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。     

猪附红细胞体PCR诊断方法的建立及应用

根据基因库中已登录的猪附红细胞体新的基因组DNA序列设计引物,从疑似猪附红细胞体(Mycoplasma suis)感染猪全血样品基因组DNA中扩增出了预期长度666 bp的目的DNA片段,通过对24份临床疑似病例样品的PCR扩增及其他病原微生物基因组DNA的特异性扩增试验,建立了E.suis的PCR诊断方法;进一步对PCR产物克隆、测序分析表明,与国外已报道的AJ504999株相关区域核苷酸、氨基酸序列同源性分别为98.19%和96.85%,表明我国分离株与国外株基因组存在差异。     

猪弓形虫特异性PCR诊断方法的建立及应用

以猪弓形虫核糖体DNA第一内转录间隔区(ITS1)序列为模板自行设计引物,建立了猪弓形虫病特异PCR诊断方法,并从弓形虫国际标准强毒株RH速殖子和疑似T.gondii感染猪全血及肺脏组织样品基因组DNA中扩增出了预期长度273bp的目的DNA片段。敏感性和特异性试验结果显示,该PCR方法能检测到的最低DNA量为0.001ng,且与相关的9种对照寄生虫、细菌和病毒无交叉反应。用建立的PCR诊断方法对临床30份猪弓形虫疑似病料和60份健康猪抗凝全血样品进行检测,结果30份病料中有24份呈现阳性;60份健康猪血中有5份为阳性;随机取两个临床样品的阳性PCR扩增片段进行克隆测序表明,二者序列与Gen-Bank中已登录的猪弓形虫ITS1基因相应部分序列完全相同。以上表明所建立的PCR方法具有高度的敏感性和特异性;本研究为猪弓形虫病的快速诊断提供了一种新方法。     

非电泳法PCR牛早期胚胎性别鉴定研究

为选出更高效、实用的牛胚胎性别鉴定方法，分别用成年牛血样提取的基因组DNA和冷冻的牛早期胚胎细胞DNA为样本，以电泳法和非电泳法用相应的性染色体DNA引物做胚胎PCR性别鉴定实验，以相对比。血液模板DNA结果与胚胎样本结果都表明，使用DYZ-1引物的非电泳法在比使用SE引物的电泳节约1h以上时间的同时，具有比SE更高的灵敏度。这次研究在我国首次成功地把非电泳PCR法应用到牛胚胎性别鉴定之中，减少了胚胎性别鉴定的操作步骤，并大大缩短了性别鉴定所需要的时间，从而使胚胎移植现场性别鉴定更加可行。     

羊泰勒虫PCR检测方法的建立和初步应用

利用羊泰勒虫18SrRNA基因的序列特点,设计合成种特异性引物,建立羊泰勒虫PCR检测方法,该方法能特异性扩增398bp的羊泰勒虫18SrRNA基因片段,而对羊巴贝斯虫、羊无浆体、牛环形泰勒虫和牛伊氏锥虫的基因组DNA没有扩增带出现。对羊泰勒虫基因组DNA的最小检测量为0.12fgDNA。通过检测124份临床样品,24份为羊泰勒虫感染阳性,其余为阴性。结果表明,建立的PCR检测方法具有极高的敏感性和特异性,可用于羊泰勒虫病和临床健康带虫羊的诊断。     

Bovine cysticercosis—Development of a real-time PCR to enhance classification of suspect cysts identified at meat inspection

Laboratory confirmation methods are important in bovine cysticerosis diagnosis as other pathologies can result in morphologically similar lesions resulting in false identifications. We developed a probe-based real-time PCR assay to identify Taenia saginata in suspect cysts encountered at meat inspection and compared its use with the traditional method of identification, histology, as well as a published nested PCR. The assay simultaneously detects T. saginata DNA and a bovine internal control using the cytochrome c oxidase subunit 1 gene of each species and shows specificity against parasites causing lesions morphologically similar to those of T. saginata. The assay was sufficiently sensitive to detect 1 fg (Ct 35.09 ± 0.95) of target DNA using serially-diluted plasmid DNA in reactions spiked with bovine DNA as well as in all viable and caseated positive control cysts. A loss in PCR sensitivity was observed with increasing cyst degeneration as seen in other molecular methods. In comparison to histology, the assay offered greater sensitivity and accuracy with 10/19 (53%) T. saginata positives detected by real-time PCR and none by histology. When the results were compared with the reference PCR, the assay was less sensitive but offered advantages of faster turnaround times and reduced contamination risk. Estimates of the assay's repeatability and reproducibility showed the assay is highly reliable with reliability coefficients greater than 0.94.     

Effects of temperature and time in transit on polymerase chain reaction detection of feline herpesvirus DNA.

