Detection and identification of Mycoplasma conjunctivae in infectious keratoconjunctivitis by PCR based on the 16S rRNA gene.

A specific PCR assay based on unique sequences of the rrs genes (16S rRNA) of Mycoplasma conjunctivae was developed for direct detection and identification of this pathogen from clinical material. DNA from eye swabs was amplified after a simple lysis step by either a single PCR with the M. conjunctivae specific primer pair McoR1 and McoF1, or by a nested PCR with the Mycoplasma genus specific primer pair MOLIGEN1-L and 16UNI-R in the first step and McoR1 and McoF1 in the second step. The specificity of the primer pair McoR1 and McoF1 was verified with purified DNA from the type strain, from 17 field isolates of M. conjunctivae and from several Mollicutes which are phylogenetically related to M. conjunctivae or which can be isolated from the same host animals. This method identified mycoplasma isolates from goat, sheep, ibex and chamois originating from different countries as M. conjunctivae. No cross amplifications with other mycoplasmas which are related to M. conjunctivae were observed. Eye swab samples containing known numbers of M. conjunctivae cells were analysed after direct lysis of the material. The detection level was estimated to be 20 cells per swab when the nested PCR procedure was used and 2 x 10(5) by the single PCR method. In an experimental infection model of sheep, the nested PCR method for detection of M. conjunctivae gave results which were comparable to mycoplasmal culture. These are the implications for diagnostic purposes: M. conjunctivae isolates can be identified by the one-step PCR method, whereas for detection and identification of M. conjunctivae in clinical material the two-step method should be used (higher sensitivity).     

猪附红细胞体PCR检测方法的建立和初步应用

基于猪附红细胞体广东株16S rRNA基因的序列特点，设计合成种特异性引物，建立了猪附红细胞体PCR检测方法。该方法能特异性扩增523bp的猪附红细胞体16SrRNA基因片段，而对猪丹毒杆菌G4T10株、猪链球菌STl71株、多杀性巴氏杆菌E0630株、猪胸膜肺炎放线杆菌、猪肺炎支原体、鸡毒支原体和猫血巴尔通氏体CA株的基因组DNA没有扩增带出现。对猪附红细胞体基因组DNA的最小检测量为160pg。通过对38份临床样品的检测，8份为猪附红细胞体感染阳性，其余为阴性。结果表明，建立的PCR检测方法具有极高的敏感性和特异性，可用于急性猪附红细胞体病和临床健康带菌猪的诊断。     

利用半套式PCR扩增16S rRNA基因检测牛和猪附红细胞体

根据GenBank收录的猪和牛附红细胞体16SrRNA基因序列设计1对通用引物，在其上游引物内侧叉设计1条分别针对猪和牛附红细胞体的特异性引物。以这4条引物对出现附红细胞体痛典型症状及疑似症状的猪和牛的血样DNA进行半套式-PCR扩增。结果显示，该反应阳性率为58．3％，低于临床解剖和镜检结果。对谈基因的序列测定结果进行分析，表明不同动物附红细胞体的16SrRNA基因同源性在80％以上。从谈基因来看，附红细胞体与立克次氏体没有同源性，而与肺炎支原体和穿透支原体亲垮关系较近。     

16S rRNA基因在细菌菌种鉴定中的应用

本文综述了应用16S rRNA基因作为靶基因对细菌进行鉴定的各种分子生物学技术，并指出应用16S rRNA基因在乳酸菌鉴定方面的研究进展。     

一株猪源棒状杆菌的分离及其16S rRNA基因分析鉴定

四川某商品猪场仔猪出现以体温升高,背、腹和腿部皮肤发绀,淋巴结出血肿大,肺、脾脏出血、化脓为主要特征的疾病。通过对分离细菌的纯化培养、形态学观察、生化试验、致病性试验和药物敏感性试验,鉴定出一株致病菌。应用通用引物对其16S rRNA基因进行克隆和序列分析,序列在NCBI上进行BLAST比对,选择同源性较高的棒状杆菌属中25株不同种的菌株16S rRNA序列进行比对分析,构建遗传进化树。分离纯化的细菌在鲜血琼脂平板厌氧条件下生长良好,为革兰氏染色阳性杆状菌,能发酵部分糖类,能致死小白鼠,对头孢类抗生素敏感,16S rRNA序列与棒状杆菌属细菌的同源性最高,在78.2%~98.0%之间,遗传进化树分析结果表明,该菌株与棒状杆菌属细菌属于同一分类群,分离菌鉴定为棒状杆菌。     

