CN106011154B - A kind of cause hepatapostema Klebsiella Pneumoniae molecular detection kit and its application - Google Patents

A kind of cause hepatapostema Klebsiella Pneumoniae molecular detection kit and its application Download PDF

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CN106011154B
CN106011154B CN201610669762.XA CN201610669762A CN106011154B CN 106011154 B CN106011154 B CN 106011154B CN 201610669762 A CN201610669762 A CN 201610669762A CN 106011154 B CN106011154 B CN 106011154B
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hepatapostema
klebsiella pneumoniae
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pago
luxr
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CN106011154A (en
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张彦亮
陶臻
黄岩
俞杨
黄金伟
江建平
叶美萍
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Nanjing First Hospital
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Abstract

The invention discloses a kind of cause hepatapostema Klebsiella Pneumoniae molecular detection kit and its applications, and the present invention provides cause hepatapostema Klebsiella Pneumoniae gene specific sequencepagOWithluxR, the two gene specifics be present in cause hepatapostema Klebsiella Pneumoniae in, can be used as the diagnostic marker of Klebsiella Pneumoniae hepatapostema.Primer based on the design of the two genes, which can be used for preparing, causes hepatapostema Klebsiella Pneumoniae molecular detection kit, can be used for the diagnosis or its early diagnosis of Klebsiella Pneumoniae hepatapostema, has great commercial development value.

Description

A kind of cause hepatapostema Klebsiella Pneumoniae molecular detection kit and its application
Technical field
The present invention relates to medical diagnosis on disease fields, and in particular to a kind of cause hepatapostema Klebsiella Pneumoniae molecular detection kit And its application.
Background technique
Klebsiella Pneumoniae (K.pneumoniae subsp.pneumonia), belongs to enterobacteriaceae lactobacteriaceae.Often parasitize Human skin, pharynx nasalis and enteron aisle etc. are conditioned pathogen.Clinically, pneumonia and urinary tract infections etc. can be caused (Podschun R,Ullmann U.Klebsiella spp.as nosocomial pathogens:epidemiology, taxonomy,typing methods,and pathogenicity factors.Clinical microbiology reviews.1998;11(4):589-603).1980 to nineteen ninety, Taiwan Liu et al. people reported 7 by high poison for the first time Serious hepatapostema is with entophthamia case (Liu Y, Cheng D, Lin C.Klebsiella caused by power Klebsiella Pneumoniae pneumoniae liver abscess associated with septic endophthalmitis.Arch Intern Med 1986;146:1913–16).Hereafter, Klebsiella Pneumoniae hepatapostema starts Global prevalence, especially in Asia.With it is common Klebsiella Pneumoniae compare, cause that hepatapostema Klebsiella Pneumoniae invasiveness is strong, lethality is high.In addition to leading to hepatapostema, liver is caused Abscess Klebsiella Pneumoniae can also cause serious meningitis, entophthamia and pulmonary abscess etc. (Siu LK, Yeh KM, Lin JC, Fung CP,Chang FY.Klebsiella pneumoniae liver abscess:a new invasive syndrome.The Lancet Infectious diseases.2012;12(11):881-7).For the lung of virulence high in this way Scorching Klebsiella infection, diagnoses as early as possible, treats in time, the generation to severe complication is reduced, and improving prognosis has important face Bed value.But it is used to cause the Testing and appraisal of hepatapostema Klebsiella Pneumoniae currently without a kind of fast and convenient method.
