CN104328174B - A kind of detect the LAMP primer of Mus Klebsiella pneumonia, test kit and method - Google Patents
A kind of detect the LAMP primer of Mus Klebsiella pneumonia, test kit and method Download PDFInfo
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- CN104328174B CN104328174B CN201410583258.9A CN201410583258A CN104328174B CN 104328174 B CN104328174 B CN 104328174B CN 201410583258 A CN201410583258 A CN 201410583258A CN 104328174 B CN104328174 B CN 104328174B
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Abstract
The invention discloses and a kind of detect the LAMP primer of Mus Klebsiella pneumonia, test kit and method, it is to design LAMP primer by Klebsiella pneumonia tyrB gene order, sets up and be applicable to clinical sample detection, high specificity, highly sensitive Mus Klebsiella pneumonia visible detection method；Can be detected the existence of Klebsiella pneumonia fast and accurately by the presence or absence of observation green fluorescence, lowest detection is limited to 5.6 copy numbers/reaction.4 primers of present invention design and the screening identification to the distinguished sequence district of target sequence, it is ensured that the high degree of specificity of LAMP amplification, is suitable for basic unit's scene application.
Description
Technical field
The invention belongs to medical microbial detection technique field, relate to a kind of LAMP detecting Mus Klebsiella pneumonia and draw
Thing and detection method.
Background technology
Klebsiella pneumonia is Gram-negative, non-motor type, have pod membrane, lactate fermentation, amphimicrobian shaft-like carefully
Bacterium.Klebsiella pneumonia generally resides in the intestinal of big mice and other animals.As opportunist, e coil k 1 pneumonia
Bacterium once enters respiratory tract, can infect big mice, causes severe lung to damage, and this bacterium takes in antibiotic-resistant nude mice
For the higher growth tendency of other antibacterials, for experiment one of rodentine common health monitor control index.
The most conventional determination of Klebsiella pneumoniae method includes using monitoring swab direct bed board method and colour developing to cultivate
Base method and Standard PCR method/fluorescence quantitative PCR method, all can detect effectively.But the existence of bacterial cultivation relatively additive method is difficult to
Standardization, the longest, culture medium, operating procedure or condition of culture are in shortcomings such as different experiments room difference are bigger, therefore result may
The false Yin/Yang of inconsistent or appearance.Standard PCR method and fluorescence quantitative PCR method, need to through degeneration, anneal, extend, add that DNA carries
Round a process probably need 2～within 4 hours, just can go out result, and need accurate expensive instrument and reagent, basic unit is opened
Open up fast and convenient molecular diagnosis unfavorable.
Notomi et al. was in invention ring mediated isothermal amplification (LAMP) technology in 2000, and through progressively improving, this technology is borrowed
Help 6 specific primers and a kind of archaeal dna polymerase with strand displacement characteristic, can be quick, high special and clever under isothermal conditions
Quick amplification target sequence.
Summary of the invention
It is an object of the invention to provide and a kind of detect the LAMP primer of Mus Klebsiella pneumonia, test kit and method.
For reaching above-mentioned purpose, present invention employs techniques below scheme:
A kind of LAMP primer detecting Mus Klebsiella pneumonia, including following 2 pairs of primers: outer primer F3 and B3 and interior
Primers F IP and BIP；The nucleotide sequence of FIP as shown in SEQ.ID.NO.1, the nucleotide sequence of BIP such as SEQ.ID.NO.2 institute
Showing, the nucleotide sequence of F3 is as shown in SEQ.ID.NO.3, and the nucleotide sequence of B3 is as shown in SEQ.ID.NO.4.
A kind of LAMP kit detecting Mus Klebsiella pneumonia, this test kit includes 40 μm ol.L-1FIP 1.0 μ
L, 40 μm ol.L-1BIP 1.0 μ L, 10 μm ol.L-1F30.5 μ L and 10 μm ol.L-1B30.5 μ L；F3 and B3 is for draw outward
Thing, FIP and BIP is inner primer, and the nucleotide sequence of FIP is as shown in SEQ.ID.NO.1, and the nucleotide sequence of BIP is such as
Shown in SEQ.ID.NO.2, the nucleotide sequence of F3 as shown in SEQ.ID.NO.3, the nucleotide sequence of B3 such as SEQ.ID.NO.4 institute
Show.
Described test kit also includes 2 × reaction buffer 12.5 μ L, 8U/ μ L Bst polymerase 1 μ L, 25mM dNTP 1.5 μ
L and fluorescent dye 1 μ L.
Described fluorescent dye is the calcein aqueous solution of mass fraction 0.5%.
