16S-23S rDNA内转录间隔区序列寡核苷酸探针鉴定分支杆菌菌种的研究

目的研究以16S-23S rDNA内转录间隔区(intemal transcribed spacer,ITS)序列为靶基因设计分支杆菌菌种寡核苷酸探针,应用PCR-反向杂交技术快速鉴定分支杆菌菌种.方法应用PCR-反向杂交技术检测26种36株分支杆菌标准株,24株分支杆菌临床分离株.结果分支杆菌标准株和临床分离株经PCR扩增,依菌种不同可见一条约340bp～450bp范围DNA片段.探针特异性试验表明,21种寡核苷酸探针除草分支杆菌探针MPH与微黄分支杆菌亦杂交外,其余探针均为特异的.5株结核分支杆菌临床分离株鉴定为结核分支杆菌复合群,19株非结核分支杆菌临床分离株鉴定至种水平.结论 16S-23S rDNA ITS PCR-反向杂交鉴定分支杆菌菌种简便、快速、准确,具有较高应用价值.     

利用基因芯片快速检测多种临床常见致病菌及其耐药性基因

目的快速、准确、灵敏地检测临床常见的致病菌及其耐药基因。方法采用基因芯片技术，利用细菌23S rRNA基因序列信息和某些耐药基因作为检测靶基因，设计针对不同菌属的寡核苷酸探针和耐药基因探针的基因芯片，聚合酶链反应（PCR）扩增并荧光标记目的DNA片段，通过杂交反应检测致病菌及其耐药基因。结果在理想状态下（检测试剂盒抽提的细菌基因组DNA）检测的结果与国内外文献报道的灵敏度相当（10^3～10^6细菌／ml），并在部分临床分离株、耐药标准菌株中进行验证，显示该方法有良好的特异性及可重复性。细菌种类能鉴别到种水平的有16种，能鉴别到属水平的有7类。覆盖了临床常见的多种病原菌，并且还可同期检测超广谱β内酰胺酶（ESBLs）基因耐药。结论DNA芯片检测具有快速、高特异性和高灵敏度的特点，是常规鉴定方法的一种有益补充。     

人工喷泉中一株军团菌的系统遗传学鉴定

目的检测喷泉水中的1株军团菌并进行分子生物学鉴定和系统发育分析。方法采集潍坊市一处人工喷泉水水样,用细菌基因组试剂盒提取水样中的总细菌基因组DNA,使用针对军团菌属16S rRNA基因片段的特异性引物PCR扩增军团菌属16S rRNA基因片段并测序,与从GenBank获得的另外41株军团菌的16S rRNA的基因序列进行对比分析,采用PAUP*4.0b10软件对16S rRNA基因片段序列数据矩阵进行最大简约法分析并绘制基因进化树。结果 PCR扩增喷泉水提取物中军团菌属特异性16S rRNA基因片段,片段碱基数654 bp。测序分析该菌株(命名为WF-B)的16S rRNA基因序列与Legionella beliardensis 16S rRNA基因序列的遗传距离较近,相似度达99.8%,在构建的最大简约进化树中该菌与L.beliardensis以自检值97%聚类为一枝。结论该喷泉水中检出的军团菌WF-B与L.beliardensis的亲缘关系较近,相关部门应加强监管力度,降低其感染风险。     

16S-23SrDNA间隔区序列PCR扩增及探针杂交用于偶然分支杆菌暴发感染的研究

目的　从基因水平上确认福建省南平市注射后偶然分支杆菌暴发感染的致病菌,并建立PCR结合DNA探针杂交快速鉴定偶然分支杆菌的方案。方法 根据偶然分支杆菌16S-23S rDNA间隔区序列,设计合成一段寡核苷酸探针,采用PCR扩增、RFLP和DNA斑点杂交技术,对29株偶然分支杆菌临床分离株进行鉴定。结果 29株偶然分支杆菌临床分离株均被PCR扩增出一条约470bp的DNA条带,DNA探针杂交也出现特异的杂交斑点。结论 16S23SrDNA间隔区序列PCR扩增及DNA探针杂交在基因水平上确认引起此次注射后暴发感染的致病菌为偶然分支杆菌,该方法具有灵敏、特异的特点。     

