一起蜡样芽孢杆菌10型引起食物中毒的快速诊断与分子分型研究

目的对引起一起食物中毒的蜡样芽孢杆菌进行快速诊断和分子分型。方法对中毒人员的呕吐物、肛拭子、可疑食品等样品用国标方法进行实验室检测,同时采用自主建立的荧光PCR方法进行快速检测。所分离的菌株PCR扩增vrrA基因多态性位点,产物进行基因双向测序和比较分析。结果在10份呕吐物、肛拭子、可疑食品中用传统方法和荧光PCR方法同时检出8份蜡样芽孢杆菌阳性,生物分型为10型。PCR测序结果显示它们有99%的同源性。结论这是一起食用了由蜡样芽孢杆菌10型污染的食品引起的呕吐型食物中毒,用蜡样芽孢杆菌呕吐毒素基因cesB为检测靶标的荧光PCR方法可以快速灵敏地对此类食物中毒进行初步诊断。以vrrA基因为多态性位点的PCR基因测序方法可用于蜡样芽孢杆菌的分子分型和食品污染源的准确追踪。     

rpoB作为蜡样芽胞杆菌群快速检测的标志基因的实验研究

目的探讨常规PCR和实时荧光定量PCR（Q-PCR）方法检测蜡样芽胞杆菌群rpoB基因的特异性和敏感性。方法提取蜡样芽胞杆菌群和其他各种对照细菌的基因组DNA,合成蜡样芽胞杆菌群rpoB基因扩增引物,采用常规PCR和SYBRgreen实时定量PCR两种方法扩增rpoB基因片段,并将PCR产物克隆到pMD18-T载体后进行DNA测序。结果常规PCR和Q-PCR均能扩增出蜡样芽胞杆菌群rpoB基因的174bpDNA片段,而各种对照菌株均未见扩增。序列比对发现蜡样芽胞杆菌群细菌在该片段中存在5处核苷酸的不同,差异率为2.88%。以炭疽芽胞杆菌基因组DNA系列稀释作为扩增模板显示常规PCR最小检出量为3.42pg,Q-PCR的敏感性达到171fg,3次重复实验显示Q-PCR检测rpoB基因的灵敏度为（3.32×101±7.45×100）拷贝。结论以rpoB基因为检测靶基因的Q-PCR方法具有高度的特异性和良好的敏感性,能实现对蜡样芽胞杆菌群快速而准确的检测。     

炭疽芽胞杆菌基因组中串联重复序列拷贝数的分析

目的研究炭疽芽胞杆菌基因组中多位点串联重复序列遗传标记的遗传变异规律。方法根据文献上发表的串联重复序列位点，利用已发表的13对引物，对88株炭疽芽胞杆菌基因组DNA进行PCR扩增，扩增产物进行琼脂糖和聚丙烯酰胺凝胶电泳，利用凝胶影像分析软件对PCR产物DNA片段的碱基含量进行测算，计算出串联重复拷贝数。对部分PCR扩增产物DNA片段进行测序，利用DNAStar软件进行序列比对，分析不同菌株间的串联重复序列遗传变异规律。结果（1）炭疽芽胞杆菌基因组中的串联重复序列位置，同一菌株具有相对稳定的串联重复拷贝数。（2）88株炭疽芽胞杆菌DNA上的13个串联重复序列遗传标记中，有的串联重复序列拷贝数变异较小，有的却存在着复杂的多态性；（3）有些串联重复序列单位内的核苷酸数目不变，但核苷酸的排列组合有差异，不过其重复单位内都包含着一个相同的稳定不变的核心核苷酸序列。结论炭疽芽胞杆菌基因组DNA中串联重复序列可以精确定位，测定结果可以数值化，并且串联重复序列在菌株DNA中具有相对的稳定性，因此，串联重复序列是研究炭疽芽胞杆菌遗传特征的较好指标，具有鉴别炭疽芽胞杆菌菌株间差别的能力。     