As what the increase and cause hepatapostema Klebsiella Pneumoniae of Klebsiella Pneumoniae hepatapostema Case report were studied gos deep into, Several phenotypes relevant to hepatapostema Klebsiella Pneumoniae is caused are put forward one after another, including bacterium colony high viscosity phenotype and capsular polysaccharide blood Clear type K1 type/K2 type etc..Klebsiella Pneumoniae can secrete polysaccharose substance in cell surface, so that bacterium colony be made to generate high viscosity table Type, to resist the phagocytosis of macrophage and neutrophil leucocyte.But recently the study found that only 50% less than cause hepatapostema lung Scorching klebsiella shows as bacterium colony high viscosity (Qu TT, Zhou JC, Jiang Y, Shi KR, Li B, Shen P, et al.Clinical and microbiological characteristics of Klebsiella pneumoniae liver abscess in East China.BMC infectious diseases.2015;15:161).Capsular polysaccharide serotypes Antigen K1 type and K2 type are the predominant serotypes for causing hepatapostema Klebsiella Pneumoniae, but still have 20% or more cause hepatapostema pneumonia Klebsiella is not belonging to K1/K2 serotype.In addition, serotype K1 type or K2 type are also found to be present in pneumonia klebsiella (Sun Y,Wu H,Shen D.Clinical and Molecular Analysis of Klebsiella pneumoniae Causing Liver Abscess in China.Journal of molecular microbiology and biotechnology.2016;26(4):245-51).Therefore, in order to which in molecular level, more rapidly effectively identification causes liver Abscess Klebsiella Pneumoniae, we pass through to the genome ratio for causing hepatapostema Klebsiella Pneumoniae and pneumonia klebsiella Compared with analysis, the specific gene sequences for causing hepatapostema Klebsiella Pneumoniae are found.Using these specific sequences, by simple PCR method, can rapidly identify cause hepatapostema Klebsiella Pneumoniae, be the infection as caused by the pathogen it is timely diagnosis with Treatment improves patient's prognosis offer basis.
Summary of the invention
The object of the present invention is to provide cause hepatapostema Klebsiella Pneumoniae gene specific sequence pagO, the base Because specific sequence pagO is shown in SEQ ID NO.1.
It is another object of the present invention to provide based on cause hepatapostema Klebsiella Pneumoniae gene specific sequence The primer of pagO design, primer are as follows: pagO_F:TGCTCTTGAAACTATCCCTCC, pagO_R:GGCAATAACTCCCGTCCA.
It is also an object of the present invention to provide cause hepatapostema Klebsiella Pneumoniae gene specific sequence luxR, institutes The gene specific sequence luxR stated is shown in SEQ ID NO.2.
It is also an object of the present invention to provide based on cause hepatapostema Klebsiella Pneumoniae gene specific sequence The primer of luxR design, primer are as follows: luxR_F:CTTTGCCGGCATGGAACATA, luxR_R: TGAGCCAAATGTATGCCAAGGA。
It is also an object of the present invention to provide cause hepatapostema Klebsiella Pneumoniae gene specific sequence pagO or Primer based on pagO design causes the application in hepatapostema Klebsiella Pneumoniae detection kit in preparation, including is used to prepare lung Application in scorching klebsiella hepatapostema early diagnosis kit.
It is also an object of the present invention to provide cause hepatapostema Klebsiella Pneumoniae gene specific sequence luxR or Primer based on luxR design causes the application in hepatapostema Klebsiella Pneumoniae detection kit in preparation, including is used to prepare lung Application in scorching klebsiella hepatapostema early diagnosis kit.
Final object of the present invention is the provision of a kind of cause hepatapostema Klebsiella Pneumoniae molecular detection kit, The kit includes primer:
PagO_F:TGCTCTTGAAACTATCCCTCC
PagO_R:GGCAATAACTCCCGTCCA
LuxR_F:CTTTGCCGGCATGGAACATA
LuxR_R:TGAGCCAAATGTATGCCAAGGA.
To achieve the goals above, the present invention uses following technical measures:
Causing hepatapostema Klebsiella Pneumoniae gene specific sequence pagO, the gene specific sequence pagO is SEQ Shown in ID NO.1.
Primer based on pagO sequence design is protection scope of the present invention, it is preferred that the primer of pagO are as follows: pagO_ F:TGCTCTTGAAACTATCCCTCC;PagO_R:GGCAATAACTCCCGTCCA.
Causing hepatapostema Klebsiella Pneumoniae gene specific sequence luxR, the gene specific sequence luxR is SEQ Shown in ID NO.2.
Primer based on luxR sequence design is protection scope of the present invention, it is preferred that the primer of luxR are as follows: luxR's Primer are as follows: luxR_F:CTTTGCCGGCATGGAACATA;LuxR_R:TGAGCCAAATGTATGCCAAGGA.
Protection scope of the present invention further includes causing hepatapostema Klebsiella Pneumoniae gene specific sequence pagO or being based on The primer of pagO design causes the application in hepatapostema Klebsiella Pneumoniae detection kit in preparation, including prepares kerekou pneumonia primary Bacterium hepatapostema early diagnosis kit.
