. A method using probes or amplification primers or both which are specific, ubiquitous and sensitive for determining the presence or amount of nucleic acids:

from a bacterial antibiotic resistance gene selected from the group consisting of bla_tem, bla_rob, bla_shv, aadB, aacC1, aacC2, aacC3, aacA4, mecA, vanA, vanH, vanX, satA, aacA-aphH, vat, vga, msrA sul, and int, and

from specific bacterial species selected from the group consisting of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis, Streptococcus pneumoniae, Staphylococcus aureus, Staplylococcus epidermidis, Enterococcus faecalis, Staphylococcus epidermidis, Enterococcus faecalis, Staphylococcus saprophyticus, Streptococcus pyogenes, Haemophilus influenzae, and Moraxella catarrhalis, in any sample suspected of containing said nucleic acids,

wherein each of said nucleic acids comprises a selected target region hybridizable with said probes or primers;

said method comprising the steps of contacting said sample with said probes or primers and detecting the presence or amount of hybridized probes or amplified products as an indication of the presence or amount of said specific bacterial species simultaneously with said bacterial antibiotic resistance gene;

said probes or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with said bacterial species and with any one of;

SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7 and a complementary sequence thereof, for determining the presence or amount of Escherichia coli;

SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11, and a complementary sequence thereof, for determining the presence or amount of Klebsiella pneumoniae;

SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20 and a complementary sequence thereof, for determining the presence or amount of Pseudomonas aeruginosa;

SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15 and a complementary sequence thereof, for determining the presence or amount of Proteus mirabilis;

SEQ ID NO. 30, SEQ ID NO. 31, SEQ ID NO. 34, SEQ ID NO. 35 and complementary sequence thereof, for determining the presence or amount of Streptococcus pneumoniae;

SEQ ID NO. 37 and a complementary sequence thereof, for determining the presence or amount of Staplylococcus aureus;

SEQ ID NO. 36 and a complementary sequence thereof, for determining the presence or amount of Staphylococcus epidermidis;

SEQ ID NO. 1, SEQ ID NO. 2 and a complementary sequence thereof, for determining the presence or amount of Enterococcus faecalis;

SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, and a complementary sequence thereof, for determining the presence or amount of Staphylococcus saprophyticus;

SEQ ID NO. 32, SEQ ID NO. 33 and a complementary sequence thereof, for determining the presence or amount of Streptococcus pyogenes;

SEQ ID NO. 25, SEQ ID NO. 26, SEQ ID NO. 27 and a complementary sequence thereof, for determining the presence or amount of Haemophilus influenzae; and

SEQ ID NO. 28, SEQ ID NO. 29 and a complementary sequence thereof, for determining the presence or amount of Moraxella catarrhalis.

2. The method of any one of claim 1, which is performed directly on a sample obtained from human patients, animals, environment or food.

3. The method of claim 1, which is performed directly on a sample consisting of one or more bacterial colonies.

4. The method of claim 1, wherein said nucleic acids are amplified by a method selected from the group consisting of:

a) polymerase chain reaction (PCR),

b) ligase chain reaction,

c) nucleic acid sequence-based amplification,

d) self-sustained sequence replication,

e) strand displacement amplification

f) branched DNA signal amplification,

g) nested PCR, and

h) multiplex PCR.

5. The method of claim 4 wherein said nucleic acids are amplified by PCR.

6. The method of claim 5 wherein said nucleic acids are all simultaneously detected.

7. The method of claim 6 wherein the PCR protocol achieves within one hour the determination of the presence of said nucleic acids by performing for each amplification cycle an annealing step of only one second at 55°

C. and a denaturation step of only one second at 95°

C. without any time specifically allowed to an elongation step.

33. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to β

-lactam antibiotics mediated by the bacterial antibiotic resistance gene bla_tem directly from a test sample or from bacterial colonies, which comprises the steps of;

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 161 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to β

-lactam antibiotics mediated by the bacterial antibiotic resistance gene bla_tem.

34. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to β

-lactam antibiotics mediated by the bacterial antibiotic resistance gene bla_rob directly from a test sample or from bacterial colonies, which comprises the steps of;

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 162 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to β

-lactam antibiotics mediated by the bacterial antibiotic resistance gene bla_rob.

35. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to β

-lactam antibiotics mediated by the bacterial antibiotic resistance gene bla_shv directly from a test sample or from bacterial colonies, which comprises the steps of;

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 163 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to β

-lactam antibiotics mediated by the bacterial antibiotic resistance gene bla_shv.

36. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to aminoglycoside mediated by the bacterial antibiotic resistance gene aadB directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 164 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aadB.

37. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacC1 directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 165 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacC1.

38. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacC2 directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 166 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacC2.

39. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacC3 directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 167 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacC3.

40. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacA4 directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 168 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacA4.

41. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to β

-lactam antibiotics mediated by the bacterial antibiotic resistance gene mecA directly from a test sample or from bacterial colonies, which comprises the steps of;

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 169 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to β

-lactam antibiotics mediated by the bacterial antibiotic resistance gene mecA.

42. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to vancomycin mediated by the bacterial antibiotic resistance genes vanH, vanA and vanX directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 170 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to vancomycin mediated by the bacterial antibiotic resistance genes vanH, vanA and vanX.

43. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to streptogramin A mediated by the bacterial antibiotic resistance gene satA directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence ha at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 173 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to streptogramin A mediated by the bacterial antibiotic resistance gene satA.

44. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacA-aphD directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 174 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to aminoglycoside antibiotics mediated by the bacterial antibiotic resistance gene aacA-aphD.

45. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to virginiamycin mediated by the bacterial antibiotic resistance gene vat directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 175 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to virginiamycin mediated by the bacterial antibiotic resistance gene vat.

46. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to virginiamycin mediated by the bacterial antibiotic resistance gene vga directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 176 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to virginiamycin mediated by the bacterial antibiotic resistance gene vga.

47. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to erythromycin mediated by the bacterial antibiotic resistance gene msrA directly from a test sample or from bacterial colonies, which comprises the steps of:

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 177 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to erythromycin mediated by the bacterial antibiotic resistance gene msrA.

48. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to β

-lactams, aminoglycosides, chloramphenicol or trimethoprim mediated by the bacterial antibiotic resistance gene int directly from a test sample or from bacterial colonies, which comprises the steps of;

a) contacting the bacterial DNA with a probe or with amplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 171 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to β

-lactams, aminoglycosides, chloramphenicol or trimethoprim mediated by the bacterial antibiotic resistance gene int.

49. A method as defined in claim 1, which comprises the evaluation of the presence of a bacterial resistance to β

-lactams, aminoglycosides, chloramphenicol or trimethoprim mediated by the bacterial antibiotic resistance gene sul directly from a test sample or from bacterial colonies, which comprises the steps of;

a) contacting the bacterial DNA with a probe or withamplification primers, said probe or primers comprising at least one single stranded nucleic acid which nucleotidic sequence has at least twelve nucleotides in length capable of hybridizing with the nucleotide sequence defined in SEQ ID NO. 172 or a sequence complementary thereof under conditions such that the nucleic acid of said probe or primers can selectively hybridize with said gene; and

b) detecting the presence of a hybridization complex or of an amplification product as an indication of a bacterial resistance to β

-lactams, aminoglycosides, chloramphenicol or trimethoprim mediated by the bacterial antibiotic resistance gene sul.

55. A diagnostic kit for the detection and/or quantification of the nucleic acids of any combination of the bacterial resistance genes defined in any one of claims 33 to 49 comprising any combination of probes or primers defined therein.

57. A diagnostic kit for the simultaneous detection and/or quantification of nucleic acids of any bacterial antibiotic resistance genes selected from the group consisting of:

bla_tem, bla_rob, bla_shv, aadB, aacC1, aacC2, aacC3, aacA4, mecA, vanA, vanH, vanX, satA, aacA-aphD, vat, vga, msrA, sul and int, and of any combination of the bacterial species defined in claim 1, comprising any combination of the bacterial probes defined in claim 1 and any combination of the probes to the antibiotic resistance genes defined in any one of SEQ ID NOs;

161 to 177 in whole or in part.

