微卫星多重PCR在水生动物亲权分析中的研究进展

微卫星标记作为共显性标记具有分布广泛、中性遗传的特点,在群体遗传结构分析和亲子鉴定(即亲权鉴定)方面已有了广泛应用,通过微卫星标记技术可以清楚有效地分析子代的遗传背景。本文就目前微卫星多重PCR在水生动物亲权关系分析、系谱认证方面的研究进展进行了综述。     

microRNA在水产动物中的研究进展

mi RNAs是一类在真核生物中广泛存在的非编码小分子RNA,通过与靶m RNA互补配对在转录水平上对基因的表达进行负调控,导致m RNA的翻译抑制或降解。大量研究表明,mi RNA在躯体发育、癌症、细胞分化、细胞增殖与凋亡、脂肪代谢等方面发挥作用。近来在水产动物中,有关mi RNA的研究取得了众多的科研成果,然而对其进行全面总结的报道较缺乏。本文综述了mi RNA在水产动物中的研究进展,结果显示mi RNA在水产动物中表现为多样化的生物学功能,本文也对其研究前景进行了展望,旨在为以后更好地研究水产动物mi RNA的功能提供参考。     

应用聚合酶链式反应(PCR)检测锦鲤疱疹病毒

为建立并优化锦鲤疱疹病毒检测方法,针对目前国内集约化养殖鲤鱼大面积流行的病死现象进行有针对性的检测,对在疫区采集到的病鱼肾脏、肝胰脏、肠等组织,提取基因组DNA,应用锦鲤疱疹病毒特异性引物进行PCR反应,同时设立阴性对照(TE buffer)。通过1%琼脂糖凝胶进行鉴定,与阴性对照比较,在484bp处出现特异性目的条带。经序列测定,所得PCR产物的基因序列与NCBI上锦鲤疱疹病毒的同源率达到99%以上。对同一批次的样品进行重复检测,结果表明该方法具有较好的可重复性,可据此判定结果。通过对锦鲤疱疹病毒的检测,确定了疫区引起框镜鲤(Cyprinus carpio)和建鲤(Cyprinus carpio var Jian)大批死亡的病原为锦鲤疱疹病毒(Koi Herpesvirus,KHV),从而对疫区控制、防治方案的制定提供了理论依据。建议尽快在鲤鱼主要养殖区开展KHV流行病学、诊断与检测及免疫预防等方面的研究。     

Ultra highly sensitive method for detecting Flavobacterium psychrophilum using high‐gradient immunomagnetic separation with a polymerase chain reaction

We attempted to develop an ultrahigh sensitive method for detecting Flavobacterium psychrophilum using high‐gradient immunomagnetic separation (HGIMS) with a polymerase chain reaction (PCR). HGIMS is a magnetic separation method in which the magnetic force is strengthened by introducing a magnetic gradient between the magnetic filter and nearby column. Because immunomagnetic beads specifically react with target cells, target cells are collected efficiently. Accumulated beads are released from the filter by removing the external magnetic force. After concentrating the samples using the HGIMS system, DNA was extracted from the samples, and PCR was applied to detect F. psychrophilum. Our primers did not react with reference bacteria and reacted specifically with F. psychrophilum. The detection sensitivity using the HGIMS system was higher than that of the method without the HGIMS system, and the total assay time, including sample preparation, was <3.5 h. PCR products of the expected size were obtained from samples of concentrated 4 × 10^?1 to 4 × 10³ cfu mL^?1F. psychrophilum more than 80% of the time using the HGIMS system. Furthermore, our proposed method could be useful for the specific detection of F. psychrophilum from actual samples. Our proposed method is suitable for the highly sensitive detection of F. psychrophilum.     