A kind of LAMP method detecting Mus Klebsiella pneumonia, comprises the following steps:
1) DNA of object to be detected (such as rat, mice) is extracted；
2) following component is mixed, build the 25 μ L LAMP reactions including 2 pairs of primers F 3 and B3 and FIP and BIP
System:
2 × reaction buffer 12.5 μ L, 40 μm ol.L-1FIP 1.0 μ L, 40 μm ol.L-1BIP 1.0 μ L, 10 μ
mol.L-1F30.5 μ L, 10 μm ol.L-1B30.5 μ L, 8U/ μ L Bst polymerase 1 μ L, 25mM dNTP 1.5 μ L, to be detected
The DNA 2 μ L of object, fluorescent dye 1 μ L, ultra-pure water complements to 25 μ L；The nucleotide sequence of FIP as shown in SEQ.ID.NO.1,
The nucleotide sequence of BIP as shown in SEQ.ID.NO.2, the nucleotide sequence of F3 as shown in SEQ.ID.NO.3, the nucleotides sequence of B3
Row are as shown in SEQ.ID.NO.4；
3) at 63 DEG C, LAMP reaction system being heated 40min, then heat 5min at 85 DEG C, reaction completes；
4) judgement of result is carried out after question response completes in the following manner:
The most coloured change of LAMP reaction system is observed, if LAMP reaction system color changes after having reacted
Then for positive reaction, show Klebsiella pneumonia to be detected in object to be detected；If LAMP reaction system color does not occurs
Change is then negative reaction, shows to be not detected by Klebsiella pneumonia in object to be detected.
The extracting method of the DNA of described object to be detected is:
The blood of object to be detected, tissue fluid or suppuration liquid are inoculated in broth bouillon, then under the conditions of 37 DEG C
Cultivate 24h and obtain bacterium solution, take bacterium solution and be centrifuged, the centrifugal supernatant DNA test kit obtained is extracted DNA.
Positive control and negative control is set up the most respectively, with Klebsiella pneumonia genomic DNA as the positive when detection
Comparison, with ultra-pure water as negative control；When carrying out the judgement of result, also compare with positive control and negative control, if to be checked
Survey LAMP reaction system corresponding to object and the LAMP reaction system corresponding to positive control all in green, then judge to be checked
The testing result surveying object is positive reaction, if corresponding to the LAMP reaction system corresponding to object to be detected and negative control
LAMP reaction system all in crocus, then judge that the testing result of object to be detected is as negative reaction.
Compared with prior art, the present invention has a following useful technique effect:
The present invention uses Klebsiella pneumonia tyrB gene to become LAMP primer as detection Object combine, it is achieved that to lung
Scorching klebsiella is easy, fast, detect accurately；This gene is after NCBI blast search, in Klebsiella pneumonia kind
Between genus, aberration rate is low and takes into account the conserved sequence between different serotypes, the lowest with the homology of other kind antibacterials, therefore
Can be as versatility gene test Klebsiella pneumonia.
The LAMP method of the detection Mus Klebsiella pneumonia that the present invention provides, its high specificity: the feminine gender detected is right
According to result the most no positive with big mouse genome.
The LAMP method of the detection Mus Klebsiella pneumonia that the present invention provides, its detection sensitivity is high: Standard PCR detects
Method sensitivity is 100pg/reaction (100copy number/reaction) order of magnitude, uses detection method,
Monitoring lower-cut is that 13.5fg/ reacts (5.6 copy numbers/reaction)
The LAMP method of the detection Mus Klebsiella pneumonia that the present invention provides, detection is rapid for it, it is convenient to go out result: conventional
The whole process of PCR just can go out result 2～4 hours, and quantitative fluorescent PCR is also required to 1～1.5 hours, and the present invention provides
Detection method i.e. may occur in which positive findings at about 50 minutes.And easy and simple to handle, low to instrument requirements, it is only necessary to common water-bath
Pot, it is possible to by the direct observed result of dyestuff, eliminate the step of electrophoresis, can be at basic unit's detection Mus Klebsiella pneumonia
Practice has wide practical use, is that one is laboratory animal department simplicity, detects Mus e coil k 1 pneumonia fast, accurately
The method of bacterium, and the use of applicable basic unit.
