CN115341040A - Primer group for identifying mycobacterium tuberculosis and application thereof - Google Patents

Primer group for identifying mycobacterium tuberculosis and application thereof Download PDF

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CN115341040A
CN115341040A CN202110521377.1A CN202110521377A CN115341040A CN 115341040 A CN115341040 A CN 115341040A CN 202110521377 A CN202110521377 A CN 202110521377A CN 115341040 A CN115341040 A CN 115341040A
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mycobacterium tuberculosis
detected
primer
identifying
bacteria
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张福仁
刘红
潘晴
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Dermatology Hospital Affiliated To Shandong First Medical University
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    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
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    • C12Q1/6851Quantitative amplification

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Abstract

The invention discloses a primer group for identifying mycobacterium tuberculosis and application thereof. The primer group consists of a primer 1, a primer 2 and a probe, and the nucleotide sequences of the primer group are respectively shown as a sequence 1, a sequence 2 and a sequence 3 in a sequence table. The invention also successfully establishes a method for detecting the mycobacterium tuberculosis by adopting a real-time fluorescent quantitative PCR technology based on the primer group, and the detection method has the advantages of high speed, high sensitivity and strong specificity, and provides an effective technical means for early diagnosis and treatment of patients infected by the mycobacterium tuberculosis.

Description

Primer group for identifying mycobacterium tuberculosis and application thereof
Technical Field
The invention relates to the technical field of biology, in particular to a primer group for identifying mycobacterium tuberculosis and application thereof.
Background
Tuberculosis, a chronic infectious disease caused by infection with mycobacterium tuberculosis. The mycobacterium tuberculosis can invade various organs of the whole body of a human body and invade the lung, so that the pulmonary tuberculosis is caused; the mycobacterium tuberculosis in the tuberculosis focus of other organs can also invade the skin or spread to skin tissues through blood circulation or lymphatic system to cause skin tuberculosis, thereby causing serious threat to human life health.
The traditional detection method for mycobacterium tuberculosis comprises the following steps: smear method, culture method, and drug sensitivity test method. However, the traditional detection method has the defects of low sensitivity and long time consumption, and is not beneficial to early diagnosis and early treatment of diseases. Currently, molecular biology techniques are increasingly used for the detection and identification of pathogenic pathogens. The real-time fluorescent quantitative PCR technology is a method of adding fluorescent group into common PCR reaction system, utilizing fluorescent signal accumulation to monitor whole PCR process in real time, and finally making quantitative analysis on unknown template by means of standard curve. The method has the advantages of high accuracy, sensitivity, strong specificity and quick detection.
Disclosure of Invention
The invention aims to solve the technical problem of establishing a method for detecting mycobacterium tuberculosis by adopting a real-time fluorescent quantitative PCR technology.
In order to solve the above technical problems, the present invention firstly provides a primer set for identifying or assisting in identifying mycobacterium tuberculosis.
The primer group for identifying or assisting in identifying the mycobacterium tuberculosis consists of a primer 1, a primer 2 and a probe;
the primer 1 is a 1) or a 2) as follows:
a1 A single-stranded DNA molecule shown as a sequence 1 in a sequence table;
a2 A single-stranded DNA molecule obtained by substituting and/or deleting and/or adding one or more nucleotides to the sequence 1 and having the same function as the sequence 1;
the primer 2 is a 3) or a 4) as follows:
a3 A single-stranded DNA molecule shown in a sequence 2 in a sequence table;
a4 A single-stranded DNA molecule obtained by substituting and/or deleting and/or adding one or more nucleotides to the sequence 2 and having the same function as the sequence 2;
the probe is a 5) or a 6) as follows:
a5 A single-stranded DNA molecule shown in a sequence 3 in a sequence table;
a6 Single-stranded DNA molecule obtained by substituting and/or deleting and/or adding one or more nucleotides to the sequence 3 and having the same function as the sequence 3.
In the primer set, the molar ratio of the primer 1, the primer 2 and the probe is 5.
In order to solve the technical problems, the invention also provides a new application of the primer group.