泛耐药鲍曼不动杆菌整合子Ⅰ和ISCR1结构及基因分型研究

目的研究从临床分离的鲍曼不动杆菌的整合子Ⅰ和ISCR1的分布及结构情况,并对其进行基因分型。方法分离自临床的57株鲍曼不动杆菌,PCR检测整合酶Ⅰ、整合子Ⅰ、ISCR1以及ISCR1可变区,PCR产物进行限制性片段长度多态性（RFLP）分型并进行测序分析可变区携带的耐药基因盒,ERIC-PCR进行基因分型。结果 49株整合酶I阳性,其中47株整合子I扩增阳性,RFLP分为2型,测序结果为aacA4-catB8-aadA1和drf17-aadA5。3株ISCR1以及ISCR1可变区扩增均阳性,可变区经RFLP分为1型,测序结果为orf513-qnrA1-ampR-qacEdeltal,ISCR1阳性菌整合子I均阳性,经ERIC-PCR检测将57株鲍曼不动杆菌分为27个基因型。结论Ⅰ类整合子广泛存在于鲍曼不动杆菌中,ISCRI携带率较低,氨基糖苷类、甲氧苄啶类和β-内酰胺类耐药基因盒较常见,ERIC-PCR可用于临床鲍曼不动杆菌的分子流行病学研究。     

鲍曼不动杆菌armA基因的分布与耐药性的研究

目的 调查我院鲍曼不动杆菌中16S rRNA甲基化基因armA的分布以及与鲍曼不动杆菌耐药谱的关系,并初步探讨其在分子流行病学分析中的作用.方法 收集72株鲍曼不动杆菌,采用K-B法对鲍曼不动杆菌进行药物敏感试验,后采用PCR筛选鲍曼不动杆菌的16S rRNA甲基化基因armA,并利用随机扩增多态性DNA法(RAPD)技术进行基因分型.统计各鲍曼不动杆菌菌株对多种氨基糖苷类药物的药敏结果,并分析基因型与耐药性的关系.结果 根据PCR产物片段大小,72株鲍曼不动杆菌共有armA基因阳性菌株20株(27.8%).含有armA基因型鲍曼不动杆菌菌株对庆大霉素、妥布霉素和阿米卡星的耐药率均为90%;随机扩增多态性DNA法显示20株armA基因阳性的鲍曼不动杆菌主要分为7型,A型为优势克隆株.结论 产16S rRNA甲基化基因armA的鲍曼不动杆菌菌株可对多种氨基糖苷类抗生素高水平耐药.同一克隆菌株在病房内和病房间的传播为我院armA基因传播的主要方式.     

临床分离耐喹诺酮类铜绿假单胞菌gyrA基因单点突变研究

目的 研究临床分离铜绿假单胞菌耐喹诺酮类药物的分子机制，对PCR－RFLP－SSCP分析铜绿假单胞菌gyrA基因突变的可行性评价。方法 以铜绿假单胞菌gyrA基因序列为靶序列，用PCR、PCR－SSCP、PCR－RFLP、DNA测序、OMIGA软件分析等方法，对铜绿假单胞菌gyrA基因突变进行研究。结果 在铜绿假单胞菌10株耐药突变株中，有8株的gyrA基因的83位表现出高频的单点突变，其突变方式全为ACC→ATC。gyrA的PCR扩增产物Sac Ⅱ酶切片段与测序结果一致。SSCP带谱与测序结果比较，除1株（PSA2）其SSCP带谱与标准株相同，但测序结果有点突变外，其余菌株与测序结果一致。结论 临床分离的铜绿假单胞菌耐喹诺酮类药物分子机制主要表现为gyrA基因83位氨基酸密码子突变（Thr-83→Ile)，利用PCR－SSPC－RFLP系统，可快速、准确地检测耐喹诺酮类药物的铜绿假单胞菌gyrA中至少1个碱基的差异。     

聚合酶链式反应技术在肾综合征出血热病毒基因分型中的应用

用聚合酶链反应（ＰＣＲ）方法对２５株国内外病毒进行分型。病毒ＲＮＡ逆转录成ｃＤＮＡ后，用Ⅰ型（ＨＡＮ）和Ⅱ型（Ｒ２２）两种分型引物进行体外扩增。产物经凝胶电泳、核苷酸序列分析和打点杂交等技术证实其特异性。结果表明，Ⅰ型引物仅扩增野鼠型病毒ｃＤＮＡ；Ⅱ型引物也只扩增家鼠型病毒，无交叉反应。扩增片段的大小与预计一致。两种引物和探针可将２５株病毒明确地分为两种基因型，与血清学分型结果完全吻合。     

