Detection of Burkholderia cepacia DNA from Artificially Infected EDTA‐blood and Lung Tissue Comparing Different DNA Isolation Methods

Bacterial DNA (Burkholderia cepacia) was prepared from artificially infected equine ethylenediaminetetraacetic acid (EDTA)‐blood and lung tissue by using four standard methods (lysis buffer containing proteinase K, phenol/chloroform/isoamylalcohol‐extraction, microwave‐treatment, heat treatment) and six commercially available kits (Puregene®, High Pure PCR Template Preparation Kit®, InstaGene®, QiaAmp Tissue Kit®, DNAzol® and Elu‐Quik®). After a subsequent polymerase chain reaction (PCR), their efficacy and sensitivity were compared. Concerning the detection limits, the simple lysis with a proteinase K‐containing buffer led to the best results for EDTA‐blood as well as for artificially infected lung tissue.     

Comparison of DNA isolation methods and detection of Salmonella spp. from animal faeces and dust using invA real-time PCR

There is a strong interest to reduce the expenditure for the detection of Salmonella spp. from animal faeces and environmental samples from primary production according to ISO 6579:2002 Annex D by including a rapid and effective method to detect Salmonella spp. already after pre-enrichment in BPW. It has been shown that real-time PCR methods are very effective to detect Salmonella organisms after pre-enrichment of foods. However, materials from primary animal production compose of much higher amounts of substances which might inhibit the sensitivity of real-time PCR. Different techniques of DNA isolation after pre-enrichment of artificially inoculated bovine faecal material were used to compare their detection limit and detection probability using an invA 5' nuclease real-time PCR approach. A detection probability of 100% was shown at 10(5) cfu/ml using the QIAamp DNA Stool Mini Kit (Qiagen, Germany), at 10(4) cfu/ml using the High Pure PCR Template Preparation Kit (Roche, Germany) and at 10(3) cfu/ml using thermal cell lysis or an in-house lab protocol, respectively. In comparison DNA isolation by thermal cell lysis revealed a very good detection limit, low costs and almost no risks of contamination. Furthermore, caecal contents from pigs were analysed by ISO 6579:2002 Annex D and the invA real-time PCR using thermal cell lysis for DNA extraction. As a result neither false positive nor false negative findings were obtained. Inclusion of the real-time PCR after pre-enrichment of samples in BPW followed by bacterial detection of Salmonella only with samples positive with real-time PCR might be a valuable tool to fulfil the international standard of ISO 6579:2002 Annex D but also to diminish the expenditures. However, it must be stated that the modification of an international standard method and its use in routine diagnostic requires the validation and registration of national and/or international competent authorities.     

Use of the bead beater for preparation of Mycobacterium paratuberculosis template DNA in milk.

Mycobacterium paratuberculosis is a recognized chronic enteric pathogen that can affect many different species of animals, including primates. It has been suggested that this organism is associated with Crohn's disease in humans, and that milk is a potential source of human exposure to this organism. The limit of the detection of M. paratuberculosis in milk samples by direct PCR was 10(5) cfu/mL if the traditional boiling method was used for template DNA preparation. In this study, an improved method for template DNA preparation was examined. The method involves the use of a bead beater, which breaks up bacterial cell wall mechanically by vibrating bacteria with microbeads at high speed. The effectiveness of this method for lysing M. paratuberculosis cells was compared to that of the freeze-thaw method, and use of commercial kits such as the InstaGene Matrix and the QIAamp Tissue Kit. The bead beater procedure was tested in combination with various cell lysis and template DNA preparation procedures to determine which of these steps improved the limit of detection of PCR assay that amplifies a 413 bp fragment of the IS900 gene. Results showed that the use of the bead beater, in combination with the use of lysis buffer, boiling, and isopropanol precipitation, decreased the limit of detection of M. paratuberculosis in milk by the PCR to 10(2) cfu/mL. The limit of detection was further decreased to 10 cfu/mL when 0.0037% bovine serum albumin was included in the PCR reaction mixtures. The improved assay was 10- to 10(4)-fold more sensitive than the PCR assays using template DNA prepared by other lysis procedures including boiling alone, freeze-thaw plus boiling, or use of commercial kits for lysis.     

