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LUMINEX-MPMA和NGS技術(shù)在中樞神經(jīng)系統(tǒng)感染性疾病診斷中的應(yīng)用研究

發(fā)布時(shí)間:2019-06-12 20:37
【摘要】:中樞神經(jīng)系統(tǒng)感染性疾病具有進(jìn)展迅速,致死致殘率高等特征。導(dǎo)致中樞神經(jīng)系統(tǒng)感染的病原體種類達(dá)100多種,包括病毒,細(xì)菌,真菌,寄生蟲等。但目前的病原體檢測方法(如鏡檢、培養(yǎng)、ELISA檢測、生化、PCR檢測等)陽性率低、診斷周期長,且無法達(dá)到高通量檢測病原體的要求。由于缺乏高通量、陽性率高的診斷方法,60%-85%的患者無明確病原學(xué)診斷[1],患者被給予經(jīng)驗(yàn)型治療,不僅導(dǎo)致了抗生素的濫用及微生物的耐藥,并且給患者帶來了沉重的經(jīng)濟(jì)負(fù)擔(dān)。因此,為有效降低該類疾病的不良影響,在臨床上對(duì)導(dǎo)致疾病的病原體進(jìn)行高特異性、高通量、快速的檢測的方法是迫切需要的。本研究利用Luminex TM-200和NGS技術(shù),以疑診病毒性腦(膜)炎患者腦脊液為標(biāo)本,建立能同時(shí)篩查18種病原體的Luminex TM-200平臺(tái)及探索性研究二代測序分析技術(shù)能否應(yīng)用于腦脊液標(biāo)本檢測并發(fā)現(xiàn)未知病原體。第一部分 基于LuminexTM-200平臺(tái)高通量檢測18種病原體方法的建立目的:通過LuminexTM-200平臺(tái)建立一種通量高、特異性強(qiáng)的可同時(shí)檢測18種中樞神經(jīng)系統(tǒng)常見病原體的核酸檢測平臺(tái)。方法:建立基于Luminex TM-200為平臺(tái)的MPMA-PCR體系,該體系應(yīng)用Luminex磁珠微陣列標(biāo)記,多重PCR及溫度轉(zhuǎn)移擴(kuò)增等三種策略,可同時(shí)擴(kuò)增18種病原體(hsv-1,hsv-2,vzv,cmv,eb,mev,muv,jcv,jev,echo,ev71,ca16,hev,c.neoforman,m.tuberculosis,s.pneumonia,t.gondii,a.cantonensis)。首先,針對(duì)18種病原體的特異性基因序列構(gòu)建質(zhì)粒并作為標(biāo)準(zhǔn)品,對(duì)標(biāo)準(zhǔn)品檢測的基礎(chǔ)之上建立mpma-pcr體系并以pcr產(chǎn)物測序結(jié)果作為金標(biāo)準(zhǔn),驗(yàn)證mpma-pcr體系的特異性。通過檢測倍比稀釋的標(biāo)準(zhǔn)品檢測mpma-pcr體系95%最低檢出濃度。其次,收集177例腦脊液樣本(包括138例疑診病毒性腦(膜)炎腦脊液樣本,19例經(jīng)商業(yè)化試劑盒檢測的腦脊液樣本,20例非腦(膜)炎腦脊液樣本),使用mpma-pcr體系進(jìn)行檢測,并以測序結(jié)果評(píng)價(jià)該體系檢測臨床樣本的可行性、特異性及靈敏度。結(jié)果:(1)mpma-pcr體系的建立:通過標(biāo)準(zhǔn)品質(zhì)粒的檢測,確認(rèn)mpma-pcr體系可針對(duì)18種病原體特異性基因同時(shí)檢測。mpma-pcr體系檢測結(jié)果與測序驗(yàn)證實(shí)驗(yàn)結(jié)果一致,特異性為100%。應(yīng)用probit模型分析mpma-pcr各引物的95%最低檢出限hsv-2、vzv、eb和muv的引物的95%最低檢出限為103copy/reaction。其余14對(duì)引物95%最低檢出限均高于100copy/reaction。(2)臨床樣本的檢測:應(yīng)用mpma-pcr體系檢測177例腦脊液樣本病原核酸陽性率23.16%(41/177):hsv-1病毒檢出率為7.9%(14/177);hsv-2病毒檢出率6.21%(11/177);eb病毒和?刹《緳z出率為2.25%(4/177);巨細(xì)胞病毒和帶狀皰疹病毒各2例;腮腺炎病毒、ca16、ev71和ev68各1例。陰性對(duì)照樣本,未檢測到病原體。mpma-pcr體系檢測結(jié)果與測序驗(yàn)證結(jié)果達(dá)到95.48%的一致性。結(jié)論:建立一種基于luminextm-200平臺(tái)高通量、高特異性的mpma-pcr體系,該體系可同時(shí)檢測18種中樞神經(jīng)系統(tǒng)感染病原體。mpma-pcr體系檢測標(biāo)準(zhǔn)品檢測結(jié)果與測序驗(yàn)證達(dá)到100%的符合率。通過對(duì)臨床疑診病毒性腦(膜)炎患者腦脊液標(biāo)本檢測,mpma-pcr體系病原體檢出率可達(dá)23.16%,特異性達(dá)到100%。針對(duì)檢出率較低,我們主要考慮兩方面原因,第一,導(dǎo)致出現(xiàn)類似病毒性腦膜炎癥狀的原因可能超出mpma-pcr體系目標(biāo)檢測范圍。第二,疑似腦(膜)炎的病例,可能由于致病病原體數(shù)量少,才導(dǎo)致癥狀不典型,且核酸含量低于mpma-pcr檢測的最低檢測濃度。綜合以上原因,mpma-pcr體系,靈敏度并不太理想。但是結(jié)合金標(biāo)準(zhǔn)比對(duì)結(jié)果顯示,該體系具有較高的特異性。第二部分 NGS技術(shù)在中樞神經(jīng)系統(tǒng)感染未知病原體檢測的探索性研究目的:實(shí)驗(yàn)第一部分結(jié)果顯示,MPMA-PCR體系具有較高的特異性,但是靈敏度缺乏。仍有部分腦脊液樣本病原體信息不能明確,為進(jìn)一步明確這些樣本的病原體信息,我們探索性應(yīng)用靈敏度更高的二代測序平臺(tái)(NGS),以期發(fā)現(xiàn)其它可能導(dǎo)致中樞神經(jīng)系統(tǒng)感染的病原體。方法:收集經(jīng)第一部分實(shí)驗(yàn)仍無明確病原體信息的腦脊液樣本21例(為未知病源組)和12例明確診斷為隱球菌腦膜炎患者腦脊液樣本(為隱球菌組)作為陽性對(duì)照,利用NGS技術(shù)對(duì)33例未知病原體樣本檢測進(jìn)行探索性研究;NGS陽性結(jié)果利用qPCR方法進(jìn)行驗(yàn)證。結(jié)果:12例隱球菌腦膜炎樣本經(jīng)NGS檢測,83.33%(10/12)樣本中存在隱球菌序列。