应用多重PCR检测水生动物源气单胞菌安徽分离株的毒力基因型分布

粘附素(aha1)、气溶素(aerA)和细胞兴奋性肠毒素(alt)是气单胞菌的主要毒力因子。根据aha1、aerA和alt基因序列设计三对引物建立了可同时检测三种毒力基因的多重PCR方法(MPCR)。该方法扩增出气单胞菌的aha1大小为1087bp,aerA为721bp,alt为480bp,其敏感度为102CFU·mL-1。而对金黄色葡萄球菌、恶臭假单胞菌、拟态弧菌以及非致病性气单胞菌均未扩增出任何条带。用限制性内切酶EcoRⅤ、BamHⅠ和FbaⅠ分别酶切PCR扩增产物,均获得与预期一致的酶切图谱。用建立的MPCR对15株水生动物源气单胞菌安徽分离株进行毒力基因检测,结果显示在13株致病性气单胞菌中10株细菌的毒力基因型为alt aha1 aerA ,2株为alt aha1-aerA-,1株为alt aha1 aerA-;alt、aha1和aerA基因在气单胞菌中的携带率分别为100%、84.62%和76.92%。表明气单胞菌安徽分离株的主要毒力基因型是alt aha1 aerA 的高毒力表型,alt毒力基因普遍存在于不同表型种气单胞菌中。     

TaqMan real-time polymerase chain reaction assay for rapid detection of Flavobacterium columnare

Flavobacterium columnare is a ubiquitous Gram-negative bacterium that causes columnaris disease in a wide variety of fish worldwide. Timely detection of this bacterium is important to prevent its spreading and to reduce the economic loss to fish farmers. We developed a TaqMan-based real-time polymerase chain reaction (PCR) targeting a 113 bp nucleotide region of the chondroitin AC lyase gene of F. columnare G₄. Specificity of the assay evaluated with 20 isolates of F. columnare and 15 other taxonomically or ecologically related bacteria revealed that the primers and probe were 100% specific for detection of F. columnare. The sensitivity limit of detection of F. columnare in pure cultures, over a range of dilutions [3.1 × 10⁰–3.1 × 10⁶ colony-forming units (CFU) mL⁻¹], was observed to be ∼3 bacterial cells. The lowest limit of detection in nucleic acids from pure culture of F. columnare was 5.4 fg and the assay was linear with the log of amount of nucleic acid (R²=0.994) over that range (5.4 ng–5.4 fg). In tissues (blood, gills and kidney) of F. columnare experimentally infected fish, the bacterial numbers measured by TaqMan real-time PCR ranged from 3.4 × 10⁰ to 9.5 × 10⁵ CFU mL⁻¹. In both F. columnare experimentally infected and spiked samples, positive PCR results were confirmed by bacteriological culture with 100% agreement. The TaqMan real-time PCR developed in this study is specific, sensitive and reproducible for the detection and quantitation of F. columnare in infected fish.     

Development of a multiplex PCR assay for Photobacterium damselae subsp. piscicida identification in fish samples

A multiplex polymerase chain reaction protocol for the detection of Photobacterium damselae and subspecies piscicida and damselae discrimination, with internal amplification control, was developed. Assay specificity was assessed by testing 19 target and 25 non-target pure cultures. The detection limit was 500 fg, corresponding to 100 genome equivalents. The optimized protocol was also prevalidated with spleen, kidney and blood samples from infected and uninfected sea bass, without any culture step, and it can be proposed as a valid alternative to culture standard methods for the rapid and specific diagnosis of photobacteriosis in fish.     