山羊绒毛干中线粒体DNA和核DNA的提取与PCR扩增

本研究以PCR缓冲液、MgCl2溶液和蛋白酶K为裂解提取液,建立了一种从山羊绒毛干中快速提取DNA的方法。结果表明,该方法不仅能从山羊绒毛干中提取出线粒体DNA和核DNA,而且能够有效地进行线粒体基因和核基因组基因的PCR扩增,为拓展羊绒样品在个体识别、遗传资源评价、分子进化和分子标记辅助育种等研究领域中的应用奠定基础。     

Comparison of nested PCR and real-time PCR for the detection of Toxoplasma gondii in biological samples from naturally infected cats

There are different protocols of molecular diagnosis methods available including DNA extraction methods to diagnose of Toxoplasma gondii, being necessary to perform comparative studies in biological samples. The aim of this study is to compare real-time PCR (rtPCR) and nested PCR (nPCR) to evaluate the detection of T. gondii in naturally infected cats. Biological samples of Toxoplasma-seropositive cats were assayed for detection of T. gondii DNA - extracted by both the lysis buffer and proteinase K (LB proteinase K) method and the acid guanidinium thiocyanate (GuSCN) method - using rtPCR and nPCR. T. gondii DNA was detected by nPCR in 43.6% and 40.8% of the samples from which it was extracted by the LB proteinase K and the GuSCN method, respectively. With rtPCR these figures fell significantly to 33.8% and 14.1%. Despite of nPCR showed higher sensitivity, the agreement observed between two PCRs was good; this agreement, however, was affected by the DNA extraction method used, LB proteinase K method showed better results.     

分支杆菌DNA的不同提取方法在PCR反应中的定性评价

采用已报道过的分支杆菌DNA7种不同提取方法分别对标准BCG菌株和结核病鹿肺样本DNA提取后比较并进行聚合酶链反应(PCR)扩增,通过PCR反应对几种DNA提取方法做出定性评价。结果表明:方法5和7有100%临床样本检测率,方法7所得DNA浓度和纯度最高。说明临床样本分支杆菌DNA提取过程中使用物理和化学方法裂解细胞,使用蛋白酶K和氯仿纯化、异丙醇沉淀DNA是十分必要的。     

Detection of genomic DNA of the crayfish plague fungus Aphanomyces astaci (Oomycete) in clinical samples by PCR

A diagnostic procedure, based on a polymerase chain reaction method (PCR) was developed to detect infection of crayfish with the Oomycete Aphanomyces astaci. A set of oligonucleotide primers was designed to specifically amplify A. astaci DNA in the ITS region surrounding the 5.8S rDNA gene. The PCR amplifies a 115 bp amplicon. The specificity of the primers was demonstrated by testing on 27 A. astaci strains and against 20 non-A. astaci Oomycetes and 5 fungal species. Most of the non-A. astaci Oomycete or fungal species included in the study are either known parasites of freshwater crayfish cuticle or can be found in their natural environment. Specificity was also tested against crayfish tissue and some known parasites and bacteria infecting crayfish.

A protocol for the extraction of A. astaci DNA from infected crayfish tissue was developed. The optimised method allows the detection of two genome equivalents of purified A. astaci genomic DNA.

The method was tested on noble crayfish (Astacus astacus), artificially infected with A. astaci. Detection of A. astaci was possible at the very first time of sampling, which was 2 days after the beginning of spore exposure.     

Detection of toxoplasmosis in experimentally infected goats by PCR

PCR was used to diagnose toxoplasmosis in two pairs of Barbari goats infected by oral administration of doses of either 10(4) or 10(5) oocysts of Toxoplasma gondii. Blood and lymph node aspirates were collected from the infected goats and control goat at intervals, and tissues were also collected from a fetus that was aborted and a doe that died during the trial. Both processed and unprocessed samples were used for the PCR, using primers directed to the multicopy B1 gene. None of the blood samples was positive, but a specific signal was obtained from the lymph node aspirates after partial DNA extraction. Direct PCR of the lung, muscle and mesenteric lymph node of the doe and lung tissue of the aborted fetus yielded the target fragment. The simplified PCR protocols, including partial DNA extraction and direct assay of lung tissue, were effective for the diagnosis of toxoplasmosis.     

