Hybridization probes for detecting neisseria strains

Claim 2

Probe for detecting one or more Neisseria strains, containing : - either a sequence belonging to a nucleic acid selected from the following groups of nucleic acids and which includes itself of from 10 to the maximum number of nucleotides of the selected nucleic acid -or a variant sequence which distinguishes of any of the preceding sequences (4) to (18) . either by addition to or removal from any of their respective extremities of one or several nucleotides, . or changing within any of said sequences of one or more nucleotides, . or both, yet provided that in any of the above circumstances said probe still hybridizes with the same RNA or DNA target as the corresponding unmodified sequence.

Claim 3

The probe of claim 1, containing : - either a sequence belonging to a nucleic acid selected from the following groups of nucleic acids and which includes itself of from 10 to the maximum number of nucleotides of the selected nucleic acid - or a variant sequence which distinguishes of any of the preceding sequences (1) to (18) . either by addition to or removal from any of their respective extremities of one or several nucleotides, . or changing within any of said sequences of one or more nucleotides, . or both, yet provided that in any of the above circumstances said probe still hybridizes with the same RNA or DNA target as the corresponding unmodified sequence.

Claim 4

Probe for detecting one or more Neisseria strains, which targets one of the sequences defined hereunder or the corresponding complementary sequence, when the hybridization medium or the wash medium or both as appropriate are the following ones : hybridization medium : containing about 3xSSC, (SSC = 0.15M NaCl, 0.015M sodium citrate, pH 7.0) about 25 mM of phosphate buffer pH 7.1, 20% deionized formamide 0.02% ficoll, 0.02% bovine serum albumin, 0.02% polyvinylpyrrolidone, and about 0.1 mg/ml sheared, denatured salmon sperm DNA, wash medium : containing about 3XSSC, 25 mM phosphate buffer pH 7.1, and 20% deionized formamide wherein said target sequences and the corresponding relevant hybridization temperatures (HT) and wash temperatures (WT) respectively are as follows :

Claim 5

Probe for detecting one or more Neisseria strains, which targets one of the sequences defined hereunder or the corresponding complementary sequence, when the hybridization medium or the wash medium or both as appropriate are the following ones : hybridization medium : containing about 3xSSC, (SSC = 0.15M NaCl, 0.015M sodium citrate, pH 7.0) about 25 mM of phosphate buffer pH 7.1, 20% deionized formamide 0.02% ficoll, 0.02% bovine serum albumin, 0.02% polyvinylpyrrolidone, and about 0.1 mg/ml sheared, denatured salmon sperm DNA, wash medium : containing about 3XSSC, 25 mM phosphate buffer pH 7.1, and 20% deionized formamide wherein said target sequences and the corresponding relevant hybridization temperatures (HT) and wash temperatures (WT) respectively are as follows :

Claim 6

Probe for detecting one or more Neisseria gonorrhoeae strains from other bacterial strains, and in particular from other Neisseria strains, containing - either a sequence belonging to a nucleic acid selected from the following groups of nucleic acids and which includes itself of from 10 to the maximum number of nucleotides of the selected nucleic acid - or a variant sequence which distinguishes of any of the preceding sequences (1) to (18) . either by addition to or removal from any of their respective extremities of one or several nucleotides, . or changing within any of said sequences of one or more nucleotides, . or both, yet provided that in any of the above circumstances said probe still hybridizes with the same RNA or DNA target as the corresponding unmodified sequence.

Claim 7

Probe for detecting one or more Neisseria gonorrhoeae strains from other bacterial strains, and in particular from other Neisseria strains, containing - either a sequence belonging to a nucleic acid selected from the following groups of nucleic acids and which includes itself of from 10 to the maximum number of nucleotides of the selected nucleic acid - or a variant sequence which distinguishes of any of the preceding sequences (1) to (18) . either by addition to or removal from any of their respective extremities of one or several nucleotides, . or changing within any of said sequences of one or more nucleotides, . or both, yet provided that in any of the above circumstances said probe still hybridizes with the same RNA or DNA target as the corresponding unmodified sequence.