16 S rRNA在细菌分类鉴定研究中的应用

细菌的16S核糖体RNA（ribosome RNA,rRNA）以其在进化上的特征性序列,现已被广泛用于细菌分类和鉴定的分子指标。其具体操作是,以聚合酶链式反应（PCR）分离细菌样本中的16SrRNA的基因片段,通过克隆、测序或酶切、探针杂交获得其序列信息,再与16SrRNA数据库中的序列数据进行比较,确定其在进化中的位置,从而鉴定样本中可能存在的微生物种类。文章综述了16SrRNA作为微生物系统分子分类鉴定的理论基础和方法,以及在细菌分类鉴定中的应用。     

鸡卡氏杆菌的分离与16S rRNA基因的分析鉴定

四川雅安某种鸡场种鸡出现消瘦,腹部膨大,肝脏肿大破裂出血,腹膜和输卵管炎为主要特征的疾病。为诊断和预防此病的发生,通过对细菌分离纯化、形态学观察、生化试验、药物敏感性试验鉴定出1株致病菌,应用通用引物对细菌的16S rRNA基因进行克隆和测序,测序结果于NCBI上进行BLAST比对,选择同源性较高的巴氏杆菌科15个属的29株细菌16S rRNA序列进行比对分析,构建遗传进化树。结果表明,分离纯化的细菌能在血平板上生长,革兰氏染色阴性短杆状,能发酵大多数糖和醇类,对头孢类抗生素敏感,16S rRNA序列与卡氏杆菌属细菌的同源性最高,在92.2%～99.5%之间,特别是与鸭卡氏杆菌同源在97.5%～99.5%之间。遗传进化树分析结果表明,该菌株与卡氏杆菌属细菌属于同一大分类群,与鸭卡氏杆菌位于同一个小分支,最终诊断该鸡场为卡氏杆菌感染。     

鸡卡氏杆菌的分离与16S rRNA基因的分析鉴定

四川雅安某种鸡场种鸡出现消瘦,腹部膨大,肝脏肿大破裂出血,腹膜和输卵管炎为主要特征的疾病.为诊断和预防此病的发生,通过对细菌分离纯化、形态学观察、生化试验、药物敏感性试验鉴定出1株致病菌,应用通用引物对细菌的16S rRNA基因进行克隆和测序,测序结果于NCBI上进行BLAST比对,选择同源性较高的巴氏杆菌科15个属的29株细菌16S rRNA序列进行比对分析,构建遗传进化树.结果表明,分离纯化的细菌能在血平板上生长,革兰氏染色阴性短杆状,能发酵大多数糖和醇类,对头孢类抗生素敏感,16S rRNA序列与卡氏杆菌属细菌的同源性最高,在92.2%～99.5%之间,特别是与鸭卡氏杆菌同源在97.5%～99.5%之间.遗传进化树分析结果表明,该菌株与卡氏杆菌属细菌属于同一大分类群,与鸭卡氏杆菌位于同一个小分支,最终诊断该鸡场为卡氏杆菌感染.     

Detection of Renibacterium salmoninarum in tissue samples by sequence capture and fluorescent PCR based on the 16S rRNA gene

The 16S rRNA genes from eight isolates of Renibacterium salmoninarum with different origins and dates of isolation were sequenced to evaluate the possibility to construct a diagnostic PCR system with target sites within this gene. The sequences were found to be identical but for one single position in one of the isolates, and two regions with an adequate number of nucleotide differences as compared to closely related species were identified. Species-specific fluorescent PCR primers complementary to these regions were constructed as well as oligonucleotides for DNA preparation by sequence capture. A mimic molecule was constructed to be used as an internal control. The PCR was specific and allowed the detection of DNA equivalent to 1-10 R. salmoninarum genomes per reaction. The DNA preparation with sequence capture and analysis by PCR with a mimic was found to be a reliable method for analysis of kidneys from fish with BKD. The amount of PCR inhibiting substances present in the tissue was reduced, and the relevant DNA was concentrated in the capture step. Furthermore, the use of the mimic molecule in the system assured that false negative results could be identified.     

应用16S rRNA基因序列鉴定柞蚕空胴病病原菌

20世纪70年代末,采用形态分类学方法,将引起柞蚕空胴病的致病菌鉴定为柞蚕链球菌(Streptococcus pernyi sp.nov)。分别提取已分离柞蚕空胴病的5株病原菌株的基因组DNA,PCR扩增16S rRNA基因片段,经克隆、测序后,与GenBank中登录的相关肠球菌、链球菌菌株的16S rRNA基因序列进行同源性比对并构建系统进化树。结果表明,供试的5株菌株的16S rRNA基因序列相似性在99.5%～99.9%之间,相互之间存在着10个可变位点,推测5株菌株属于同一个菌种;5株菌株的16S rRNA基因序列与肠球菌属(Enterococcus)16S rRNA基因序列的相似性较高,在92.4%～99.8%之间,而与链球菌属(Streptococcus)16S rRNA基因序列的相似性相对较低,在87.3%～87.8%之间;5株菌株与肠球菌属在系统进化树上聚为一类。基于菌株的16S rRNA基因序列分析,鉴定柞蚕空胴病的病原菌应归属于肠球菌属。     