A multiplex real-time PCR for differential detection and quantification of Salmonella spp., Salmonella enterica serovar Typhimurium and Enteritidis in meats

Salmonella (S.) Typhimurium and S. Enteritidis are the major causative agents of food-borne illnesses worldwide. Currently, a rapid detection system using multiplex real-time polymerase chain reaction (PCR) has been applied for other food-borne pathogens such as Escherichia coli, Staphylococcus aureus and Streptococcus spp. A multiplex real-time PCR was developed for the simultaneous detection of Salmonella spp., especially S. Typhimurium and S. Enteritidis, in beef and pork. For the specific and sensitive multiplex real-time PCR, three representative primers and probes were designed based on sequence data from Genbank. Among the three DNA extraction methods (boiling, alkaline lysis, and QIAamp DNA Mini Kit), the QIAamp DNA Mini Kit was the most sensitive in this study. The optimized multiplex real-time PCR was applied to artificially inoculated beef or pork. The detection sensitivity of the multiplex real-time PCR was increased. The specificity of the multiplex real-time PCR assay, using 128 pure-cultured bacteria including 110 Salmonella isolates and 18 non-Salmonella isolates, was 100%, 100% and 99.1% for Salmonella spp., S. Typhimurium and S. Enteritidis, respectively. The sensitivity was 100%, 100% and 91.7% for Salmonella spp., S. Typhimurium and S. Enteritidis, respectively. The multiplex real-time PCR assay developed in this study could detect up to 0.54 ± 0.09 and 0.65 ± 0.07 log₁₀ CFU/ml for S. Typhimurium and S. Enteritidis for beef, 1.45 ± 0.21 and 1.65 ± 0.07 log₁₀ CFU/ml for S. Typhimurium and S. Enteritidis for pork, respectively, with all conditions optimized. Our results indicated that the multiplex real-time PCR assay developed in this study could sensitively detect Salmonella spp. and specifically differentiate S. Typhimurium from S. Enteritidis in meats.     

Evidence of Neospora caninum DNA in wild rodents

Seventy-five house mice (Mus musculus), 103 rats (Rattus norvegicus) and 55 field mice (Apodemus sylvaticus) from North-West Italy were PCR analysed for Neospora caninum infection. Brain, kidney and muscle tissues collected from the above mentioned animals were tested by PCR using Np6 and Np21 primers. The brain tissue from 2 house mice and 2 rats, the kidney from 4 rats, 1 house mouse and 1 field mouse and muscle from 10 rats, 8 house mice and 1 field mouse were tested positive for N. caninum. Sequencing showed a 96-97% identity of PCR products with N. caninum NC1 sequence. Our findings support previous report on house mouse and rat, and for the first time, provides the evidence of the infection also in field mice. Based on our data, it could be hypothesized that mice can act as a reservoir of N. caninum, and they can play a role in maintaining/spreading N. caninum infection also in the sylvatic cycle. The possibility that dogs could be infected by eating infected house mice suggests new opportunities for N. caninum prophylaxis and control.     

1株猪鼻支原体的分离鉴定及致病性

猪鼻支原体是猪场感染率极高的一种支原体,可引起多发性浆膜炎、关节炎等症状。目前尚未建立标准的猪鼻支原体发病模型,也缺乏标准强毒株。本研究从某猪场发病猪的关节液中分离得到一株支原体,通过PCR检测、菌落形态观察、菌体形态电镜分析、菌株MLST分型等方法对其进行了鉴定,确认其为猪鼻支原体。为评价菌株致病性,将该分离株接种1月龄自然分娩不吃初乳猪（SF-pCD猪）,试验猪在感染后出现关节肿胀、跛行等临床症状,日增重显著低于对照组,并出现部分死亡。剖检结果显示感染组出现胸膜炎、腹膜炎、心包炎及关节炎,肺部组织病理分析显示为间质增宽,无虾肉样病变。从发病猪的扁桃体、肺、心及关节积液中可再次分离到攻毒株。综上,本研究分离获得一株猪鼻支原体,人工感染猪后可出现典型的发病症状,猪鼻支原体发病模型的建立为致病机制及疫苗研究奠定了重要的基础。     