Claim 8

Probe for detecting one or more Neisseria gonorrhoeae strains from other bacterial strains, and in particular from other Neisseria strains, containing - either a sequence belonging to a nucleic acid selected from the following groups of nucleic acids and which includes itself of from 10 to the maximum number of nucleotides of the selected nucleic acid provided that the probe does not consist of the following sequence: TCA TCG GCC GCC GAT ATT GGC - or a variant sequence which distinguishes of any of the preceding sequences (1) to (18) . either by addition to or removal from any of their respective extremities of one or several nucleotides, . or changing within any of said sequences of one or more nucleotides, . or both, yet provided that in any of the above circumstances said probe still hybridizes with the same RNA or DNA target as the corresponding unmodified sequence.

Claim 9

Probe for detecting one or more Neisseria gonorrhoeae strains from other bacterial strains, and in particular from other Neisseria strains, containing - either a sequence belonging to a nucleic acid selected from the following groups of nucleic acids and which includes itself of from 10 to the maximum number of nucleotides of the selected nucleic acid provided that the probe does not consist of the following sequence: TCA TCG GCC GCC GAT ATT GGC - or a variant sequence which distinguishes of any of the preceding sequences (1) to (18) . either by addition to or removal from any of their respective extremities of one or several nucleotides, . or changing within any of said sequences of one or more nucleotides, . or both, yet provided that in any of the above circumstances said probe still hybridizes with the same RNA or DNA target as the corresponding unmodified sequence.

Claim 10

Probe for detecting one or more Neisseria gonorrhoeae strains from other bacterial strains, and in particular from other Neisseria strains, which target one of the sequences defined hereunder or the corresponding complementary sequence, when the hybridization medium or the wash medium or both as appropriate are the following ones : hybridization medium : containing about 3xSSC, (SSC = 0.15M NaCl, 0.015M sodium citrate, pH 7.0) about 25mM of phosphate buffer pH 7.1, 20% deionized formamide 0.02% ficoll, 0.02% bovine serum albumin, 0.02% polyvinylpyrrolidone, and about 0.1 mg/ml sheared, denatured salmon sperm DNA, wash medium : containing about 3XSSC, 25 mM phosphate buffer pH 7.1, and 20% deionized formamide wherein said target sequences and the corresponding relevant hybridization temperatures (HT) and wash temperatures (WT) respectively are as follows :

Claim 11

Probe for detecting one or more Neisseria gonorrhoeae strains from other bacterial strains, and in particular from other Neisseria strains, which target one of the sequences defined hereunder or the corresponding complementary sequence, when the hybridization medium or the wash medium or both as appropriate are the following ones : hybridization medium : containing about 3xSSC, (SSC = 0.15M NaCl, 0.015M sodium citrate, pH 7.0) about 25mM of phosphate buffer pH 7.1, 20% deionized formamide 0.02% ficoll, 0.02% bovine serum albumin, 0.02% polyvinylpyrrolidone, and about 0.1 mg/ml sheared, denatured salmon sperm DNA, wash medium : containing about 3XSSC, 25 mM phosphate buffer pH 7.1, and 20% deionized formamide wherein said target sequences and the corresponding relevant hybridization temperatures (HT) and wash temperatures (WT) respectively are as follows :

Claim 12

Process for detecting Neisseria strains in a biological sample from other bacterial strains, wherein said process comprises contacting said biological sample in which the nucleic acids (DNAs and RNAs) of the strains have been made accessible to hybridization, if need be, under suitable denaturation conditions with a probe according to any one of claims 1 to 6 under conditions enabling hybridization between the probe and complementary nucleic acids of the Neisseria strains, which may be present in the sample, and detecting the hybrids possibly formed.

Claim 13

Process for detecting Neisseria strains from other bacterial strains in a biological sample, according to claim 7, wherein the probes used are the ones hybridizing both with DNA and RNA of Neisseria strains which may be present in the biological sample.