Accompanying drawing explanation
Fig. 1 is the color-distinctive schematic diagram of positive reaction and negative reaction；
Fig. 2 is LAMP specificity experiments result schematic diagram；
Fig. 3 is the LAMP testing result schematic diagram after gradient dilution；
In figure: POS represents the testing result of positive control, K.p represents object to be detected (pneumonia infection klebsiella)
Testing result, Kp represents the testing result of Klebsiella pneumonia genomic DNA, and Sa represents staphylococcus aureus gene group
The testing result of DNA, H2O represents the testing result of negative control, and P.a represents the testing result of bacillus pyocyaneus genomic DNA,
Rat represents the testing result of rat genomic dna, and Mouse represents the testing result of mouse gene group DNA, a represents 5.6 ×
106The testing result of copies/ μ L, b represents 5.6 × 105The testing result of copies/ μ L, c represents 5.6 × 104copies/μL
Testing result, d represents 5.6 × 103The testing result of copies/ μ L, e represents 5.6 × 102The testing result of copies/ μ L, f
Representing the testing result of 5.6 × 10copies/ μ L, g represents the testing result of 5.6copies/ μ L, and h represents 5.6 × 10- 1The testing result of copies/ μ L.
Detailed description of the invention
With embodiment, the present invention is elaborated below in conjunction with the accompanying drawings, described in be explanation of the invention rather than limit
Fixed.
The invention discloses a kind of test experience LAMP method with Mus Klebsiella pneumonia, this detection method is based on ring
Mediated isothermality amplification is carried out.
The present invention is directed to Klebsiella pneumonia tyrB gene (gene accession number AF074934), devise and include outer drawing
Thing, the specific primer of inner primer.Only need to add sample in the LAMP reaction system set up can be by observation green fluorescence
With or without detecting the existence of Klebsiella pneumonia fast and accurately, lowest detection is limited to 5.6 copy numbers/reaction, for quickly inspection
Survey big mice Klebsiella pneumonia and provide the convenient method of an applicable basic unit.
1, design of primers and synthesis:
In view of specificity and the accuracy of detection, use Klebsiella pneumonia tyrB gene as detection Object combine
Becoming LAMP primer, this is that between Klebsiella pneumonia kind, aberration rate is low owing to tyrB gene is after NCBI blast search
And take into account the conserved sequence between different serotypes, and the lowest with the homology of other kind antibacterials, therefore can be as general
Property gene test Klebsiella pneumonia.
Use primer-design software Primer Explorer 4.0, guarding for Klebsiella pneumonia tyrB gene
District devises 4 LAMP primer, including forwards/reverse inner primer FIP/BIP, forwards/reverse outer primer F3/B3, described primer
With tyrB (gene accession number: AF074934) gene 150～a part for the nucleotide sequence of 333 or its complementary strand thereof.Tool
The primer sequence of body is shown in Table 1.
Table 1 LAMP method detection Mus Klebsiella pneumonia primer sequence
The extraction of bacterial genomes DNA profiling 2.1, to be detected
For the ease of the explanation to detection method, specifically used bacterial genomes is extracted test kit and is extracted e coil k 1 pneumonia
Bacterium and (bacillus pyocyaneus, staphylococcus aureus, the sramana Li Ding Salmonella) strain gene group DNA as comparison, through nucleic acid-protein
Quantitative instrument is quantitatively rear standby.
2.2, mice to be checked uses the method cutting tail first to obtain blood sample, is inoculated in fresh broth bouillon, 37
Cultivate 24h under the conditions of DEG C and obtain bacterium solution, take bacterium solution and be centrifuged, utilize Genomic Purification Kit according to explanation the centrifugal supernatant obtained
The method of book extracts DNA.
3, LAMP reaction system (25 μ L) is built
Fluorescent dye is the calcein aqueous solution of mass fraction 0.5%.Template is the DNA extracted.2 × reaction buffering
Liquid and Bst polymerase are purchased from New England Biolabs..
4, foundation and the primer availability of Klebsiella pneumonia LAMP detection method detects
Joining in reaction system using the DNA extracting from described mice to be checked as template, course of reaction is as follows: reaction temperature
Spending 63 DEG C, 40 minutes time, then heat 5 minutes at 85 DEG C, reaction terminates.
Use positive control (Klebsiella pneumonia genomic DNA) and negative control (ultra-pure water) by above-mentioned reaction system
Carry out with condition.
5, the qualification of Klebsiella pneumonia LAMP product
Owing to adding the fluorescent dye of 1 μ L before reaction in LAMP reaction system, detect by an unaided eye LAMP reaction system face
Complexion changed, and comparing with negative and positive, reactant liquor be green be positive reaction (seeing POS and K.p in Fig. 1), in crocus be
Negative reaction (sees H2O in Fig. 1).
Amplification process can be formed substantial amounts of pyrophosphate ion.Manganese ion in fluorescent dye is tied with calcein
Conjunction causes fluorescent quenching, and dye colour is crocus simultaneously.When amplified reaction forms pyrophosphate ion, manganese ion and burnt phosphorus
Acid ion combines and forms manganese pyrophosphate, causes the generation of fluorescence signal, and dye colour becomes green simultaneously.After i.e. LAMP reaction
Having expanded a large amount of target dna, addition calcein i.e. may react and presents green.