致病性嗜水气单胞菌多重PCR检测方法的建立

致病性嗜水气单胞菌(Aeromonas hydrophila)是近年中国各地大规模流行的淡水养殖鱼类暴发性疾病的主要病原,本研究针对GenBank中登录的致病性嗜水气单胞菌的气溶素基因(hlyA)、溶血素基因(aerA)以及为气单胞菌属所特有的内参照基因16S rRNA保守区设计了3对特异性引物,通过进行多重PCR反应体系优化,多重PCR产物的测序鉴定与特异性和敏感性实验,试图建立一种检测致病性嗜水气单胞菌的多重PCR检测方法。对8株嗜水气单胞菌、16株相关菌株进行多重PCR检测,结果显示,非致病性分离株均未扩增出毒力基因hlyA和aerA,而致病性分离株则至少含有hlyA基因;对40份送检的水产动物样品进行多重PCR检测,结果与常规微生物学检测符合率为97.5%。多重PCR检测方法具有较高的敏感性与特异性,最低可检测模板量为10 ng的样品。该方法的建立对水产动物嗜水气单胞菌病的快速诊断和分子流行病学的调查有重要意义。     

Application of the rpoS gene for the detection of Vibrio anguillarum in flounder and prawn by polymerase chain reaction

Vibrio anguillarum , an opportunistic fish pathogen, is the main species responsible for vibriosis, a disease that affects feral and farmed fish and shellfish, and causes considerable economic losses in marine aquaculture. In this study, we used polymerase chain reaction (PCR) to detect V. anguillarum . PCR specificity was evaluated by amplifying the rpoS gene, a general stress regulator, in six strains of V. anguillarum and 36 other bacterial species. PCR amplified a species-specific fragment (689 bp) from V. anguillarum . Furthermore, the PCR assay was sensitive enough to detect rpoS expression from 3 pg of genomic DNA , or from six colony-forming units (CFU) mL⁻¹ of cultured V. anguillarum . However, the assay was less sensitive when genomic DNA from the infected flounder and prawn was used (limit of detection, 50 ng and 10 ng g⁻¹ tissue, respectively). These data demonstrate that PCR amplification of the rpoS gene is a sensitive and species-specific method to detect V. anguillarum in practical situations.     

应用多聚酶链反应检测生鸡肉中沙门氏菌的研究

目的:建立快速、特异、灵敏的PCR方法以检测生鸡肉中的肠炎沙门氏菌。方法:以肠炎沙门氏菌的sefA基因作为靶序列设计一对引物,将样品增菌后用煮沸法提取细菌基因组DNA进行检测。结果:每克生鸡肉污染3.0×10°CFU肠炎沙门氏菌,经16h增菌培养后可扩增出500bp特异性性DNA带,对28份屠宰场样品的检测结果与传统方法相符合。结论:PCR法适于生鸡肉中肠炎沙门氏菌的快速、准确检测。     

基于核酸适配体的PCR法检测溶藻弧菌及其灭活菌

溶藻弧菌(Vibrio alginolyticus)分布广,数量多,发病率高,是水产养殖中常见的条件致病菌,而对溶藻弧菌进行快速准确的识别鉴定是其病害防治的前提和基础。核酸适配体,因为具有较高的亲和特异性,在微生物的识别鉴定方面展现出了巨大的优势。本文利用核酸适配体和适配体筛选产物,通过结合、洗涤、加热分离、PCR扩增以及电泳检测等步骤,对溶藻弧菌进行了检测鉴定。结果表明,适配体和筛选产物都能对溶藻弧菌及其灭活菌进行较好的识别鉴定,适配体筛选产物对溶藻弧菌的检测下限为10~3cfu/mL,而对其灭活菌的检测下限为10~2cfu/mL,适配体对溶藻弧菌及其灭活菌的检测下限都可达到10 cfu/mL。该方法对溶藻弧菌有较好的亲和特异性,并能较好地区分溶藻弧菌与哈维氏弧菌等水产常见病原菌,在水产病害的检测中显示了较好的应用前景。     

Design standards for experimental and field studies to evaluate diagnostic accuracy of tests for infectious diseases in aquatic animals