Claim 14

Process for detecting Neisseria strains from other bacterial strains, according to claim 7 or 8, wherein the hybridization medium contains about 3xSSC, (SSC = 0,15M NaCl, 0,015M sodium citrate, pH 7.0) about 25mM of phosphate buffer pH 7.1, 20% deionized formamide, 0.02% ficoll, 0.02% bovine serum albumin, 0.02% polyvinylpyrrolidone, and about 0.1 mg/ml sheared, denatured salmon sperm DNA, or the wash medium contains about 3XSSC, 25 mM phosphate buffer pH 7.1, and 20% deionized formamide, and wherein the probe used is anyone of the probes (1), (1bis), (1ter) or (1quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 55°C, preferably of about 53°C, and/or the wash temperature to the range of about 55°C, preferably of about 53°C, or anyone of the probes (2), (2bis), (2ter) or (2quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 60°C and/or the wash temperature to the range of about 60°C, or anyone of the probes (3), (3bis), (3ter) or (3quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 60°C and/or the wash temperature to the range of about 60°C, or anyone of the probes (4), (4bis), (4ter) or (4quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 65°C and/or the wash temperature to the range of about 65°C, or anyone of the probes (5), (5bis), (5ter) or (5quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 55°C and/or the wash temperature to the range of about 55°C, or anyone of the probes (9), (9bis), (9ter), or (9quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 60°C and/or the wash temperature to the range of about 60°C, or anyone of the probes (6), (6bis), (6ter) or (6quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 65°C and/or the wash temperature to the range of about 65°C to about 70°C, or anyone of the probes (7), (7bis), (7ter) or (7­quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 55°C and/or the wash temperature to the range of about 55°C, or anyone of the probes (8), (8bis), (8ter) or (8quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 55°C and/or the wash temperature to the range of about 55°C to about 60°C, or anyone of the probes (10), (10bis), (10ter) or (10quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 55°C and/or the wash temperature to the range of about 55°C to about 60°C or anyone of the probes (11), (11bis), (11ter) or (11quater) of claim 2, the hybridization temperature being suitably adjusted to about 55°C and/or the wash temperature to about 55°C. or anyone of the probes (12), (12bis), (12ter) or (12quater) of claim 2, the hybridization temperature being suitably adjusted to range of about 55°C to about 60°C and/or the wash temperature to range of about 55°C to about 60°C. or anyone of the probes (13), (13bis), (13ter) or (13quater) of claim 2, the hybridization temperature being suitably adjusted to range of about 45°C and/or the wash temperature to range of about 45°C. or anyone of the probes (14, (14bis), (14ter) or (14quater) of claim 2, the hybridization temperature being suitably adjusted to range of about 40°C to about 45°C and/or the wash temperature to range of about 40°C to about 45°C. or anyone of the probes (15), (15bis), (15ter) or (15quater) of claim 2, the hybridization temperature being suitably adjusted to range of about 50°C to about 55°C and/or the wash temperature to range of about 50°C to about 55°C. or anyone of the probes (16), (16bis), (16ter) or (16quater) of claim 2, the hybridization temperature being suitably adjusted to range of about 50°C to about 60°C and/or the wash temperature to range of about 50°C to about 60°C. or anyone of the probes (17), (17bis), (17ter) or (17quater) of claim 2, the hybridization temperature being suitably adjusted to range of about 50°C to about 55°C and/or the wash temperature to range of about 50°C to about 55°C. or anyone of the probes (18), (18bis), (18ter) or (18quater) of claim 2, the hybridization temperature being suitably adjusted to range of about 45°C and/or the wash temperature to range of about 45°C.

