For detecting target sequence and the test kit of New Delhi metal beta lactamase-1 gene
Technical field
The invention belongs to technological field of biochemistry, be specifically related to target sequence and test kit that a kind of application Fluorescence PCR assay detects New Delhi metal beta lactamase-1 (NDM-1) gene.
Background technology
2010, in India, a kind of novel bacteria mutated genes that the South Asian nations such as Pakistan occur is likely at global spread, have the bacterium of this gene to comprising cephalosporin, carbapenems, most microbiotic such as aminoglycoside has resistance (at present only to replacing family's ring element and polymyxin two kinds of antibiotic sensitive), therefore this unnamed gene is New Delhi metal beta lactamase-1 (NewDelhimetallo-β-lactamase1 by medical expert, be called for short NDM-1) gene, originally it be present on the plasmid of the bacteriums such as intestinal bacteria, express the enzyme produced and can decompose above-mentioned microbiotic, NDM-1 gene can be propagated along with the transfer of plasmid between bacterium, cause the bacterium obtaining this gene to the antibiotic resistance (YongD of major part, etal.AntimicrobialAgentsandChemotherapy, 2009, 53 (12): 5046-5054.RolainJM, etal, ClinicalMicrobiologyandInfection, 2010, 16 (12): 1699-1701.).So far, microbiotic multi-drug resistant bacteria containing this super drug resistant gene of NDM-1 has spread from South Asia region to be propagated to the whole world, successively and domestic discovery national in Britain, the U.S., Canada, Australia, Holland etc., to the health of the mankind define new threat (
www.theLancet.com/Infection, publishedonlineAugust11,2010DOI:10.1016/S1473-3099 (10) 70143-2).
Clinically to the traditional detection of this microbiotic multi-drug resistant bacteria be separation and Culture in conjunction with susceptibility authentication method, need the soonest to go out detected result week more than one, far can not meet the needs clinically to Pathogenic Microorganisms On Tropical and medication guide.Therefore adopt molecular biology method qualification to be inevitable choice clinically containing the multi-drug resistant bacteria of NDM-1 gene, wherein fluorescence PCR method is especially due to sensitive, feature and have advantage fast.
Summary of the invention
The object of this invention is to provide one utilizes Fluorescence PCR assay to detect target sequence and the test kit of New Delhi metal beta lactamase-1 (NDM-1) gene, test kit contains primer and the probe of with good grounds target sequence SEQIDNO:1 design, thus the accuracy of real-time PCR detection NDM-1 gene can be improved, be suitable for the microbiotic multidrug resistant pathogenetic bacteria of clinical Rapid identification containing NDM-1 gene.
1. the Design and synthesis of real-time fluorescence PCR primer probe
By inquiring about New Delhi metal beta lactamase-1 gene order in GenBank, compare by the gene order of molecular biology professional software to various source, select high conservative and the sequence SEQIDNo:1 with good homology as detection target sequence, according to the principle of TaqMan fluorescent PCR design, devise according to this target sequence the conservative region that a pair NDM-1 gene-specific primer increase on this gene, and detect in real time with the specificity T aqMan probe of 5 ' end FAM mark.Primer and probe base sequence as follows:
Upstream primer is 5 '-ggCggggATTgCgACTTATg-3 ', as shown in SEQIDNO:2;
Downstream primer is 5 '-AATACCTTgAgCgggCCAAAg-3 ', as shown in SEQIDNO:3;
Fluorescent probe is 5 '-AATgCgTTgTCgAACCAgCTTgCC-3 ' (5 ' flag F AM, 3 ' mark TAMRA or BHQ-1), as shown in SEQIDNO:4.
By above-mentioned design, obtain pair of primers and probe sequence by NDM-1 gene special, it is 25 μMs that above-mentioned primed probe is dissolved to concentration with aseptic double-distilled water after being synthesized by business sequent synthesis company (Shanghai Sangon Biological Engineering Technology And Service Co., Ltd etc.) ,-20 DEG C of preservations.
2. the preparation of test kit
NDM-1 gene by fluorescence PCR detection kit (32 person-portion) main ingredient designed for target sequence SEQIDNO:1 is as follows:
(1) PCR damping fluid 672 μ l, main component has Tris-HCl (pH8.3), KCl, gelatin, dATP, dGTP, dCTP, dUTP, MgCl
2, upstream and downstream primer (SEQIDNo:2 and 3).
(2) fluorescent probe 96 μ l, containing fluorescent probe (SEQIDNo:4).
(3) Taq enzyme 64 μ l, containing Taq DNA polymerase 40U and uracil-DNA glycosylase (UNG enzyme) 16U.
(4) negative control 200 μ l is culture of Escherichia coli, 10
4individual bacterium/ml.
(5) positive control 200 μ l is the artificial constructed culture of Escherichia coli containing SEQIDNo:1 sequence plasmid, 10
3individual bacterium/ml.
(6) DNA extraction liquid 1.5ml, main component is 50mmol/LNaOH, 5mMEDTA, 1%TritonX-100,1%NP-40.
