Method for detecting mycoplasma

• US 10,640,834 B2
• Filed: 09/07/2015
• Issued: 05/05/2020
• Est. Priority Date: 09/10/2014
• Status: Active Grant

• Current Assignee: Lymphotec Inc. (GC Cell Corporation), Tokyo Medical and Dental University
• Original Assignee: National University Corporation Tokyo Medical and Dental University
• Inventors: Shimizu, Norio, Takahashi, Hideyuki
• Primary Examiner(s): Woolwine, Samuel C
• Application Number:
  US15/509,430
• Publication Number:
  US 20170240959A1
• Time in Patent Office: 1,702 Days
• Field of Search: None
• CPC Class Codes: C12N 15/09 Recombinant DNA-technology
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

An object of the present invention is to provide a detection method for Mycoplasma by which a greater number of Mycoplasma species can be more quickly and easily detected with high sensitivity and accuracy, a set of a forward primer, a reverse primer and a probe for the detection and a kit containing the set. Mycoplasma in a test sample is detected by a multiplex real time quantitative PCR using one or more forward primers, each of which is an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 30 nucleotides in the nucleotide sequence represented by SEQ ID No: 1, and which contains a nucleotide sequence at nucleotide positions 14 to 24 in SEQ ID No: 1; reverse primers, each of which is an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26 nucleotides in the one or more nucleotide sequences represented by SEQ ID Nos: 14 and 17 to 20; and a probe(s), which is an oligonucleotide, which consists of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26 nucleotides in the nucleotide sequence represented by SEQ ID No: 33, or which consists of a complementary nucleotide sequence thereto.

Claims

1. A kit for detecting Mycoplasma in a test sample by a multiplex real time quantitative PCR, wherein

the kit comprises one or more forward primers, two or more reverse primers, one or more probes and a solid support;

the probe(s) is immobilized onto the solid support;

the probe is a probe for specifically detecting products amplified by use of the forward primer and at least any one of the reverse primers;

the forward primer(s) is an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 30 nucleotides in the nucleotide sequence of SEQ ID No;

1, and which contains a nucleotide sequence (caaggtatccs) at nucleotide positions 14 to 24 in SEQ ID No;

1;

the reverse primers each are an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26 nucleotides in one or more nucleotide sequences of SEQ ID Nos;

14 and 17 to 20; and

the probe(s) is an oligonucleotide, which consists of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26 nucleotides in the nucleotide sequence of SEQ ID No;

33, or which consists of a complementary nucleotide sequence thereto.

2. The kit according to claim 1, wherein the one or more forward primers are one or more oligonucleotides each consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 30 nucleotides in the nucleotide sequence of SEQ ID No:

1, and which contains a nucleotide sequence (caaggtatccstac) at nucleotide positions 14 to 27 in SEQ ID No;

1.

3. The kit according to claim 1, wherein the one or more forward primers are two or more oligonucleotides and at least one of the oligonucleotides in said two or more oligonucleotides are selected from the following (A) and at least one of the oligonucleotides in said two or more oligonucleotides are selected from the following (B):

(A) a forward primer, which is an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 30 nucleotides in the nucleotide sequence of SEQ ID No;

2, and which contains a nucleotide sequence at nucleotide positions 14 to 24 in SEQ ID No;

2, and

(B) a forward primer, which is an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 30 nucleotides in the nucleotide sequence of SEQ ID No;

3, and which contains a nucleotide sequence at nucleotide positions 14 to 24 in SEQ ID No;

3.

4. The kit according to claim 1, containing two forward primers, wherein the two forward primers are an oligonucleotide consisting of any one nucleotide sequence selected from SEQ ID Nos:

4 to 7, 11 and 12, and an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

13.

5. The kit according to claim 1, wherein at least one of the reverse primers is an oligonucleotide containing a nucleotide sequence (wsccaaggcatccaccah) at nucleotide positions 3 to 20 in SEQ ID No:

14.

6. The kit according to claim 1, wherein the two or more reverse primers are two or more oligonucleotides selected from the following (C1), (C2-1), (C2-2), (C2-3), (D), (E1), (E2), (F) and (G):

(C1) an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26nucleotides in the nucleotide sequence of SEQ ID No;

15,

(C2-1) an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26nucleotides in the nucleotide sequence of SEQ ID No;

16 where m at nucleotide position 20 is a, and w at nucleotide position 22 is a,

(C2-2) an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26nucleotides in the nucleotide sequence of SEQ ID No;

16 where m at nucleotide position 20 is c, and w at nucleotide position 22 is a,

(C2-3) an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26nucleotides in the nucleotide sequence of SEQ ID No;

16 where m at nucleotide position 20 is a, and w at nucleotide position 22 is t,

(D) an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26nucleotides in the nucleotide sequence of SEQ ID No;

17,

(E1) an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 24nucleotides in the nucleotide sequence of SEQ ID No;

18 where s at nucleotide position 2 is g, and r at each of nucleotide positions 4 and 9 is g,

(E2) an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 24nucleotides in the nucleotide sequence of SEQ ID No;

18 where s at nucleotide position 2 is c, and r at each of nucleotide positions 4 and 9 is a,

(F) an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 25nucleotides in the nucleotide sequence of SEQ ID No;

19, and

(G) an oligonucleotide consisting of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 23nucleotides in the nucleotide sequence of SEQ ID No;

20.

