CN116640867B - A primer pair and probe combination for detecting Streptococcus dysgalactiae by RAA-LFD and its application - Google Patents
A primer pair and probe combination for detecting Streptococcus dysgalactiae by RAA-LFD and its application Download PDFInfo
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Abstract
Description
技术领域Technical Field
本发明属于致病菌检测技术领域,具体涉及一种RAA-LFD检测停乳链球菌的引物对和探针组合及其应用。The invention belongs to the technical field of pathogenic bacteria detection, and specifically relates to a primer pair and a probe combination for detecting Streptococcus dysgalactiae by RAA-LFD and an application thereof.
背景技术Background Art
停乳链球菌不仅能够导致牛、猪和羊等多种动物的乳房炎,多关节炎,败血症等疾病,还可感染人类,引起菌血症、心内膜炎、脑膜炎、脓毒性关节炎、呼吸道和皮肤感染等疾病。停乳链球菌作为水产养殖中一种新出现的病原体,它可以在许多养殖鱼类中引起严重疾病,包括斑点叉尾鮰(channel catfish)、高体鰤(Seriola dumerili)、鰤鱼(Seriolaquinqueradiata)、黄尾鰤(Seriola lalandi)、鲳参鱼(Trachinotus blochii)、白斑鲷(Lutjanus stellatus)、杂交红罗非鱼(Oreochromis sp.)、尼罗罗非鱼(Oreochromisniloticus)、鲻鱼(Mugil cephalus)、军曹鱼(Rachycentron canadum)和鲻鱼(Lizahaematocheila)以及不同种类的养殖鲟鱼(Acipenser baerii,Acipenser schrenckii和Acipenser gueldenstaedti),给水产养殖带来巨大的威胁。Streptococcus dysgalactiae can not only cause mastitis, polyarthritis, sepsis and other diseases in a variety of animals such as cattle, pigs and sheep, but can also infect humans, causing bacteremia, endocarditis, meningitis, septic arthritis, respiratory and skin infections and other diseases. Streptococcus dysgalactiae is an emerging pathogen in aquaculture. It can cause serious diseases in many farmed fish species, including channel catfish, greater amberjack (Seriola dumerili), yellowtail amberjack (Seriola quinqueradiata), yellowtail amberjack (Seriola lalandi), pomfret (Trachinotus blochii), white snapper (Lutjanus stellatus), hybrid red tilapia (Oreochromis sp.), Nile tilapia (Oreochromis niloticus), mullet (Mugil cephalus), cobia (Rachycentron canadum) and grey mullet (Liza haematocheila) as well as different species of farmed sturgeon (Acipenser baerii, Acipenser schrenckii and Acipenser gueldenstaedti), posing a huge threat to aquaculture.
免疫原性分泌蛋白(Immunogenic Secreted Protein,ISP)基因序列高度保守,其编码的蛋白具有很强的免疫原性,是停乳链球菌的主要抗原。有研究表明,根据停乳链球菌ISP基因设计的特异性引物进行PCR,均能扩增出目的条带。将其PCR扩增产物的测序结果与GenBank中的相应序列进行比对,分析该序列同源性为94.2%~100%,证明ISP基因是停乳链球菌的高度保守序列,可根据ISP基因设计引物用来检测停乳链球菌。The gene sequence of immunogenic secreted protein (ISP) is highly conserved, and the protein it encodes has strong immunogenicity and is the main antigen of Streptococcus dysgalactiae. Studies have shown that PCR with specific primers designed based on the ISP gene of Streptococcus dysgalactiae can amplify the target band. The sequencing results of its PCR amplification product were compared with the corresponding sequence in GenBank, and the sequence homology was analyzed to be 94.2% to 100%, proving that the ISP gene is a highly conserved sequence of Streptococcus dysgalactiae, and primers can be designed based on the ISP gene to detect Streptococcus dysgalactiae.