The invention provides an application of the primer group in any one of the following b 1) -b 8):
b1 Preparing a product for identifying or assisting in identifying whether the bacteria to be detected is mycobacterium tuberculosis;
b2 Identifying or assisting in identifying whether the test bacterium is mycobacterium tuberculosis;
b3 Preparing a product for diagnosing or assisting in diagnosing whether a subject is infected with mycobacterium tuberculosis;
b4 To diagnose or aid in diagnosing whether a subject is infected with mycobacterium tuberculosis;
b5 Preparing a product for detecting or assisting in detecting whether a sample to be detected contains mycobacterium tuberculosis;
b6 Detecting or assisting in detecting whether the sample to be detected contains mycobacterium tuberculosis;
b7 Preparing a product for identifying or assisting in identifying mycobacterium tuberculosis from other mycobacteria;
b8 ) or to aid in the identification of Mycobacterium tuberculosis from other Mycobacteria.
In order to solve the technical problems, the invention also provides a kit containing the primer group;
the function of the kit is any one of the following c 1) -c 4):
c1 Identifying or assisting in identifying whether the test bacterium is mycobacterium tuberculosis;
c2 To diagnose or aid in diagnosing whether a subject is infected with mycobacterium tuberculosis;
c3 Detecting or assisting in detecting whether the sample to be detected contains mycobacterium tuberculosis;
c4 ) or to aid in the identification of Mycobacterium tuberculosis from other Mycobacteria.
Further, the kit may further comprise other reagents for identifying mycobacterium tuberculosis. In the present invention, the other reagent for identifying Mycobacterium tuberculosis may be TaqMan Gene Expression Master Mix.
Still further, the kit may include a negative control (e.g., ddH) 2 O) and positive control (e.g. Mycobacterium tuberculosis Standard Strain: (A)
Figure BDA0003064108960000021
27294 TM ) Genomic DNA of (4).
The preparation method of the kit also belongs to the protection scope of the invention.
The preparation method of the kit comprises the following steps of d 1) or d 2):
d1 Respectively and individually packaging each primer in the primer group;
d2 Each primer in the primer set is mixed together in proportion.
Further, in the d 2), the primer 1, the primer 2 and the probe in the primer group are mixed together according to a molar ratio of 5.
In order to solve the technical problem, the invention also provides a method for identifying or assisting in identifying whether the bacteria to be detected is mycobacterium tuberculosis.
The method for identifying or assisting in identifying whether the bacteria to be detected are mycobacterium tuberculosis comprises the following steps: extracting nucleic acid of bacteria to be detected, and performing real-time fluorescence quantitative PCR by using the primer group by using the nucleic acid of the bacteria to be detected as a template; and after the reaction is finished, judging whether the bacteria to be detected are mycobacterium tuberculosis or not through the amplification curve and the CT value: if the bacteria to be detected have an S-type amplification curve and the CT value is less than 35, the bacteria to be detected are or are selected as mycobacterium tuberculosis; otherwise, the bacteria to be tested is not or is not candidate to be the mycobacterium tuberculosis.
In order to solve the above technical problems, the present invention also provides a method for diagnosing or aiding in diagnosing whether a subject is infected with mycobacterium tuberculosis.
The method for diagnosing or assisting in diagnosing whether a person to be tested is infected with mycobacterium tuberculosis comprises the following steps: extracting nucleic acid of a person to be detected, and performing real-time fluorescence quantitative PCR by using the primer group by using the nucleic acid of the person to be detected as a template; and (3) judging whether the person to be detected is infected with the mycobacterium tuberculosis through the amplification curve and the CT value after the reaction is finished: if the person to be tested has an S-type amplification curve and the CT value is less than 35, the person to be tested is infected or candidate infected with mycobacterium tuberculosis; otherwise, the tested person is not infected or candidate is not infected with the mycobacterium tuberculosis.
In order to solve the technical problem, the invention also provides a method for detecting or assisting in detecting whether a sample to be detected contains mycobacterium tuberculosis.
The method for detecting or assisting in detecting whether a sample to be detected contains mycobacterium tuberculosis comprises the following steps: extracting nucleic acid of a sample to be detected, and performing real-time fluorescence quantitative PCR by using the primer group by using the nucleic acid of the sample to be detected as a template; and (3) judging whether the sample to be detected contains the mycobacterium tuberculosis or not through the amplification curve and the CT value after the reaction is finished: if the sample to be detected has an S-shaped amplification curve and the CT value is less than 35, the sample to be detected contains or is candidate to contain the mycobacterium tuberculosis; otherwise, the sample to be tested does not contain or candidate does not contain the mycobacterium tuberculosis.