Presence of Maedi Visna Virus (MVV)‐Proviral DNA in the Genital Tissues of Naturally Infected Ewes

Maedi Visna virus (MVV) causes progressive degenerative inflammatory disease in multiple organs including the lungs (pneumonia, ‘maedi’), mammary gland, joints and nervous system (meningoencephalomyelitis, ‘visna’) in sheep. Maedi Visna Virus has been detected in macrophages of several tissues and epithelial cells in vivo: bone marrow, cells of the central nervous system, lung and bronchial tissues, milk epithelial cells recovered from milk samples and epithelial cells of mammary tissue. However, the presence of MVV in the genital tracts of naturally infected ewes has not previously been studied. The aim of this study was to use nested‐PCR, targeting the gag gene, to determine whether genital tissues (ovaries, oviducts and uterus) from 83 ewes originating from various breeding herds in the South‐East of France were positive for MVV‐proviral DNA. Peripheral blood mononuclear cells (PBMC) tested positive for MVV‐proviral DNA, using nested‐PCR analysis, in 57.8% of ewes (48/83). The provirus was also identified in 47% (78/166) of the ovaries, 38.6% (64/166) of the oviducts and 45.8% (38/83) of the uteri sampled. These findings clearly demonstrate, for the first time, that tissue samples from the genital tract of ewes (ovary, oviduct and uterus) can be infected with MVV. This suggests that there is a risk of vertical and/or horizontal transmission of MVV during embryo transfer from embryos produced in vivo or in vitro.     

一种高效提取桑树根围土壤微生物总DNA的方法

为了建立桑树根围土壤微生物群落结构的分子生态学试验技术体系,采取不同的细胞裂解方法及DNA沉淀方法直接提取桑树根围土壤微生物总DNA,并以采用试剂盒提取的桑树根围土壤微生物总DNA为参照,筛选出一种能有效提取高纯度、多样性土壤微生物总DNA的方法:以十六烷基三甲基溴化铵(CTAB)、溶菌酶、蛋白酶K、十二烷基磺酸钠(SDS)为裂解液,经反复冻融裂解细胞,在DNA提取液中添加聚乙烯吡咯烷酮K30(PVP K30)、牛血清蛋白(BSA)、CaCl2去除腐殖酸,并结合聚乙二醇8000(PEG8000)沉淀和纯化DNA。该方法简便、快速,获得的桑树根围土壤微生物基因组DNA分子长度在23 kb以上,土壤鲜样的微生物DNA产率为11.2μg/g,且纯度较高,D(260 nm)/D(230 nm)=1.42,D(260 nm)/D(280 nm)=1.37,可直接用于PCR扩增及变性梯度凝胶电泳(DGGE)分析。     

Determination of an efficient and reliable method for DNA extraction from ticks

Molecular detection of pathogenic microorganisms in ticks is based on DNA amplification of the target pathogen; therefore, extraction of DNA from the tick is a major step. In this study, we compared three different tick DNA extraction protocols based on an enzymatic digestion by proteinase K followed by DNA extraction by a commercial kit (method 1), or on mortar crushing, proteinase K digestion and phenol/chloroform DNA extraction (method 2) and fine crushing with a beads beater, proteinase K digestion and DNA extraction using a commercial kit (method 3). The absence of PCR inhibitors and the DNA quality were evaluated by PCR amplification of the tick mitochondrial 16S rRNA gene using tick-specific primers. With method 1, 23/30 (77%) of the samples were extracted; with method 2, 30/31 (97%) of the samples were extracted and with method 3, 30/30 (100%) of the samples were extracted. DNA extraction efficiency using method 3 is significantly higher than DNA extraction efficiency using method 1 (100% versus 77%, P < 0.05). There was no significant difference between methods 2 and 3. Method 3 was however more adapted to cohort studies than method 2. This technique was validated for cohort tick DNA extraction and applicable to the treatment of small samples such as nymphs and soft ticks with 100% efficiency.     

