PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed,paraffin-embedded tissues

The polymerase chain reaction (PCR) was used to amplify specific segments of the 16S ribosomal RNA gene of Clostridium chauvoei, a major pathogen of ruminants. Three sets of primers were used to produce amplicons of 159, 836 and 959 base pairs (bp), respectively. The PCR was evaluated by testing clinically important strains of Clostridium, including 21 strains of C. chauvoei, five strains each of Clostridium septicum and Clostridium perfringens and two strains each of Clostridium novyi, Clostridium histolyticum and Clostridium sordellii. Both purified DNA and biomass from pure cultures of each of these microorganisms were evaluated as templates in the PCR. In addition, extracts of formalin-fixed, paraffin-embedded tissues of eight sheep experimentally inoculated with C. chauvoei or C. septicum (four animals each) were also tested by the PCR using the three sets of primers. Purified DNA template of all C. chauvoei strains produced PCR amplicons of the expected size for all three primer pairs. However, when biomass from pure cultures of C. chauvoei or tissue extracts were used as templates, only the primer pair designed to produce the 159bp amplicon gave consistently positive results. No positive results were obtained with any primer pair when purified DNA or biomass from pure cultures of non-target clostridial species were used as templates. Therefore, the PCR primer sets appear to be very specific for identifying C. chauvoei in both cultures and tissues.     

Quantitative real-time PCR for detection of neurotoxin genes of Clostridium botulinum types A,B and C in equine samples

Botulism in horses in the USA is attributed to Clostridium botulinum types A, B or C. In this study, a duplex quantitative real-time PCR (qPCR) for detection of the neurotoxin genes of C. botulinum types A and B, and a singleplex qPCR for detection of the neurotoxin gene of C. botulinum type C, were optimized and validated for equine gastrointestinal, faecal and feed samples. The performance of these assays was evaluated and compared to the standard mouse bioassay (MBA) using 148 well-characterized samples, most of which were acquired from a repository of veterinary diagnostic samples from cases of botulism: 106 samples positive for C. botulinum (25 type A, 27 type B, 28 type C, 1 type D and 25 type E) and 42 negative samples. The sensitivities of the qPCR assays were 89%, 86% and 96% for C. botulinum types A, B and C, respectively. The overall sensitivity of the mouse bioassay for types A, B and C was 81%. The specificities of the qPCR assays were 99–100% and the specificity of the mouse bioassay was 95%.     

鉴别牛早期胚胎性别PCR方法引物的设计与筛选

根据牛Y-染色体特异重复序列、睾丸特异蛋白基因以及性别决定基因序列设计合成5对公牛Y-染色体特异引物，依据牛骨胳肌α肌动蛋白前体基因和微卫星DNA序列设计合成4对牛DNA特异引物(内标引物)。单重PcR扩增牛基因组DNA，筛选出4对牛Y-染色体特异引物和1对牛DNA特异内标引物。将不同的Y-染色体特异引物与内标引物组合，多重PCR扩增牛基因组DNA、已知性别的牛成纤维细胞和克隆胚胎，筛选出2个可用于牛早期胚胎性别鉴别的PCR引物组合：B34／A12和B78／A12。     

Preliminary study on differentiation of Leptospira grippotyphosa and Leptospira sejroe from other common pathogenic leptospiral serovars in canine urine by polymerase chain reaction assay.