經(jīng)qPCR平行驗(yàn)證陽性率為33.33%(4/12);21例未知病原體樣本中,28.57%(5/21)高度可能病原菌包括:克雷伯桿菌1例,肺炎鏈球菌1例,無乳鏈球菌1例,結(jié)核桿菌1例,假單胞菌1例;14.28%(3/21)的樣本經(jīng)qPCR確認(rèn)樣本(包括1例克雷伯桿菌,1例肺炎鏈球菌,1例無乳鏈球菌)。NGS在本次腦脊液樣本建庫成功率僅為72%(24/33)。結(jié)論:針對(duì)隱球菌陽性對(duì)照樣本檢測,83.33%的樣本中存在隱球菌序列,但qPCR驗(yàn)證檢測僅33.33%的樣本檢出隱球菌。這一結(jié)果表明根據(jù)隱球菌組二代測序技術(shù)的靈敏度高于qPCR。根據(jù)陽性對(duì)照樣本的NGS檢測結(jié)果表明,NGS技術(shù)針對(duì)腦脊液中病原體核酸檢測具有可行性,且高靈敏度。經(jīng)NGS技術(shù)檢測未知病原體組,28.57%的樣本可檢測到高度懷疑的病原體序列。經(jīng)qPCR驗(yàn)證得到陽性率為14.28%。21例未知病原體樣本中檢測到其他病原體核酸,表明了NGS技術(shù)對(duì)MPMA-PCR體系靈敏度的補(bǔ)充。但是目前72%的建庫成功率相對(duì)較低,建庫的成功了將直接影響NGS技術(shù)的靈敏度。但是目前NGS平臺(tái)針對(duì)腦脊液標(biāo)本檢測并沒有成熟的文庫建立方法,所以如何解決病原體核酸載量低的問題尚需更多實(shí)驗(yàn)研究和探索。
[Abstract]:The infectious diseases of the central nervous system have the characteristics of rapid progress, high death rate and the like. The types of pathogens that lead to the infection of the central nervous system are more than 100, including viruses, bacteria, fungi, parasites, and the like. But the current pathogen detection method (such as microscopic examination, culture, ELISA detection, biochemistry, PCR detection, etc.) has the advantages of low positive rate, long diagnosis period and no requirement of high-flux detection of the pathogen. Due to the lack of high flux and high positive rate of the diagnosis,60% to 85% of the patients have no clear etiological diagnosis[1], and the patient is treated with an empirical type, which not only leads to the abuse of the antibiotics and the drug resistance of the microorganisms, but also brings a heavy economic burden to the patients. Therefore, in order to effectively reduce the adverse effect of the disease, the method of high specificity, high-throughput and rapid detection of the pathogen causing the disease is urgently needed. Luminex (TM-200) and NGS (NGS) technology were used in this study to establish a Luminex TM-200 platform and an exploratory study on the screening of 18 pathogens. The first part is based on the aim of high-throughput detection of 18 pathogen methods based on the Luminex TM-200 platform: a nucleic acid detection platform with high flux and strong specificity can be established through the Luminox TM-200 platform, and the common pathogens of the 18 central nervous systems can be detected at the same time. Methods: An MPMA-PCR system based on Luminex TM-200 as a platform was established. The system applied the three strategies of Luminex magnetic bead microarray labeling, multiplex PCR and temperature transfer amplification, and can simultaneously amplify 18 pathogens (hsv-1, hsv-2, vzv, cmv, eb, mev, muv, jcv, jv, echo, ev71, ca16, hev, c. neoforman, m. tubulosis, s. pneumonia, T. gondii, a. canonensis). First, a plasmid was constructed for the specific gene sequence of 18 pathogens and used as the standard, and the mpma-pcr system was established on the basis of the standard product detection and the result of the