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。     

16s rDNA序列分析在腹泻粪便标本菌群分析应用

目的应用16s rDNA序列分析方法,对临床实验室没有分离到已知病原菌的腹泻病人粪便标本进行菌群分析,为腹泻病人的病原学诊断提供线索。方法根据细菌16s rDNA保守区序列设计通用引物,以腹泻病人粪便标本中的总DNA为模板,PCR扩增16s rDNA片段。将获得的片段克隆入T载体进行测序,与数据库中发表序列的进行比对,判断标本中细菌的种类和比例;PCR扩增常见的五类致病性大肠杆菌的特征基因应用于排除诊断。结果在3份粪便标本中,大肠杆菌为优势菌群(所占比例分别为84%、65%和81%);其他种群细菌为拟杆菌属(Bacteroides)、柠檬酸杆菌属(Citrobacter)和普雷沃氏菌属(Prevotella)等;实验室常规培养方法没有分离到常见的五类致病性大肠杆菌;PCR扩增没有发现常见的五类致病性大肠杆菌的特征基因。结论引起三例病人腹泻的病原菌可能是一种新的大肠杆菌;16s rDNA序列分析方法可应用于腹泻粪便标本菌群分析,为常规的病原培养方法提供补充,对疾病的诊断提供线索。     

一种快速检测患者血液标本猪链球菌方法的研究

目的建立一种快速检测患者血液标本中猪链球菌的方法。方法收集患者血液标本。提取细菌金基因组DNA；根据猪链球菌6个特异基因设计引物，采用PCR技术对这些基因进行检测，并对PCR扩增阳性的基因产物进行序列分析验证，并分析该方法诊断猪链球菌病的特异性和敏感性。结果取唾液链球菌等6种链球菌进行验证，该检测方法的特异性为100％。模拟标本（细菌含量〉10^3个／ml）的敏感性为100％，血培养阳性病人标本的敏感性为100％。通过对90份血培养阴性临床标本的检测，9份PCR结果阳性，序列分析结果证实扩增片段为目的基因。结论该方法灵敏、特异、快速。可直接用于患者血液标本的猪链球菌特异性基因的检测，为猪链球菌感染的早期诊断提供实验室依据。     

细菌基因检测在慢性前列腺炎诊断中的应用研究

目的建立基于16SrRNA基因的PCR细菌学检测方法，用于慢性前列腺炎患者EPS的细菌学检查，以指导临床诊断和治疗。方法建立细菌PCR检测方法，对58例慢性前列腺炎患者的EPS或VB3标本和30例健康对照标本进行检测，并作细菌培养检查。结果PCR扩增产物经1%琼脂糖凝胶电泳，在1 500 bp处有一明显条带，经过优化的PCR方法检测细菌的敏感性为103/ml（每毫升中细菌的个数，下同）。慢性前列腺炎患者的EPS标本PCR检测阳性率46.6%（27/58），培养法阳性率为6.9%（4/58），以PCR法的阳性率较高（χ^2=9.772，P〈0.05）。对照组标本PCR检测阳性率为10.0%（3/30）。结论基于16SrRNA基因的PCR方法具有快速、简便、稳定、不受干扰等优点，可用于慢性前列腺炎患者EPS的细菌检测。     

采用通用引物PCR及RFLP快速检测下呼吸道感染常见病原菌的临床研究

目的 采用聚合酶链反应(PCR)配合限制性酶切片段多态性(restriction fragment length polymorphism,RFLP)分析检测下呼吸道感染的常见病原菌,探讨其在临床快速诊断细菌感染中的应用价值.方法 在下呼吸道感染的住院患者中筛选出合格痰标本125例,分为2份,1份行痰培养作为对照,另1份以16S rRNA基因为靶序列,在其保守区建立通用引物进行PCR扩增,再分别用限制性内切酶HaeⅢ、MnlⅠ、AluⅠ、DdeⅠ和BstBⅠ酶切,进一步行RFLP分析,根据下呼吸道常见病原菌建立的特异酶切图谱诊断鉴定细菌,比较两种方法的检测结果.结果 125例合格痰标本中,PCR配合RFLP检测阳性85例,阳性率为68.0%,痰培养阳性72例,阳性率为57.6%,前者明显高于痰培养(P<0.01),其中肺炎链球菌及流感嗜血杆菌阳性率明显高于痰培养,部分革兰阴性杆菌阳性率也高于培养组,但部分革兰阳性球菌(溶血葡萄球菌、表皮葡萄球菌及屎肠球菌)阳性率较培养组低于痰培养.结论 PCR配合RFLP分析方法检测下呼吸道感染病原菌较常规培养方法敏感快捷,是一种具有临床应用价值的快速诊断方法.     