A multiplex polymerase chain reaction (PCR) method using primer sets of G1/G2 and B64-I/B64-II was validated to detect pathogenic leptospira serovars from canine urine samples. The PCR method was found to be specific and sensitive with a detection limit of 100 cells of Leptospira icterohaemorrhagiae per milliliter of urine. The primer set previously designated and erroneously transcribed B64-I/B64-II amplified a DNA fragment of 352 base pairs from Leptospira grippotyphosa and Leptospira sejroe but not from Leptospira autumnalis, Leptospira bratislava, Leptospira canicola, Leptospira hardjo, Leptospira icterohaemorrhagiae, and Leptospira pomona. From 100 diagnostic canine urine samples, 5 were found positive for Leptospira grippotyphosalsejroe with a PCR product of 352 base pairs and 6 were positive for other pathogenic leptospira serovars with a PCR product of 285 base pairs. One 285-base pair product was sequenced and found to be 99.3% homologous to the G1/G2 PCR fragment sequence reported previously. All 352-base pair PCR products of clinical samples and pure cultures of L. grippotyphosa and L. sejroe were sequenced. The 352-base pair fragment sequences of L. grippotyphosa and L sejroe were identical. Only 2 base pairs were found different between the sequences from pure cultures and those from clinical samples. Serum samples from 3 positive cases that generated a PCR product of 352 base pairs were tested by the microscopic agglutination test, and 2 were found to be positive for L. grippotyphosa (1:10,240 and 1:5,120), 1 was positive for L. grippotyphosa (1:320) or L. icterohaemorrhagiae (1:320). The results of this study suggest that the multiplex PCR with the primer set G1/G2 and the erroneously transcribed B64-I/B64-II may be able to differentiate L. grippotyphosa or L. sejroe from other pathogenic leptospira serovars commonly tested for in Canadian diagnostic laboratories.     

Diagnosis of botulism types C and D in cattle by a monoclonal antibody-based sandwich ELISA

This study was undertaken to evaluate two monoclonal antibody-based sandwich ELISAs (sELISAs) for the detection of Clostridium botulinum neurotoxins (BoNTs) types C and D from culture-enriched intestinal content samples from cattle. To validate the diagnostic significance of the presence of cultivable, toxin-producing C botulinum in the intestines of cattle, samples from both suspect and non-suspect botulism cases were examined. BoNT was detected by both sELISAs in a greater number of suspect animals than by direct testing of uncultured samples by mouse bioassay. One sELISA detected two BoNT C and one BoNT Group III mosaic isoform in three animals that were missed by the other, and both sELISAs failed to identify samples from two mouse bioassay-positive BoNT C animals. BoNT D was also detected in one non-suspect sample by one of the sELISAs.     

牛病毒性腹泻病毒一步法RT-PCR检测方法的建立

根据牛病毒性腹泻/粘膜病病毒5'端非结构蛋白基因序列,设计合成1对特异性引物,建立检测牛病毒性腹泻/粘膜病病毒244 bp片段的RT-PCR一步法。该方法对牛病毒性腹泻/粘膜病病毒NADL、OregonC24V和长春184毒株各标准毒株检测,结果均为阳性。对标准毒株的细胞毒进行检测,其敏感度达0.1 TCID50;而对牛传染性鼻气管炎病毒、猪瘟病毒、牛轮状病毒和牛冠状病毒的细胞培养物进行检测,结果均为阴性。检测460份不同样品,与病毒分离试验比较,符合率100%,证明该方法特异性强,敏感性高。初步结果表明所建立的一步法RT-PCR技术可用于牛病毒性腹泻/粘膜病的检测及流行病学调查。     

Polymerase chain reaction with a primer pair in the 16S-23S rRNA spacer region for detection of Mycoplasma pulmonis in clinical isolates

To develop a diagnostic tool to identify Mycoplasma pulmonis (M. pulmonis) in clinical isolates, we developed a polymerase chain reaction (PCR) assay using primers specific for the 16S-23S rRNA intergenic spacer region (SR) of M. pulmonis. One pair of PCR primers reacted specifically with two reference strains of M. pulmonis tested and seven samples isolated from naturally infected rats. The primer pair did not produce PCR products of the correct size from any other rodent or human mycoplasmas or cellular DNA from rodent lungs. Specificity of the PCR assay was confirmed by Southern blotting with probe specific for the SR of M. pulmonis. The PCR assay for detection of M. pulmonis established in this study is suitable for diagnosis of M. pulmonis infection in clinical cases.     