sequencing of the pcr product was used as the gold standard to verify the specificity of the mpma-pcr system. The minimum detectable concentration of the mpma-pcr system was detected by the test of the standard product diluted in comparison to the dilution. Then,177 cerebrospinal fluid samples (including 138 cerebrospinal fluid samples of suspected viral encephalitis (membrane),19 cerebrospinal fluid samples detected by the commercial kit and 20 non-brain (membrane) inflammatory cerebrospinal fluid samples) were collected and tested using the mpma-pcr system. The feasibility, specificity and sensitivity of the system were evaluated by sequencing. Results: (1) The establishment of the mpma-pcr system: the detection of the standard quality particles confirmed that the mpma-pcr system can be used for simultaneous detection of 18 pathogen-specific genes. The results of the mpma-pcr system were consistent with the results of the sequencing validation, and the specificity was 100%. The detection limit of the detection limit of 95% of the primers of the mma-pcr primers was analyzed by using the probit model, and the detection limit of the 95% of the primers for the vzv, b and muv was 103 copy/ action. The minimum detection limit of the remaining 14 pairs of primers was higher than 100 copy/ reaction. (2) The detection of clinical samples: The positive rate of pathogenic nucleic acid in 177 patients with cerebrospinal fluid sample was 23.16% (41/177) by using the mpma-pcr system. The detection rate of hsov-1 virus was 7.9% (14/177), the detection rate of hsov-2 virus was 6.21% (11/177), the detection rate of eb virus and Esmovirus was 2.25% (4/177),2 cases of cytomegalovirus and herpes zoster virus, and ca16, 1 case of ev71 and ev68. Negative control sample, no pathogen detected. The results of the detection of the mpma-pcr system and the results of the sequencing verification reached 95.48%. Conclusion: A high-flux and high-specificity mpma-pcr system based on luminextm-200 is established, which can detect the pathogens of 18 central nervous systems at the same time. The results of the detection of the mma-pcr system and the sequencing verification reached 100%. By means of the detection of cerebrospinal fluid in the patients with viral encephalitis (membrane), the detection rate of the mma-pcr system can reach 23.16%, and the specificity can reach 100%. In view of the low detection rate, we mainly consider two reasons, first, the cause of similar viral meningitis symptoms may exceed the target detection range of the mpma-pcr system. Second, cases of suspected brain (membrane) inflammation may cause the symptoms to be not typical due to the small number of pathogenic agents, and the nucleic acid content is lower than the lowest detection concentration detected by the mpma-pcr. For the above reasons, the mpma-pcr system is not ideal for sensitivity. However, the