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。     

4种病原菌特异基因片段阳性蜱的16S rRNA基因克隆文库分析

目的 建立16S rRNA基因克隆文库分析蜱媒菌群的方法,观察该方法对蜱寄生病原菌的检测效率以及对细菌群落多样性分析和对病原菌的筛检能力.方法 用伯氏疏螺旋体、汉赛巴通体、嗜吞噬细胞无形体和查菲埃立克体4种病原菌特异基因设计引物,扩增蜱标本提取的核酸,以上述4种病原菌特异基因片段扩增均阳性的蜱核酸提取物做模板,用16S rRNA基因的通用引物进行PCR扩增、纯化、连接、克隆和测序,建立16S rRNA基因克隆文库,将测序结果与数据库进行比对,计算克隆文库Coverage值和Shannon-Wiener多样性指数.结果 测出103个有效序列,检出16种已知种属的细菌,其中8个是优势类型(克隆子数>5个);检测到伯氏疏螺旋体、汉赛巴通体和立克次体3种病原菌,但这3种病原菌均不是优势类型(克隆子数均<5个).Coverage值为96.11%,Shannon-Wiener多样性指数为2.40.克隆序列分析结果表明,蜱寄生细菌主要为α、γ变形菌纲,占56.25%(9/16).结论 16S rRNA基因序列分析可以对蜱标本进行菌群相对定量研究,可以同时检出多种病原菌,是一种较好的细菌菌群多样性分析和病原菌筛检方法.     

快速检测细菌并革兰分型的半巢式聚合酶链反应及其初步应用

目的以半巢式聚合酶链反应(PCR)检测细菌及作革兰阴、阳性分型,并与细菌培养法比较。方法以细菌16SrRNA基因为靶序列,采用一对通用引物(pm1,pm3)和一条革兰阴性型特异性引物(pm2),以半巢式PCR方法扩增实验室保留菌株的DNA并作出革兰染色分型;以人类外周血白细胞基因组DNA、HBVDNA阳性血清以及白假丝酵母菌为对照,检测此方法的特异性;采用倍比稀释菌液作敏感性实验;与细菌培养法比较,验证此方法检测临床标本的敏感性。结果对17个实验室保留菌株进行检测,以通用引物对作第1次PCR均得到371bp长度的DNA片段;再以革兰阴性菌特异引物对(pm2,pm3)作第2次PCR,9种阴性菌均得到353bp的DNA片段,而8种阳性菌未被扩增。特异性实验表明,此通用引物与人类基因组DNA、真菌及病毒无交叉反应。敏感性实验表明,采用半巢式PCR可检测出3个CFU的细菌。对120份临床标本检测,半巢式PCR检测阳性率(29.2%)显著高于细菌培养法检测阳性率(17.5%)。结论此半巢式PCR检测细菌方法,具有特异、敏感、快速的特点,并能对细菌进行革兰阴性、阳性分型,可用于临床感染性疾病的初步诊断。     

细菌感染患者早期病原学分子诊断技术

目的 建立细菌感染患者早期病原及耐药性分子诊断技术，以便尽早实施有效的抗感染治疗方案，改善患者预后。方法 扩增细菌23S rRNA基因序列，同时扩增多种耐药基因，设计探针，通过基因芯片杂交技术识别其差异序列，鉴别细菌，检测耐药基因，用于病原早期诊断和耐药谱测定；收集血培养标本223份，脑脊液、胸水、腹水标本339份，尿液标本514份，比较所建立方法与传统方法的一致性，验证所建立技术的可靠性。结果 基因诊断方法可正确检出常见病原菌，并检测其是否携带mecA、SHV、CTX-M-1组和CTX-M-2组耐药基因。检测血、尿及脑脊液等无菌体液标本时，所建立的快速检测方法与常规方法的符合率分别为96．4％、99．8％和99．7％，总体符合率为99．1％，耐药性检测与传统药物敏感结果的符合率为95．7％，其准确性与常规方法相当，检测时间比常规方法平均减少（2．09±1．15）d。结论 多重PCR-基因芯片杂交技术可用于耐药菌感染的病原早期诊断和耐药感染的同步检测，应用于临床可望改善患者的预后。     