Protection scope of the present invention further includes causing hepatapostema Klebsiella Pneumoniae gene specific sequence luxR or being based on The primer of luxR design causes the application in hepatapostema Klebsiella Pneumoniae detection kit in preparation, including prepares kerekou pneumonia primary Bacterium hepatapostema early diagnosis kit.
A kind of cause hepatapostema Klebsiella Pneumoniae detection kit, comprising:
PagO_F:TGCTCTTGAAACTATCCCTCC
PagO_R:GGCAATAACTCCCGTCCA
LuxR_F:CTTTGCCGGCATGGAACATA
LuxR_R:TGAGCCAAATGTATGCCAAGGA.
Compared with prior art, the invention has the characteristics that:
1. there is no the molecular marker well for causing hepatapostema Klebsiella Pneumoniae to identify at present, the present invention passes through survey 2 plants of the sequence cause hepatapostema Klebsiella Pneumoniaes for being isolated from China's Mainland and 1 plant of non-cause hepatapostema Klebsiella Pneumoniae, joint are online 45 plants announced cause hepatapostema Klebsiella Pneumoniae and 103 plants of non-full-length genome data for causing hepatapostema Klebsiella Pneumoniae, lead to Comparison analysis is crossed, two sections of sequences for the high special in causing hepatapostema Klebsiella Pneumoniae have been obtained.
2. the 2 sections provided by the invention sequences for causing hepatapostema Klebsiella Pneumoniae special can be used as preparation and cause hepatapostema Klebsiella Pneumoniae detection kit
3. the 2 sections provided by the invention sequences for causing hepatapostema Klebsiella Pneumoniae special, can be used as molecular marker, use In the early diagnosis of Klebsiella Pneumoniae hepatapostema.Especially in the Bacteria culturing result of other body fluid source samples such as blood Before reporting out, using blood samples of patients sample or liver vomica fester, is detected using quick PCR method and cause hepatapostema kerekou pneumonia The presence or absence of primary bacterium specific gene pagO or/and luxR can be quickly to pneumonia in conjunction with patients with clinical manifestations and imaging data Klebsiella hepatapostema makes diagnosis, improves the success rate of Klebsiella Pneumoniae hepatapostema.
Specific embodiment
The invention will be further described for specific embodiment.Technical solution of the present invention is if not otherwise specified this The conventional scheme in field.
Embodiment 1:
The exploitation and verifying of specific sequence:
The screening process combination second generation sequencing technologies (Next-Generation of specific gene sequences Sequencing, NGS), comparative genomics (Comparative Genomics) and bioinformatics (Bioinformatics) method, and using the statistical method of science, to sequence in multiple Klebsiella Pneumoniae genomes The specificity of distribution is tested, and in isolated cause hepatapostema Klebsiella Pneumoniae and non-cause hepatapostema Klebsiella Pneumoniae Middle progress PCR verifying, to determine that sequence is causing the specificity in hepatapostema Klebsiella Pneumoniae.Specific implementation process is as follows:
Choose 2 plants of cause hepatapostema Klebsiella Pneumoniaes for being isolated from China's Mainland and 1 plant of non-cause hepatapostema kerekou pneumonia primary Bacterium is used for genome sequencing, and sequencing result spliced with SPAdes (v3.5) software, with PATRIC on-line analysis platform into Row predictive genes and functional annotation.Obtained sequencing result joint US National Bioinformatics Institute (National Center For Bi otechnology Information, NCBI) announce 45 plants of cause hepatapostema Klebsiella Pneumoniaes and 103 plants of non-causes The full-length genome data of hepatapostema Klebsiella Pneumoniae are analyzed by comparing, and screening, which exists only in, causes hepatapostema kerekou pneumonia primary Gene in bacterium genome has obtained sequence pagO (the SEQ ID of two sections of high specials in causing hepatapostema Klebsiella Pneumoniae Shown in NO.1) and luxR (shown in SEQ ID NO.2) based on this two sections of special primers, exploitation obtains a set of be used for Identification causes the primer of hepatapostema Klebsiella Pneumoniae:
The primer of pagO are as follows:
PagO_F:TGCTCTTGAAACTATCCCTCC
PagO_R:GGCAATAACTCCCGTCCA
The primer of luxR are as follows:
LuxR_F:CTTTGCCGGCATGGAACATA
LuxR_R:TGAGCCAAATGTATGCCAAGGA.