In order to solve the above technical problems, the present invention finally provides a method for identifying or assisting in identifying M.tuberculosis from other Mycobacteria.
The method for identifying or assisting in identifying the mycobacterium tuberculosis and other mycobacteria comprises the following steps: extracting nucleic acid of bacteria to be detected, and performing real-time fluorescent quantitative PCR by using the primer group by using the nucleic acid of the bacteria to be detected as a template; and after the reaction is finished, judging whether the bacteria to be detected is mycobacterium tuberculosis or other mycobacteria through an amplification curve and a CT value: if the bacteria to be detected have an S-type amplification curve and the CT value is less than 35, the bacteria to be detected are or are selected as mycobacterium tuberculosis; otherwise, the bacteria to be tested are or are selected as other mycobacteria.
Any of the above methods further comprises the steps of: and (3) judging the result on the premise that the negative control has no amplification curve or the CT value is more than 35, the positive control has an S-shaped amplification curve and the CT value is less than 35.
In any of the above methods, the final concentration of each of the primer 1 and the primer 2 in the real-time fluorescence quantitative PCR system may be 7.5 μ M, and the final concentration of the probe in the real-time fluorescence quantitative PCR system may be 6 μ M.
The real-time fluorescent quantitative PCR system can be composed of 15 muL TaqMan Gene Expression Master Mix, 0.75 muL primer 1, 0.75 muL primer 2, 0.6 muL probe, 2 muL template and 10.9 muL ddH 2 And (C) O.
The real-time fluorescent quantitative PCR reaction program can be specifically 50 ℃ for 2min,95 ℃ for 10min and 40 cycles (95 ℃ for 15s and 60 ℃ for 1 min).
In any of the above methods, the nucleic acid is genomic DNA.
In any of the above uses or kits or methods, the other mycobacterium may be at least one of the following mycobacteria: mycobacterium marinum, mycobacterium cheloni, mycobacterium fortuitum, mycobacterium haemophilus.
The invention takes the specific gene IS6110 of mycobacterium tuberculosis as a target gene, and designs a specific primer and a probe thereof. Then, using Mycobacterium tuberculosis standard strain (H37 RV) as positive control, extracting standard strain genome DNA, measuring its nucleic acid concentration to 1562 ng/microliter, diluting by continuous 10-fold gradient to x 10 -1 To x 10 -8 The detection is carried out by respectively adopting a commercially available mycobacterium tuberculosis nucleic acid detection kit (Daan Gen-Kung Co., ltd. Of Zhongshan university) and the specific primer and probe of the invention. The results showed that both had comparable sensitivity and could be detected at X10 -6 . The invention also carries out specificity analysis on the specific primer and the probe, selects the cultured colonies of the skin tissue samples of 1 case of mycobacterium tuberculosis, 100 cases of mycobacterium marinum, 1 case of mycobacterium cheloni, 2 cases of mycobacterium fortuitum and 2 cases of mycobacterium haemophilus infection patients which are clinically and definitely diagnosed as an experimental group, simultaneously sets a blank control group, and adopts the specific primer and the probe for detection. The results show that: only 1 case of mycobacterium tuberculosis infected patients in the experimental group have positive cultured bacterial colonies, and the accuracy reaches 100 percent; the rest are negative, and the specificity reaches 100%. The invention successfully establishes miningThe method for detecting the mycobacterium tuberculosis by using the real-time fluorescent quantitative PCR technology has the sensitivity equivalent to that of a commercially available dalan kit, and provides an effective technical means for early diagnosis and treatment of a mycobacterium tuberculosis infected patient.
Detailed Description
The following examples are given to facilitate a better understanding of the invention, but do not limit the invention.
The test methods in the following examples are all conventional methods unless otherwise specified.
The test materials used in the following examples were purchased from a conventional biochemical reagent store unless otherwise specified.
The quantitative tests in the following examples, all set up three replicates and the results averaged.
