Optimization of a 3'-minor groove binder-DNA probe targeting the uidA gene for rapid identification of Escherichia coli O157:H7 using real-time PCR

Enterohemorrhagic Escherichia coli are harmful human pathogens capable of causing bloody diarrhea and vomiting. An important serotype commonly associated with human illness is the E. coli O157:H7 serotype. Unlike other real-time polymerase chain reaction (PCR) methods for identifying E. coli O157:H7, this study describes the development and optimization of a real-time PCR method targeting a conserved point mutation at +93 in the uidA (gusA) gene that is unique to O157:H7, distinguishing it from non-O157:H7 serotypes. A TET-labeled Minor Groove Binder (MGB) DNA probe was designed for use in a 5' nuclease PCR assay. Using a panel of two E. coli O157:H7 strains, three E. coli non-O157:H7 strains, and one non-E. coli species, the assay was optimized for the specific detection of the E. coli O157:H7 strains. Optimal conditions were identified at high anneal/extend temperatures, low magnesium concentrations, and low probe concentrations, resulting in correct identification of E. coli O157:H7 and non-O157:H7 strains. The improved specificity of MGB probes for single base pair mismatches such as the +93 uidA mutation provides a novel approach towards rapid identification of E. coli O157:H7.     

空肠弯曲菌、单增李斯特菌和大肠杆菌O157多重PCR分子检测研究

目的建立同时检测空肠弯曲菌、单核细胞增生性李斯特菌（简称单增李斯特菌）和大肠杆菌O157的多重聚合酶链反应（PCR）检测技术。方法根椐空肠弯曲菌mapA基因序列、单增李斯特菌的编码溶血素（hly）基因序列和大肠杆菌的O157抗原（rfbE）基因序列,分别设计了3对特异引物,PCR扩增的目的基因片段为589 bp、360 bp和194bp;并对反应条件进行了优化。结果对3种致病菌检测,多重PCR检测DNA的敏感度分别为空肠弯曲菌2.264 ng、单增李斯特菌37.92 ng、大肠杆菌2.100 ng,样品检测时间6-8 h。结论该方法操作简便,检测周期短,特异性和敏感度高,为同时检测污染样品中空肠弯曲菌、单增李斯特菌和大肠杆菌O157奠定了基础。     

Application of real-time PCR and RT-PCR assays for the detection and quantitation of VT 1 and VT 2 toxin genes in E. coli O157:H7

Real-time PCR assays, based on hybridisation probes and LightCycler technology, were developed for VT 1 and VT 2 genes and applied to the detection and quantitation of DNA and mRNA of Escherichia coli O157:H7. The qualitative consensus PCR assay for the detection of VT 1 and/or VT 2 genes had a detection limit of 100 fg of E. coli O157:H7 genomic DNA and did not detect DNA from 13 non-VTEC isolates. When E. coli O157:H7 was inoculated into minced beef, enriched and recovered by immunomagnetic separation, the real-time consensus PCR assay had a detection limit of log(10)3.5 ml(-1) E. coli O157:H7 cells. Nineteen E. coli O157:H7 isolates, derived from food, bovine samples and human faeces, were analysed and compared for mRNA expression of three genes, VT 1, VT 2 and gapA (housekeeping gene), using quantitative real-time PCR assays. While there was no statistically significant difference for the expression of the VT 1 (p=0.134) or VT 2 (p=0.52) mRNA in the E. coli O157:H7 isolates from food, bovine and human sources, three clinical isolates did show lower expression of VT 2 compared to other isolates in the study. The study indicates that the consensus qualitative real-time PCR assay for VT 1 and VT 2 is rapid and sensitive and that the quantitative assays reported here have the potential to be used as an alternative method to more conventional methods for studying VT 1 and VT 2 virulence gene expression in E. coli O157:H7 with potential application in other pathogenic E. coli species.     