基因芯片技术在常见肠道致病菌感染检测中的应用

目的 建立一种运用PCR结合基因芯片技术检测和鉴定引起腹泻的常见肠道致病菌方法.方法 根据生物信息学技术以细菌16S rDNA和23S rDNA序列设计各细菌的特异型探针和引物,在基因芯片制备基础上,通过对靶基因的扩增、杂交和对杂交结果的分析,对常见肠道致病菌的检测和鉴定效果进行评价,同时对临床采集100份腹泻患者粪便标本通过细菌培养结果,比较基因芯片技术的灵敏性和特异性.结果 100份临床粪便标本中,采用基因芯片技术共检出50份(50％)携带肠道致病菌;细菌培养鉴定出47份(47％)携带肠道致病菌,其中42份基因芯片与细菌培养结果一致,准确率为79.25％,与基因芯片比较差异无统计学意义(x2=5.28,P＞0.05).结论 我们所建立的基因芯片系统具有高通量和高准确性,可以作为临床鉴定细菌的一个重要的工具,而且适用于流行病学调查研究.     

人感染藤黄短小杆菌的分离与鉴定

目的研究从患儿颌下淋巴结穿刺脓液中分离的纯G^＋棒状样杆菌的生物学地位。方法常规方法分离培养细菌，并做生化反应。提取细菌DNA，采用聚合酶链反应（PCR）扩增目的基因，琼脂糖凝胶电泳回收目的基因并测序。结果分离菌的一般生物学特性与生化反应与藤黄短小杆菌基本相同，16S rRNA基因长1387bp，与藤黄短小杆菌16S rRNA基因相似度达99．7％。结论通过生化反应和16S rRNA基因的序列测定确定此菌为藤黄短小杆菌，初步认为是藤黄短小杆菌的新亚型。     

肺炎链球菌临床分离株PBP2b基因序列分析及其应用探索

目的通过分析肺炎链球菌PBP2b基因转肽酶编码区的序列差异，建立可区分对青霉素敏感肺炎链球菌（PSSP）与青霉素不敏感肺炎链球菌（PNSSP）的分子生物学方法。方法检测青霉素对肺炎链球菌的最低抑菌浓度（MIC），对菌株PBP2b转肽酶编码区进行PCR扩增和序列分析，根据序列差异设计相应引物和探针，并采用PCR-反向杂交方法区分PSSP与PNSSP。结果43株肺炎链球菌（42株临床分离株及1株标准株）中8株为PSSP，30株为青霉素中介株（PISP），5株为青霉素耐药株（PRSP）。经PBP2b基因限制性片段长度多态性分析（RFLP）及测序分析，PSSP与PNSSP（PISP＋PRSP）存在谱型及序列差异。根据序列差异建立的检测方法可正确区分PSSP与PNSSP。结论肺炎链球菌PSSP和PNSSP菌株的PBP2b基因转肽酶编码区之间存在可供鉴别的序列差异，据此可建立快速、特异的分子生物学方法，有望为该菌耐药基因的快速诊断提供客观依据。     

PCR-反向点杂交基因分型与实时荧光定量PCR检测人乳头瘤病毒的研究

目的评价PCR-反向点杂交基因分型与实时荧光定量PCR在检测人乳头瘤病毒(HPV)的意义。方法同时采用PCR-反向点杂交基因分型和实时荧光定量PCR对121例女性宫颈脱离细胞标本进行HPV检测。其中PCR-反向点杂交基因分型能检测23种HPV亚型,实时荧光定量PCR定量检测常见的13种高危HPV亚型。结果 PCR-反向点杂交基因分型检测HPV的阳性率为28.10%(34/121),实时荧光定量PCR检测HPV的阳性率为16.53%(20/121),差异有统计学意义(P<0.05);二者检测的符合率为93.39%(113/121)。结论 PCR-反向杂交基因分型适用于HPV感染的筛查,而实时荧光定量PCR适用于HPV感染相关疾病的疗效与预后的判断。PCR-反向杂交基因分型与实时荧光定量PCR联合检测可提高HPV检测的特异性和敏感度,对于生殖道HPV感染以及子宫颈癌的早期发现、预防和治疗具有重要意义。     