重组酶介导的等温扩增技术(Recombinase-aided amplification,RAA)是一种不需要热稳定酶和复杂热循环仪的扩增技术,该技术利用单链DNA结合蛋白(single strandDNA binding protein,SSB)、重组酶和DNA聚合酶即可完成反应。目前,等温扩增技术逐渐增多,根据不同的反应原理设计不同的等温扩增技术,常用等温扩增技术有:核酸依赖性扩增检测技术(Nuclear acid sequence-based amplification,NASBA)、环介导等温扩增技术(Loop-mediated isothermal amplification method,LAMP)和重组酶介导的等温扩增技术(RAA)等。然而NASBA需要预热;LAMP需要设计4~6对引物;并且NASBA和LAMP术需要较高的应温度温度。RAA因其高效、敏感性好、用时短等的优点,近年来在病原微生物检测、疾病诊断等领域广泛应用。RAA-LFD技术在细菌检测的应用稍晚于病毒检测。但细菌基因组为DNA核酸,较一些RNA病毒而言无需反转录的过程,更利于脱离实验室环境,应用到现场检测中。Recombinase-aided amplification (RAA) is an amplification technology that does not require thermostable enzymes and complex thermal cyclers. This technology uses single strand DNA binding protein (SSB), recombinase and DNA polymerase to complete the reaction. At present, isothermal amplification technologies are gradually increasing. Different isothermal amplification technologies are designed according to different reaction principles. Commonly used isothermal amplification technologies include: nuclear acid sequence-based amplification detection technology (NASBA), loop-mediated isothermal amplification method (LAMP) and recombinase-mediated isothermal amplification technology (RAA). However, NASBA requires preheating; LAMP requires the design of 4 to 6 pairs of primers; and NASBA and LAMP require a higher reaction temperature. RAA has been widely used in pathogenic microorganism detection, disease diagnosis and other fields in recent years due to its advantages such as high efficiency, good sensitivity and short time. The application of RAA-LFD technology in bacterial detection is slightly later than that in virus detection. However, the bacterial genome is DNA nucleic acid, which does not require reverse transcription compared to some RNA viruses. It is more conducive to being out of the laboratory environment and applied to on-site testing.
目前,缺乏简单,有效且灵敏度高,技术要求低的检测停乳链球菌的方法,因此提供一种特异性引物用于停乳链球菌的检测,使其具有反应温度易达到、反应所需时间短、特异性强、灵敏度高以及检测结果符合率高等优点的检测停乳链球菌的方法在致病菌检测领域具有十分重要的意义。At present, there is a lack of a simple, effective, sensitive and low technical requirement method for detecting Streptococcus dysgalactiae. Therefore, a specific primer is provided for the detection of Streptococcus dysgalactiae, which has the advantages of easy reaction temperature, short reaction time, strong specificity, high sensitivity and high consistency of test results. The method for detecting Streptococcus dysgalactiae is of great significance in the field of pathogenic bacteria detection.
发明内容Summary of the invention
针对现有技术的上述不足,本发明提供一种用于检测停乳链球菌的引物对和探针组合及其应用,采用本发明引物对和探针进行RAA-LFD检测,具有反应温度易达到、反应所需时间短、特异性强、灵敏度高以及检测结果符合率高等优点,并且本发明对设备及试验人员操作技术要求低,适合在野外或缺乏实验室检测设备的场景下开展停乳链球菌的检测。In view of the above-mentioned deficiencies in the prior art, the present invention provides a primer pair and a probe combination for detecting Streptococcus dysgalactiae and an application thereof. The primer pair and the probe of the present invention are used for RAA-LFD detection, which has the advantages of easy reaction temperature, short reaction time, strong specificity, high sensitivity and high detection result compliance rate. In addition, the present invention has low requirements on the operating technology of equipment and test personnel, and is suitable for detecting Streptococcus dysgalactiae in the field or in scenarios where there is a lack of laboratory testing equipment.