Detection of Shiga toxin genes stx1, stx2, and the +93 uidA mutation of E. coli O157:H7/H-using SYBR Green I in a real-time multiplex PCR

Enterohemorrhagic Escherichia coli (EHEC) is a major foodborne pathogen capable of causing diarrhea and vomiting, but more serious complications such as hemorrhagic colitis and hemolytic-uremic syndrome (HUS) can result. A real-time PCR method to detect the presence of Shiga toxin producing E. coli (STEC) and E. coli O157:H7 was investigated using SYBR Green I (SG). Primers were designed to target the Shiga toxin genes (stx1 and stx2) and a highly conserved base substitution at +93 of the beta-glucuronidase gene (uidA) unique to E. coli O157:H7. An initial test panel of five E. coli and non-E. coli isolates was tested with individual primer sets (simplex assay) and all primer sets including stx1, stx2, and uidA (multiplex assay). All strains were correctly identified in both assays. Average melt temperatures (Tm's, degrees C) for PCR products were 85.42--stx1, 81.93--stx2, and 88.25--uidA in simplex assays and 85.20--stx1, 81.20--stx2, and 88.16--uidA when multiplexed. Each of the three gene targets in one multiplex reaction could be distinguished by melt curve data with significantly different Tm's. The assay was expanded to a panel of 138 isolates consisting of STEC, E. coli O157:H7, non-toxigenic E. coli, and non-E. coli isolates with melt peaks consistent with those stated above.     

空肠弯曲菌、单增李斯特菌和大肠杆菌O157多重PCR分子检测研究

目的建立同时检测空肠弯曲菌、单核细胞增生性李斯特菌(简称单增李斯特菌)和大肠杆菌O157的多重聚合酶链反应(PCR)检测技术。方法根椐空肠弯曲菌mapA基因序列、单增李斯特菌的编码溶血素(hly)基因序列和大肠杆菌的O157抗原(rfbE)基因序列,分别设计了3对特异引物,PCR扩增的目的基因片段为589 bp、360 bp和194bp;并对反应条件进行了优化。结果对3种致病菌检测,多重PCR检测DNA的敏感度分别为空肠弯曲菌2.264 ng、单增李斯特菌37.92 ng、大肠杆菌2.100 ng,样品检测时间6~8 h。结论该方法操作简便,检测周期短,特异性和敏感度高,为同时检测污染样品中空肠弯曲菌、单增李斯特菌和大肠杆菌O157奠定了基础。     

多重PCR检测肠出血性大肠埃希菌O157：H7

目的 建立一种快速、特异的检测肠出血性大肠埃希菌O157:H7菌株的多重PCR方法。 方法 针对O157:H7菌株的O157、H7抗原特异基因rfbE O157、fliC H7以及stx1、stx2、eaeA和hlyA四种毒力基因设计相应引物,在同一扩增体系中进行PCR反应,通过优化多重PCR 反应条件和循环参数,建立检测O157:H7菌株的多重PCR方法,并测定其特异性和灵敏度。 结果 6 对特异性引物各自扩增相应的基因片段,检测结果与常规PCR 获得的结果一致。细菌纯培养物的检测灵敏度为1.33×10⁴ CFU。 结论 该多重PCR方法能在一次检测中同时反映待测菌株是否为肠出血性大肠埃希菌O157:H7及其携带毒力基因的情况,可为O157:H7大肠埃希菌感染的诊断及流行病学调查提供一种简便、快速的检测手段。     

Rapid PCR detection of enterohemorrhagic Escherichia coli (EHEC) in bovine food products and feces

Although Escherichia coli (E. coli) O157:H7 is a major cause of foodborne illness, other types of E. coli can also cause illness. E. coli that possess the eae gene for attachment and effacing have the potential to cause disease. Many real-time, molecular-based assays have been developed to detect Enterohemorrhagic E. coli (EHEC) including E. coli O157:H7. However, no assay currently exists to detect the eae gene present in E. coli O157:H7 and other EHEC strains with a confirmed positive or negative result in less than 12 h. Raw beef food products (raw ground beef and raw boneless beef) at 25 and 375 g samples and bovine fecal samples at 2 g were inoculated with 10(1), 10(3), 10(4), and 10(5) organisms of E. coli O157:H7 to test the sensitivity of this assay. Fourteen different foodborne bacteria (including E. coli O157:H7) and 19 various E. coli strains, obtained from the United States Department of Agriculture-Agricultural Research Service (USDA-ARS) were tested for specificity. E. coli O157:H7 was detected at the level of 10(1) organisms in both 25 and 375 g samples of raw ground and raw boneless beef products as well as 2 g samples of bovine feces after pre-enrichment and concentration. None of the 14 foodborne bacteria screened for cross-reactivity was detected. All USDA E. coli strains confirmed to contain the eae gene were detected.     