The 30 μ l reaction systems be made up of after adding template 4 μ l after mixing mentioned reagent box component PCR damping fluid 21 μ l, fluorescent probe 3 μ l, Taq enzyme 2 μ l, containing Tris-HCl (pH8.3) 10mM, KCl50mM, gelatin 0.1mg/ml, dATP, dGTP, dCTP, dUTP each 0.2-0.4mM, MgCl
2the each 0.2-0.5 of 1.5-5mM, primer μM, fluorescent probe 0.1-0.5 μM, Taq DNA polymerase 1-5U, UNG enzyme 0.1-1U, fluorescent PCR instrument carries out amplified reaction.
More specifically, Tris-HCl (pH8.3) 10mM, KCl50mM, gelatin 0.1mg/ml, dATP, dGTP, dCTP, dUTP each 0.2mM, MgCl is contained in the reaction system that said components is mixed with
2each 0.35 μM of 3.5mM, primer, fluorescent probe 0.2 μM, Taq DNA polymerase 1.25U, UNG enzyme 0.5U, fluorescent PCR instrument carries out amplified reaction.
The test kit that said components is assembled into is at-20 DEG C of storage and transport.
3. test kit using method
Test kit of the present invention containing one of use step in NDM-1 gene microbiotic multidrug resistant pathogenetic bacteria testing process is being:
(1) sample preparation
Get clinical sample or the enrichment liquid of collection, be placed in centrifuge tube 13,000rpm centrifugal 6 minutes, carefully inhale with pipettor and abandon supernatant (for preventing siphoning away precipitation, 5 μ l raffinates can be retained), in precipitation, add 1ml physiological saline, after vortex oscillation mixing, repeated centrifugation is inhaled and is abandoned supernatant.In precipitation, add 50 μ lDNA extracting solutions, latter 100 DEG C of vortex vibration mixing keeps 10 minutes, and 13,000rpm gets supernatant in centrifugal 2 minutes and carries out fluorescent PCR augmentation detection.Test kit is negative identical with sample liquid with positive control treatment process.
(2) augmentation detection
According to detected sample number n+2, get test kit PCR damping fluid 21 μ l × (n+2), fluorescent probe 3 μ l × (n+2), Taq enzyme 2 μ l × (n+2) component, each amplification pipe packing 26 μ l after mixing, adds the test kit negative control, positive control and each 4 μ l of the above-mentioned n handled well a sample form that handle well respectively.Each reaction tubes volume is 30 μ l, is put into by above-mentioned amplification pipe on two channels real-time fluorescence PCR instrument and runs according to the circulate program of 40 times of 94 DEG C of 10sec after 50 DEG C of 2min, 94 DEG C of 2min, 60 DEG C of 45sec.
(3) result judges
Use after fluorescent PCR instrument end of run and carry software analysis result, test kit negative control should be that feminine gender, positive control Ct value < 30 are for positive without Ct value.Sample amplification Ct value < is for containing NDM-1 gene masculine, and sample infects NDM-1 gene pathogenic bacteria of drug-resistant; Detected result is NDM-1 gene negative without Ct value person; If 38 < Ct value <, for detecting gray area, need duplicate detection 2 times, as detected result at least 1 Ct value < 40 judges that this pipe is NDM-1 gene masculine, otherwise, judge that this pipe is as negative.
4. beneficial effect
The present invention is according to the primed probe of above-mentioned design and technical scheme, and be developed into NDM-1 gene by fluorescence PCR detection kit by optimizing reaction system and amplification condition, its principal feature is as follows:
(1) test kit adopts the NDM-1 gene target sequence of Auele Specific Primer probe in detecting high conservative, ensure that detection specificity and sensitivity;
(2) test kit stopped pipe detects, fast easy and simple to handle, can report detected result in 2 hours;
(3) the dUTP-UNG enzyme system in amplification system further avoids the result false positive that gene-amplification product pollution causes.
The These characteristics of test kit, is the primed probe combined with fluorescent round pcr Combination application that adopt and design according to preferred target sequence and directly causes.From the principle, test kit of the present invention passes through the analysis to real-time fluorescent PCR amplification signal in NDM-1 genopathy substance clinical sample detects, judge the existence of NDM-1 gene nucleic acid specific fragment, as a kind of means of NDM-1 gene nucleic acid rapid detection, Technical Design of the present invention is reasonable, can be widely used in clinical in Rapid identification containing the super drug resistant gene pathogenetic bacteria of NDM-1.
Embodiment
Below in conjunction with specific embodiment, set forth the present invention further.Should be understood that these embodiments are only not used in for illustration of the present invention to limit the scope of the invention.In addition should be understood that those skilled in the art can do various technical change or amendment by technology general knowledge to the present invention, and these equivalent form of values fall within the application's appended claims limited range equally after the content of having read the present invention's instruction.
Main agents involved in the present invention illustrates:
Taq DNA polymerase, uracil-DNA glycosylase (UNG enzyme), dNTPs (dATP, dUTP, dCTP, dGTP) are Shanghai Hong Yi company and produce, and primed probe and other chemical reagent are purchased from Shanghai Sangon Biological Engineering Technology And Service Co., Ltd.