The standard strain of Mycobacterium tuberculosis (H37 RV) in the following examples is the product of ATCC, with the number
Figure BDA0003064108960000041
27294 TM
Example 1 primer set for rapid identification of Mycobacterium tuberculosis and method for identifying the same
1. Primer group for rapidly identifying mycobacterium tuberculosis
The specific gene IS6110 of the mycobacterium tuberculosis IS taken as a target gene, a specific Primer and a probe of the specific gene are designed through Primer Express Software for Real-Time PCR Version 3.0 Software, and the specific sequence IS shown in table 1. The single-stranded DNA molecule shown in the sequence 1, the single-stranded DNA molecule shown in the sequence 2 and the single-stranded DNA molecule shown in the sequence 3 form a primer group for rapidly identifying the mycobacterium tuberculosis.
TABLE 1 specific primers and probes
Figure BDA0003064108960000051
2. qPCR method for rapidly identifying mycobacterium tuberculosis
1. Experimental equipment
(1) The instrument comprises the following steps: biosafety cabinet, carbon dioxide incubator, 4-degree refrigerator, -20-degree refrigerator, -80-degree refrigerator, micropipettor, dry type constant temperature metal bath, centrifuge, water purifier, nanoDrop TM 8000 Spectrophotometer (Thermo Scientific, america), american ABI 7500 real-time fluorescence quantitative PCR instrument.
(2) Reagent: DNA extracts, primers and probes (invitrogen), taqMan Gene Expression Master Mix (Thermo Fisher, applied BioSystems, 00826956).
(3) Consumable material: spear head, 1.5mL ep tube, eight tubes, etc.
2. Experimental methods
(1) And (4) after the ultraviolet lamp of the biological safety cabinet irradiates for 30 minutes, taking out the cultured bacterial colony of the bacteria to be detected from the carbon dioxide incubator, and placing the bacterial colony in the biological safety cabinet. A small amount of each colony was scraped with an inoculating loop and placed in a 1.5mL ep tube.
(2) Adding 80 mu L of DNA extracting solution into a 1.5mL ep tube containing colonies, carrying out vortex oscillation for 10s, and then centrifuging at 10000r/min for 10s to enable the colonies and the DNA extracting solution to be positioned at the bottom of the ep tube.
(3) And (5) placing the mixture in a dry constant-temperature metal bath at 100 ℃ for 10min to extract colony DNA.
(4) Taking out the ep tube from the dry constant-temperature metal bath, centrifuging at 10000r/min for 30s, and obtaining supernatant fluid containing the nucleic acid of the bacterial colony. And then storing in a refrigerator at minus 80 ℃ for later use.
(5) A PCR system (30. Mu.L) was prepared according to the recipe shown in Table 2, and the final concentrations of the primer F, the primer R and the probe in the PCR system were 7.5. Mu.M, 7.5. Mu.M and 6. Mu.M, respectively. And simultaneously setting a negative control and a positive control, wherein the negative control comprises the following steps: ddH 2 O, positive control: mycobacterium tuberculosis Standard Strain: (A)
Figure BDA0003064108960000052
27294 TM )。
TABLE 2 reaction System
Components 1×(μL)
TaqMan Gene Expression Master Mix 15
F 0.75
R 0.75
probe 0.6
ddH 2 O 10.9
DNA template 2
(6) Detection was carried out using an ABI StepOnePlus fluorescent quantitative PCR instrument with the reaction program of 50 ℃ for 2min,95 ℃ for 10min, and 40 cycles (95 ℃ for 15s, 60 ℃ for 1 min).
3. Determination of results
And on the premise that the negative and positive controls are qualified (no amplification curve or the CT value is more than 35 in the negative control, and an S-type amplification curve and the CT value are in the positive control and less than 35 in the positive control), if the bacteria to be detected have the S-type amplification curve and the CT value is less than 35, the bacteria to be detected are mycobacterium tuberculosis, otherwise, the bacteria to be detected are not mycobacterium tuberculosis.