Claim 15

Process for detecting Neisseria gonorrhoeae strains from other bacterial strains and and particularly from other Neisseria strains, wherein said process comprises contacting said biological sample, in which the nucleic acids (DNAs and RNAs) have been made accessible to hybridization, if need be, under suitable denaturation conditions, with a probe of the invention specific for Neisseria gonorrhoeae strains and selected from the probes (1), (1bis), (1ter), (1quater), (2), (2bis), (2ter), 2(quater), (3), (3bis), (3ter), (3quater), (40), (4bis), (4ter), (4quater), (5), (5bis), (5ter), (5quater), (9), (9bis), (9ter), (9quater), (11), (11bis), (11ter), (11quater), (13), (13bis), (13ter), (13quater), (18), (18bis), (18ter) and (18quater) of claim 2, whenever required under hybridization and washing conditions adjusted such as to ensure specific hybridization with complementary nucleic acids of the Neisseria gonorrhoeae strains, which may be present in the sample, yet not with complementary DNA or RNA of other Neisseria species, and detecting the hybrids possibly formed.

Claim 16

Process for detecting N. gonorrhoeae strains from other bacterial strains and in particular from other Neisseria strains, according to claim 10, wherein the hybridization medium contains about 3xSSC, (SSC = 0,15M NaCl, 0,015M sodium citrate, pH 7.0) about 25mM of phosphate buffer pH 7.1, 20% deionized formamide, 0.02% ficoll, 0.02% bovine serum albumin, 0.02% polyvinylpyrrolidone, and about 0.1 mg/ml sheared, denatured salmon sperm DNA, or the wash medium contains about 3XSSC, 25 mM phosphate buffer pH 7.1, and 20% deionized formamide, and wherein the probe used is anyone of the probes (1), (1bis), (1ter) or (1quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 55°C, preferably of about 53°C, and/or the wash temperature to the range from about 55°C to about 65°C, preferably from about 53°C to about 65°C and preferably of about 53°C, and the probe used is anyone of the probes (2), (2bis), (2ter) or (2quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 60°C and/or the wash temperature to the range of about 65°C to about 70°C, or anyone of the probes (3), (3bis), (3ter) or (3quater) of claim 2, the hybridization temperature being suitably adjusted to the range of abut 60°C and/or the wash temperature to the range of about 65°C to about 70°C, or anyone of the probes (4), (4bis), (4ter) or (4quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 65°C and/or the wash temperature to the range of about 70°C to about 75°C, or anyone of the probes (5), (5bis), (5ter) or (5quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 60°C and/or the wash temperature to the range of about 65°C, or anyone of the probes (9), (9bis), (9ter) or (9quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 60°C to about 65°C and/or the wash temperature to the range of about 65°C, or more preferably anyone of the probes (1), (1bis), (1ter) or (1quater) of claim 2, the hybridization temperature being suitably adjusted to the range of about 55°C and/or the wash temperature to the range of about 55°C to about 65°C or anyone of the probes (11), (11bis), (11ter) or (11quater) of claim 2, the hybridization temperature being suitably adjusted to about 65°C and/or the wash temperature to about 65°C or anyone of the probes (13), (13bis), (13ter) or (13quater) of claim 2, the hybridization temperature being suitably adjusted to range about 50°C to about 55°C and/or the wash temperature to range about 50°C to about 55°C, or anyone of the probes (18), (18bis), (18ter) or (18quater) of claim 2, the hybridization temperature being suitably adjusted to about 60°C and/or the wash temperature to about 60°C.

Claim 17

Kit for the detection in vitro of a large number, preferably all Neisseria strains in a biological sample, said kit containing : - at least one probe selected among any of those according to claims 1 to 4 ; - the buffer or components necessary for producing the buffer enabling hybridization reaction between these probes and the DNAs and/or RNAs of a large number, preferably all strains of Neisseria to be carried out ; - when appropriate means for detecting the hybrids resulting from the preceding hybridization.