Embodiment 2:
Gene specific verifying:
PagO and luxR causes verifying of the hepatapostema Klebsiella Pneumoniae specific gene in Clinical isolation, specific Step is:
1. the cause hepatapostema being clinically separated and non-cause hepatapostema Klebsiella Pneumoniae bacterial strain are selected, for detecting pagO (SEQ ID N O.1 shown in) and luxR (shown in SEQ ID NO.2) cause hepatapostema Klebsiella Pneumoniae in specificity.Select liver purulence The 40 plants of Klebsiella Pneumoniaes separated in swollen patient's vomica are as detection group (causing hepatapostema group), alternative negated Klebsiella Pneumoniae 36 plants of the Klebsiella Pneumoniae separated in hepatapostema patient are used as negative control group (non-cause hepatapostema group).It also has chosen and faces simultaneously Other the common pathogenic bacteria (other pathogenic bacteria groups) separated on bed are causing hepatapostema kerekou pneumonia further to verify these factors Specificity in primary bacterium: including staphylococcus aureus, escherichia coli, Acinetobacter bauamnnii, enterococcus faecium, enterococcus faecalis.
2. the design of 2 predicted gene specific primers: for pagO and luxR specific sequence design primer such as Under:
The primer of pagO are as follows:
PagO_F:TGCTCTTGAAACTATCCCTCC
PagO_R:GGCAATAACTCCCGTCCA
The primer of luxR are as follows:
LuxR_F:CTTTGCCGGCATGGAACATA
LuxR_R:TGAGCCAAATGTATGCCAAGGA
3. the extraction of bacterial genomes: 76 plants of Klebsiella Pneumoniaes of selection are extracted DNA in a conventional manner.
4.PCR detects pagO and luxR gene and (causes hepatapostema group, non-cause hepatapostema group and other pathogenic bacteria in three groups of bacterium Group) in there are situations: PCR reaction use Premix TaqVersion 2.0 (TaKaRa, Code:D331A) kit.Root Illustrate according to kit, the PCR reaction system of setting is 25ul, wherein Premix Taq 12.5ul, genomic DNA template 1ul (about 100ng), upstream and downstream primer 0.5ul (10uM), adds deionized water 10.5ul to be supplemented to total volume 25ul.
PCR condition are as follows: 94 DEG C of denaturation 5min;95 DEG C of 30s, 55 DEG C of 30s, 72 DEG C of 30s, 30 circulations;72℃7min;Reaction After respectively take 5ul reaction product for DNA agarose gel electrophoresis, running gel ethidium bromide (Ethi dium Bromid after) dyeing 5min, the photographic analysis on U.S. Bole (Bio-Rad) gel image analyser.
It the results are shown in Table 1, as shown in table 1, pagO and luxR are causing the detection positive rate in hepatapostema Klebsiella Pneumoniae point Not Wei 100%, and it is non-cause hepatapostema Klebsiella Pneumoniae in be all 2.78%.In other pathogenic bacteria groups, including it is golden yellow Color staphylococcus, escherichia coli, Acinetobacter bauamnnii, enterococcus faecium, enterococcus faecalis are feminine gender.
Result above it can be proved that pagO or luxR cause hepatapostema Klebsiella Pneumoniae in have very high specificity, Respectively or the molecular marked compound of diagnosis of pneumonia klebsiella hepatapostema can be combined as.
The result of PCR detection of table 1 pagO and luxR in clinical strains
Embodiment 3:
PagO and luxR sequence is preparing Klebsiella Pneumoniae hepatapostema diagnostic reagent based on the primer of its sequence design Application in box:
This experimental design thinking is as follows: the blood culture sample that clinic obtains being divided into blood culture with positive bacteria group and Healthy People is negative Group, wherein blood culture with positive bacteria group refers to the sample that bacterium is turned out in all blood, is not limited solely to turn out kerekou pneumonia in blood Primary bacterium, the sample including turning out other pathogenic bacteria.It is detected with PCR special in positive blood culture sample and negative blood culture sample Sex factor (i.e. pagO and luxR) there are situations, finally PCR result and the final clinical diagnosis correspondence analysis of patient, come with this Judge method provided by the invention to the recall rate of Klebsiella Pneumoniae hepatapostema.