58. A diagnostic kit for the simultaneous detection and/or quantification of nucleic acids of any antibiotic resistance genes selected from the group consisting of:

bla_tem, bla_rob, bla_shv, aadB, aacC1, aacC2, aacC3, aacA4, mecA, vanA, vanH, vanX, satA, aacA-aphD, vat, vga, msrA, sul and int, and of any combination of the bacterial species defined in claim 1, comprising any combination of the pairs of primers defined in claim 1 and any combination of pairs of primers that anneal to the antibiotic resistance genes defined in any one of SEQ ID NOs;

161 to 177.

59. A diagnostic kit for the simultaneous detection and/or quantification of any bacterial species, of any bacterial antibiotic resistance genes selected from the group consisting of:

bla_tem, bla_rob, bla_shv, aadB, aacC1, aacC2, aacC3, aacA4, mecA, vanA, vanH, vanX, satA, aacA-aphD, vat, vga, msrA, sul and int, and of any combination of the bacterial species defined in claim 1, comprising any combination of pairs of primers defined in claim 1, a pair of universal primers and any combination of pairs of primers that anneal to the antibiotic resistance genes defined in any one of SEQ ID NOs.;

161 to 177.

60. The method of claim 1, wherein the probe for detecting nucleic acid sequences from said bacterial species has at least twelve nucleotides in length and is capable of hybridizing with any sequence selected from the group consisting of the following probes for the detection of the following species:

SEQ ID NO;

44, SEQ ID NO;

45, SEQ ID NO;

48, SEQ ID NO;

49, SEQ ID NO;

50, SEQ ID NO;

51, SEQ ID NO;

52, SEQ ID NO;

53, SEQ ID NO;

54, and a sequence complementary thereof for the detection of Escherichia coli;

SEQ ID NO;

70, SEQ ID NO;

71, SEQ ID NO;

72, SEQ ID NO;

73, SEQ ID NO;

76, SEQ ID NO;

77, SEQ ID NO;

80, SEQ ID NO;

81, SEQ ID NO;

82, and a sequence complementary thereof for the detection of Proteus mirabilis;

SEQ ID NO;

96, SEQ ID NO;

97, SEQ ID NO;

100, SEQ ID NO;

101, SEQ ID NO;

102, SEQ ID NO;

103, SEQ ID NO;

104, and a sequence complementary thereof for the detection of Staphylococcus saprophyticus;

SEQ ID NO;

108, SEQ ID NO;

109, SEQ ID NO;

110, SEQ ID NO;

111, SEQ ID NO;

114, SEQ ID NO;

115, SEQ ID NO;

116, SEQ ID NO;

117, and a sequence complementary thereof for the detection of Moraxella catarrhalis;

SEQ ID NO;

87, SEQ ID NO;

88, SEQ ID NO;

89, SEQ ID NO;

90, SEQ ID NO;

91, SEQ ID NO;

92, SEQ ID NO;

93, SEQ ID NO;

94, SEQ ID NO;

95, and a sequence complementary thereof for the detection of Pseudomonas aeruginosa;

SEQ ID NO;

105, SEQ ID NO;

106, SEQ ID NO;

107, and a sequence complementary thereof for the detection of Haemophilus influenzae; and

SEQ ID NO;

120, SEQ ID NO;

121, and a sequence complementary thereof for the detection of Streptococcus pneumoniae.

8. A method for the detection, identification or quantification of Escherichia coli directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Escherichia coli and capable of hybridizing with any one of SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Escherichia coli in said test sample.

9. A method for detecting the presence or amount of Escherichia coli in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Escherichia coli DNA and of any one of SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Escherichia coli in said test sample.

10. The method of claim 9, wherein said at least one pair of primers is selected from the group consisting of:

a) SEQ ID NO;

42 and SEQ ID NO;

43,

b) SEQ ID NO;

46 and SEQ ID NO;

47,

c) SEQ ID NO;

55 and SEQ ID NO;

56, and

d) SEQ ID NO;

131 and SEQ ID NO;

132.