Example 2 sensitivity test
1. Experimental materials
A standard strain of Mycobacterium tuberculosis with a concentration of 1562 ng/. Mu.L (
Figure BDA0003064108960000061
27294 TM ) The genomic DNA solution of (1) was subjected to successive dilution at a ratio of 1562X 10 in order of concentration -1 ng/μL、1562×10 -2 ng/μL、1562×10 - 3 ng/μL、1562×10 -4 ng/μL、1562×10 -5 ng/μL、1562×10 -6 ng/μL、1562×10 -7 ng/μL、1562×10 - 8 ng/. Mu.L of Mycobacterium tuberculosis DNA solution.
2. Experimental methods and results
And (3) respectively taking the mycobacterium tuberculosis DNA solutions with different concentrations as templates, and respectively adopting the method in the step two of the example 1 and a mycobacterium tuberculosis nucleic acid detection kit (Daan Gen-Kung Ltd of Zhongshan university, the product number is DA 0051) to carry out detection and result judgment.
The results show that: the method of the invention has the detection sensitivity equivalent to that of a commercial kit, and both can reach 1562 multiplied by 10 -6 ng/μL。
Example 3 specificity test
1. Experimental materials
Experimental materials: cultured colonies of skin tissue samples from patients infected with mycobacteria. The mycobacterial patients were as follows: 1 Mycobacterium tuberculosis infected patient, 100 Mycobacterium marinum infected patients, 2 Mycobacterium haemophilus infected patients, 1 Mycobacterium cheloni infected patient and 2 Mycobacterium fortuitum infected patients, all of whom were clinically confirmed and informed.
2. Experimental methods and results
Genomic DNAs were extracted from the test materials in the first step, and the fluorescent quantitative PCR and the result judgment were performed by the method in the second step of example 1 using the extracted DNA solutions as templates. Simultaneously with ddH 2 O is blank control.
The results show that: only 1 case of the Mycobacterium tuberculosis colonies are positive, the accuracy reaches 100 percent, the rest colonies and the blank control group are negative, and the specificity reaches 100 percent.
The foregoing is only a preferred embodiment of the present invention, and it should be noted that, for those skilled in the art, various modifications and decorations can be made without departing from the technical principle of the present invention, and these modifications and decorations should also be regarded as the protection scope of the present invention.
Sequence listing
<110> university of Shandong first medical university affiliated dermatological Hospital (institute for prevention and treatment of skin disease and STD in Shandong province, hospital for skin disease in Shandong province)
<120> primer group for identifying mycobacterium tuberculosis and application thereof
<160> 3
<170> PatentIn version 3.5
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<212> DNA
<213> Artificial Sequence
<400> 1
gccctgatgt gtaggttgca 20
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<212> DNA
<213> Artificial Sequence
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cgtcgagagc accgatcat 19
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<212> DNA
<213> Artificial Sequence
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ctcatctgga tcagctc 17

Claims (10)

1. The primer group for identifying or assisting in identifying the mycobacterium tuberculosis consists of a primer 1, a primer 2 and a probe;
the primer 1 is a 1) or a 2) as follows:
a1 A single-stranded DNA molecule shown as a sequence 1 in a sequence table;
a2 A single-stranded DNA molecule obtained by substituting and/or deleting and/or adding one or more nucleotides in the sequence 1 and having the same function as the sequence 1;
the primer 2 is a 3) or a 4) as follows:
a3 A single-stranded DNA molecule shown in a sequence 2 in a sequence table;
a4 A single-stranded DNA molecule obtained by substituting and/or deleting and/or adding one or more nucleotides to the sequence 2 and having the same function as the sequence 2;
the probe is a 5) or a 6) as follows:
a5 A single-stranded DNA molecule shown in a sequence 3 in a sequence table;
a6 Single-stranded DNA molecule obtained by substituting and/or deleting and/or adding one or more nucleotides to the sequence 3 and having the same function as the sequence 3.
2. The primer set according to claim 1, wherein: the molar ratio of the primer 1, the primer 2 and the probe is 5.
3. Use of the primer set of claim 1 or 2 in any one of the following b 1) -b 8):
b1 Preparing a product for identifying or assisting in identifying whether the bacteria to be detected are mycobacterium tuberculosis;
b2 Identifying or assisting in identifying whether the test bacterium is mycobacterium tuberculosis;
b3 Preparing a product for diagnosing or assisting in diagnosing whether a subject is infected with Mycobacterium tuberculosis;
b4 To diagnose or aid in diagnosing whether a subject is infected with mycobacterium tuberculosis;
b5 Preparing a product for detecting or assisting in detecting whether a sample to be detected contains mycobacterium tuberculosis;
b6 Detecting or assisting in detecting whether the sample to be detected contains mycobacterium tuberculosis;
b7 Preparing a product for identifying or assisting in identifying mycobacterium tuberculosis from other mycobacteria;
b8 ) or to assist in the identification of Mycobacterium tuberculosis from other Mycobacteria.