MA120微生物鉴定/药敏分析系统在临床微生物鉴定与药物敏感性测定中的效果评价

目的评价国产微生物鉴定/药敏分析系统(MA120)在临床微生物鉴定和药物敏感性测定的效果。方法收集解放军第三〇二医院2013年1月—2014年12月间的临床分离株1803株,包括革兰阴性菌1205株及革兰阳性菌598株,共28个菌属,107个菌种,菌种经16S r DNA测序(测序)鉴定确认。用MA120进行细菌的鉴定与药敏检测,鉴定结果与测序确认结果比较,计算种的鉴定符合率;药敏结果与VITEK 2全自动细菌鉴定/药敏分析系统(VITEK 2)的药敏检测结果比较,计算耐药的符合率。结果 MA120鉴定革兰阴性菌19个菌属67个菌种1205株,与测序结果总体符合率为91.12%;鉴定革兰阳性菌9个菌属40个菌种598株,与测序结果总体符合率为94.31%。MA120药敏卡涵盖常见的抗生素,耐药率与VITEK2的符合率分别为:肠杆菌科89.54%,非发酵菌86.11%,葡萄球菌属94.74%,肠球菌属与链球菌属82.61%。结论 MA120在常见临床微生物的鉴定与药敏中的应用具有较好的效果,鉴定细菌种类涵盖临床常见的致病菌,且具有的药敏抗生素种类齐全,并可根据美国临床和实验室标准协会的建议及临床需求及时完善,应用灵活。     

产丙酮酸棒状杆菌的鉴定及微生物学性状研究

目的对临床分离于皮脂腺囊肿标本中的菌株进行表型和基因型鉴定,描述该菌株的生物学特性及致病性,为临床诊断提供准确地病原学依据。方法对分离菌株进行革兰氏染色等,并使用VITEK 2Compact全自动微生物分析仪进行鉴定。采用K-B法进行药敏试验。提取分离菌株DNA,采用通用引物对16S rRNA基因进行PCR扩增并测序,将测序结果与GenBank中收录的16S rRNA基因序列进行BLAST同源性对比。结果分离菌株经VITEK 2Compact鉴定为玫瑰色库克菌,后经16S rRNA序列测定方法鉴定,分离菌株为产丙酮酸棒状杆菌。药敏试验显示该菌株对四环素、万古霉素、利福平敏感,对青霉素、红霉素、克林霉素、环丙沙星、左氧氟沙星、复方新诺明、头孢吡肟、亚胺培南、庆大霉素等均耐药。结论对于表现型不易鉴定或鉴定不准确的细菌,采用16SrRNA序列测定的方法进行鉴定是最准确的。产丙酮酸棒状杆菌是引起患者疾病的致病菌。在完善产丙酮酸棒状杆菌生化反应信息的同时,探索出有效可行的生物学鉴定方法。     

16SrRNA基因PCR加反相杂交技术检测细菌DNA

目的探讨聚合酶链反应（ＰＣＲ）加反相杂交技术在细菌ＤＮＡ检测中的应用。方法以１６ＳｒＲＮＡ基因为靶序列，设计引物及寡核苷酸探针，采用ＰＣＲ法加反相杂交检测标准菌株及临床标本细菌ＤＮＡ。结果对２０株不同标准菌株进行ＰＣＲ扩增，均出现３７１ｂｐ长度的ＤＮＡ片段，敏感性试验可检测出１０－１２ｇ的细菌ＤＮＡ，与人基因组及病毒无交叉反应；２２份血培养阳性标本及４份脑脊液培养阳性标本均扩增出３７１ｂｐ长度ＤＮＡ条带，反相杂交区分革兰阳性／阴性细菌与培养结果相符。结论１６ＳｒＲＮＡ基因ＰＣＲ加反相杂交技术检测细菌ＤＮＡ，具有敏感、快速、准确的特点，为细菌感染的临床诊断提供了科学的依据。     

Molecular approaches for identification and characterization of lactic acid bacteria

The last few years have produced a revolution in the development of very sensitive, rapid, automated, molecular detection methods for a variety of various species of lactic acid bacteria (LAB) associated with food and dairy products. Nowadays many such strains of LAB are considered probiotics. The genome-based methods are useful in identifying bacteria as a complementary or alternative tool to phenotypical methods. Over the years, identification methodologies using primers that target different sequences, such as the 16S ribosomal RNA (rRNA)-encoding gene, the 16S-23S rRNA intergenic spacer region, the 23S rRNA-encoding, recA and ldhD genes; randomly amplified polymorphic DNA, restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, amplification rDNA restriction analysis, restriction enzyme analysis, rRNA, pulse field gel electrophoresis and amplification fragment length polymorphism have played a significant role in probiotic bacteriology. Hence, the aim of this review is to provide an overview of some rapid and reliable polymerase chain reaction-based molecular methods used for identifying and differentiating closely related species and strains of LAB associated with food and industry.     