78. A diagnostic kit for the detection or quantification of the nucleic acids of any combination of the bacterial species defined in any one of claims 9, 10, 12, 13, 15, 16, 18, 19, 21, 22, 24, 25, 27, 28, 30, 31, 62, 63, 65, 66, 68, 69, 71, 72, 74 and 75 comprising any combination of pairs of primers defined therein.

11. A method for the detection, identification or quantification of Moraxella catarrhalis directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Moraxella catarrhalis and capable of hybridizing with any one of SEQ ID NO. 29 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Moraxella catarrhalis in said test sample.

77. A diagnostic kit for the detection and/or quantification of the nucleic acids of any combination of the bacterial species defined in any one of claims 8, 11, 14, 17, 20, 23, 26, 29, 60, 61, 64, 67 and 70, comprising any combination of probes defined therein.

12. A method for detecting the presence or amount of Moraxella catarrhalis in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Moraxella catarrhalis DNA and of SEQ ID NO. 29, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Moraxella catarrhalis in said test sample.

13. The method of claim 12, wherein said at least one pair of primers is selected from the group consisting of:

a) SEQ ID NO;

118 and SEQ ID NO;

119, and

b) SEQ ID NO;

160 and SEQ ID NO;

119.

14. A method for the detection, identification or quantification of Pseudomonas aeruginosa directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Pseudomonas aeruginosa and capable of hybridizing with any one of SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Pseudomonas aeruginosa in said test sample.

15. A method for detecting the presence or amount of Pseudomonas aeruginosa in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Pseudomonas aeruginosa DNA and of any one of SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Pseudomonas aeruginosa in said test sample.

16. The method of claim 15, wherein said at least one pair of primers is selected from the group consisting of:

a) SEQ ID NO;

83 and SEQ ID NO;

84, and

b) SEQ ID NO;

85 and SEQ ID NO;

86.

17. A method for the detection, identification or quantification of Staphylococcus epidermidis directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Staphylococcus epidermidis and capable of hybridizing with any one of SEQ ID NO. 36 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Staphylococcus epidermidis in said test sample.

18. A method for detecting the presence or amount of Staphylococcus epidermidis in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Staphylococcus epidermidis DNA and of SEQ ID NO. 36, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Staphylococcus epidermidis in said test sample.

19. The method of claim 18, wherein said at least one pair of primers is selected from the group consisting of:

a) SEQ ID NO;

145 and SEQ ID NO;

146, and

b) SEQ ID NO;

147 and SEQ ID NO;

148.

20. A method for the detection, identification or quantification of Staphylococcus aureus directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Staphylococcus aureus and capable of hybridizing with any one of SEQ ID NO. 37 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Staphylococcus aureus in said test sample.

21. A method for detecting the presence or amount of Staphylococcus aureus in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Staphylococcus aureus DNA and of SEQ ID NO. 37, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Staphylococcus aureus in said test sample.

22. The method of claim 21, wherein said at least one pair of primers is selected from the group consisting of:

a) SEQ ID NO;

149 and SEQ ID NO;

150,

b) SEQ ID NO;

149 and SEQ ID NO;

151, and

c) SEQ ID NO;

152 and SEQ ID NO;

153.

23. A method for the detection, identification or quantification of Streptococcus pneumoniae directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Streptococcus pneumoniae and capable of hybridizing with any one of SEQ ID NO. 30, SEQ ID NO. 31, SEQ ID NO. 34, SEQ ID NO. 35 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Streptococcus pneumoniae in said test sample.

24. A method for detecting the presence or amount of Streptococcus pneumoniae in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Streptococcus pneumoniae DNA and of any one of SEQ ID NO. 30, SEQ ID NO. 31, SEQ ID NO. 34, SEQ ID NO. 35, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Streptococcus pneumoniae in said test sample.

25. The method of claim 24, wherein said at least one pair of primers is selected from the group consisting of;

a) SEQ ID NO;

78 and SEQ ID NO;

79,

b) SEQ ID NO;

156 and SEQ ID NO;

157, and

c) SEQ ID NO;

158 and SEQ ID NO;

159.