The purpose of this study was to report methods currently recommended by commercial laboratories for collecting, shipping, and processing of samples for feline herpesvirus type 1 (FHV-1) testing using polymerase chain reaction (PCR) and to determine the effect of temperature and time on the ability of 1 PCR method to detect FHV-1 DNA in experimental and clinical samples. Eleven laboratories offering FHV-1 PCR were surveyed. There was notable variation in sample types and shipping conditions recommended and PCR protocols used by these laboratories. Subsequently, using a single PCR method, FHV-1 DNA was detected in samples exposed to various temperatures within the laboratory. Finally, FHV-1 PCR was performed on paired clinical samples collected from 25 cats and shipped at ambient temperatures via US Postal Service (USPS) or with an ice pack via a courier. Samples sent by USPS were exposed to significantly longer transit time and arrived at significantly higher temperature than did samples sent by courier. Despite this, all sample pairs yielded concordant results when tested for FHV-1 DNA using this PCR method. Although it may not be necessary for samples collected for detection of FHV-1 DNA using this PCR method to be shipped under the most expedient or temperature-controlled conditions, this should be verified for a variety of PCR assays and sample types.     

Detection of Mycobacterium avium subsp. paratuberculosis in faeces using different procedures of pre-treatment for real-time PCR in comparison to culture

One of the most relevant aspects in the diagnosis of paratuberculosis (Johne’s disease) in cattle is the availability of a method for the rapid and sensitive detection of Mycobacterium avium subsp. paratuberculosis (MAP) in order to facilitate the prompt removal of pathogen-shedding animals from a herd. To meet this requirement, methods for pre-treatment of bovine faecal samples and subsequent extraction of DNA for detection of MAP by real-time PCR were compared with MAP culture results. A total of 116 bovine faecal samples that showed weak (64.7%), moderate (18.1%) or strong (17.2%) growth of MAP on solid HEY medium were investigated.For PCR, supernatants, sediments or bacterial pellets were obtained from faecal samples by pre-treatment before extraction of MAP DNA based on silica membranes or magnetic particles. Samples then were tested by MAP IS900 and ISMav2 real-time PCR with an analytical sensitivity of 6 and 28 genome equivalents (GE) per mL, respectively.The best results were obtained by including a microfiltration step in the sample pre-treatment in combination with silica membrane-based mini-columns or magnetic particles for DNA extraction. This approach enhanced the detection rate of MAP in IS900 real-time PCR from 58.6% to 84.5% using silica membrane mini-columns and from 61.2% to 64.7% using magnetic particles.     

Sexing of pre-implantation ovine embryos through polymerase chain reaction-based amplification of GAPDH,SRY and AMEL genes

The ability to identify the sex of embryo and control of sex ratio has a great commercial importance to livestock industry. Prediction of embryonic sex could be useful in the management decisions of sex selection in breeding programs. Several methods have been attempted to determine the sex but the polymerase chain reaction (PCR)-based sexing method is generally favoured, as it is cost effective, simple and reliable. The aim of the present study was to identify sex of sheep embryos produced in vitro through amplification of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), sex-determining region Y (SRY) and amelogenin genes present in genomic DNA (gDNA) of embryos through PCR. To avoid false interpretation of the result by no amplification of SRY in female embryos, a duplex PCR was approached to amplify combinedly SRY and GAPDH genes. Sex-specific blood was used in PCR as positive control. In vitro sheep embryos were produced as per standardized protocol of laboratory. Sexing of sex-specific blood and in vitro produced embryos were approached though PCR to amplify the respective genes using gDNA present in the sample without its traditional isolation. The accuracy of sex prediction for embryos was 100% by this procedure.     

Detection of Leishmania infantum DNA by real-time PCR in canine oral and conjunctival swabs and comparison with other diagnostic techniques

The use of non invasive sampling, such as collection of conjunctival swabs, as a diagnostic tool for the detection of Leishmania DNA is of interest. The purpose of this study was to evaluate the diagnostic utility of detecting Leishmania infection with the use of conjunctival swab samples in dogs living in a highly endemic area for leishmaniosis and to investigate, for the first time, the presence of Leishmania DNA in oral swabs in the same population. One hundred sixty-three dogs living outdoor and recruited in various provinces of Sicily were studied. Leishmania infantum indirect fluorescent antibody test (IFAT), delayed-type hypersensitivity reaction to leishmanin (DTH) and real-time PCR of blood (BL), lymph node (LN), conjunctival (CS) and oral swab (OS) samples were performed. The positive PCR percentages in LN, CS, OS and BL samples were: 24.5%, 22.1%, 8.7% and 5.5%, respectively. Serological and DTH positive percentages were 27.0% and 73.8%, respectively. Seropositive and LN-PCR positive dogs had a high likelihood to be positive by CS-PCR. The similar positive PCR percentages found in CS and LN samples suggest the use of CS-PCR as non-invasive alternative technique to LN-PCR for the detection of Leishmania infection in dogs. In addition, this study demonstrated, for the first time, the presence of Leishmania DNA in oral swabs in dogs.     