本发明采用以下技术方案:The present invention adopts the following technical solutions:
一种RAA-LFD检测停乳链球菌的引物对和探针,该引物对为:ISP-F1/ISP-R1、ISP-F1/ISP-R2、ISP-F2/ISP-R1、ISP-F2/ISP-R2、ISP-F3/ISP-R1或ISP-F3/ISP-R2;其中,ISP-F1、ISP-F2、ISP-F3、ISP-R1和ISP-R2的核苷酸序列如下:A primer pair and a probe for detecting Streptococcus dysgalactiae by RAA-LFD, wherein the primer pair is: ISP-F1/ISP-R1, ISP-F1/ISP-R2, ISP-F2/ISP-R1, ISP-F2/ISP-R2, ISP-F3/ISP-R1 or ISP-F3/ISP-R2; wherein the nucleotide sequences of ISP-F1, ISP-F2, ISP-F3, ISP-R1 and ISP-R2 are as follows:
ISP-F1:5’-AATTTAAATCAGAGGCAAAAGGTGACCACGGAA-3’(SEQ ID NO.1);ISP-F1: 5’-AATTTAAATCAGAGGCAAAAGGTGACCACGGAA-3’ (SEQ ID NO. 1);
ISP-F2:5’-AATGCTCCACATAGGCCGCATAAGTATTAACAGA-3’(SEQ ID NO.2);ISP-F2: 5’-AATGCTCCACATAGGCCGCATAAGTATTAACAGA-3’ (SEQ ID NO. 2);
ISP-F3:5’-TCCCAAAGAACTTTCTGACATGGCAATAGCAAC-3’(SEQ ID NO.3);ISP-F3: 5’-TCCCAAAGAACTTTCTGACATGGCAATAGCAAC-3’ (SEQ ID NO. 3);
ISP-R1:5’-ATCTGATGTTCTTAATCCTGCAGAGCCTACTCG-3’(SEQ ID NO.4);ISP-R1: 5’-ATCTGATGTTCTTAATCCTGCAGAGCCTACTCG-3’ (SEQ ID NO. 4);
ISP-R2:5’-GATGTTCTTAATCCTGCAGAGCCTACTCGTCCA-3’(SEQ ID NO.5);ISP-R2: 5’-GATGTTCTTAATCCTGCAGAGCCTACTCGTCCA-3’ (SEQ ID NO. 5);
所述探针的核苷酸序列为:The nucleotide sequence of the probe is:
5’-TATCTCCAAATTTAAATCAGAGGCAAAAGGT GACCACGGAAGAGGTGT-3’(SEQ ID NO.6)。5'-TATCTCCAAATTTAAATCAGAGGCAAAAGGT GACCACGGAAGAGGTGT-3' (SEQ ID NO. 6).
进一步地,上述下游引物的5’端标记有生物素,所述探针的5’端标记有荧光素,3’端标记C3 Spacer,在探针30bp处,将碱基T替换为dSpacer;Furthermore, the 5' end of the downstream primer is labeled with biotin, the 5' end of the probe is labeled with fluorescein, the 3' end is labeled with C 3 Spacer, and at 30 bp of the probe, the base T is replaced with dSpacer;
所述探针为:The probe is:
5’-FAM-TATCTCCAAATTTAAATCAGAGGCAAAAGG/dSpace5’-FAM-TATCTCCAAATTTAAATCAGAGGCAAAAGG/dSpace
r/GACCACGGAAGAGGTGT(C3 Spacer)-3’。r/GACCACGGAAGAGGTGT(C 3 Spacer)-3'.
上述引物对和探针组合在检测停乳链球菌中的应用。Application of the primer pair and probe combination in detecting Streptococcus dysgalactiae.
一种用于检测停乳链球菌的试剂盒,包括上述引物对和探针。A kit for detecting Streptococcus dysgalactiae comprises the above primer pair and probe.
一种检测停乳链球菌的方法,包括以下步骤:提取待测样本DNA,采用上述引物对和探针组合进行RAA扩增,利用LFD对RAA扩增产物进行检测。A method for detecting Streptococcus dysgalactiae comprises the following steps: extracting DNA of a sample to be tested, performing RAA amplification using the primer pair and probe combination, and detecting the RAA amplification product using LFD.