E.coli O157：H7 LAMP检测方法的建立

目的建立检测E.coli O157：H7环介导的等温扩增方法（LAMP）。方法选取E.coli O157：H7的rfbE基因设计LAMP引物,优化建立LAMP检测体系。并用该体系和国标法对76份人工污染样品进行了检测。结果所建立的E.coli O157：H7 LAMP体系具有良好的特异性,用该体系对9属13种41株菌进行检测,结果只有E.coli O157：H7的扩增产物电泳结果为阶梯状条带,非E.coli O157：H7均未产生扩增产物,灵敏性为2.7×101CFU/mL。样品及培养基对反应体系没有影响或影响很小。对76份样品进行了检测,E.coli O157：H7 LAMP检测方法与国标法的总符合率为96.1%,2h内即可完成检测。结论本研究建立的E.coli O157：H7的LAMP法不但解决了分子生物学检测对实验室仪器设备的高要求问题,而且检测方法简便、快捷,非常便于基层实验室和现场检测使用。     

Multiplex PCR for detection of trait and virulence factors in enterohemorrhagic Escherichia coli serotypes

A multiplex PCR assay was developed which allowed the simultaneous detection of five trait genes or virulence markers in enterohemorrhagic Escherichia coli (EHEC) serotypes. A primer pair, designed to detect a single base-pair mutation in the uidA gene, is specific only for the prototypic EHEC of O157:H7 serotype and its toxigenic, non-motile variants. In a similar way, primers to the eaeA gene of the gamma-intimin derivative specifically detects strains in the EHEC 1 clonal group, which consists mostly of O157:H7 and some O55:H7 serotypes. The other three primer pairs, specific for stx1, stx2 and both variants of ehxA genes, will detect the presence of these virulence genes in all EHEC serotypes. Analysis of 34 strains, including various serotypes of EHEC, Shiga toxin-producing E. coli and enteropathogenic E. coli, confirmed that the multiplex PCR assay detected the presence of these genes in a manner consistent with the known genotype of each respective strains.     

江苏省徐州市出血性大肠埃希菌O157∶H7 感染性腹泻的监测研究

目的 系统监测肠出血性大肠埃希菌O157∶H7(O157∶H7)感染并发肾衰(HUS)、腹泻患者、宿主动物、蝇类、食品携带O157∶H7的状况,为预警监测体系建立提供参考依据。 方法 采集徐州市疫情暴发点和监测点腹泻患者粪便、蝇类和食品标本分离菌株。应用PCR技术检测志贺毒素基因stx。 结果 1999-2011年徐州市累计报告O157∶H7引起的感染性腹泻并发HUS 132例。腹泻患者带菌率1.2%、蝇类带菌率0.5%、食品带菌率1.0%、宿主动物带菌率3.1%。菌株带毒由stx1和stx2共存发展为以不带毒为主。 结论 江苏省徐州市O157∶H7感染自1999年、2000年暴发流行后,该市疫情一直稳定。腹泻患者带菌率、宿主动物带菌率、蝇类带菌率、食品带菌率及菌株带毒情况发生了改变。     

Development of a triplex PCR assay for the specific detection of Campylobacter jejuni,Salmonella spp., and Escherichia coli O157:H7

A triplex PCR assay was developed and evaluated for efficacy in detecting Campylobacter jejuni, Salmonella spp., and Escherichia coli O157:H7 in a variety of raw and ready-to-eat food products. Following a short enrichment period, artificially contaminated food samples were subjected to a triplex PCR assay, which incorporated published primers for each food pathogen, a protocol for sample collection, and a PCR procedure designed specifically for the assay. The selected primers amplified fragment sizes of 159 bp, 252 bp, and 360 bp for C. jejuni, E. coli O157:H7, and Salmonella spp., respectively. This assay provides specific and reliable results and allows for the cost-effective detection of all three bacterial pathogens in one reaction tube.     

Emerging foodborne pathogens: enterohemorrhagic Escherichia coli.