6, the specificity experiments of LAMP
Non-Klebsiella pneumonia (bacillus pyocyaneus, the Staphylococcus aureus that Klebsiella pneumonia and experimental mouse are often sent out
Bacterium, sramana Li Ding Salmonella) genomic DNA and big mouse gene group DNA, set up LAMP according to above-mentioned reaction system and condition
Detection method, carries out specific test.Arranging Klebsiella pneumonia genomic DNA is positive control, and ultra-pure water is negative right
According to.Result shows, positive reaction occurs in only Klebsiella pneumonia genome, remaining the most negative (seeing Fig. 2).
7, LAMP sensitivity tests
After Klebsiella pneumonia genomic DNA is carried out 10 times of gradient dilutions, negative control (ultra-pure water) is set, according to
Above-mentioned reaction system and condition set up LAMP detection method, to determine the sensitivity of detection method.
Seeing Fig. 3, result shows: the Mus Klebsiella pneumonia LAMP detection method of foundation can detect in sample 5.6 and copy
The Klebsiella pneumonia DNA of shellfish number/reaction.
From the point of view of the present invention, the more conventional PCR of LAMP amplification method and fluorescence PCR method have:
High specificity: only by whether amplification i.e. can determine that the presence or absence of genes of interest, thus complete antibacterial and virus
Qualitative detection.
Highly sensitive: Standard PCR detection method sensitivity is that 100pg/ reacts (100 copy numbers/reaction) order of magnitude, uses
Detection method, Monitoring lower-cut is that 13.5fg/ reacts (5.6 copy numbers/reaction).
Operate and identify simple and efficient: the whole process of Standard PCR just can go out result, quantitative fluorescent PCR 2～4 hours
Being also required to 1～1.5 hours, the detection method that the present invention provides i.e. may occur in which positive findings at 50 minutes.And it is easy and simple to handle,
Low to instrument requirements, it is only necessary to light water bath, it is possible to by the direct observed result of dyestuff, to eliminate the step of electrophoresis,
The practice of basic unit detection Mus kerekou pneumonia uncle has wide practical use.
Claims (4)
1. the LAMP primer detecting Mus Klebsiella pneumonia, it is characterised in that: use Klebsiella pneumonia tyrB base
Because becoming LAMP primer, including following 2 pairs of primers: outer primer F3 and B3 and inner primer FIP and BIP as detection Object combine；
The nucleotide sequence of FIP as shown in SEQ.ID.NO.1, the nucleotide sequence of BIP as shown in SEQ.ID.NO.2, the nucleotide of F3
Sequence is as shown in SEQ.ID.NO.3, and the nucleotide sequence of B3 is as shown in SEQ.ID.NO.4.
2. the LAMP kit detecting Mus Klebsiella pneumonia, it is characterised in that: this test kit uses kerekou pneumonia primary
Salmonella tyrB gene becomes LAMP primer, including 40 μm ol L as detection Object combine-1FIP 1.0 μ L, 40 μm ol L-1
BIP 1.0 μ L, 10 μm ol L-1F3 0.5 μ L and 10 μm ol L-1B3 0.5 μ L；F3 and B3 is outer primer, FIP
Be inner primer with BIP, the nucleotide sequence of FIP as shown in SEQ.ID.NO.1, the nucleotide sequence of BIP such as SEQ.ID.NO.2 institute
Showing, the nucleotide sequence of F3 is as shown in SEQ.ID.NO.3, and the nucleotide sequence of B3 is as shown in SEQ.ID.NO.4.
A kind of LAMP kit detecting Mus Klebsiella pneumonia the most as claimed in claim 2, it is characterised in that: described reagent
Box also includes 2 × reaction buffer 12.5 μ L, 8U/ μ L Bst polymerase 1 μ L, 25mM dNTP 1.5 μ L and fluorescent dye 1 μ
L。
A kind of LAMP kit detecting Mus Klebsiella pneumonia the most as claimed in claim 3, it is characterised in that: described fluorescence
Dyestuff is the calcein aqueous solution of mass fraction 0.5%.
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| CN109628621B (en) * | 2019-02-02 | 2022-02-15 | 广西壮族自治区兽医研究所 | Real-time quantitative LAMP primer group and kit for detecting Klebsiella pneumoniae |
| CN111500751B (en) * | 2020-04-10 | 2023-10-27 | 刘洋 | Detection method and kit for rapidly detecting high-virulence klebsiella pneumoniae |
| CN114898800B (en) * | 2022-07-14 | 2022-09-16 | 中国医学科学院北京协和医院 | Method and system for predicting sensitivity of klebsiella pneumoniae to ceftriaxone |
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