7. The kit according to claim 1, wherein the two or more reverse primers are two or more oligonucleotides selected from the following oligonucleotides:

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

21,

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

22,

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

24,

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

25,

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

26,

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

27,

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

17,

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

28,

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

29,

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

19, and

an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

20.

8. The kit according to claim 1, wherein the probe is an oligonucleotide containing a nucleotide sequence (sggrtggaty) at nucleotide positions 7 to 16 in SEQ ID No:

33 or a complementary nucleotide sequence thereto.

9. The kit according to claim 1, wherein the one or more probes are one or more oligonucleotides selected from the following (H) to (L):

(H) an oligonucleotide, which consists of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26nucleotides in the nucleotide sequence of SEQ ID No;

34, or which consists of a complementary nucleotide sequence thereto,

(I) an oligonucleotide, which consists of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26nucleotides in the nucleotide sequence of SEQ ID No;

35, or which consists of a complementary nucleotide sequence thereto,

(J) an oligonucleotide, which consists of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26nucleotides in the nucleotide sequence of SEQ ID No;

36, or which consists of a complementary nucleotide sequence thereto,

K) an oligonucleotide, which consists of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26nucleotides in the nucleotide sequence of SEQ ID No;

37, or which consists of a complementary nucleotide sequence thereto, and

(L) an oligonucleotide, which consists of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26 nucleotides in the nucleotide sequence of SEQ ID No;

38, or which consists of a complementary nucleotide sequence thereto.

10. The kit according to claim 1, wherein the one or more probes are one or more oligonucleotides selected from the following (h) to (l):

(h) an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

39,

(i) an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

40,

(j) an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

41,

(k) an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

42, and

(l) an oligonucleotide consisting of the nucleotide sequence of SEQ ID No;

43.

11. A set of a forward primer, a reverse primer and a probe for detecting Mycoplasma in a test sample by a multiplex real time quantitative PCR, wherein the set contains one or more forward primers, two or more reverse primers and one or more probes;

the probe(s) is a probe for specifically detecting products amplified by use of the forward primer and at least any one of the reverse primers and the probe is labeled with a fluorescent substance;

the forward primer(s) is an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 30 nucleotides in the nucleotide sequence of SEQ ID No;

1, and which contains a nucleotide sequence (caaggtatccs) at nucleotide positions 14 to 24 in SEQ ID No;

1;

the reverse primers each are an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26 nucleotides in one or more nucleotide sequences of SEQ ID Nos;

14 and 17 to 20; and

the probe(s) is an oligonucleotide, which consists of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26 nucleotides in the nucleotide sequence of SEQ ID No;

33, or which consists of a complementary nucleotide sequence thereto.

12. A method for detecting Mycoplasma in a test sample by a multiplex real time quantitative PCR, comprising

(a) Step a of extracting DNA from the test sample,

(b) Step b of performing a multiplex real time quantitative PCR using the DNA extracted in Step a as a template, and one of more forward primers and two or more reverse primers, and

(c) Step c of detecting the presence of Mycoplasma in the test sample by detecting a product amplified by the multiplex real time quantitative PCR in Step b by use of one or more probes;

the probe(s) is a probe for specifically detecting products amplified by use of the forward primer and at least any one of the reverse primers;

the forward primer(s) is an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 30 nucleotides in the nucleotide sequence of SEQ ID No;

1, and which contains a nucleotide sequence (caaggtatccs) at nucleotide positions 14 to 24 in SEQ ID No;

1;

the reverse primers each are an oligonucleotide consisting of a nucleotide sequence, which is selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26 nucleotides in one or more nucleotide sequences of SEQ ID Nos;

14 and 17 to 20; and

the probe(s) is an oligonucleotide, which consists of a nucleotide sequence selected from the group consisting of nucleotide sequences each consisting of continuous 17 to 26 nucleotides in the nucleotide sequence of SEQ ID No;

33, or which consists of a complementary nucleotide sequence thereto.

13. The method for detecting Mycoplasma according to claim 12, wherein the product amplified by the multiplex real time quantitative PCR in Step c is detected by detecting whether or not a specific hybridization with the probe as defined in claim 12 occurs.

14. The method for detecting Mycoplasma according to claim 12, wherein the detection limit in sensitivity of one or more Mycoplasma species selected from the group consisting of Mycoplasma arginini, Mycoplasma buccale, Mycoplasma faucium, Mycoplasma hominis, Mycoplasma orale, Mycoplasma salivarium, Mycoplasma fermentans, Mycoplasma lipophilum, Mycoplasma primatum, Mycoplasma hyorhinis, Mycoplasma synoviae, Mycoplasma genitalium, Mycoplasma pneumoniae, Acholeplasma laidlawii, Ureaplasma urealyticum, Mycoplasma gallisepticum and Spiroplasma citri, is 10 cfu/mL or less.