应用单一和双重荧光定量PCR法快速检测军团菌

目的 建立单一和双重荧光定量PCR方法分别和同时进行军团菌属及嗜肺军团菌的检测.方法 利用军团菌属16 S rRNA基因和嗜肺军团菌mip基因设计引物和探针,两条基因探针分别标记FAM和HEX,并将相关反应体系和条件进行优化.分别应用单一基因探针(单一荧光定量PCR)和双重基因探针(双重荧光定量PCR)对嗜肺军团菌、非嗜肺军团菌及非军团菌进行检测,并验证两种方法的特异度、敏感度.应用双重荧光定量PCR检测空调水样滤膜样品和DNA提取样品,比较两者结果的一致性.结果 针对军团菌属及嗜肺军团菌,应用荧光定量PCR,16 S rRNA基因和mip基因均能较好的检出,16S rRNA和mip的最低检出限分别为8和10个拷贝.经优化得到了最佳反应体系.单一荧光定量PCR方法所检的8株嗜肺军用菌及4株非嗜肺军团菌16 S rRNA基因均为阳性,嗜肺军团菌mip基因阳性,非嗜肺军团菌mip基因阴性.双重荧光定量PCR方法所检的23株嗜肺军团菌中有2株为假阴性,9株非嗜肺军团菌和非军团菌属中有1株为假阳性.49份空调水样滤膜直接检测和提取DNA后检测的结果一致,其中26份水样军团菌阳性,20份为嗜肺军团菌,6份为非嗜肺军团菌;1份弗朗西斯菌检测HEX阳性(假阳性),占实际培养分离的1/26.结论 单一及双重荧光定量PCR法特异、快速、敏感,一次同时检测嗜肺与非嗜肺军团菌,满足对空调和环境水样军团菌监测的要求.     

实时荧光PCR快速检测嗜肺军团菌的研究

目的 建立TaqMan-MGB探针实时荧光PCR快速检测嗜肺军团菌技术,为临床和环境样品检测嗜肺军团菌提供可实用工具.方法 在对嗜肺军团菌mip序列进行分析、比较基础上,设计一对特异性引物和TaqMan-MGB探针,通过实时荧光PCR反应条件和反应体系的优化,实现对嗜肺军团菌的快速检测;用克隆到pMD-19T载体上的嗜肺军团菌mip基因阳参片段和不同菌株验证方法的敏感性和特异性.结果 当用热裂解法提取DNA,25μl的反应体系中包括上、下游引物(20μmol/L)各0.6μl,探针(20μmol/L)0.4μl,模板DNA 6.0μl,反应条件为预变95℃20 S,变性95℃10 s,退火50℃ 40 s,40个循环时,TaqMan-MGB探针实时荧光PCR技术对嗜肺军团菌mip基因阳参片段最低检测浓度为0.71拷贝/μl,其循环阈值(Ct值)与模板浓度具有极好的对应关系(r=0.999);1株嗜肺军团菌标准株、12株嗜肺军团菌分离株的Ct值在13.23～16.04之间,而包括金黄葡萄球菌、鼠伤寒沙门菌、副溶血性弧菌、大肠埃希菌、铜绿假单胞菌、痢疾志贺菌共计76株其他菌PCR Ct值均大于30;整个检测过程仅需1.5 h.结论 TaqMan-MGB探针的嗜肺军团菌实时荧光PCR检测方法具有特异性和敏感性、易操作、结果准确可靠等优点,可用于嗜肺军团菌检测.     

肝螺杆菌TaqMan MGB探针实时荧光定量PCR快速检测方法的建立及应用研究

目的 建立特异、敏感、快速检测肝螺杆菌的TaqMan MGB探针实时荧光定量PCR方法.方法 针对肝螺杆菌flaB 基因的保守区设计特异性引物和探针,建立肝螺杆菌TaqMan MGB探针实时荧光定最PCR方检测方法,验证方法的特异性、敏感性和稳定性.对2008-2011年期间采集的1081份临床样本中的肝螺杆菌进行检测,同时进行分离培养和常规PCR检测.结果 建立的TaqMan MGB探针实时荧光定量PCR方法对肝螺杆菌的检测具有高度的特异性,对幽门螺杆菌、空肠弯曲菌、泰泽氏菌、侵肺巴斯德氏菌、大肠埃希菌、铜绿假单胞菌均无交叉反应,检测的灵敏度达8.3拷贝.标准曲线显示各浓度范围内具有良好的线性关系,相关系数为0.999,斜率为-3.227,TaqManMGB探针实时荧光定量PCR效率为100％.对1081份临床样本进行检测,TaqMan MGB探针实时荧光定量PCR和常规PCR均能检出86份肝螺杆菌阳性样本,而细菌分离培养则仅检出4份阳性.结果显示,建立的TaqMan MGB探针实时荧光定量PCR方法比细菌分离培养方法更敏感,能够直接从临床样本中检出肝螺杆菌DNA,检测时间仅为2h.结论 研究建立的TaqMan MGB探针实时荧光定量PCR方法具有可靠、特异、敏感的特点,适用于肝螺杆菌的快速检测.     