Design and reporting quality of diagnostic accuracy studies (DAS) are important metrics for assessing utility of tests used in animal and human health. Following standards for designing DAS will assist in appropriate test selection for specific testing purposes and minimize the risk of reporting biased sensitivity and specificity estimates. To examine the benefits of recommending standards, design information from published DAS literature was assessed for 10 finfish, seven mollusc, nine crustacean and two amphibian diseases listed in the 2017 OIE Manual of Diagnostic Tests for Aquatic Animals. Of the 56 DAS identified, 41 were based on field testing, eight on experimental challenge studies and seven on both. Also, we adapted human and terrestrial‐animal standards and guidelines for DAS structure for use in aquatic animal diagnostic research. Through this process, we identified and addressed important metrics for consideration at the design phase: study purpose, targeted disease state, selection of appropriate samples and specimens, laboratory analytical methods, statistical methods and data interpretation. These recommended design standards for DAS are presented as a checklist including risk‐of‐failure points and actions to mitigate bias at each critical step. Adherence to standards when designing DAS will also facilitate future systematic review and meta‐analyses of DAS research literature.     

[鱼师]诺卡菌特异性PCR快速检测方法的建立

[鱼师]诺卡菌（Nocardia seriolae）是危害中国南方大口黑鲈（Micropterus salmoides）养殖业的主要病原之一,由于该菌在培养基上生长缓慢,对其分离鉴定造成诸多不便。文章根据[鱼师]诺卡菌16S-23S转录间隔区（ITS）序列设计特异性引物建立了[鱼师]诺卡菌特异性PCR快速检测方法。试验结果表明,利用设计的特异性PCR引物只能扩增出[鱼师]诺卡菌特异性片段,检出限为5pg模板DNA。在此基础上研制了PCR快速检测试剂盒并对[鱼师]诺卡菌人工感染的大口黑鲈组织进行了检测,结果显示该试剂盒能从未出现明显发病症状的大口黑鲈组织中检出阳性片段,阳性率为100％,比传统细菌分离鉴定方法更加灵敏、快速且高效,具有较好的应用前景。     

鰤诺卡菌特异性PCR快速检测方法的建立

鰤诺卡菌（Nocardia seriolae）是危害中国南方大口黑鲈（Micropterus salmoides）养殖业的主要病原之一,由于该菌在培养基上生长缓慢,对其分离鉴定造成诸多不便。文章根据鰤诺卡菌16S~23S转录间隔区（ITS）序列设计特异性引物,建立了鰤诺卡菌特异性PCR快速检测方法。试验结果表明,利用我们设计的特异性PCR引物只能扩增出鰤诺卡菌特异性片段,检出限为5 pg模板DNA。在此基础上研制了PCR快速检测试剂盒并对鰤诺卡菌人工感染的大口黑鲈组织进行了检测,结果显示该试剂盒能从未出现明显发病症状的大口黑鲈组织中检出阳性片段,阳性率为100%,比传统细菌分离鉴定方法更加灵敏、快速且高效,具有较好的应用前景。     

Detection of Koi herpesvirus: impact of extraction method,primer set and DNA polymerase on the sensitivity of polymerase chain reaction examinations

Since virus isolation is seldom successful, KHV infection is commonly detected by PCR examination. A number of different PCR assays have been described in recent years. However, at present no commonly accepted PCR method is used amongst different laboratories. The aim of this study was to check if the examination of infected fish by different PCR methods yielded comparable results. We used tissue samples of three KHV‐infected koi, one KHV‐infected common carp, one KHV‐infected goldfish and one non‐infected common carp. DNA was extracted with DNAzol Reagent, High Pure PCR Template DNA Preparation Kit and QIAamp DNA Mini Kit. The DNA was tested by PCR with different combinations of published primer sets –KHV‐F and ‐R, KHV‐Gray‐2F and ‐2R and KHV‐TKf and ‐TKr – plus different DNA polymerases – a standard Taq DNA polymerase, a Platinum (hotstart) Taq DNA polymerase and a Platinum (hotstart) Pfx DNA polymerase with proofreading activity. The different extraction methods produced DNA solutions with different yields of DNA and different degrees of homogeneity. Also, the sensitivity of the PCR depended on the choice of the primer set and polymerase. Not all infected fish could be identified with all methods; there were large differences in the sensitivity between methods.     