In 1982, a new pathogen caused an outbreak of hemorrhagic colitis in this country. This new pathogen, Escherichia coli O157:H7, was not a known enteropathogen prior to this time. Since 1982, this organism has become the most commonly isolated pathogen from patients with bloody stools. Health officials estimate that E. coli O157:H7 causes 20,000 cases of hemorrhagic colitis annually in the U.S. Approximately 5% of all hemorrhagic colitis patients experience serious sequelae involving hemolytic anemia, thrombocytopenia, and kidney failure, and about 250 patients die each year with E. coli O157:H7 hemorrhagic colitis and sequelae. Even as many clinical laboratories become more efficient at detecting E. coli O157:H7 using simple media, other strains of enterohemorrhagic E. coli are appearing as causes of hemorrhagic colitis and hemolytic uremic syndrome. These non-O157:H7 are more difficult to detect and identify, and present a challenge to clinical microbiologists.     

Semi-automated fluorogenic PCR assays (TaqMan) forrapid detection of Escherichia coli O157:H7 and other shiga toxigenic E. coli.

Semi-automated detection of Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 and non-O157:H7 Shiga toxin-producing E. coli (STEC) was achieved using fluorogenic polymerase chain reaction (PCR). These PCR assays were designed to amplify 80, 120 and 150 bp regions of virulence genes stx1, stx2 and eaeA, respectively, using specific primers. The fluorogenic probes were used for specific detection of amplified products of the stx1 and stx2 genes of STEC, and the eaeA gene of EHEC O157:H7. For multiplex PCR assay, the three sets of primers and fluorogenic probes were included in one reaction to simultaneously amplify and detect any of the three targeted virulence genes. In non-multiplex PCR assay, each of the three virulence genes was amplified and detected in independent reactions. The specificity of these assays was evaluated using suspensions of STEC and other bacterial species lacking stx1, stx2 and eaeA. The multiplex assay detected all STEC harbouring any combination of three virulence genes. Three non-multiplex PCR reactions identified types of Shiga toxin genes carried by a STEC and identified STEC as either EHEC O157:H7 or non-O157:H7 STEC. Sensitivity limits of these assays in beef and faeces inoculated with EHEC O157:H7 were 5.8 to 580 cfu and 1.2 to 1200 cfu, respectively. These assays can be completed within 8-10 h when performed simultaneously or within 13 h if the multiplex assay is used as an initial screen for detecting STEC and the non-multiplex assay is used for subsequent detection of stx1 and stx2 of STEC and eaeA of EHEC O157:H7 Copyright 1999 Academic Press.     

一株不产志贺毒素的肠出血性大肠杆菌O157:H7菌株的鉴定

目的 对一株不产志贺毒素的肠出血性大肠杆菌O157:H7菌株进行血清生化特征及毒力基因鉴定.方法 对154菌株进行常规血清生化鉴定,使用聚合酶链反应(PCR)方法检测该菌的志贺毒素基因及其他毒力因子,同时以southern杂交、Hela细胞毒实验进行证实.结果 菌株154的志贺毒素PCR检测、shouthern杂交为阴性,Hela细胞毒定量结果显示该菌株不产生志贺毒素,毒力因子eae,hly检测为阳性.结论 菌株154是不产志贺毒素的肠出血性大肠杆菌O157:H7菌株,且具有O157:H7菌株特异性的毒力因子.     

聚合酶链反应检测出血性大肠埃希菌

为建立一种针对出血性大肠埃希菌的特异性聚合酶链反应（ＰＣＲ）诊断方法，根据Ｏ１５７：Ｈ７血清型大肠埃希菌ｈｌｙＡＢ基因的ＤＮＡ序列，设计８个引物，使用３２株Ｏ１５７：Ｈ７血清型。结果表明，引物ＲＨ２８－ＲＨ３０和ＲＨ２６－ＲＨ３１敏感性和特异性好，达１００％。ＲＨ２６－ＲＨ３１产物的分子量较大，为２ｋｂ。ＲＨ２８－ＲＨ３０的产物为３３８ｂｐ，比较适合检验使用。研究还发现，使用煮沸法制备ＰＣＲ模板，方法简便、快速、实用，且对ＰＣＲ反应的特异性和敏感性无影响。ｈｌｙＡＢ基因片段作为出血性大肠埃希菌ＤＮＡ探针的特异性和敏感性是明显的，且实用性好。根据出血性大肠埃希菌独特的ｈｌｙＡＢ基因序列设计的ＰＣＲ引物，在理论和实际应用方面均有其优越性。     