Rapid detection of pseudorabies virus genomic sequences in biological samples from infected pigs using polymerase chain reaction DNA amplification

The presence of the pseudorabies virus (PRV) genome in infected hosts has previously been studied by standard hybridization techniques, which showed the viral genome to be present at very low levels in infected tissues. The recently introduced polymerase chain reaction (PCR) procedure provides an alternative and rapid means of amplifying small quantities of specific DNA sequences. We applied this technique to a study of pigs infected by PRV. The sequence selected for amplification consisted of 222 base pairs lying in the gene coding for the glycoprotein gp50. We used a pair of 20-mer oligonucleotides flanking this sequence as primer and a cloned Stu-Nde fragment containing the sequence as target DNA. To avoid the tedious DNA extraction procedure we performed PCR directly on disrupted cells and detected specific amplification after 25 cycles of PCR with the thermostable Taq DNA polymerase. Amplified products were detected by gel electrophoresis directly. Nasal samples from experimentally and naturally infected pigs were tested by this PCR technique. When compared with tissue culture and serological tests, detection by gel electrophoresis of PCR amplified fragments provided excellent specificity and sensitivity. We concluded that PCR amplification will be a valuable tool for rapid diagnosis of PRV infection in pigs, taking less than 1 h to complete.     

A polymerase chain reaction assay for the detection of Leptospira spp. in bovine semen.

A rapid and specific method for the detection of pathogenic Leptospira spp. in bovine semen using the polymerase chain reaction (PCR) is described. The primers used were derived from an EcoR1/BamH1 fragment that hybridized strongly to chromosomal DNA from the hardjobovis serovar. Three different extraction methods were evaluated in this study: phenol-chloroform extraction method, proteinase K (PK) in 1% SDS, followed by phenol-chloroform, and phenol-chloroform followed by 1% cetyltrimethylammonium bromide (CTAB). A PCR product of approximately 500 base pairs (bp) in length was obtained when DNA from pure Leptospira culture was used as a template for PCR, regardless of the DNA extraction method used. The product was consistent with that predicted from the gene sequence. However, in semen seeded in vitro, as well as in semen from infected bulls, a PCR product was obtained only when the leptospiral DNA was extracted from the specimen using the CTAB method. In contrast, other methods used for DNA extraction did not generate suitable templates for the PCR procedure. This is the first PCR protocol developed to detect Leptospira in bovine semen. The PCR protocol provided a direct and unequivocal demonstration that Leptospira can be detected in semen of infected animals. The CTAB method was also used successfully in detecting Leptospira in the urine of infected animals. The PCR procedure was shown to be more sensitive than either the fluorescent antibody test (FAT) or culture for detecting the organism in urine.     

3种犬细小病毒感染诊断方法比较

本研究应用犬细小病毒抗原快速检测试剂盒、血凝/血凝抑制试验和PCR方法对120份具有腹泻/呕吐症状的患犬粪便样本进行了犬细小病毒检测。结果显示,3种方法检测阳性份数分别为60,49,68。犬细小病毒抗原快速检测试剂盒与血凝/血凝抑制(HA/HI)试验相比较,敏感性、特异性及总符合率分别为100.0%,84.5%,90.8%;与PCR法相比较,敏感性、特异性及总符合率分别为85.3%,96.2%,90.0%。从试验结果看,HA/HI法具有较高的特异性,但敏感性较低;PCR具有高度敏感性和特异性,但不适合临床推广;细小病毒抗原快速检测试剂盒,在正确操作下结果可靠,是临床诊断犬细小病毒感染的首选方法。     