多重PCR快速检测奶牛乳房炎3种主要病原体

奶牛乳房炎是引起奶牛业经济损失的一种重要疫病,目前还没有快速、特异检测奶牛乳房炎主要致病原的方法。本试验根据金黄色葡萄球菌、无乳链球菌、大肠杆菌各自保守的16S或23S rRNA基因序列,合成了3对特异性引物,建立了三重PCR检测方法。特异性试验表明,该方法对所有参与测试的金黄色葡萄球菌、无乳链球菌和大肠杆菌都能扩增出各自的阳性条带,而对所有参与测试的对照菌株则不能扩增出任何条带。敏感性试验表明该方法能检测到4个菌的金黄色葡萄球菌、无乳链球菌和2个菌的大肠杆菌。对送检的乳房炎奶样36份直接进行PCR检测,金黄色葡萄球菌阳性7份,无乳链球菌阳性2份,大肠杆菌阳性6份。     

Multiplex real-time PCR SYBR Green for detection and typing of group III Clostridium botulinum

Clostridium botulinum type C and type D belonging to the group III organisms, are mainly responsible for animal botulism outbreaks. Clinical signs alone are often insufficient to make a diagnosis of botulism and a laboratory confirmation is required. Laboratory confirmation can be performed by demonstrating the presence of botulinum neurotoxins in serum, gastrointestinal contents, liver, wound of sick or dead animals, or by demonstrating the presence of C. botulinum in gastrointestinal contents, liver, and wound. Demonstration of spores in gastrointestinal contents or tissue of animals with clinical signs indicative of botulism reinforces the clinical diagnosis. With the aim of detecting and typing C. botulinum group III organisms, a multiplex real-time PCR SYBR Green was developed and in-house validated. Selectivity, limit of detection, relative accuracy, relative specificity, relative sensitivity, and repeatability of the method were investigated. The multiplex real-time PCR SYBR green used showed a 100% selectivity, 100% relative accuracy, 100% relative specificity, 100% relative sensitivity and a limit of detection of 277 and 580 DNA copies for C. botulinum type C and C. botulinum type D, respectively. The method reported here represents a suitable tool for laboratory diagnosis of type C and D botulism and for testing a large number of samples collected during the animal botulism surveillance and prevention activities.     

Detection and identification of salmonellas from poultry-related samples by PCR

A polymerase chain reaction (PCR) assay was developed for the generic detection of Salmonella sp. and the identification of S. Enteritidis (SE), S. Gallinarum (SG), S. Pullorum (SP) and S. Typhimurium (ST) in material collected in the field from poultry. The specificity and sensitivity of the assay combined with Rappaport-Vassiliadis selective enrichment broth (PCR-RV) were determined, and field samples were analyzed to verify the validity of the method application. Specificity of the assay was tested using 29 SE, 11 SG, 10 ST and 10 SP strains, along with 75 strains of 28 other Salmonella serovars and 21 strains of other bacterial genera. The assay was 100% specific for Salmonella detection and ST identification. The primer pair for SE, SG and SP also detected S. Berta. PCR detection limits for Salmonella at the genus level were 2 ST, 8 SE, 1.1x10(3) SG and 1.8x10(5) SP cells. At the serovar level, detection limits were 7 ST, 1.2x10(3) SE, 4.4x10(7) SG and 1.8x10(6) SP cells. At the genus level, PCR-RV detected approximately 128% more positive field samples than the standard microbiological techniques and results were ready in 48h instead of 7 days. PCR-RV method is diagnostic of Salmonella at the genus level and ST at the serovar level, although other tests are needed to identify SE, SG and SP to serovar level.     

Detection of feline immunodeficiency proviral DNA in peripheral blood lymphocytes by the polymerase chain reaction.