Claim 18

Kit for the detection in vitro of Neisseria gonorrhoeae strains in a biological sample, said kit containing : - at least one probe specific for N. gonorrhoeae as above defined, e.g. a probe selected from the probes (2), (2bis), (2ter), (2quater), (3), (3bis), (3ter), (3quater), (4), (4bis), (4ter), (4quater), (5), (5bis), (5ter), (5quater), (9), (9bis), (9ter), (9quater), (11), (11bis), (11ter), (11quater), (13), (13bis), (13ter), (13quater), (18), (18bis), (18ter) and (18quater), according to claim 2, or more preferably a probe selected from anyone of the probes (1), (1bis), (1ter) or (1quater) according to claim 2 ; - the buffer or components necessary for producing the buffer enabling hybridization reaction between these probes and the DNAs and/or RNAs of a strain of Neisseria gonorrhoeae to be carried out, - when appropriate means for detecting the hybrids resulting from the preceding hybridization.

Claim 19

Process for detecting N. gonorrhoeae strains from other bacterial strains and in particular from other Neisseria strains, wherein said process comprises contacting said biological sample, in which the nucleic acids (DNA and RNAs) have been made accessible to hybridization, if need be, under suitable denaturation conditions, with two probes of anyone of claims 1 to 6, which are specific for Neisseria gonorrhoeae strains and are respectively not able to hybridize to the same non-target strains, and in particular, selected from the following combinations: - probe of group 9 and anyone of the probes of the following groups: 1, 2, 3, 5 and 13. - probe of group 13 and anyone of the probes of the following groups: 1, 2, 3 and 5. - probe of group 18 and anyone of the probes of the following groups: 1, 2, 3, 5, 9 and 13. - probe of group 5 and anyone of the probes of the following groups: 1, 2 and 3 and more particularly, selected from the following combinations: - probe of group 9 and one of group 5. - probe of group 18 and one of the probes of the following groups: 5 and 9, whenever required under hybridization and washing conditions adjusted such as to ensure specific hybridization with complementary nucleic acids of the Neisseria gonorrhoeae strains, which may be present in the sample, yet not with complementary DNA or RNA of other Neisseria species, and detecting the hybrids possibly formed.

Claim 20

Kit for sandwich hybridization assay, for the detection in vitro of Neisseria gonorrhoeae strains in a biological sample, said kit containing : - at least two probes specific for N. gonorrhoeae selected from the following combinations: - probe of group 9 and anyone of the probes of the following groups: 1, 2, 3, 5 and 13. - probe of group 13 and anyone of the probes of the following groups: 1, 2, 3 and 5. - probe of group 18 and anyone of the probes of the following groups: 1, 2, 3, 5, 9 and 13. - probe of group 5 and anyone of the probes of the following groups: 1, 2 and 3. and more particularly from the following combinations: - probe of group 9 and one of group 5. - probe of group 18 and one of the probes of the following groups: 5, and 9 - the buffer or components necessary for producing the buffer enabling hybridization reaction between these probes and the DNAs and/or RNAs of a strain of Neisseria gonorrhoeae to be carried out, - when appropriate means for detecting the hybrids resulting from the preceding hybridization.

Claim 21

Kit for sandwich hybridization assay, for the detection in vitro of Neisseria gonorrhoeae strains in a biological sample, said kit containing : - at least two probes specific for N. gonorrhoeae selected from the following combinations: - probe of group 9 and anyone of the probes of the following groups: 1, 2, 3, 5 and 13. - probe of group 13 and anyone of the probes of the following groups: 1, 2, 3 and 5. - probe of group 18 and anyone of the probes of the following groups: 1, 2, 3, 5, 9 and 13. - probe of group 5 and anyone of the probes of the following groups: 1, 2 and 3. and more particularly from the following combinations: - probe of group 9 and one of group 5. - probe of group 18 and one of the probes of the following groups: 5, and 9 - the buffer or components necessary for producing the buffer enabling hybridization reaction between these probes and the DNAs and/or RNAs of a strain of Neisseria gonorrhoeae to be carried out, - when appropriate means for detecting the hybrids resulting from the preceding hybridization.