进一步地,上述RAA扩增体系为:tris缓冲液23~25μL、10μM正向引物1.8~2.2μL、10μM反向引物1.8~2.2μL,10μM探针0.5~0.7μL、待测样品DNA与ddH2O共17~17.3μL;优选的,缓冲液25μL、10μM正向引物2.1μL、10μM反向引物2.1μL,10μM探针0.6μL、待测样品DNA与ddH2O共17.2μL。Furthermore, the RAA amplification system is: 23-25 μL of tris buffer, 1.8-2.2 μL of 10 μM forward primer, 1.8-2.2 μL of 10 μM reverse primer, 0.5-0.7 μL of 10 μM probe, and 17-17.3 μL of the sample DNA to be tested and ddH 2 O; preferably, 25 μL of buffer, 2.1 μL of 10 μM forward primer, 2.1 μL of 10 μM reverse primer, 0.6 μL of 10 μM probe, and 17.2 μL of the sample DNA to be tested and ddH 2 O.
进一步地,上述RAA扩增程序为39℃~44℃,15~30min;优选为39℃,15min。Furthermore, the above RAA amplification procedure is 39°C to 44°C for 15 to 30 min; preferably 39°C for 15 min.
采用上述技术方案,本发明的有益效果为:By adopting the above technical solution, the beneficial effects of the present invention are as follows:
本发明提供了一种RAA-LFD检测停乳链球菌的引物和探针组合及其应用,本发明方法根停乳链球菌ISP基因序列同时设计引物和探针,以降低假阳性的概率,从而提高RAA-LFD检测方法成功的可行性;通过反复优化反应体系及反应条件,确定其最佳反应温度是39℃,最低反应时间为15min,本发明特异性好,最低检测灵敏度可达1.002×102pg/μL。采用本发明建立的RAA-LFD法和传统PCR法对50尾攻毒的斑马鱼样本进行检测,结果表明两种方法的阳性符合率为97.6%,阴性符合率为90.0%,总符合率为98.0%,而与传统PCR法相比,RAA-LFD法的ROC曲线下面积(Area Under the ROC Curve,AUC)为0.950,敏感性和特异性分别为100%和90%。因此,本发明采用根停乳链球菌ISP基因序列同时设计的引物和探针结合RAA-LFD检测方法具有反应温度易达到、反应所需时间短、特异性强、灵敏度高以及检测结果符合率高等优势,并且对设备及试验人员操作技术要求低,适合在缺乏实验室检测设备的场景下开展停乳链球菌的检测。The invention provides a primer and probe combination for detecting Streptococcus dysgalactiae by RAA-LFD and its application. The method of the invention designs primers and probes based on the ISP gene sequence of Streptococcus dysgalactiae at the same time to reduce the probability of false positive, thereby improving the feasibility of the successful RAA-LFD detection method; by repeatedly optimizing the reaction system and reaction conditions, it is determined that the optimal reaction temperature is 39°C and the minimum reaction time is 15min. The invention has good specificity and the minimum detection sensitivity can reach 1.002×10 2 pg/μL. The RAA-LFD method established by the invention and the traditional PCR method are used to detect 50 zebrafish samples infected with poison. The results show that the positive coincidence rate of the two methods is 97.6%, the negative coincidence rate is 90.0%, and the total coincidence rate is 98.0%. Compared with the traditional PCR method, the RAA-LFD method has an area under the ROC curve (AUC) of 0.950, and the sensitivity and specificity are 100% and 90% respectively. Therefore, the present invention adopts the primers and probes designed simultaneously based on the ISP gene sequence of Streptococcus dysgalactiae in combination with the RAA-LFD detection method, which has the advantages of easy reaction temperature, short reaction time, strong specificity, high sensitivity and high compliance rate of detection results, and has low requirements on the operating skills of equipment and test personnel, and is suitable for the detection of Streptococcus dysgalactiae in scenarios where there is a lack of laboratory testing equipment.
附图说明BRIEF DESCRIPTION OF THE DRAWINGS
图1为停乳链球菌RAA-LFD引物对筛选图。FIG1 is a screening diagram of the RAA-LFD primer pair for Streptococcus dysgalactiae.
图2为不同温度下停乳链球菌RAA-LFD引物对的筛选图。FIG. 2 is a screening diagram of RAA-LFD primer pairs of Streptococcus dysgalactiae at different temperatures.