The preparation of embodiment 1:NDM-1 gene by fluorescence PCR detection kit
(1) primed probe synthesis
Business sequent synthesis company (Shanghai Sangon Biological Engineering Technology And Service Co., Ltd) is entrusted to synthesize following sequence:
Upstream primer is 5 '-ggCggggATTgCgACTTATg-3 ', as shown in SEQIDNo:2;
Downstream primer is 5 '-AATACCTTgAgCgggCCAAAg-3 ', as shown in SEQIDNO:3;
Fluorescent probe is 5 '-AATgCgTTgTCgAACCAgCTTgCC-3 ' (5 ' flag F AM, 3 ' mark TAMRA or BHQ-1), as shown in SEQIDNo:4.
Being dissolved to concentration with aseptic double-distilled water is respectively 25 μMs ,-20 DEG C of preservations.
(2) NDM-1 gene PCR damping fluid is prepared
Containing Tris-HCl (pH8.3) 14.2mM, KCl71.4mM, gelatin 0.14mg/ml, dATP, dGTP, dCTP, dUTP each 0.29mM, MgCl
25mM, each 5 μMs of upstream and downstream primer (SEQIDNo:2 and 3), according to 672 μ l/ pipe packing.
(3) fluorescent probe is prepared
Containing NDM-1 gene by fluorescence probe (SEQIDNo:4) 2 μMs, according to 96 μ l/ pipe packing.
(4) Taq enzyme is prepared
Containing Taq DNA polymerase 40U and uracil-DNA glycosylase (UNG enzyme) 16U, according to 64 μ l/ pipe packing.
(5) DNA extraction liquid is prepared
Containing 50mmol/LNaOH, 5mMEDTA, 1%TritonX-100,1%NP-40.According to the packing of 1.5ml/ pipe.
(6) test kit feminine gender, positive reference substance is prepared
Cultivate intestinal bacteria, intestinal bacteria containing SEQIDNO:1 artificial sequence plasmid respectively, and measure nutrient solution concentration by viable plate count method, be diluted to 1 × 10
4individual bacterium/ml and 1 × 10
3individual bacterium/ml, respectively as test kit negative control and positive control.According to 200 μ l/ pipe packing.
(7) kind of the component of 5 after above-mentioned packing is placed in same container, is assembled into test kit, encapsulation.
Preparation technology is summarized as follows:
(1) primed probe synthesized quantitatively is prepared, Concentration Testing, sampling quality inspection.
(2) PCR damping fluid, fluorescent probe, Taq enzyme, DNA extraction liquid is aseptic subpackaged, sampling quality inspection.
(3) feminine gender, positive reference substance are carried out concentration determination, packing, sampling quality inspection.
(4) assemble finished product test kit, be stored in-20 DEG C.
The application of embodiment 2:NDM-1 gene by fluorescence PCR detection kit
(1) sample preparation
Get clinical sample or enrichment liquid 20 example of collection, be placed in centrifuge tube 13,000rpm centrifugal 6 minutes, carefully inhale with pipettor and abandon supernatant (for preventing siphoning away precipitation, 5 μ l raffinates can be retained), in precipitation, add 1ml physiological saline, after vortex oscillation mixing, repeated centrifugation is inhaled and is abandoned supernatant.In precipitation, add 50 μ lDNA extracting solutions, latter 100 DEG C of vortex vibration mixing keeps 10 minutes, and 13,000rpm gets supernatant in centrifugal 2 minutes and carries out fluorescent PCR augmentation detection.Test kit is negative identical with sample liquid with positive control treatment process.
(2) augmentation detection
According to detected sample number n+2 (n=20), get test kit PCR damping fluid 21 μ l × (n+2), fluorescent probe 3 μ l × (n+2), Taq enzyme 2 μ l × (n+2) component, each amplification pipe packing 26 μ l after mixing, adds respectively according to the test kit negative control of sample processing method process, positive control and each 4 μ l of the above-mentioned n handled well a sample form.Each reaction tubes volume is 30 μ l, is put into by above-mentioned amplification pipe on ABI7500 fluorescent PCR instrument and runs according to the circulate program of 40 times of 94 DEG C of 10sec after 50 DEG C of 2min, 94 DEG C of 2min, 60 DEG C of 45sec.
(3) result judges
Use after fluorescent PCR instrument end of run and carry software analysis result, test kit negative control should be judged as feminine gender without Ct value, positive control Ct value < 30 is judged as the positive.Sample amplification Ct value < is NDM-1 gene masculine, containing NDM-1 gene pathogenic bacteria of drug-resistant in sample; Sample amplification is that NDM-1 gene resistant organism is negative without Ct value person; If 38 < Ct value < 40, be judged as detecting gray area, need duplicate detection 2 times, as detected result at least 1 Ct value < 40 judges that this pipe is NDM-1 gene masculine, otherwise, judge that this pipe is as negative.
According to the above results determination methods, have 1 example to detect Ct value < 38, be judged as that NDM-1 gene pathogenic bacteria of drug-resistant is positive in the 20 routine samples that experiment detects, all the other 19 examples are that NDM-1 gene pathogenic bacteria of drug-resistant is negative.