1. the collection of clinical blood culture sample: collecting 2 groups of blood culture samples, 69 bottles of blood culture with positive bacteria group, Healthy People blood altogether Negative 40 bottles of the group of culture.
2.PCR detect pagO and luxR in blood culture sample there are situations:
The preparation of 2.1 templates: aseptically, the blood in 3ml culture bottle is extracted, 8000rpm is centrifuged 2min.It abandons Supernatant is removed, precipitating is mixed into suspension with the piping and druming of 200ul distilled water.Suspension boils 10min at 100 DEG C, then uses 13000rpm, from Heart 5min, the template that supernatant is detected as PCR.
2.2PCR detect pagO and luxR gene order marker and combinations thereof in two groups of blood culture samples there are feelings Condition: PCR reaction uses Premix TaqVersion2.0 (TaKaRa, Code:D331A) kit.Illustrated according to kit, if The PCR reaction system set is 25ul, wherein Premix Taq 12.5ul, genomic DNA template 2ul, upstream and downstream primer 0.5ul (10uM) adds deionized water 10.5ul to be supplemented to total volume 25ul.PCR reaction condition are as follows: 94 DEG C of denaturation 5min;95 DEG C of 30s, 55 DEG C 30s, 72 DEG C of 30s, 30 circulations;72℃7min;Ago-Gel of the 5ul reaction product for DNA is respectively taken after reaction Electrophoresis, after running gel dyes 5min with ethidium bromide (Ethidium bromid), Bole (Bio-Rad) gel imaging in the U.S. Photographic analysis on analyzer.
The primer of pagO are as follows:
PagO_F:TGCTCTTGAAACTATCCCTCC
PagO_R:GGCAATAACTCCCGTCCA
The primer of luxR are as follows:
LuxR_F:CTTTGCCGGCATGGAACATA
LuxR_R:TGAGCCAAATGTATGCCAAGGA
PCR testing result and final patient's confirmed result are shown in Table 2 in blood culture with positive bacteria group.In regulation, pagO and luxR only It is the positive that want an amplification, which be positive i.e. sample,.Healthy People blood culture feminine gender group is expanded without any band, is feminine gender, Therefore result is not shown in table 2 and table 3." confirmed result " column "+" indicates that the last diagnostic of patient is kerekou pneumonia primary in table 2 Bacterium hepatapostema, "-" indicate that patient excludes the diagnosis of Klebsiella Pneumoniae hepatapostema, are other diseases.Atopen column (i.e. " pa GO ", " luxR ", " pagO+luxR ") in "+" indicate that >=1 marker amplification is the positive, "-" indicates the factor detected It is complete negative.
The final confirmed result of 2 blood culture with positive bacteria group patient of table and PCR amplification result
Wherein in table 2, atopen PCR result in the blood culture sample of No. 10 cases is all positive, but at the beginning No. 10 cases clinically and have not been diagnosed as Klebsiella Pneumoniae hepatapostema, and applicant suspects that false positive occurs in the factor;But two Zhou Hou, with disease progression, Finding case hepatapostema is diagnosed as Klebsiella Pneumoniae hepatapostema, thus eliminate it is specific because Sub- false positive results;This case also illustrates that atopen has the function of early diagnosing Klebsiella Pneumoniae hepatapostema.
The positive rate and false positive rate of each marker in 3 blood culture with positive bacteria group of table
PagO PCR positive rate in the blood culture sample of Klebsiella Pneumoniae hepatapostema patient is 97.37%, in non-pneumonia Positive rate in klebsiella hepatapostema patient's blood culture sample is only 0%, is 0% in the positive rate of blood culture feminine gender group; LuxR PCR positive rate in the blood culture sample of Klebsiella Pneumoniae hepatapostema patient is 92.11%, in non-Klebsiella Pneumoniae Positive rate in hepatapostema patient's blood culture sample is 0%, is 0% in the positive rate of blood culture feminine gender group;PagO+luxR is in lung PCR positive rate is 97.37% in the blood culture sample of scorching klebsiella hepatapostema patient, in non-Klebsiella Pneumoniae hepatapostema Positive rate in patient's blood culture sample is only 0%, is 0% in the positive rate of blood culture feminine gender group.These results suggest that pagO With luxR there is very high specificity in Klebsiella Pneumoniae hepatapostema patient's blood culture with positive bacteria sample, can distinguish or combines Molecular marker as Klebsiella Pneumoniae hepatapostema quick diagnosis.