Molecular detection of bacterial contamination in gnotobiotic rodent units

Gnotobiotic rodents provide an important technique to study the functional roles of commensal bacteria in host physiology and pathophysiology. To ensure sterility, these animals must be screened frequently for contamination. The traditional screening approaches of culturing and Gram staining feces have inherent limitations, as many bacteria are uncultivable and fecal Gram stains are difficult to interpret. Thus, we developed and validated molecular methods to definitively detect and identify contamination in germ-free (GF) and selectively colonized animals. Fresh fecal pellets were collected from rodents housed in GF isolators, spontaneously contaminated ex-GF isolators, selectively colonized isolators and specific pathogen-free (SPF) conditions. DNA isolated from mouse and rat fecal samples was amplified by polymerase chain reaction (PCR) and subjected to quantitative PCR (qPCR) using universal primers that amplify the 16S rRNA gene from all bacterial groups. PCR products were sequenced to identify contaminating bacterial species. Random amplification of polymorphic DNA (RAPD) PCR profiles verified bacterial inoculation of selectively colonized animals. These PCR techniques more accurately detected and identified GF isolator contamination than current standard approaches. These molecular techniques can be utilized to more definitively screen GF and selectively colonized animals for bacterial contamination when Gram stain and/or culture results are un-interpretable or inconsistent.     

应用16S-23S rRNA基因区间对败血症常见菌的鉴定

目的：建立检测不同菌种细菌的16S－23S rNA基因区间的特异图谱。方法：应用聚合酶链反应（PCR），限制性内切酶片段长度多态性分析（RFLP），分子克隆及测序技术，对临床常见的代表20个属26个种的标准菌株及相应的临床分离菌株共61株进行PCR扩增，同时对临床标本进行培养并与PCR－RFLP比较，探讨其在临床应用中的价值。结果：26株不同的标准菌株行PCR扩增后，分别出现1条带，2条带，3条带及多条带的不同DNA图谱，其敏感性为2．5CFU，与人类基因组DNA，真菌及病毒无交叉反应，其中14种菌经PCR扩增即可区分，另10种经Hinf I或AluI酶切后才能区分，肺炎克雷伯菌与坚韧肠球菌间的差异在第779位碱基上不同，Xma Ⅲ酶能进行区别，临床42例血培养15例阳性，阳性率35．7％；而PCR阳性27例，阳性率达64．3％，其阳性率明显高于血培养（P＜0．01），6例脑脊液标本中1例培养为表皮葡萄球菌，其PCR也阳性，2例培养阴性标本，其PCR也阳性，经图谱分析为葡萄球菌，1例培养为新型隐球菌的脑脊液标本PCR检测为阴性，另2例PCR及培养均阴性。结论：建立了PCR加RFLP技术快速检测细菌16S－23S rRNA基因区间的方法，进一步为临床细菌感染的病原诊断提供了新的科学依据。     

16S rRNA基因芯片诊断新生儿败血症

目的建立16SrRNA基因加基因芯片检测新生儿败血症的诊断技术，以提高临床检测细菌的速度及准确性。方法对125例拟诊为败血症的新生儿血标本及部分脑脊液标本进行细菌16SrRNA基因及基因芯片检测．包括DNA提取、设计引物和探针、聚合酶链反应（PCR）扩增、基因芯片的制备、杂交、激光扫描与读片。结果125例中PCR检测血标本阳性64例，占51．2％；血培养阳性32例，占25．6％；非特异性指标41例，占32．8％，差异有统计学意义（P〈0．01）。若以血培养阳性和／或非特异指标至少两项阳性为诊断标准，PCR灵敏度为90．3％（56／62），特异度为87．3％（55／63），正确诊断指数为0．776。3例脑脊液标本中PCR阳性2例，培养阳性仅1例。对64例PCR阳性血标本进一步作基因芯片检测，结果通用探针均阳性。其中G^＋探针阳性60份。G探针阳性4份。30份PCR和血培养均阳性的标本中其探针菌株与血培养细菌阳性结果相符。2例脑脊液标本PCR阳性，基因芯片检测结果与培养结果相符。结论168 rRNA基因PCR加基因芯片杂交可为新生儿败血症提供早期、敏感的病原学诊断依据。     

PCR和DNA斑点杂交分析贝氏柯克斯体的核酸标识

目的确认贝氏柯克斯体特异的核酸标识。方法用PCR法特异扩增贝氏柯克斯体24kDa,27kDa、30kDa、34kDa、热休克蛋白B等表面蛋白基因,以及23SrRNA插入序列和16S23SrRNA间区序列等基因片段,从DNA电泳凝胶中回收纯化PCR扩增的目的DNA片段,用地高辛随机引物标记法标记目的DNA片段作探针,行DNA斑点杂交。结果PCR扩得的7个贝氏柯克斯体DNA片段探针只能与贝氏柯克斯体基因组DNA杂交而不能与其他种属的立克次体的基因组杂交,每种探针检测同源目的基因的灵敏度可达到10pg。结论这7种贝氏柯克斯体DNA片段是贝氏柯克斯体特异的DNA片段,可作为贝氏柯克斯体的核酸标识,基于它们的序列设计的引物和探针具有极高的贝氏柯克斯体种特异性。     