B型肉毒神经毒素基因的PCR检测

本研究用一对Ｂ型肉毒神经毒素基因特异的寡核苷酸引物，扩增Ｂ型基因轻链区域一段２５３ｂｐ的ＤＮＡ片段，对２２株Ｂ型肉毒梭菌进行了鉴定，所试２２株Ｂ型肉毒梭菌其ＰＣＲ均为阳性。用Ｂ型肉毒梭菌ＣＭＣＣ（Ｂ）６４３５２对ＰＣＲ的检测灵敏度进行检查，可从６０个细菌中得到明显的扩增产物。用其它各型肉毒梭菌及其它梭状芽胞杆菌共５３株对ＰＣＲ的特异性进行了检测，除一株Ａ型肉毒梭菌（ＬＣＬ００１）ＰＣＲ为阳性外，其余菌株均为阴性。ＬＣＬ００１的扩增产物其分子量以及限制性内切酶消化产物和Ｂ型肉毒梭菌的扩增产物完全一致，认为该株菌中带有不表达的Ｂ型肉毒神经毒素基因，应为Ａ（Ｂ）型。由此可见，该ＰＣＲ扩增系统不仅具有灵敏度高，特异性强等特点，而且可检测出不表达的Ｂ型肉毒神经毒素基因，用于肉毒梭菌的鉴定具有其它方法不可比拟的优点。     

肠道细菌基因间重复序列基因分型方法研究副溶血性弧菌的基因多态性

目的 采用肠道细菌基因间重复序列(enterobacterial repetitive intergenic consensus,ERIC)基因分型技术对副溶血性弧菌进行分型,评估其基因多态性,探讨其在鉴别该菌散发和暴发中的应用.方法 采用ERIC-PCR分型方法对187例分离自患者、海产品和环境中的副溶血性弧菌基因组模板进行扩增,根据PCR产物中不同产物片段组合模式获得基因型,采用进化树分析软件直观评价不同基因型的相似性,并根据离散程度分为不同的族,同时进行血清分型.结果 187例菌株可获得产物长度160～2780 bp共16种大小不同的PCR产物片段,所有菌株根据扩增片段分布可分为59种基因指纹模式,通过进化树软件可分为12族,血清分型结果表明O3∶K6为86％ (161/187),O2、O4和O12占4％ (8/187),10％ (18/187)无法分型.结论 ERIC-PCR分型结果表明,我国分离的副溶血性弧菌具有较高基因多态性,ERIC-PCR具有高分辨力,可用于快速基因分型.     

人巨细胞病毒UL149基因在临床低传代分离株中的多态性研究

目的研究人巨细胞病毒(humancytomegalovirus,HCMV)UL149序列在临床低传代分离株中的多态性,探讨HCMV基因多态性与其感染引起不同临床症状之间的关系。方法对29株经荧光定量PCR方法(QPCR)检测HCMVDNA为阳性的临床低传代分离株的细胞培养上清液进行HCMVUL149全序列PCR扩增,并对PCR扩增产物进行序列测定及分析。结果29株临床低传代分离株有26株PCR扩增阳性,与HCMVToledo株进行序列比较分析,26株临床分离株UL149开放阅读框架(openreadingframe,ORF)之间存在着高度的多态性,种系进化树分析结果显示26个序列可分为3个型,黄疸患儿分布以G1型为主;小头畸形以G3型为主;巨结肠仅见于G1、G2型,G3型未见。部分临床分离株存在CKP位点的缺失及TKP位点增加。结论HCMVUL149基因在临床分离株中存在着高度的多态性。来自不同临床症状分离株的UL149基因及其编码蛋白具有一定的结构特点,并与基因型呈一定的相关性。     

Reassessment of sequence-based targets for identification of bacillus species

The Bacillus genus is a large heterogeneous group in need of an efficient method for species differentiation. To determine the current validity of a sequence-based method for identification and provide contemporary data, PCR and sequencing of a 500-bp product encompassing the V1 to V3 regions of the 16S rRNA gene were undertaken using 65 of the 83 type strains of this genus. This region proved discriminatory between most species (70.0 to 100% similarity), the exceptions being clinically relevant B. cereus and B. anthracis as well as nonpathogenic B. psychrotolerans and B. psychrodurans. Consequently, 27 type and clinical strains from the B. cereus group were used to test alternate targets (rpoB, vrrA, and the 16S-23S spacer region) for identification. The rpoB gene proved the best alternate target, with a conserved 4-nucleotide difference between B. cereus and B. anthracis. The high 16S rRNA gene sequence similarities between some strains demonstrated the need for a polyphasic approach to the systematics of this genus. This approach is one focus of the Ribosomal Differentiation of Medical Microorganisms mandate. Accordingly, the 16S rRNA gene sequences generated in this study have been submitted for inclusion into its publicly accessible, quality-controlled database at http://www.ridom_rdna.de/.     