26. A method for the detection, identification or quantification of a bacterial species bearing exotoxin A gene speA directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of a bacterial species bearing exotoxin A gene speA and capable of hybridizing with any one of SEQ ID NO. 33 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of a bacterial species bearing exotoxin A gene speA in said test sample.

74. A method as defined in claim 26, wherein said bacterial species is Streptococcus pyogenes and said probe further comprises at least one single stranded nucleic acid which nucleotide sequence is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Streptococcus pyogenes and with any one of SEQ ID NO. 32 and a complementary sequence thereof, whereby Streptococcus pyogenes and associated exotoxin A speA gene are both detectable.

27. A method for detecting the presence or amount of a bacterial species bearing exotoxin A gene speA in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of a bacterial species bearing exotoxin A gene speA DNA and of SEQ ID NO. 33, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of a bacterial species bearing exotoxin A gene speA in said test sample.

28. The method of claim 27, wherein said at least one pair of primers is SEQ ID NO:

143 and SEQ ID NO;

144.

75. A method as defined in claim 27, wherein said bacterial species is Streptococcus pyogenes and said at least one pair of primers further comprises at least one pair of primers having at least twelve nucleotides in length and being capable of hybridizing with any one of SEQ ID NO. 32 and a sequence complementary thereof, whereby Streptococcus pyogenes and associated exotoxin A speA gene are both detectable.

76. The method as defined in claim 27, wherein said at least one pair of primers further comprises SEQ ID NO:

141 and SEQ ID NO;

142 specific and ubiquitous for Streptococcus pyogenes, whereby Streptococcus pyogenes and associated exotoxin A speA gene are both detectable.

29. A method for the detection, identification or quantification of Enterococcus faecalis directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Enterococcus faecalis and capable of hybridizing with any one of SEQ ID NO. 1, and SEQ ID NO. 2 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Enterococcus faecalis in said test sample.

30. A method for detecting the presence or amount of Enterococcus faecalis in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Enterococcus faecalis DNA and of any one of SEQ ID NO. 1 and SEQ ID NO. 2, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Enterococcus faecalis in said test sample.

31. The method of claim 30, wherein said at least one pair of primers is selected from the group consisting of:

a) SEQ ID NO;

38 and SEQ ID NO;

39, and

b) SEQ ID NO;

40 and SEQ ID NO;

41.

32. A method for detecting the presence or amount of any bacterial species in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing a pair of universal primers which sequence is defined in SEQ ID NO;

126 and SEQ ID NO;

127, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said any bacterial species DNA that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of said any bacterial species in said test sample.

50. A nucleic acid having the nucleotide sequence of any one of SEQ ID NO:

3, SEQ ID NO;

4, SEQ ID NO;

29, SEQ ID NO;

36, SEQ ID NO;

37, a part thereof and variants thereof which, when in single stranded form, ubiquitously and specifically hybridize with a target bacterial DNA as a probe or as a primer.

51. An oligonucleotide having a nucleotide sequence of any one of SEQ ID NOs:

38 to 43, SEQ ID NOs;

83 to 86, SEQ ID NO;

118, SEQ ID NO;

119, SEQ ID NO;

127, SEQ ID NO;

131, SEQ ID NO;

132, SEQ ID NOs;

141 to 153, SEQ ID NO;

158, SEQ ID NO;

159 and SEQ ID NO;

160.

52. A recombinant plasmid comprising a nucleic acid as defined in claim 51.

53. A recombinant host which has been transformed by a recombinant plasmid according to claim 52.

54. A recombinant host according to claim 53 wherein said host is Escherichia coli.

56. A diagnostic kit for the detection and/or quantification of nucleic acids of any bacterial species comprising the primers defined in SEQ ID NOs. 126 and 127.

61. A method for the detection, identification or quantification of Klebsiella pneumoniae directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Klebsiella pneumoniae and capable of hybridizing with any one of SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Klebsiella pneumoniae in said test sample.

62. A method for detecting the presence or amount of Klebsiella pneumoniae in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Klebsiella pneumoniae DNA and of any one of SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Klebsiella pneumoniae in said test sample.