4. A kit containing the primer set according to claim 1 or 2;
the function of the kit is any one of the following c 1) -c 4):
c1 Identifying or assisting in identifying whether the test bacterium is mycobacterium tuberculosis;
c2 To diagnose or aid in diagnosing whether a subject is infected with mycobacterium tuberculosis;
c3 Detecting or assisting in detecting whether the sample to be detected contains mycobacterium tuberculosis;
c4 ) or to assist in the identification of Mycobacterium tuberculosis from other Mycobacteria.
5. The method for preparing the kit according to claim 4, wherein the method is d 1) or d 2):
d1 Separately packaging each primer in the primer set according to claim 1 or 2;
d2 Mixing the respective primers in the primer set according to claim 1 or 2 together in proportion.
6. The method of claim 5, wherein: in the d 2), the primer 1, the primer 2 and the probe in the primer group are mixed together according to a molar ratio of 5.
7. A method for identifying or assisting in identifying whether a bacterium to be detected is mycobacterium tuberculosis comprises the following steps: extracting nucleic acid of bacteria to be detected, and carrying out real-time fluorescent quantitative PCR by using the primer group of claim 1 by using the nucleic acid of the bacteria to be detected as a template; and after the reaction is finished, judging whether the bacteria to be detected are mycobacterium tuberculosis or not through the amplification curve and the CT value: if the bacteria to be detected have an S-type amplification curve and the CT value is less than 35, the bacteria to be detected are or are selected as mycobacterium tuberculosis; otherwise, the bacteria to be detected is not or is not candidate to be the mycobacterium tuberculosis.
8. A method of diagnosing or aiding in the diagnosis of whether a subject is infected with mycobacterium tuberculosis, comprising the steps of: extracting nucleic acid of a person to be detected, and carrying out real-time fluorescent quantitative PCR by using the primer group of claim 1 by using the nucleic acid of the person to be detected as a template; and after the reaction is finished, judging whether the person to be detected is infected with the mycobacterium tuberculosis through the amplification curve and the CT value: if the person to be tested has an S-type amplification curve and the CT value is less than 35, the person to be tested is infected or candidate infected with mycobacterium tuberculosis; otherwise, the tested person is not infected or candidate is not infected with the mycobacterium tuberculosis.
9. A method for detecting or assisting in detecting whether a sample to be detected contains mycobacterium tuberculosis comprises the following steps: extracting nucleic acid of a sample to be detected, and carrying out real-time fluorescence quantitative PCR by using the primer group of claim 1 by using the nucleic acid of the sample to be detected as a template; and (3) judging whether the sample to be detected contains the mycobacterium tuberculosis or not through the amplification curve and the CT value after the reaction is finished: if the sample to be detected has an S-shaped amplification curve and the CT value is less than 35, the sample to be detected contains or is candidate to contain the mycobacterium tuberculosis; otherwise, the sample to be tested does not contain or is candidate to contain the mycobacterium tuberculosis.
10. A method for identifying or aiding in the identification of mycobacterium tuberculosis from other mycobacteria comprising the steps of: extracting nucleic acid of bacteria to be detected, and carrying out real-time fluorescent quantitative PCR by using the primer group of claim 1 by using the nucleic acid of the bacteria to be detected as a template; and after the reaction is finished, judging whether the bacteria to be detected is mycobacterium tuberculosis or other mycobacteria through an amplification curve and a CT value: if the bacteria to be detected have an S-type amplification curve and the CT value is less than 35, the bacteria to be detected are or are selected as mycobacterium tuberculosis; otherwise, the bacteria to be tested are other mycobacteria or are candidate to be other mycobacteria.
CN202110521377.1A 2021-05-13 2021-05-13 Primer group for identifying mycobacterium tuberculosis and application thereof Pending CN115341040A (en)

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