Application of multiplex quantitative polymerase chain reaction methods to detect common bacterial fish pathogens in Nile tilapia,Oreochromis niloticus,hatcheries in Costa Rica

Edwardsiella spp., Streptococcus spp., and Francisella noatunensis subsp. orientalis are some of the most important fish pathogens affecting global tilapia, Oreochromis spp., aquaculture. In Costa Rica, the aquaculture industry is dominated by freshwater‐cultured Nile tilapia, Oreochromis niloticus, which are raised in all seven national provinces. At present, little is known regarding the diversity of pathogens present in these facilities, and definitive identification of agents associated with disease outbreaks are rare. To evaluate the prevalence of common bacterial pathogens in these systems, this study used multiplex quantitative polymerase chain reaction (qPCR) assays targeting Edwardsiella, Streptococcus, and Francisella species as a diagnostic and surveillance tool. In 2017, seven different tilapia hatcheries were visited, and 350 fingerlings were subjected to necropsy and molecular diagnostic evaluation. Fish exhibiting gross signs of disease were subjected to histological and microbiological analysis. For the first time, Edwardsiella anguillarum was recovered and molecularly confirmed from diseased tilapia in Costa Rica. In addition, F. noatunensis subsp. orientalis was identified in a region of Costa Rica where it had not been previously reported.     

Quantitative analysis of an experimental white spot syndrome virus (WSSV) infection in Penaeus monodon Fabricius using competitive polymerase chain reaction

White spot syndrome virus (WSSV) has been a major pathogen of cultured Penaeus monodon Fabricius in Malaysia since 1994. As quantitative study on the replication of WSSV is in its infancy, competitive polymerase chain reaction (PCR) was used for quantitative study of an experimental WSSV infection per os in growout P. monodon . Gills, abdominal integument and abdominal muscle were selected for viral quantification. Infection was detectable as early as 14 h postinfection (h p.i.) in both gills and integument, but the infection in muscle was only detected at 24 h p.i. Gill tissue had the highest viral load, followed by integument and muscle. Typical viral growth curves were obtained for all organs with distinct phases of eclipse (0–24 h p.i.), logarithmic (24–48 h p.i.) and the plateau (48–120 h p.i.). Cumulative mortality rapidly increased from 48 h p.i. and reached 100% at the end of the plateau phase at 120 h p.i. Gross signs of white spots and reddish discoloration were also obvious in moribund individuals from the plateau phase. Based on the three phases of viral growth, WSSV infection was classified into light, moderate and heavy infection stages.     

Development of real-time PCR assays for detection of megalocytiviruses in imported ornamental fish

Megalocytiviruses have been associated globally with severe systemic disease and economic loss in farmed food fish and ornamental fish. The viruses have been spread internationally by translocation of live fish. In New Zealand, megalocytiviruses are regarded as exotic. A potential pathway for introduction has been identified, namely imported ornamental fish. In the present study, real‐time PCR assays were developed for detection of megalocytiviruses using a conserved major capsid protein gene. A SYBR green assay was developed to target all known megalocytiviruses. A second real‐time PCR assay using a molecular beacon was developed to specifically target gourami, Trichogaster trichopterus, iridovirus, a species of iridovirus previously linked to ornamental fish imports in Australia. The analytical sensitivity for the SYBR green and molecular beacon assays were 10 and 100 fg, respectively. The analytical specificity of the real‐time PCR assays determined using genomic DNA templates from three target viruses, 12 non‐target viruses and 25 aquatic bacterial species were 100%. The intra‐run and inter‐run coefficients of variation of both assays were <5%. The real‐time PCR assays developed in this study provide rapid, sensitive, and specific detection of megalocytiviruses and gourami iridovirus.