Feline immunodeficiency virus (FIV) proviral DNA was detected by the polymerase chain reaction method (PCR). PCR products were detected by gel electrophoresis and ethidium bromide staining. The P-10, P-15 and P-24 regions of the gag gene of FIV were chosen as the target sequences for amplification, and three primer pairs were prepared. The PCR products subjected to amplification with each primer pair were found to possess sites of digestion by a restriction enzyme, as hypothesized. They did not react with feline leukemia virus (FeLV)-infected or feline syncytium-forming virus (FeSFV)-infected cell-derived DNA, and specifically amplified FIV-infected cell-derived DNA. FIV proviral DNA was detected by the PCR method with either primer pair (one-step amplification: single PCR) in DNA derived from peripheral blood lymphocytes (PBL) from 7 of 12 FIV antibody-positive cats. When PCR products in each of the 12 cats were subjected to a second amplification using the same primer pair (two-step amplification: double PCR), FIV proviral DNA was detected in all of the cats. When PBL samples collected from three cats that were negative and three that were positive in the single PCR were cultured for a few weeks in the presence of interleukin 2, FIV proviral DNA was detected in all six cats by the single PCR method. The results suggest that either the use of cultured PBL as the sample or the performance of the double PCR method enables simple and specific detection of FIV proviral DNA in PBL.     

Identification of genotypes of Giardia intestinalis isolates from dogs in Japan by direct sequencing of the PCR amplified glutamate dehydrogenase gene

Giardia has been detected in domestic dogs in Japan, but the genotype of isolates has remained unclear because identification has relied on conventional microscopy. Here we tried to identify the genotypes of four isolates from dogs in Japan by direct sequencing of the PCR amplified Giardia glutamate dehydrogenase (GDH) gene. The primer pair GDHF3 and GDHB5, targeting the GDH gene, was designed to prime a region of the GDH gene sequence conserved in the strains found to have the dog-specific genotype. The specific PCR product (approximately 220 bp), amplified with this primer pair, was only observed when Giardia DNA was used as the template. The sequences of the diagnostic fragments were identical among the isolates from dogs, and were differed by 15 bp or 1 bp from the strains, which were found to be the dog-specific genotypes, Assemblage C or D respectively. To verify the identity of the amplified DNA, a phylogenetic analysis was performed. Consequently, the sequence of the isolates from dogs clearly clustered with the strain found to be Assemblage D with neighbor-joining analyses. Therefore, all the isolates from dogs examined were identified as the dog-specific genotype, Assemblage D. In the present study, we revealed the genotype of Giardia isolates in Japan, and showed that direct sequencing of the PCR product amplified with the primer pair GDHF3 and GDHB5 was a useful tool for distinguishing between the zoonotic and dog-specific genotypes.     

检测和鉴别犬瘟热病毒强、弱毒株的复合反转录-套式聚合酶链式反应(RT-nPCR)的建立及初步应用

根据GenBank上登录的犬瘟热病毒（Canine distemper virus，CDV）基因组全序列，选择CDV强、弱毒株间有区别保守区设计了一对通用引物P1和P4，并在该对引物跨越区域的内部设计了CDV强毒株特异性引物P2及弱毒株特异性引物P3，用引物P1／P4进行RT—PCR，然后用引物P2／P3／P4进行复合套式PCR，建立了一种能区分CDV强、弱毒株的复合反转录-套式聚合酶链式反应（RT—nPCR）的鉴别诊断方法。应用该方法从CDV强、弱毒株的基因组中分别扩增出了大小为247bp和177bp的特异性片段，从两种病毒基因组混合物中扩增出了大小为247bp和177bp的两条特异性片段，与犬细小病毒、犬腺病毒、犬冠状病毒、狂犬病病毒、新城疫病毒的细胞培养物以及正常细胞对照组进行复合RT—nPCR扩增时均为阴性。对从黑龙江省和吉林省采集的20份疑似CDV病料进行的检测结果表明，有15份类似CDV强毒，5份类似CDV弱毒。本研究建立的复合RT—nPCR可以有效检测CDV感染，能够将强、弱毒株区分开，可用于临床快速检测、流行病学监测以及追踪疫苗免疫效果等。     