嗜肺军团菌生物膜的形成与毒力基因表达量分析

目的 初步探讨生物膜相关军团菌独特的毒力基因表达特征.方法 在富营养条件下建立静止状态的单细胞嗜肺军团菌生物膜模型.运用反转录real-time PCR技术,比较和分析浮游和生物膜状态下嗜肺军团菌部分毒力基因的表达,毒力基因包括mip、flaA和fliA基因.结果 对数生长后期与对数生长期浮游菌的mip、flaA和fliA基因表达量比值分别为0.53、4.45、3.67,对数生长期浮游菌显示复制态军团菌的毒力基凶表达特征,对数生长后期表达转移态军团菌特点.生物膜相关军团菌与对数生长期浮游菌的mip、flaA和fliA基因表达量比值为4.42、5.24、16.21;与对数生长后期浮游菌的比值为8.39、1.18、4.43,生物膜相关军团菌同时表达复制态和转移态军团菌毒力基因特征.结论 生物膜相关军团菌毒力基因的表达具有其特殊性,有待进一步研究.

Abstract：

Objective To investigate the physiological state of L. pneumophila in biofilm. Methods Genes previously identified as good markers for the transmissive and replicative phases of the L. pneumophila life cycle during growth in Acanthamoeba castellanii were examined for their expression fold change in the sessile cells as compared to planktonic cells using real-time RT PCR. Results Mature L. pneumophila biofilms were formed at 37t in 75 cm2 cell culture treated flasks for 18 days. The ratio of gene (mip, flaA and fliA) expression in post-exponential cells compared to exponential cells is 0. 53, 4. 45 and 3. 67. The exponential phase cultures display replicative traits and post-exponential bacteria express transmissive factors. The ratio of gene (mip, flaA and fliA) expression in sessile cells compared to exponential cells is 4.42, 5.24 and 16.21, while the sessile cells compared to exponential cells is 8.39, 1. 18 and 4. 43, respectively. Conclusion The violence gene expression of L pneumophila in biofilm is unique.     

空调冷却水军团菌污染调查

目的 调查某市城区空调系统军团菌(Lp)污染的现状,为军团菌肺炎的预防和控制工作提供参考.方法 采取随机抽样研究方法,抽取某市城区空调冷却塔水样32份,作军团菌污染情况检测.结果 在32份冷却塔水样中,有13份水样检出了军团菌(Lp1型和Lp2-14型),其阳性检出率为41%.结论 该市空调冷却塔水军团菌污染较普遍,应当引起高度重视,加强空调系统的定期和不定期的清洗、消毒工作非常必要.     

多重实时荧光定量PCR检测肠出血性大肠杆菌O157:H7

目的 利用多重荧光定量PCR技术,建立一种快速、准确、特异检测肠出血性大肠杆菌O157:H7的定量方法.方法 选取肠出血性大肠杆菌O157:H7编码脂多糖基因(rfbE)和编码鞭毛抗原基因(fliC)作为检测的靶基因,设计引物和TaqMan-MGB探针,探针的5'端分别用FAM和HEX进行荧光标记,3'端标记MGB.优化PCR扩增体系,对多重实时荧光定量PCR方法的特异性、灵敏度、重复性评价,同时进行一定数量临床样本鉴定,与常规方法进行比较.结果 本研究所建立的多重实时荧光定量PCR方法可准确、特异地检测和鉴定肠出血性大肠杆菌O157:H7,能够有效甄别肠出血性大肠杆菌O157:H7与非H7菌株,其他菌株均无阳性结果;该方法的灵敏度可达到10 CFU/ml;定量检测的批间和批内变异系数均小于5%;对66例临床样本进行评价,结果显示15例肠出血性大肠杆菌O157:H7阳性,2例为肠出血性大肠杆菌O157:非H7阳性,其中16例与常规培养法结果符合,符合率达到98.49%.结论 本研究建立的检测肠出血性大肠杆菌O157:H7多重实时荧光定量PCR方法快速,结果准确、可靠,操作简便,为肠出血性大肠杆菌O157:H7的临床诊断、现场流行病学调查和食品安全监测提供了新的鉴定方法.     