A new phylogenetic cluster of cereulide-producing Bacillus cereus strains

Phenotypic and molecular studies have established that cereulide-producing strains of Bacillus cereus are a distinct and probably recently emerged clone within the Bacillus population. We analyzed a set of B. cereus strains, both cereulide producers and nonproducers, by multilocus sequence typing. Consistent with earlier reports, nonproducers demonstrated high heterogeneity. Most cereulide-producing strains and all flagellar antigen type H1 strains were allocated to the known sequence type of exclusively emetic B. cereus strains. Several cereulide-producing strains, however, were recovered at a new phylogenetic location, all of which were serotype H3 or H12. We hypothesize that the group of cereulide producers is diversifying progressively, probably by lateral transfer of the corresponding gene complex.     

血清学指定HLA-B座位纯合型误差分析及HLA-B座位表达变异检测的意义

目的 :用DNA分型法对HLA B座位抗原纯合型进行分型 ,探明是否存在HLA B基因发生变异引起结果差异。方法 :经血清学鉴定HLA B座位纯合型样本 75例 ,用PCR SSP法进行DNA分型和表达变异筛查。结果 :75例血清学鉴定为纯合型后经DNA分型证实有 12例存在第二基因 ,经PCR SSP法进行变异筛查发现有 1例存在第四外显子额外胞嘧啶插入 ,经DNA分型发现的第二基因实为沉默基因。结论 :用PCR SSP法进行HLA B基因分型可弥补血清学方法的不足 ,同时筛查表达变异使分型结果更加准确 ,能有效地指导临床应用。     

Specific detection and typing of adenovirus types 40 and 41 in stool specimens by dot-blot hybridization.

A dot-blot hybridization test was developed which allowed the direct detection of fastidious enteric adenovirus DNA in stool specimens from children with diarrhea and simultaneous typing of the viruses as adenovirus type 40 (Ad40) or Ad41. Cloned PstI fragments of Ad40 and Ad41 were used as 32P-labeled probes in the test, which allowed detection of picogram quantities of viral DNA in 20 to 40 microliter of stool suspension. Results were obtained within 48 h. The type specificity of the test was evaluated with 76 specimens known to contain either Ad40 or Ad41 by restriction enzyme analysis. Sixty-one specimens had sufficient DNA to be detected without any removal of protein. Thirty-one adenoviruses were typed as Ad40, and 30 were typed as Ad41, giving 100% correlation with the results of restriction enzyme analysis. The other 15 specimens were detected and typed as Ad40 or Ad41 only after removal of protein by a phenol extraction method. The dot-blot hybridization method is particularly useful for identifying those Ad40 and Ad41 strains which defy all attempts at culture and will be a useful tool in the epidemiology of fastidious enteric adenovirus infections.     

Comparison of sequencing of the por gene and typing of the opa gene for discrimination of Neisseria gonorrhoeae strains from sexual contacts

Typing of gonococcal strains is a valuable tool for the biological confirmation of sexual contacts. We have developed a typing method based on DNA sequencing of two overlapping por gene fragments generated by a heminested PCR. We compared sequencing of the por gene (POR sequencing) and typing of the opa gene (OPA typing) for the characterization of strains from 17 sexual partnerships. Both methods were highly discriminatory. A different genotype was detected in 15 of the 17 epidemiologically unconnected couples by POR sequencing and in 16 of the 17 couples by OPA typing with restriction enzyme HpaII. Within partnerships, identical genotypes were obtained from 16 of the 17 known sex contacts by POR sequencing and from 15 of the 17 by OPA typing. Compared to OPA typing, which relies on interpretation of bands in a gel, DNA sequence data offer the advantage of being objective and portable. As costs for sequencing decline, the method should become affordable for most laboratory personnel who wish to type gonococcal strains.     

Simple and Accurate PCR-Based System for Typing Vacuolating Cytotoxin Alleles of Helicobacter pylori

Alleles of the vacuolating cytotoxin gene (vacA) of Helicobacter pylori vary between strains, particularly in the region encoding the signal sequence (which may be type s1 or s2) and the midregion (which may be type m1 or m2). Using a PCR-based typing system developed in the United States, we showed that 36 strains from Asia and South America were all vacA signal sequence type s1; 3 were midregion type m1 and 11 were m2, but 22 could not be typed for the vacA midregion. All strains possessed cagA (cytotoxin-associated gene A), another virulence marker. vacA nucleotide sequence analysis showed that midregion typing failure was due to base substitutions at the primer annealing sites. Using the new sequence data, we developed two new PCR-based vacA midregion typing systems, both of which correctly typed 41 U.S. strains previously typed by the old system and successfully typed all 36 of the non-U.S. strains. All previously untypeable strains were vacA m1, other than one m1/m2 hybrid. In summary, we describe and validate a simple PCR-based system for typing vacuolating cytotoxin (vacA) alleles of H. pylori and show that this system correctly identifies the signal and midregion types of vacA in 77 strains from Asia and North and South America.     