牛早期胚胎性别鉴定PCR反应体系优化的研究

根据牛SRY基因序列设计合成2对巢式PCR引物作为性别鉴定引物,根据牛-珠蛋白基因序列设计了一对引物作为内标引物建立了牛胚胎性别鉴定的PCR反应体系。公牛可以扩增出187bp的SRY基因片段和255 bp的-珠蛋白基因片段,母牛只能扩增出255 bp的-珠蛋白基因片段。由于巢式PCR只需3～8个细胞就可以在紫外灯下看到扩增结果,而常规PCR则需要较多的细胞,所以胚胎性别鉴定时使用巢式PCR效果更好。     

RT-PCR evaluation for identification and sequence analysis of foot-and-mouth disease serotype O from 2006 to 2007 in Punjab, Pakistan

FMD clinically positive 250 tissue samples (mouth and hoof epithelium and vesicle swabs, tongue tissue) and 175 secretion samples (milk, saliva, serum, plasma) were evaluated by RT-PCR for the diagnosis of FMD with different pair of universal and serotype-specific primers from 2006 to 2007 in Punjab, Pakistan. Universal primer pair P1/P2 from VP1 gene detected FMD in 182 out of 250 (72.8%) tissues and 92 out of 175 (52.6%) secretion samples, while universal primer 1F/1R from 5′UTR region detected FMD in 218 out of 250 (87.2%) tissues and 142 out of 175 (81.1%) secretion samples. 1F/1R proved better than the P1/P2 primer pair for primary diagnosis of FMD, direct from the clinical positive samples. Direct sequencing of the universal primer pair P1/P2 revealed that O serotype of FMD was circulating in this region. O serotype of FMD was detected with O-1C(ARS4)/PNK 61, AU(O)/AU(rev), AU(O)/PNK61 primer pairs, these primer pairs also compared with each other. AU(O)/AU(rev) and AU(O)/PNK61 detected O serotype of FMD in 88.9% tissue and swab (mouth and hoof vesicle swabs) samples and 71.9% different secretion (milk, saliva, serum, plasma) samples, while O-1C(ARS4)/PNK 61 detected 48.1% tissue and swab (mouth and hoof vesicle swabs) samples and 37.5% different secretion (milk, saliva, serum, plasma) samples. AU(O)/AU(rev), AU(O)/PNK61 primer pairs detected 40.8% more tissue and swab samples, while these pairs detected 34.4% more secretion samples. Cloning of PCR product of AU(O)/AU(rev) VP1 gene and sequencing for phylogenetic studies revealed that O serotype of FMD circulating in Punjab, Pakistan was genetically very diverse from the ‘O’ serotype in Middle East and Europe. The dendrogram showed that Pakistan ‘O’ serotype was very much similar genetically to its neighbor countries (Sri Lanka, India, Iran, Iraq, and China) and PanAsia 1 lineage which caused 2001-outbreak in UK and 1994-outbreak in Saudi Arabia, etc.     

产毒素多杀性巴氏杆菌的鉴定

采用菌落多重PCR方法对分离保存的28株多杀性巴氏杆菌进行种型和毒素基因的检测,结果表明,菌株C51-6、M-4和P-2237为产毒素多杀性巴氏杆菌,菌株C51-6和P-2237为荚膜血清D型,菌株M-4为荚膜血清A型。同时用金黄色葡萄球菌抑制试验、中性吖啶黄沉淀试验和豚鼠皮肤坏死试验对PCR方法进行了验证。基于对甘露醇、卫茅醇、山梨醇、海藻糖的发酵能力和产生鸟氨酸脱羧酶的特性,3株菌株鉴定为多杀性巴氏杆菌多杀亚种。     