犬附红细胞体PCR检测方法的建立

目的 步建立犬附红细胞体PCR检测方法。方法 据已发表的附红细胞体基因序列，设计了一对特异性引物，以犬附红细胞体基因组DNA和附红细胞体可疑病犬样品DNA为模板，聚合酶链式反应（PCR）扩增，扩增产物经克隆测序分析。结果 CR扩增产物大小为541bp，序列分析表明与GenBank数据中发表的序列一致，表明这套引物成功扩增出目的基因序列，但正常犬血样品DNA和弓形虫、伊氏锥虫、吉氏巴贝斯虫、犬细小病毒、犬瘟热的DNA样品都不能扩增出目的基因片段。结论 研究建立的PCR方法可以用于犬附红细胞体的检测，为犬附红细胞体病的诊断及分子流行病学的调查提供了新的手段。     

安氏隐孢子虫PCR检测方法的建立

经BLAST检索,以HSP70基因设计一对引物(5'-CAATCGAATTGGATTCTTTGTC-3'和5'-CACCTTCAAAT-ACTTGAATAAGT-3')对奶牛安氏隐孢子虫进行了PCR试验.结果显示所建立的PCR检测方法只能特异扩增隐孢子虫GD株DNA,而对照样本如微小隐孢子虫、弓形虫、圆孢子虫、纤毛虫、肝片吸虫、血矛线虫、莫尼茨绦虫、牛粪便以及大肠杆菌均为阴性;通过对6个浓度梯度的虫体DNA进行PCR反应,结果表明当样本中含有445个隐孢子虫卵囊的DNA时,即可扩增产生清晰可辩的条带.测得该序列长度为494bp,序列分析为牛型C.andersoni.表明该引物能特异扩增C.andersoni,敏感性较高,适合于奶牛安氏隐孢子虫的检测.     

猪附红细胞体PCR检测方法的建立和初步应用

基于猪附红细胞体广东株16S rRNA基因的序列特点，设计合成种特异性引物，建立了猪附红细胞体PCR检测方法。该方法能特异性扩增523bp的猪附红细胞体16SrRNA基因片段，而对猪丹毒杆菌G4T10株、猪链球菌STl71株、多杀性巴氏杆菌E0630株、猪胸膜肺炎放线杆菌、猪肺炎支原体、鸡毒支原体和猫血巴尔通氏体CA株的基因组DNA没有扩增带出现。对猪附红细胞体基因组DNA的最小检测量为160pg。通过对38份临床样品的检测，8份为猪附红细胞体感染阳性，其余为阴性。结果表明，建立的PCR检测方法具有极高的敏感性和特异性，可用于急性猪附红细胞体病和临床健康带菌猪的诊断。     

Evaluation of PCR inhibitory effect of enrichment broths and comparison of DNA extraction methods for detection of Salmonella Enteritidis using real-time PCR assay

The best enrichment broth and DNA extraction scheme was determined for rapid and sensitive detection of Salmonella Enteritidis in steamed pork using real-time PCR. The inhibitory effect of commonly used Salmonella enrichment broths, Rappaport-Vassiliadis (RV) and Muller-Kauffmann tetrathionate with novobiocin (MKTTn), on real-time PCR was confirmed. The inhibition of PCR was statistically significant (p < 0.05) in RV and MKTTn, as compared with buffered peptone water (BPW) or phosphate-buffered saline. The inhibitory effect of the selective enrichment media was successfully removed by using a modified DNA extraction, PrepMan Ultra Reagent with an additional washing step or the DNeasy Tissue Kit. In three experiments, when applied to detection of Salmonella Enteritidis in steamed pork, the real-time PCR coupled with single 24 h enrichment with BPW performed better than double 48 h enrichment with BPW plus RV or MKTTn. The simple real-time PCR assay using BPW proved to be a rapid and sensitive test for detection of low concentrations of Salmonella Enteritidis in steamed pork samples as compared with the conventional culture method.     

Simultaneous detection and subtyping of porcine endogenous retroviruses proviral DNA using the dual priming oligonucleotide system

The purpose of this study was to develop a multiplex PCR that can detect porcine endogenous retrovirus (PERV) proviral genes (pol, envA, envB, envC) and porcine mitochondrial DNA, using a dual priming oligonucleotide (DPO) system. The primer specifically detected the PERV proviral genes pol, envA, envB, envC, and porcine mitochondrial DNA only in samples of pig origin. The sensitivity of the primer was demonstrated by simultaneous amplification of all 5 target genes in as little as 10 pg of pig DNA containing PERV proviral genes and mitochondrial DNA. The multiplex PCR, when applied to field samples, simultaneously and successfully amplified PERV proviral genes from liver, blood and hair root samples. Thus, the multiplex PCR developed in the current study using DPO-based primers is a rapid, sensitive and specific assay for the detection and subtyping of PERV proviral genes.     