SEQUENCE LISTING
<110>Nanjing No.1 Hospital
<120>a kind of cause hepatapostema Klebsiella Pneumoniae molecular detection kit and its application
<130>a kind of cause hepatapostema Klebsiella Pneumoniae molecular detection kit and its application
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<170> PatentIn version 3.1
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atgcgtagaa ttactatatt tatattattc ctgttagttg ctgtaacttg gggaaccacg 60
tggttagcta tgaagattgc tcttgaaact atccctccag tctttgctac cgggatgaga 120
tttttatttt ccgctccatt attaatcatt atcgcatggg taaaaaaaat accaatttta 180
tttcctgttg gccagcgtct atttcaactt gcaattagta tgttttattt tgccattcct 240
ttctctctaa tgatttatgg tgaggtttat gtaaacccag gacttgccgc tattatattt 300
gcaaatatgc cggtggctat tttaatagca tcatttttat ttttgaatga aaaaacaaac 360
tcaatacaga ttactggact aattatcgca ttagcttcac tttcgttcat cctcatcacg 420
gaggcgcggg aaaggacaga aagccagtgg acgggagtta ttgccctttc ttctgcagta 480
ataattcatg ccatagtata tactcaatgt aaaaaaagat gctgtaaagt ctctgttata 540
tcgtttaatg cgttaccgtg ttttatagct ggggttattc tttcgctggt ggggagtatc 600
tttgagaggc cacaattatc agctttatct ttacactcta cattagcaac aatgtattta 660
ggctgttttg ctggagtttt tgggatactg tgctattttt ctctgcagaa aagggctagc 720
gctttccagg cttcgctcgt atttctcatc ttccctctaa ttgcagtaag cttggaaagt 780
tatatatatg ggaaaaccat atcaacatac tcaatcttac tgattatccc cctcgtcatt 840
ggaatactta tcacacttat ccccaaaaaa actgtcgttg ataaaaacaa aatgaatagc 900
tga 903
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atgaaattgt gtgtcgttac aaataataat tatttctttg ccggcatgga acatattttc 60
tcagaggttc aatgctgtct ttgtagaata tcgagttatg atgtatatgc atgcactcct 120
aattcaaacg taatcatttt attggatggt gtgaatcaca aagtttcgat aaaagagtat 180
agctatctaa aaaaaatagg tttacctgtt ttttttattc tgaacacaaa ctgtaatgtt 240
aattccaccc tcatcggaat taacatcatt aacgcacgcg aggctatcac tattttaaaa 300
gatagaatga tttctctctt taatgggggg gggcagcttg attataaacc aataaatttg 360
acaaagaagg agtcttttat tcttagatta tatatagatg gattatcatt aacacagata 420
agtgaaaaaa cagccattag aaaaaaaaca cttataactc acacacgaaa tattcttaat 480
aagaccggtg taaaacacca taatcacctt aatattttaa aaaacatcct tggcatacat 540
ttggctcatt aa 552
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tgctcttgaa actatccctc c 21
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ggcaataact cccgtcca 18
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ctttgccggc atggaacata 20
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tgagccaaat gtatgccaag ga 22

Claims (3)

  1. Nucleotide sequence shown in 1.SEQ ID NO.1 or drawing for the design of nucleotide sequence shown in SEQ ID NO.1 Object causes the application in hepatapostema Klebsiella Pneumoniae detection kit in preparation.
  2. 2. application according to claim 1, it is characterised in that: the primer are as follows: pagO_F: TGCTCTTGAAACTATCCCTCC, pagO_R:GGCAATAACTCCCGTCCA.
  3. 3. a kind of cause hepatapostema Klebsiella Pneumoniae molecular detection kit, comprising:
    PagO_F:TGCTCTTGAAACTATCCCTCC
    PagO_R:GGCAATAACTCCCGTCCA
    LuxR_F:CTTTGCCGGCATGGAACATA
    LuxR_R:TGAGCCAAATGTATGCCAAGGA.
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