Design and evaluation of primer pairs for efficient detection of avian rotavirus

The use of molecular methods for rotavirus characterisation provides increased sensitivity for typing and allows the identification of putative reassortant strains. Reagents and methods for genotyping the virus need constant modification because of the reassortant nature of the virus. This study was aimed at designing and evaluating new oligonucleotide degenerate primer pairs that provide increased sensitivity and specificity for detecting avian rotavirus. Gene-specific primer pairs were designed by analysing different rotavirus strains isolated during the last decade by downloading them from the GenBank. The alignments were generated using clustal analysis from the BioEdit program. Degenerate nucleotides were included due to the reassortant nature of rotavirus. The consensus sequences were aligned using the BioEdit program and then treated with the Fast PCR software to derive the primers. The derived primer sequences were submitted for a BLAST search to ensure alignment was exclusive to the desired target genes. The designed primers had specific bands and were efficient in detecting rotavirus in faecal samples than previously published primers. Thus, a successful surveillance of rotaviruses requires that primer pairs be updated regularly in order to detect the emergence of novel or “unusual types”, which have occurred by genetic drift causing nucleotide changes at the primer binding sites that result in typing failures. We recommend the use of the proposed primers in molecular surveillance studies for efficient detection of avian rotavirus.     

Emergence of suspected type D botulism in ruminants in England and Wales (2001 to 2009), associated with exposure to broiler litter

Scanning surveillance by the Veterinary Laboratories Agency revealed the emergence of suspected botulism in ruminants in 2003, presented as flaccid paralysis. From 2003 to 2009, 168 cattle and 19 sheep incidents were recorded, with mortality between 5 and 80 per cent. All sheep incidents and 95 per cent of cattle incidents had proximity to broiler litter. From July 2006, the gut contents collected from 74 affected cattle and 10 affected sheep were tested for Clostridium botulinum toxins using mice bioassays and for organisms by culture. Type D toxin was identified in 32 per cent of cattle and 18 per cent of sheep samples. C botulinum type D organisms were identified in 40 per cent of cattle and 30 per cent of sheep samples, but broth from one sample reacted with C and D antisera. Type C botulism has previously been reported more commonly than type D in the UK and has been associated with the use of poultry litter as fertiliser, bedding or feed. The almost exclusive association with C botulinum type D toxins or organisms in the gut contents in this survey suggests a change in the source or epidemiology of botulism in the UK. The source of C botulinum type D was uncertain. Broilers may carry C botulinum type D in their gut flora subclinically. The emergence of a new type D strain, or changes in broiler husbandry and nutrition, medication and other enteric infections may have affected colonisation with C botulinum. Further investigation of poultry and farm environments for sources of type D awaits the development of tests for C botulinum toxins that do not require the use of mice.     

Study of the toxin-producing ability of Pasteurella multocida in mice

Cell-free sonicated extracts and broth cultures of Pasteurella multocida strains of pig origin were examined for their lienotoxicity in mice. P. multocida strains represented capsular types A and D with or without dermonecrotoxic (DNT) activity in the guinea pig skin test. Mouse lienotoxicity test was suitable for determining the toxigenicity of P. multocida strains only when bacterium-free extracts were tested. In that case both toxigenic type A and D strains were lethal to intravenously inoculated mice and caused a remarkable reduction in spleen mass when sublethal doses were used. The extracts of atoxic strains were not lethal and induced splenic hyperplasia. By testing viable cells no correlation was demonstrable between toxin production and virulence of P. multocida to mice. In one experiment the concentrated sterile culture fluids of a toxigenic type D P. multocida and a toxigenic B. bronchiseptica strain were compared. The former caused deaths and splenic atrophy among mice, while the latter was nontoxic and induced slight hyperplasia of the spleen. This fact indicates that P. multocida secretes its toxin into the culture fluid.