3340例ICU患者的病原菌分布及耐药性分析

目的：回顾性分析3340例ICU患者的病原菌菌群分布及其耐药性,为临床治疗提供依据。方法选择3340例ICU患者,采集痰液、血液、尿液、脑脊液、引流液、穿刺液标本对感染菌的分布及耐药情况进行分析。结果共送检标本14391份,分离病原菌5893株,阳性率为40．94％。剔除同一患者的同种菌株后病原菌共2689株,其中革兰阴性杆菌2017株,革兰阳性球菌558株,真菌114株。革兰阴性杆菌中,鲍曼不动杆菌、铜绿假单胞菌、肺炎克雷伯菌分别占27．96％、16．64％、15．40％,鲍曼不动杆菌对检测药物的耐药率均在50％以上。革兰阳性球菌中,凝固酶阴性葡萄球菌、屎肠球菌分别占28．85％、24．73％。耐甲氧西林金黄色葡萄球菌（MRSA）67株,耐万古霉素肠球菌（ VRE）5株。结论 ICU病原菌以非发酵杆菌为主,鲍曼不动杆菌和铜绿假单胞菌的耐药问题明显,多种细菌对常用抗菌药物均表现出多重耐药和高度耐药。     

Cardiobacterium valvarum临床分离株的生物学特性研究及16S rRNA鉴定

目的 采用不同的方-法描述Cardiobacterium valvarum(C. valvarum)临床分离株的生物学特性,利用16S rRNA基因测序技术进行分子鉴定。 方-法 转种阳性血培养标本到血琼脂平板上进行细菌培育,革兰染色涂片镜检,用VITEK 2 Compact全自动微生物鉴定分析仪对临床分离株进行细菌鉴定,基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS)对分离株的蛋白质进行高通量测定,E-test法对分离株作药敏试验。提取分离株的DNA,采用16S rRNA基因测序技术对PCR的产物进行测序,在NCBI的BLAST网站上与GenBank数据库上的序列做相似性比较,用MEGA7.0.26软件构建该分离株的系统进化树。结果 经细菌培养发现小而圆、光滑、不透明,灰色的菌落;经革兰染色后镜下见到小、两端圆形、革兰阴性的多形性杆菌;VITEK 2 Compact上机、MALDI-TOF-MS技术均未得到该分离株的鉴定结-果;16S rRNA基因测序技术测得该菌株基因全序列约为1 450 bp,与C. valvarum F0432的16S rRNA同源性为99.59%,鉴定为C. valvarum。结论该菌的形态、生化反应均无代表性,采用16S rRNA基因测序技术可以对C. valvarum进行鉴定,对该疾病的诊断具有重要意义。     

Usefulness of a molecular strategy for the detection of bacterial DNA in patients with severe sepsis undergoing continuous renal replacement therapy

INTRODUCTION: Sepsis is a major cause of morbidity and mortality in critically ill patients. Sepsis is associated with cell necrosis and apoptosis. Circulating plasma levels of DNA have been found in conditions associated with cell death, including sepsis, pregnancy, stroke, myocardial infarction and trauma. Plasma DNA can also derive from bacteria. We have recently implemented a method to detect bacterial DNA and, in the present study, we validated this technique comparing it to standard blood culture in terms of diagnostic efficacy. METHODS: We examined a cohort of 9 critically ill patients with a diagnosis of severe sepsis and acute renal failure requiring continuous renal replacement therapy (CRRT). We analyzed bacterial DNA in blood, hemofilters, and ultrafiltrate (UF) by polymerase chain reaction amplification of 16S rRNA gene sequence analysis. Standard blood cultures were performed for all patients. RESULTS: The blood cultures from 2 of the 9 (22%) patients were positive. However, bacterial DNA was identified in the blood of 6 patients (67%), including the 2 septic patients with positive blood cultures. In 9 (100%) patients bacterial DNA was found on the filter blood side, whereas in 7 (78%) subjects it was found in the dialysate compartment of the hemofilters. Bacterial DNA was never detected in the UF. CONCLUSIONS: Using the 16S rRNA gene, the detection of bacterial DNA in blood and adsorbed within the filter could be a useful screening tool in clinically septic, blood culture-negative patients undergoing CRRT. However, the identification of the etiologic agent is not feasible with this technique because specific primers for the defined bacteria must be used to further identify the suspected pathogenic organisms.     

Development of broad-range polymerase chain reaction (PCR) bacterial identification in diagnosis of infective endocarditis

BACKGROUND AND AIMS OF THE STUDY: The study aim was to identify the value of broad-range bacterial PCR in infective endocarditis (IE) of bacterial etiology, and to determine its specificity and sensitivity. METHODS: Thirty blood samples were taken for analysis from patients with IE (diagnosed according to Duke criteria) and acquired valvular heart disease. Two control groups of patients with (n = 10) or without (n = 15) urinary tract infection were defined. DNA was isolated, and three different primer pairs for the region of the gene coding for 16S rRNA were tested, to determine the most specific pair. Amplification products were analyzed with gel electrophoresis, stained with ethidium bromide, and located under UV light. RESULTS: Positive blood cultures were found in 25 patients with IE. A typical echocardiography picture with bacterial vegetations was found in all patients with sterile blood cultures, and in 20 patients with positive blood cultures. The highest specificity was found for forward/reverse (F/R) primers, as the relevant amplified PCR product was present in all blood samples with IE, and in four of 10 patients with urinary tract infection. CONCLUSION: Broad-range PCR in bacterial endocarditis is a rapid, sensitive and inexpensive technique for the detection of bacteria, but is far more prone to contamination than species-specific PCR. However, under controlled conditions, broad-range PCR may be valuable for the identification of non-specific infection, permitting a more rapid clinical diagnosis of endocarditis.     