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

The gene encoding the small subunit rRNA serves as a prominent tool for the phylogenetic analysis and classification of Bacteria and Archaea owing to its high degree of conservation and its fundamental function in living organisms. Here we show that the 16S rRNA genes of not-yet-cultivated large sulfur bacteria, among them the largest known bacterium Thiomargarita namibiensis, regularly contain numerous self-splicing introns of variable length. The 16S rRNA genes can thus be enlarged to up to 3.5 kb. Remarkably, introns have never been identified in bacterial 16S rRNA genes before, although they are the most frequently sequenced genes today. This may be caused in part by a bias during the PCR amplification step that discriminates against longer homologs, as we show experimentally. Such length heterogeneity of 16S rRNA genes has so far never been considered when constructing 16S rRNA-based clone libraries, even though an elongation of rRNA genes due to intervening sequences has been reported previously. The detection of elongated 16S rRNA genes has profound implications for common methods in molecular ecology and may cause systematic biases in several techniques. In this study, catalyzed reporter deposition-fluorescence in situ hybridization on both ribosomes and rRNA precursor molecules as well as in vitro splicing experiments were performed and confirmed self-splicing of the introns. Accordingly, the introns do not inhibit the formation of functional ribosomes.     

Synthesis of a large precursor to ribosomal RNA in a mutant of Escherichia coli

A mutant of E. coli, isolated by Kindler and Hofschneider as a strain defective in RNase III activity, forms a 30S precursor of ribosomal RNA ("30S pre-rRNA"). The half-life of the 30S pre-rRNA in growing cells at 30 degrees , estimated by the rate of specific (3)[H]uridine incorporation, is about 1 min. In rifampicin-treated cells, the RNA is metabolized to mature rRNA with a half-life of about 2 min.The 30S pre-rRNA has been highly purified. DNA-RNA hybridization tests demonstrate that it contains both 16S and 23S rRNA sequences. Also, in cultures treated with rifampicin, the cleavage products of radioactive 30S pre-rRNA include 25S and 17.5S RNA species, destined to becomes 23S and 16S rRNA. Thus, each 30S chain probably contains one 16S and one 23S RNA sequence, as well as additional sequences. Two independent techniques indicate that the additional portions account for about 27% of the total lenght: (1) By comparison to the sedimentation rate and electrophoretic mobility of marker RNAs, the 30S pre-RNA has an apparent molecular weight of 2.3 x 10(6) +/- 5%, or 28% more than the sum of 16S and 23S rRNA; (2) 27% of the 30S pre-rRNA is not competed away from hybridization by mature 16S and 23S rRNA.Thus, bacteria appear to make a pre-rRNA similar in some respects to that observed in eukaryotes; though in normal E. coli cells, the pre-rRNA is ordinarily cleaved endonucleolytically during its formation.     

Bacterial DNA in mixed cholesterol gallstones

OBJECTIVE: Numerous investigators have proposed a role for bacteria in biliary lithogenesis. We hypothesized that bacterial DNA is present in gallstones, and that categorical differences exist between gallstone type and the frequency of bacterial sequences. METHODS: Polymerase chain reaction (PCR) was used to amplify bacterial 16S rRNA and uidA (encoding Escherichia coli [E. coli] beta-glucuronidase) genes in different types of gallstones. PCR products were sequenced. RESULTS: Bacterial 16S rRNA and uidA DNA sequences in E. coli were detected in all brown pigment, common bile duct, and mixed cholesterol gallstones (n = 14). In contrast, only one (14%) of seven pure cholesterol gallstones yielded a PCR product. Most (88%) mixed cholesterol gallstones yielded PCR amplification products from their central, as well as their outer, portions. Sequenced products possessed 88-98% identity to 16S rRNA genes of E. coli and Pseudomonas species. CONCLUSIONS: Bacterial DNA sequences are usually present in mixed cholesterol (to 95% cholesterol content), brown pigment, and common bile duct, but rarely in pure cholesterol gallstones. The presence of bacterial beta-glucuronidase is also suggested. The role of bacteria and their products in the formation of mixed cholesterol gallstones, which comprise the majority of cholesterol gallstones, warrants further study.