单核细胞增生李斯特菌与志贺菌双重实时PCR检测技术的建立

目的 建立一种快速、特异、灵敏、准确定量的单核细胞增生(单增)李斯特菌(Listeriamonocytogenes)与志贺菌(Shigella)同步检测方法.方法 分别根据单增李斯特菌溶血素O基因hly与志贺菌侵袭性质粒抗原H基因ipaH设计合成引物和探针.构建重组质粒pGEM-T-hly与pGEM-T-ipaH,并以EcoR I单酶切使环状重组质粒线性化作为标准品.优化反应体系,分析特异性.双重荧光定量PCR对人工污染的脱脂灭菌乳进行检测.结果 成功构建了重组质粒标准品,并运用5'、3'端分别标记FAM、TAMRA的hly基因探针和5'、3'端分别标记HEX、TAMRA的ipaH基因探针成功建立了单增李斯特菌与志贺菌同步荧光定量PCR检测方法.结论 建立的方法有较强的特异性,线性范围好(105～101copies/μl,R2≥0.998),灵敏度为10 copies/PCR,同步检测人工污染脱脂灭菌乳的灵敏度为102CFU/ml.     

肾移植后BK病毒感染者实时荧光定量PCR检测

背景：对于BK病毒感染、BK病毒相关性肾病的认识缺乏规范的实验室诊断程序和标准化的无创性检验方法。 目的：建立肾移植后患者尿液和外周血BK病毒感染负荷实时荧光定量PCR检测方法。 方法：针对BK病毒基因组,自主设计特异性引物BKV-F和BKV-R,Taqman荧光探针BKV-P,Taqman荧光探针BKV-P的5’端标记有荧光基团,在除5’端外的任意一个位置上标记有淬灭基团;然后处理待测样本,进行PCR反应。 结果与结论：将检测阳性的扩增产物进行基因测序,测序结果经BLAST比对后证实为BK病毒基因序列;利用上述方法对56份样本进行检测,其中,20份BK病毒血清样本及20份BK病毒尿液样本检测均为阳性,有S型扩增曲线。动态范围测定显示在103~1010 copies/mL之间标准曲线具有良好的相关性。5份健康人尿液样本,5份血液样本及6份临床常见的其他病原体血液样本检测均为阴性,无S型扩增曲线。结果表明该方法可进行定性、定量检测,特异性好,反应快速,一般30 min即可得到反应结果,并且成本低、假阳性少。     

马尔堡、埃博拉病毒双重荧光定量PCR检测方法的建立

目的 建立一种快速、敏感、特异的双重实时荧光定量PCR方法,可同时检测马尔堡病毒和埃博拉病毒.方法 通过序列比对挑选出两种病毒基因组中高度保守的序列,分别设计引物及Taqman探针,两条探针分别标记FAM和Texas Red荧光报告基因,建立双重实时荧光定量PCR反应体系.结果 双重荧光定量PCR方法检测两种病毒阳性标准品的灵敏度分别为30.5拷贝/μl和28.6拷贝/μl,通过检测日本脑炎病毒、黄热病毒、登革热病毒无交叉反应,有较好的灵敏度和特异性.结论 建立了马尔堡、埃博拉病毒双重荧光定量PCR检测方法,实现了两种病毒同时实时定量检测,在传染病防控领域有较好的应用前景.     