16S-ribosomal DNA to diagnose culture-negative endocarditis

Culture-negative endocarditis (CNE) accounts for 2.5% to 48% of all cases of infectious endocarditis (IE). Prior or concurrent antibiotic treatment at the time blood cultures are taken accounts for 45% to 60% cases of CNE; the remainder are caused by slow-growing and fastidious organisms. Although limited in sensitivity because of potential contaminating bacterial DNA, detection of bacterial 16S ribosomal (r) DNA (from the 16S rRNA gene) is nevertheless more sensitive than culture. It is accomplished by using polymerase chain reaction (PCR) that targets highly conserved regions of the 16S rRNA gene. The identity of noncultivated infecting agents can then be determined by sequencing PCR products and comparing them with known 16S rDNA sequences from a wide range of bacteria. This has served to broaden the etiologic diagnosis of CNE. We review the benefits and limitations of PCR to diagnose IE and we propose advances that will be necessary to secure a place for PCR in guiding therapy.     

Presence of Bacterial 16S Ribosomal RNA Gene Segments in Human Intestinal Lymph Follicles

Background: There is currently no information regarding microbial agents inside the intestinal lymph follicles. Methods: Biopsy or resected specimens, mostly from macroscopically normal areas, were sectioned with a cryostat. DNA was extracted from microdissected samples, exclusively from the lymph follicle. Amplification of DNA was performed using universal primers designed from conserved regions of bacterial 16S ribosomal RNA (rRNA). Several clones with inserts of around 400 base pairs were subjected to DNA sequence analysis followed by a database homology search. Results: Bacterial 16S rRNA gene segments were detected in the lymph follicle in 2 of 14 (14%) non-inflammatory bowel disease (IBD) cases, 4 of 14 (28%) Crohn disease cases, and in 2 of 5 (40%) ulcerative colitis cases. Nineteen 16S rRNA gene segments were recognized in the eight positive cases. Five segments showed 100% identity to known bacterial 16S rRNAs, namely staphylococcus species, Streptococcus sanguis, and Paracoccus marcusii. However, the other 14 segments showed below 100% identity, indicating either the presence of unknown bacteria or of bacteria without known DNA data. No single identified or unidentified bacterium, characteristic of IBD, including Mycobacterium paratuberculosis and Listeria monocytogenes, was detected. Conclusions: The present study confirms the presence of bacterial 16S rRNA gene segments in human intestinal lymph follicles and paves the way for new investigations into the microbiology of the lymph follicle. Whether or not bacteria inside the lymph follicle is a primary stimulus in IBD has yet to be clarified.     

Presence of bacterial 16S ribosomal RNA gene segments in human intestinal lymph follicles

BACKGROUND: There is currently no information regarding microbial agents inside the intestinal lymph follicles. METHODS: Biopsy or resected specimens, mostly from macroscopically normal areas, were sectioned with a cryostat. DNA was extracted from microdissected samples, exclusively from the lymph follicle. Amplification of DNA was performed using universal primers designed from conserved regions of bacterial 16S ribosomal RNA (rRNA). Several clones with inserts of around 400 base pairs were subjected to DNA sequence analysis followed by a database homology search. RESULTS: Bacterial 16S rRNA gene segments were detected in the lymph follicle in 2 of 14 (14%) non-inflammatory bowel disease (IBD) cases, 4 of 14 (28%) Crohn disease cases, and in 2 of 5 (40%) ulcerative colitis cases. Nineteen 16S rRNA gene segments were recognized in the eight positive cases. Five segments showed 100% identity to known bacterial 16S rRNAs, namely staphylococcus species, Streptococcus sanguis, and Paracoccus marcusii. However, the other 14 segments showed below 100% identity, indicating either the presence of unknown bacteria or of bacteria without known DNA data. No single identified or unidentified bacterium, characteristic of IBD, including Mycobacterium paratuberculosis and Listeria monocytogenes, was detected. CONCLUSIONS: The present study confirms the presence of bacterial 16S rRNA gene segments in human intestinal lymph follicles and paves the way for new investigations into the microbiology of the lymph follicle. Whether or not bacteria inside the lymph follicle is a primary stimulus in IBD has yet to be clarified.     

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。