图3为停乳链球菌RAA-LFD引物对敏感性分析图。FIG. 3 is a sensitivity analysis diagram of the RAA-LFD primer pair of Streptococcus dysgalactiae.
图4为RAA-LFD检测停乳链球菌示意图。FIG. 4 is a schematic diagram of RAA-LFD detection of Streptococcus dysgalactiae.
图5为RAA-LFD法检测停乳链球菌的反应条件优化图。FIG. 5 is a diagram showing the optimization of reaction conditions for detecting Streptococcus dysgalactiae using the RAA-LFD method.
图6为RAA-LFD法检测停乳链球菌的敏感性和特异性图。FIG. 6 is a graph showing the sensitivity and specificity of the RAA-LFD method for detecting Streptococcus dysgalactiae.
图7为RAA-LFD检测临床样本的试纸条图。FIG. 7 is a test strip image of RAA-LFD testing clinical samples.
图8为PCR检测临床样本的凝胶电泳图。FIG8 is a gel electrophoresis diagram of PCR detection of clinical samples.
图9为RAA-LFD检测停乳链球菌的ROC分析图。FIG. 9 is a ROC analysis diagram of RAA-LFD detecting Streptococcus dysgalactiae.
具体实施方式DETAILED DESCRIPTION
下面对本发明的具体实施方式进行描述,以便于本技术领域的技术人员理解本发明,但应该清楚,本发明不限于具体实施方式的范围,对本技术领域的普通技术人员来讲,只要各种变化在所附的权利要求限定和确定的本发明的精神和范围内,这些变化是显而易见的,一切利用本发明构思的发明创造均在保护之列。The specific implementation modes of the present invention are described below so that those skilled in the art can understand the present invention. However, it should be clear that the present invention is not limited to the scope of the specific implementation modes. For those of ordinary skill in the art, as long as various changes are within the spirit and scope of the present invention as defined and determined by the attached claims, these changes are obvious, and all inventions and creations utilizing the concept of the present invention are protected.
实施例1引物设计及筛选Example 1 Primer design and screening
1、引物设计1. Primer design
根据停乳链球菌检测基因ISP,通过DNAMAN比对分析ISP基因序列的同源性并确定保守区域,采用Oligo 7软件根据保守区域共设计6对引物和一条探针,引物对为ISP-F1/ISP-R1、ISP-F1/ISP-R2、ISP-F2/ISP-R1、ISP-F2/ISP-R2、ISP-F3/ISP-R1和ISP-F3/ISP-R2;其中,ISP-F1、ISP-F2、ISP-F3、ISP-R1和ISP-R2的核苷酸序列如下:According to the ISP gene detected by Streptococcus dysgalactiae, the homology of the ISP gene sequence was analyzed by DNAMAN and the conserved region was determined. Oligo 7 software was used to design a total of 6 pairs of primers and a probe based on the conserved region. The primer pairs were ISP-F1/ISP-R1, ISP-F1/ISP-R2, ISP-F2/ISP-R1, ISP-F2/ISP-R2, ISP-F3/ISP-R1 and ISP-F3/ISP-R2; among them, the nucleotide sequences of ISP-F1, ISP-F2, ISP-F3, ISP-R1 and ISP-R2 are as follows:
ISP-F1:5’-AATTTAAATCAGAGGCAAAAGGTGACCACGGAA-3’(SEQ ID NO.1);ISP-F1: 5’-AATTTAAATCAGAGGCAAAAGGTGACCACGGAA-3’ (SEQ ID NO. 1);
ISP-F2:5’-AATGCTCCACATAGGCCGCATAAGTATTAACAGA-3’(SEQ ID NO.2);ISP-F2: 5’-AATGCTCCACATAGGCCGCATAAGTATTAACAGA-3’ (SEQ ID NO. 2);
ISP-F3:5’-TCCCAAAGAACTTTCTGACATGGCAATAGCAAC-3’(SEQ ID NO.3);ISP-F3: 5’-TCCCAAAGAACTTTCTGACATGGCAATAGCAAC-3’ (SEQ ID NO. 3);
ISP-R1:5’-ATCTGATGTTCTTAATCCTGCAGAGCCTACTCG-3’(SEQ ID NO.4);ISP-R1: 5’-ATCTGATGTTCTTAATCCTGCAGAGCCTACTCG-3’ (SEQ ID NO. 4);
ISP-R2:5’-GATGTTCTTAATCCTGCAGAGCCTACTCGTCCA-3’(SEQ ID NO.5);ISP-R2: 5’-GATGTTCTTAATCCTGCAGAGCCTACTCGTCCA-3’ (SEQ ID NO. 5);
探针的核苷酸序列为The nucleotide sequence of the probe is
5’-TATCTCCAAATTTAAATCAGAGGCAAAAGGT GACCACGGAAGAGGTGT-3’(SEQ ID NO:6)。5'-TATCTCCAAATTTAAATCAGAGGCAAAAGGT GACCACGGAAGAGGTGT-3' (SEQ ID NO: 6).