63. The method of claim 62, wherein said at least one pair of primers is selected from the group consisting of:

a) SEQ ID NO;

61 and SEQ ID NO;

62,

b) SEQ ID NO;

67 and SEQ ID NO;

68,

c) SEQ ID NO;

135 and SEQ ID NO;

136, and

d) SEQ ID NO;

137 and SEQ ID NO;

138.

64. A method for the detection, identification or quantification of Proteus mirabilis directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Proteus mirabilis and capable of hybridizing with any one of SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Proteus mirabilis in said test sample.

65. A method for detecting the presence or amount of Proteus mirabilis in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Proteus mirabilis DNA and of any one of SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Proteus mirabilis in said test sample.

66. The method of claim 65, wherein said at least one pair of primers is selected from the group consisting of:

a) SEQ ID NO;

74 and SEQ ID NO;

75, and

b) SEQ ID NO;

133 and SEQ ID NO;

134.

67. A method for the detection, identification or quantification of Staphylococcus saprophyticus directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Staphylococcus saprophyticus and capable of hybridizing with any one of SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Staphylococcus saprophyticus in said test sample.

68. A method for detecting the presence or amount of Staphylococcus saprophyticus in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Staphylococcus saprophyticus DNA and of any one of SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Staphylococcus saprophyticus in said test sample.

69. The method of claim 68, wherein said at least one pair of primers is selected from the group consisting of:

a) SEQ ID NO;

98 and SEQ ID NO;

99, and

b) SEQ ID NO;

139 and SEQ ID NO;

140.

70. A method for the detection, identification or quantification of Haemophilus influenzae directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from the sample or inoculating said sample or said bacterial colonies on an inert support and lysing in situ said inoculated sample or bacterial colonies to release the bacterial DNA, said bacterial DNA being made in a substantially single stranded form;

b) contacting said single stranded DNA with a probe, said probe comprising at least one single stranded nucleic acid which nucleotide sequence has at least twelve nucleotides in length and is capable of specifically and ubiquitously hybridizing with DNA from strains or representatives of Haemophilus influenzae and capable of hybridizing with any one of SEQ ID NO. 25, SEQ ID NO. 26, SEQ ID NO. 27 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of Haemophilus influenzae in said test sample.

71. A method for detecting the presence or amount of Haemophilus influenzae in a test sample which comprises the following steps:

a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers having at least twelve nucleotides in length, one of said primers being capable of hybridizing selectively with one of the two complementary strands of Haemophilus influenzae DNA and of any one of SEQ ID NO. 25, SEQ ID NO. 26, SEQ ID NO. 27, that contain a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template;

b) synthesizing an extension product of each of said primers which extension product contains the target sequence, and amplifying said target sequence, if any, to a detectable level; and

c) detecting the presence or amount of said amplified target sequence as an indication of the presence or amount of Haemophilus influenzae in said test sample.

72. The method of claim 71, wherein said at least one pair of primers comprises the following pair:

SEQ ID NO;

154 and SEQ ID NO;

155.

73. A method for the detection of the presence or amount of any bacterial species directly from a test sample or from bacterial colonies, which comprises the following steps:

a) depositing and fixing on an inert support or leaving in solution the bacterial DNA of the sample or of the bacterial colonies isolated from this sample, or inoculating said sample or said bacterial colonies on an inert support, and lysing in situ said inoculated sample or to release the bacterial DNA, said bacterial DNA being in a substantially single stranded form;

b) contacting said single stranded DNA with a universal probe which sequence is selected from the group consisting of SEQ ID NO;

122, SEQ ID NO;

123, SEQ ID NO;

124, SEQ ID NO;

125, SEQ ID NO;

128, SEQ ID NO;

129, SEQ ID NO;

130 and a sequence complementary thereof, under conditions such that the nucleic acid of said probe can selectively hybridize with said bacterial DNA, whereby a hybridization complex is formed, and

c) detecting the presence of said hybridization complex on said inert support or in said solution as an indication of the presence or amount of said any bacterial species in said test sample.