寡核苷酸微阵列技术用于检测幽门螺杆菌克拉霉素耐药相关23S rRNA基因多态性

目的 幽门螺杆菌（Hp）克拉霉素耐药与23S rRNA基因A2142G、A2143G和C2182T点突变相关。本研究旨在探索建立一种快速、简便的检测方法，获取Hp克拉霉素耐药相关23S rRNA基因多态性的流行病学资料，为临床合理用药提供依据。方法收集胃黏膜标本，用于病理检查、提取DNA。根据核苷酸位点设计相应探针，探针3′端以氨基修饰，氨基与探针序列之间以间隔臂相连，将探针用芯片点样仪点至玻片上。下游引物5′末端用Cy3荧光标记，进行不对称PCR扩增。其产物与芯片杂交，杂交后洗涤、扫描芯片，观察信号强度。非荧光标记引物扩增PCR产物克隆至T载体，测序验证芯片结果。结果（1）寡核苷酸微阵列技术与测序检测Hb 23S rRNA基因多态性结果完全一致。（2）经病理和PCR证实为场阳性的54例标本，杂交结果显示A2142位点均为野生型（54/54）；A2143G突变率为11．11％（6/54），尚未发现A2143C和A2143T的突变；C2182T突变率为12．96％（7／54），尚未发现C2182A和C2182G的突变，其余均为野生型。结论（1）利用寡核苷酸微阵列技术检测坳克拉霉素耐药的23S rRNA基因多态性，快速、简便而准确，可以高通量并直接检测胃黏膜而不需进行细菌培养，为根除Hp选择用药提供科学依据，推动个体化治疗方案的实施。（2）本研究没有发现场23SrRNA基因2142点突变，A2143G和C2182T突变率分别为11．11％和12．96％。     

Multicenter comparison of molecular methods for detection of Legionella spp. in sputum samples

Legionellosis can be diagnosed by PCR using sputum samples. In this report, the methods of nine laboratories for 12 sputum samples with Legionella pneumophila and Legionella longbeachae are compared. We conclude that (i) liquefaction prevents PCR inhibition, (ii) the employed mip gene PCRs detected L. pneumophila only, and (iii) the 16S rRNA gene PCR detected both Legionella species and is preferred for the diagnosis of legionellosis.     

Application of RNA polymerase beta-subunit gene (rpoB) sequences for the molecular differentiation of Legionella species

The nucleotide sequences of the partial rpoB gene were determined from 38 Legionella species, including 15 serogroups of Legionella pneumophila. These sequences were then used to infer the phylogenetic relationships among the Legionella species in order to establish a molecular differentiation method appropriate for them. The sequences (300 bp) and the phylogenetic tree of rpoB were compared to those from analyses using 16S rRNA gene and mip sequences. The trees inferred from these three gene sequences revealed significant differences. This sequence incongruence between the rpoB tree and the other trees might have originated from the high frequency of synonymous base substitutions and/or from horizontal gene transfer among the Legionella species. The nucleotide variation of rpoB enabled more evident differentiation among the Legionella species than was achievable by the 16S rRNA gene and even by mip in some cases. Two subspecies of L. pneumophila (L. pneumophila subsp. pneumophila and subsp. fraseri) were clearly distinguished by rpoB but not by 16S rRNA gene and mip analysis. One hundred and five strains isolated from patient tissues and environments in Korea and Japan could be identified by comparison of rpoB sequence similarity and phylogenetic trees. These results suggest that the partial sequences of rpoB determined in this study might be applicable to the molecular differentiation of Legionella species.     

Detection of Legionella pneumophila by real-time PCR for the mip gene

A real-time PCR assay for the mip gene of Legionella pneumophila was tested with 27 isolates of L. pneumophila, 20 isolates of 14 other Legionella species, and 103 non-Legionella bacteria. Eight culture-positive and 40 culture-negative clinical specimens were tested. This assay was 100% sensitive and 100% specific for L. pneumophila.     

Application of Legionella pneumophila-specific quantitative real-time PCR combined with direct amplification and sequence-based typing in the diagnosis and epidemiological investigation of Legionnaires’ disease

The detection of Legionella pneumophila DNA in clinical specimens using quantitative real-time polymerase chain reaction (qPCR) combined with direct sequence-based typing (SBT) offers rapid confirmation and timely intervention in the investigation of cases of Legionnaires' disease (LD). We assessed the utility of a specific L. pneumophila qPCR assay targeting the macrophage infectivity potentiator (mip) gene and internal process control with three clinical specimen types from confirmed LD cases. The assay was completely specific for L. pneumophila, as demonstrated by positive results for 39/39 strains from all subspecies and 16 serogroups. No cross-reaction was observed with any of the 54 Legionella non-pneumophila (0/69 strains) or 21 non-Legionella (0/58 strains). All L. pneumophila culture-positive respiratory samples (81/81) were qPCR-positive. Of 80 culture-negative samples tested, 47 (58.8%) were qPCR-positive and none were inhibitory. PCR was significantly more sensitive than culture for samples taken ≤ 2 days of hospitalisation (94.7% vs. 79.6%), with the difference being even more marked for samples taken between 3 and 14 days (79.3% vs. 47.8%). Overall, the sensitivity of the qPCR was ～30% greater than that of culture and direct typing on culture-negative PCR-positive samples resulted in full 7-allele profiles from 23/46, 5 to 6 alleles from 8/46 and ≥ 1 allele from 43/46 strains.     