An efficient protocol for genomic DNA extraction from formalin-fixed paraffin-embedded tissues

Formalin-fixed paraffin-embedded tissues (FFPET) represent the largest source of archival biological material available for genomic studies. In this work we present an advanced protocol for extraction of high quality DNA from FFPET that can be applied in several molecular studies. Although cat mammary tumours (CMT) are the third most frequent tumour in cats the recovery of significant number of samples for molecular studies are in some way restricted to FFPET samples. We were able to obtain high quality DNA from FFPET of thirty six CMT that were subjected to pre-fixation and fixation processes routinely used in the veterinary hospitals. The quality of DNA obtained was tested by PCR amplification using six sets of primers that amplify single-copy fragments. The DNA fragments obtained were further sequenced. This protocol was able to provide FFPET gDNA that can be amplified and sequenced for larger fragments up to 1182bp.     

Sensitivity of different Trypanosoma vivax specific primers for the diagnosis of livestock trypanosomosis using different DNA extraction methods

There are several T. vivax specific primers developed for PCR diagnosis. Most of these primers were validated under different DNA extraction methods and study designs leading to heterogeneity of results. The objective of the present study was to validate PCR as a diagnostic test for T. vivax trypanosomosis by means of determining the test sensitivity of different published specific primers with different sample preparations. Four different DNA extraction methods were used to test the sensitivity of PCR with four different primer sets. DNA was extracted directly from whole blood samples, blood dried on filter papers or blood dried on FTA cards. The results showed that the sensitivity of PCR with each primer set was highly dependant of the sample preparation and DNA extraction method. The highest sensitivities for all the primers tested were determined using DNA extracted from whole blood samples, while the lowest sensitivities were obtained when DNA was extracted from filter paper preparations. To conclude, the obtained results are discussed and a protocol for diagnosis and surveillance for T. vivax trypanosomosis is recommended.     

A simple and efficient method for isolation of a single Eimeria oocyst from poultry litter using a micromanipulator

The chicken, which is the host for seven species of Eimeria, typically is infected simultaneously by multiple Eimeria species and the oocysts of coccidia are excreted in the feces. A prerequisite for investigation of individual Eimeria species is to isolate a single oocyst from fecal samples. A novel method for isolating a single Eimeria oocyst from poultry litter using a micromanipulator was developed. This simple method is fast and reliable, and provides direct isolation of a single sporulated oocyst from fecal samples harboring multiple Eimeria species or samples contaminated by other species of parasite.     

A novel low-cost method for Mycobacterium avium subsp. paratuberculosis DNA extraction from an automated broth culture system for real-time PCR analysis

PCR is a highly accurate technique for confirming the presence of Mycobacterium avium subsp. paratuberculosis (Map) in broth culture. In this study, a simple, efficient, and low-cost method of harvesting DNA from Map cultured in liquid medium was developed. The proposed protocol (Universidad Austral de Chile [UACH]) was evaluated by comparing its performance to that of two traditional techniques (a QIAamp DNA Stool Mini Kit and cethyltrimethylammonium bromide [CTAB] method). The results were statistically assessed by agreement analysis for which differences in the number of cycles to positive (CP) were compared by Student''s t-test for paired samples and regression analysis. Twelve out of 104 fecal pools cultured were positive. The final PCR results for 11 samples analyzed with the QIAamp and UACH methods or ones examined with the QIAamp and CTAB methods were in agreement. Complete (100%) agreement was observed between data from the CTAB and UACH methods. CP values for the UACH and CTAB techniques were not significantly different, while the UACH method yielded significantly lower CP values compared to the QIAamp kit. The proposed extraction method combines reliability and efficiency with simplicity and lower cost.     

Further epidemiological survey for atovaquone resistant related gene of Babesia gibsoni in Japan during 2015–2018

A single-nucleotide polymorphism causing the replacement of methionine with isoleucine (M121I) in cytochrome b of Babesia gibsoni has been reported to reduce the susceptibility to atovaquone (ATV) in B. gibsoni infection. In our previous study, B. gibsoni with M121I was suggested to exist in nature. Thus, further examinations were performed. In total, 105 genomic DNA samples from B. gibsoni-infected dogs were collected from western (98 samples from 15 prefectures) and eastern areas (7 samples from 4 prefectures) in Japan. The M121I variant population was identified using allele-specific real-time PCR: it was then detected in nine samples (8.57%), which was higher than that in the previous study (4.11%). Although there are unclear points, such as the history of ATV usage, careful attention should be given to emerging ATV resistance.