results show that the system has a higher specificity than the gold standard. The first part of the experiment shows that the MPMA-PCR system has a high specificity, but the sensitivity is lacking. There are still some of the cerebrospinal fluid sample pathogen information that is not clear, and in order to further clarify the pathogen information for these samples, we have an exploratory application of the second-generation sequencing platform (NGS) with a higher sensitivity, with a view to finding other pathogens that may lead to the central nervous system infection. Methods: The cerebrospinal fluid samples (for unknown source group) and 12 cases of the cerebrospinal fluid sample of cryptococcal meningitis were collected as positive control by the first part of the experiment. An exploratory study of 33 unknown pathogen samples was performed using NGS technique, and the NGS positive results were verified by qPCR. Results:12 cases of cryptococcal meningitis were detected by NGS and the sequence of cryptococcus was found in 83.33% (10/12) samples. The positive rate of qPCR was 33.33% (4/12); in 21 unknown pathogen samples, 28.57% (5/21) of the highly probable pathogenic bacteria included:1 of Klebsiella,1 in Streptococcus pneumoniae,1 in non-dairy streptococcus,1 in Mycobacterium tuberculosis and 1 in Pseudomonas; A sample of 14.28% (3/21) was confirmed by qPCR (including 1 Klebsiella,1 Streptococcus pneumoniae,1 non-Streptococcus). The success rate of NGS in this CSF sample was only 72% (24/33). Conclusion: Cryptococcus neoformans were found in 83.33% of samples for cryptococcus positive control samples, but only 33.33% of the samples were detected by qPCR. The results showed that the sensitivity of the second generation sequencing technique was higher than that of qPCR. The results of NGS test according to the positive control sample show that the NGS technique is feasible and highly sensitive to the detection of the pathogen nucleic acid in the cerebrospinal fluid. The unknown pathogen group was detected by the NGS technique, and 28.57% of the samples were able to detect highly suspected pathogen sequences. The positive rate was 14.28% by qPCR, and the other pathogen nucleic acid was detected in 21 unknown pathogen samples, which indicated that the NGS technique was complementary to the sensitivity of the MPMA-PCR system. However, at present,72% of the construction success rate is relatively low, and the success of the building will directly affect the sensitivity of the NGS technology. However, at present, the NGS platform has no mature library establishment method for cerebrospinal fluid specimen detection, so it is necessary to study and explore the problem of how to solve the problem of low pathogen nucleic acid load.
【學(xué)位授予單位】:第四軍醫(yī)大學(xué)
【學(xué)位級(jí)別】:博士
【學(xué)位授予年份】:2016
【分類號(hào)】:R741

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