Legionella pneumophila mip gene sequencing to investigate a cluster of pneumonia cases

AIMS: To use fluorescent antibody (FA) and PCR studies on fixed lung tissue to investigate whether Legionella pneumophila was the cause of pneumonia in a cluster of three haematology patients. METHODS: Cut sections of paraffin blocks of lung tissue were examined by direct FA (DFA) using fluorescently labelled antibody to serogroup 1 and Pontiac strains of L. pneumophila. In addition, a single tube 'hanging drop' nested PCR targeting the mip gene of Legionella was performed on DNA extracted from the lung sections. Products were sequenced using dye terminator chemistry. RESULTS: Numerous fluorescing bacteria were seen on staining with both antibodies in lung tissue from two of the patients. Identical L. pneumophila mip gene sequences were amplified from both DFA-positive lung sections. Two differing L. pneumophila mip sequences were obtained on three separate occasions from the tissue sections from the third patient negative by DFA. These sequences differed slightly from those obtained from the two DFA positive lung tissues. CONCLUSIONS: There is good epidemiological evidence to link the first two cases who had been treated in the same ward prior to development of fever within two days of each other. The significance of results is controversial for the third patient.     

Detection of Legionella species in respiratory specimens using PCR with sequencing confirmation

Legionella spp. are a common cause of community-acquired respiratory tract infections and an occasional cause of nosocomial pneumonia. A PCR method for the detection of legionellae in respiratory samples was evaluated and was compared to culture. The procedure can be performed in 6 to 8 h with a commercially available DNA extraction kit (Qiagen, Valencia, Calif.) and by PCR with gel detection. PCR is performed with primers previously determined to amplify a 386-bp product within the 16S rRNA gene of Legionella pneumophila. We can specifically detect the clinically significant Legionella species including L. pneumophila, L. micdadei, L. longbeachae, L. bozemanii, L. feeleii, and L. dumoffii. The assay detects 10 fg (approximately two organisms) of legionella DNA in each PCR. Of 212 clinical specimens examined by culture, 100% of the culture-positive samples (31 of 31) were positive by this assay. By gel detection of amplification products, 12 of 181 culture-negative samples were positive for Legionella species by PCR, resulting in 93% specificity. Four of the 12 samples with discrepant results (culture negative, PCR positive) were confirmed to be positive for Legionella species by sequencing of the amplicons. The legionella-specific PCR assay that is described demonstrates high sensitivity and high specificity for routine detection of legionellae in respiratory samples.     

Identification of mip-like genes in the genus Legionella.

The mip gene of Legionella pneumophila serogroup 1 strain AA100 encodes a 24-kilodalton surface protein (Mip) and enhances the abilities of L. pneumophila to parasitize human macrophages and to cause pneumonia in experimental animals. To determine whether this virulence factor is conserved in the genus Legionella, a large panel of Legionella strains was examined by Southern hybridization and immunoblot analyses for the presence and expression of mip-related sequences. Strains representing all 14 serogroups of L. pneumophila contained a mip gene and expressed a 24-kilodalton Mip protein. Although the isolates of the 29 other Legionella species did not hybridize with mip DNA probes under high-stringency conditions, they did so at reduced stringency. In support of the notion that these strains possess mip-like genes, these species each expressed a protein (24 to 31 kilodaltons in size) that reacted with specific Mip antisera. Moreover, the cloned mip analog from Legionella micdadei encoded the cross-reactive protein. Thus, mip is conserved and specific to L. pneumophila, but mip-like genes are present throughout the genus, perhaps potentiating the intracellular infectivity of all Legionella species.     

Native valve endocarditis due to a novel strain of Legionella

Legionellae are Gram-negative bacteria which are capable of causing disease, most commonly in the form of pneumonia. We describe a case of native valve endocarditis caused by a Legionella strain which by genotypic (16S rRNA and mip gene sequencing) and phenotypic analyses is unlike previously described strains of Legionella.