A multiplex PCR for the detection of Brucella spp. and Leptospira spp. DNA from aborted bovine fetuses

Bovine brucellosis and leptospirosis are important causes of bovine abortion around the world. Both diseases can be serologically diagnosed, but many factors may cause false positive and negative results. Direct methods based on bacteriological isolation are usually employed, but they are difficult, time consuming and dangerous. Monoplex polymerase chain reaction (PCR) have been successfully described for the detection of Brucella spp. and Leptospira spp. Aiming at improvement in the direct diagnosis, a multiplex PCR (mPCR) for the detection of these agents in aborted bovine fetuses is described. The detection threshold of the mPCR was evaluated in experimentally contaminated bovine clinical samples using a conventional proteinase K/SDS or a boiling-based extraction protocols. The mPCR was applied to two groups of clinical samples: 63 episodes of bovine abortion and eight hamsters experimentally infected with Leptospira interrogans serovar pomona. Adopting microbiological isolation as reference, the test showed a sensitivity of 100% in both groups of clinical samples. Seven samples collected from bovine fetuses were Brucella spp. culture negative but showed positive results in mPCR. Regarding Leptospira spp. detection, similar results were observed in three bovine clinical samples. All hamsters infected with Leptospira were positive in both microbiological culture and mPCR. The boiling extraction protocol showed better results in some clinical samples, probably by the removal of PCR inhibitors by heat treatment. The high sensitivity, simplicity and the possibility of detection of both bacteria in a single tube reaction support the use of the mPCR described in the routine diagnosis.     

Use of a Mycoplasma hyopneumoniae nested polymerase chain reaction test to determine the optimal sampling sites in swine.

A number of polymerase chain reaction (PCR)-based diagnostic tests have been developed for Mycoplasma hyopneumoniae, including one from this research group. This report presents further development, optimization, and standardization of a nested PCR test. Detection sensitivity was 1 fg of M. hyopneumoniae chromosomal DNA (approximately 1 organism). This exceeded the sensitivity of or compared favorably with other published PCR tests. Polymerase chain reaction primers to porcine beta2-microglobulin were included as internal controls for amplifiable chromosomal DNA from porcine samples. To standardize the test, a number of samples from experimentally infected pigs, including nasal, tonsil, tracheobronchial swabs, lung tissue, bronchial alveolar lavage (BAL) fluid, and tracheobronchial brush samples, were examined by PCR. Samples obtained from BAL fluid and tracheobronchial sites were most predictive of infection, whereas nasal swabs and lung tissue were not reliable indicators of experimentally induced infection. In conclusion, the nested PCR developed for this study was found to be a highly sensitive and specific diagnostic tool for M. hyopneumoniae, but the enhanced sensitivity may be unnecessary if the proper sites are sampled.     

家蚕蛋白质双向电泳的样品制备方法

进行蛋白质组研究的关键是要尽可能完整地获得一个基因组在一个生物体或一个组织器官的特定时期表达的蛋白质的种类和数量 ,双向电泳技术是分离组织和器官蛋白质的核心技术 ,而蛋白质样品的制备是双向电泳的基础。以家蚕胚胎、中肠、皮肤、丝腺等组织器官为材料 ,采用磷酸缓冲液或Tris HCl缓冲液抽提蛋白质样品 ,用 6种不同的蛋白质溶解缓冲液溶解蛋白质 ,经蛋白质双向电泳和蛋白质图像软件分析 ,结果表明用磷酸缓冲液抽提、蛋白质溶解缓冲液E溶解是制备家蚕蛋白质双向电泳样品的较好方法。蛋白质磷酸抽提缓冲液 (PBS)的组成为 :32 5mmol/LK2 HPO4,2 6mmol/LKH2 PO4,4 0 0mmol/LNaCl,pH 7 6。蛋白质样品溶解缓冲液E的组成为 :8mol/L尿素 ,2mol/L硫尿 ,4 %CHAPS ,2 0mmol/LTrisbase,30mmol/LDTE ,2 %Pharmalyte(pH 3～ 10 )。