Catecholamines modulate Escherichia coli O157:H7 adherence to murine cecal mucosa

Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is an important food-borne pathogen. While the molecular mechanisms governing E. coli O157:H7 pathogenesis have been intensively investigated, the role of host factors has received less attention. In this study, we tested the hypothesis that the enteric catecholamines norepinephrine (NE) and dopamine (DA) modulate interactions of the cecal mucosa with E. coli O157:H7. Full-thickness sheets of murine cecum were mounted in Ussing chambers and short circuit current and tissue electrical conductance were periodically determined to assess active transepithelial ion transport and ionic permeability, respectively. Neurochemicals and stationary-phase E. coli O157:H7 were exposed respectively to the contraluminal and luminal aspects of the mucosa. Epithelial adherence of E. coli O157:H7 was quantified by a bacterial adhesion assay after 90 min of luminal E. coli O157:H7 exposure. DA and NE increased E. coli O157:H7 adherence relative to untreated control tissues at 50% effective concentrations of 3.8 microM and 4.2 microM respectively. Pretreatment of tissues with either the alpha-adrenergic antagonist phentolamine or the beta-adrenergic antagonist propranolol prevented the action of NE. The effect of DA was prevented by the dopamine antagonist haloperidol. The drugs did not impair tissue viability or transepithelial conductance. The present findings suggest that enteric catecholamines modulate E. coli O157:H7 adherence to the cecal epithelium. Conditions associated with elevated catecholamine release, such as stress exposure, may influence host susceptibility to E. coli O157:H7 infection.     

Quantitative detection of Escherichia coli from urine of patients with bacteriuria by real-time PCR.

INTRODUCTION: Compared with the classical urine culture method, PCR is more rapid, and can detect smaller numbers of bacteria, however it is inferior for quantification. Because of the lack of quantification in routine PCR, the meaning of a positive PCR test result has not been validated for all infections. We report on the development of a novel quantitative detection system for the urinary tract infection (UTI) Escherichia coli using real-time PCR. PATIENTS: We enrolled 200 patients with suspected bacteriuria. METHODS: The gene encoding the universal stress protein (uspA) was found to be highly specific for E. coli. We quantified the copy numbers of E. coli in the urine of patients with UTI by using a real-time PCR assay (the TaqMan system) targeting uspA genes in genomic DNAs isolated from urine samples (n=200). To evaluate the feasibility of this method, the results were compared with those of a standard urine culture. RESULTS: The incidence of positive urine cultures was 75% (150 of 200), and various doses of E. coli were detected in 84 of 150 specimens. The real-time PCR method also detected 84 cases of urinary infections of E. coli in the same specimens. Furthermore, the result of the quantification of E. coli using real-time PCR strongly correlated (r2=0.925) with the result of urine culture. CONCLUSION: Our results suggest that using quantitative-PCR means a faster and simpler diagnosis of E. coli urinary infection can be made compared with the traditional urine culture method.     

Detection by 5'-nuclease PCR of Shiga-toxin producing Escherichia coli O26, O55, O91, O103, O111, O113, O145 and O157:H7, associated with the world's most frequent clinical cases

This paper describes 5'-nuclease PCR assays for detecting eight O-serogroups, H7 flagellar antigen and stx genes from the Shiga toxin-producing Escherichia coli (STEC) associated with the world's most frequent clinical cases. A single set of primers was used to detect the genes stx1 and stx2 in the same reaction by 5'-nuclease PCR. Serotyping by 5'-nuclease PCR of STEC was based on the selection of primers and probes targeting the O-antigen gene clusters of E. coli O26, O55, O91, O111, O113, O157, the eae gene of E. coli O103, the O-island 29 of E. coli O145, and the flagellar H7 antigen gene. Results obtained on a collection of 190 strains indicate that the 5'-nuclease PCR assays used here could serve as a basis for rapid specific stx, O and H7 typing of these major pathogenic serogroups of E. coli. This work provides sensitive and specific tests for the rapid, reliable detection of the main pathogenic E. coli O-serogroups of major public health concern.