Specific identification of Gallibacterium by a PCR using primers targeting the 16S rRNA and 23S rRNA genes

Gallibacterium was recently established as a new genus including organisms previously reported as Pasteurella anatis, [Actinobacillus] salpingitidis and avian Pasteurella haemolytica-like organisms. The aim of the present study was to develop a PCR method allowing unambiguous identification of Gallibacterium. PCR primers positioned in the 16S rRNA (1133fgal) and 23S rRNA (114r) genes were defined and their specificity was subsequently tested on 122 strains. Twenty-five of the strains represented all of the presently available 15 phenotypic variants of Gallibacterium from different geographical locations, 22 other strains represented other poultry associated bacterial species or bacteria which could pose a differential diagnostic problem including members of the families Pasteurellaceae, Enterobacteriaceae and Flavobacteriaceae, and finally 75 Gallibacterium field strains isolated from Mexican chicken egg-layers. Specific amplicons were generated in all 100 Gallibacterium strains tested, whereas none of the non-Gallibacterium strains tested positive. Correct identification was confirmed by hybridization with the Gallibacterium specific probe GAN850. Two internal amplification control strategies were successfully incorporated into the PCR assay, one based on amplification of the house-keeping gene rpoB (sharing target DNA) and another based on addition of trout DNA (foreign target DNA) and amplification with beta-actin specific primers. In conclusion, the described PCR assay enables specific identification of Gallibacterium and will thus stand as a strong alternative to the present diagnostic methods.     

Intraspecific variation in the 16S rRNA gene sequences of Mycoplasma agalactiae and Mycoplasma bovis strains

Intraspecific variation in the 16S rRNA genes of 17 Mycoplasma agalactiae and eight Mycoplasma bovis isolates was investigated to determine the degree of sequence variation in these two species and to determine whether the polymorphisms in the 16S rRNA genes could be used for the construction of an evolutionary tree and as epidemiological markers. A high degree of variation was found within isolates (between operons) and between isolates of both species. In contrast to M. capripneumoniae no distinct evolutionary pattern could be seen, probably because there are functional systems for gene conversion in M. agalactiae and M. bovis. However, the non-European isolates of M. agalactiae shared three characteristic nucleotides and European isolates from the same or neighbouring countries were very similar. Differences within isolates included both polymorphic positions and sequence length differences between operons. The amount of variation within isolates of the respective species ranged from zero to seven polymorphisms for M. agalactiae and from zero to four polymorphisms for M. bovis. The high degree of variation suggests the potential for misdiagnosis of species in diagnostic PCR assays based on the 16S rRNA gene sequences. All isolates of both species had a thymidine in position 912 (E. coli numbering) that causes streptomycin resistance in several bacterial species and which is characteristic for the members of the hominis group. As expected, when five M. agalactiae and three M. bovis isolates were tested for streptomycin susceptibility, they all demonstrated streptomycin resistance. M. agalactiae and M. bovis were found to have high intraspecific variation in their 16S rRNA gene and the polymorphisms patterns indicate that gene conversion takes place.     

基于线粒体12S rRNA基因序列鉴别牛肉的种源

在提取黄牛肉、牦牛肉和水牛肉总DNA的基础上,设计通用引物进行PCR扩增,电泳回收PCR产物后双向测序,再通过构建系统进化树鉴别牛肉的物种来源.PCR扩增获得的牦牛、水牛12S rDNA基因片段大小都为440 bp,黄牛12S rDNA基因片段大小都为439bp.参照引用的不同牛种12S rDNA基因序列,构建的系统进化树能够清晰地鉴别测序样品的牛种来源.因此,结合运用PCR扩增和DNA测序技术是一种精确可靠的方法,能够有效地运用于牛肉的种源鉴别.     

副猪嗜血杆菌的分离鉴定及16S rRNA序列分析

从云南某规模化养猪场病猪肺脏分离到1株革兰氏阴性小杆菌,经细菌生化鉴定、PCR鉴定和16S rRNA序列比对鉴定为副猪嗜血杆菌。抗生素药物敏感试验结果表明,分离菌株对四环素、红霉素、氯霉素、头孢噻吩高敏;对庆大霉素、氧氟沙星、诺氟沙星中敏;对磺胺甲唑耐药。16S rRNA分析结果表明,该分离株与GenBank中的Hps参考株AB078973(基因登录号)同源性为100%,将分离菌株鉴定为副猪嗜血杆菌。16S rRNA遗传进化关系表明,分离株与副猪嗜血杆菌3株血清5型参考株AB078972、AB078973、AB078974的16S rRNA序列位于一个分支上,遗传进化关系最近,它们之间的核苷酸同源性在99.0%~99.4%之间,初步鉴定为血清5型副猪嗜血杆菌,致病性试验结果表明,分离菌株对小白鼠有强致病性,命名为YN-1株。     