罕见的CisAB与B(A)血型的基因型研究

目的　研究ABO血型系统中血清定型与基因型不一致的情况 ,通过核苷酸序列分析 ,最终阐明其真正血型。方法　应用吸收放散等实验 ,研究血清学实验中ABO正反定型不一致的情况 ,同时采用聚合酶链反应 限制性片段长度多态性方法 ,进行ABO初步基因分型 ,对二者结果矛盾的特殊标本则通过克隆测序了解他们的ABO基因第 6和第 7外显子的核苷酸序列构成。结果　在近年来收集到的并且做过基因分型的 3 5例ABO亚型标本中 ,有 7例标本血清学与基因分型不一致 ,血清学为AB亚型但基因分型却具有O基因。4例ABx ,基因分型均为A 10 2 /O ,其A基因在A 10 1的基础上 ,均有nt467(C→T)和nt80 3位 (G→C)的点突变 ,即都属于CisAB 0 1等位基因 ,真正的基因型是CisAB/O ;另外 3例血清学疑为AxB ,基因分型为BO的个体 ,除皆具有正常O基因外 ,其B基因在正常B等位基因的基础上 ,均发生单碱基突变 ,其中 1例存在nt70 0 (C→G) ,属于已经报道的B(A) 70 0等位基因 ;另外 2例无亲缘关系标本的B基因均存在新的nt64 0 (A→G)的点突变 ,导致 2 14位甲硫氨酸被缬氨酸置换。结论　通过核苷酸序列分析 ,证实 7例血清学表现为AB亚型而具有正常O基因的个体 ,4例是罕见的CisAB ,3例为B(A )型 ;同时在中国汉族ABO亚型人群中 ,检出一种新的B(A)     

Evaluation of simplified DNA extraction methods for emm typing of group A streptococci

Simplified methods of DNA extraction for amplification and sequencing for emm typing of group A streptococci (GAS) can save valuable time and cost in resource crunch situations. To evaluate this, we compared two methods of DNA extraction directly from colonies with the standard CDC cell lysate method for emm typing of 50 GAS strains isolated from children with pharyngitis and impetigo. For this, GAS colonies were transferred into two sets of PCR tubes. One set was preheated at 94 degrees C for two minutes in the thermal cycler and cooled while the other set was frozen overnight at -20 degrees C and then thawed before adding the PCR mix. For the cell lysate method, cells were treated with mutanolysin and hyaluronidase before heating at 100 degrees C for 10 minutes and cooling immediately as recommended in the CDC method. All 50 strains could be typed by sequencing the hyper variable region of the emm gene after amplification. The quality of sequences and the emm types identified were also identical. Our study shows that the two simplified DNA extraction methods directly from colonies can conveniently be used for typing a large number of GAS strains easily in relatively short time.     

Typing of Histoplasma capsulatum by restriction fragment length polymorphisms in a nuclear gene.

We previously described yps-3, a Histoplasma-specific nuclear gene probe useful in the identification of Histoplasma capsulatum. By using restriction fragment length polymorphisms (RFLPs) of DNA detected by the yps-3 gene and mitochondrial DNA, 76 clinical and soil isolates of H. capsulatum were classified. The majority of North American isolates obtained from endemic regions of the midwestern United States were members of the previously characterized class 2, although four clinical isolates from different patients with AIDS from that region were grouped in class 1 with the temperature-sensitive Downs strain. A Florida soil isolate (FLS1) was placed in class 4 on the basis of RFLP with both probes. Two American Type Culture Collection strains (G184B and G186B) from Panama were grouped into class 3 by this analysis. A group of five H. capsulatum isolates obtained from patients with AIDS in New York City were typed into a new class 5 on the basis of yps-3 polymorphisms; those organisms fell into two broad mitochondrial DNA patterns, designated 5b and 5c. Two new isolates from Panama were also members of this broad yps-3 class 5 group, but they exhibited a distinct mitochondrial DNA profile (class 5a). A sixth class was detected in DNA obtained from a patient with AIDS from Panama; that DNA had unique RFLP profiles with respect to both probes. These observations suggest that the Histoplasma-specific yps-3 gene probe is a sensitive tool for typing H. capsulatum in clinical specimens. Additionally, these studies provide molecular support for the hypothesis that AIDS-associated histoplasmosis in nonendemic areas is due to reactivation of a previously acquired infection.