基于16S rRNA基因的枯草芽孢杆菌PCR快速检测方法的建立

参照GenBank中登录的枯草芽孢杆菌16S rRNA基因,设计1对引物,扩增片段大小为460bp的基因片段,该方法对枯草芽孢杆菌检测的灵敏性为1pg总DNA量,对枯草芽孢杆菌DNA的扩增结果为阳性,对照菌株扩增结果均为阴性,成功地建立了枯草芽孢杆菌PCR检测方法。该方法具有快速、灵敏度高、特异性强等优点,为枯草芽孢杆菌的分离及鉴定奠定了良好的基础。     

Intraspecific variation in 16S rRNA gene of Mycoplasma synoviae determined by DNA sequencing

Mycoplasma synoviae (MS) is an important avian pathogen may cause both respiratory disease and joint inflammation synovitis in poultry, causing economic losses to the Brazilian poultry industry. The genotypic variation in 16S rRNA gene is unknown. Partial sequences of 16S rRNA gene of 19 strains of M. synoviae were sequenced and analyzed in order to obtain molecular characterization and evaluation of the genetic variability of strains from distinct Brazilian areas of poultry production. Different polymorphic patterns were observed. The number of polymorphic alterations in the studied strains ranged from 0 to 6. The nucleotide variations, including deletion, insertion and substitutions, ranged from 3 to 5. The genotypic diversity observed in this study may be explained by spontaneous mutations that may occur when a lineage remains in the same flock for long periods. The culling and reposition in poultry flocks may be responsible for the entry of new strains in different areas.     

副鸡嗜血杆菌16 S rDNA PCR检测方法的建立

根据副鸡嗜血杆菌的16 S rDNA基因序列设计一对特异性引物XZIC1和XZIC2,对6株副鸡嗜血杆菌进行PCR扩增。结果显示,该对引物对6株副鸡嗜血杆菌均扩增出与预期大小相一致的282bp片段,而对鸡毒支原体、禽巴氏杆菌、鸡传染性支气管炎病毒、鸡新城疫病毒、大肠埃希菌、鸡白痢沙门菌、禽流感病毒(H9)、鸡喉气管炎病毒及葡萄球菌等9种病原体的扩增结果均为阴性。该PCR敏感性结果表明,本方法可以检测到10pg的副鸡嗜血杆菌DNA模板。采用引物XZIC1和XZIC2,对分别用副鸡嗜血杆菌ctcc253、ctcc255、ctcc257、ctcc269株感染SPF鸡的临床病料DNA进行PCR扩增,均可扩增出单一的282bp的片段。     

鸭链球菌的分离鉴定及其16S rRNA基因序列分析

从一种表现为脚软、拉稀、死亡增多的新发鸭病病例中分离到1株细菌,命名为GDYJ2011。通过生长特性、染色特性及VITEK-32微生物鉴定系统生化试验鉴定为链球菌,进一步进行16SrRNA基因序列的测定与分析,鉴定为巴氏链球菌。进行人工发病试验,成功的复制出本病,该菌还表现出较强的致病力。结合药敏试验与临床治疗效果,提出了本病的防控措施。     

应用16S rRNA基因测序法鉴定兔支气管败血波氏杆菌的研究

应用16S rRNA基因测序法对兔支气管败血波氏杆菌Bb-1株进行了16SrRNA基因序列分析。结果表明,能够扩增出与预期结果相符合的片断。经Blastn比较,分离菌与兔支气管败血波氏杆菌RB50株（BX640449）同源性为99．8％。进一步的生化实验鉴定表明,Bb-1株生化反应结果符合兔支气管败血波氏杆菌生化反应特征。综合各种实验结果表明,分离菌Bb-1株为兔支气管败血波氏杆菌。     

鸭疫里氏杆菌的分离与16 S rRNA的鉴定

从疑似患有鸭疫里氏杆菌病的病死鸭群中采取的肝脏、心脏、脑等病料中分离病原,进行生化鉴定,自6只病死鸭的12份病料中分离鉴定出6株鸭疫里氏杆菌。根据鸭疫里氏杆菌16 S rRNA基因的保守序列设计特异引物,对6株鸭疫里氏杆菌进行PCR扩增,均能扩增出680 bp的特异条带;从凝胶中回收DNA目的条带并测序,测序结果与GenBank中鸭疫里氏杆菌相应序列相似率达到99.99%。