2、引物筛选2. Primer screening
采用PCR方法进行引物筛选,PCR反应体系与PCR反应运行参数如表1和表2所示,以下PCR反应均采用表1和表2中的PCR反应体系与PCR反应运行参数。The PCR method was used for primer screening. The PCR reaction system and PCR reaction operating parameters are shown in Table 1 and Table 2. The following PCR reactions all used the PCR reaction system and PCR reaction operating parameters in Table 1 and Table 2.
表1PCR反应体系Table 1 PCR reaction system
表2PCR反应运行参数Table 2 PCR reaction operating parameters
(1)初筛:以2μL的停乳链球菌DNA为模板,采用步骤1中根据停乳链球菌ISP基因设计的6对特异性引物分别进行PCR反应,通过1%琼脂糖凝胶电泳检测观察,结果如图1所示,其中M为DNA分子质量标准;NC为阴性对照;1为停乳链球菌;2为海豚链球菌;3为无乳链球菌,通过1%琼脂糖凝胶电泳检测均能够扩增出目的条带;(1) Preliminary screening: Using 2 μL of Streptococcus dysgalactiae DNA as a template, PCR reactions were performed using the 6 pairs of specific primers designed according to the ISP gene of Streptococcus dysgalactiae in step 1, and the results were observed by 1% agarose gel electrophoresis. The results are shown in FIG1 , wherein M is a DNA molecular mass standard; NC is a negative control; 1 is Streptococcus dysgalactiae; 2 is Streptococcus dolphinus; and 3 is Streptococcus agalactiae. The target bands were all amplified by 1% agarose gel electrophoresis.
(2)筛选最佳温度:以2μL的停乳链球菌DNA为模板,采用步骤1中根据停乳链球菌ISP基因设计的6对特异性引物分别在38.2℃、40.9℃、44.7℃、49.5℃和53.5℃温度下进行PCR反应,通过1%琼脂糖凝胶电泳检测观察,结果如图2所示,其中M为DNA分子质量标准;NC为阴性对照;1为ISP-F1/ISP-R1;2为ISP-F1/ISP-R2;3为ISP-F2/ISP-R1;4为ISP-F2/ISP-R2;5为ISP-F3/ISP-R1;6为ISP-F3/ISP-R2;通过1%琼脂糖凝胶电泳检测均能够扩增出目的条带,且条带明暗程度几乎一致;(2) Screening the optimal temperature: Using 2 μL of Streptococcus dysgalactiae DNA as a template, PCR was performed using the six pairs of specific primers designed according to the ISP gene of Streptococcus dysgalactiae in step 1 at 38.2°C, 40.9°C, 44.7°C, 49.5°C and 53.5°C, respectively. The results were observed by 1% agarose gel electrophoresis. The results are shown in FIG2 , wherein M is a DNA molecular mass standard; NC is a negative control; 1 is ISP-F1/ISP-R1; 2 is ISP-F1/ISP-R2; 3 is ISP-F2/ISP-R1; 4 is ISP-F2/ISP-R2; 5 is ISP-F3/ISP-R1; and 6 is ISP-F3/ISP-R2. The target bands were all amplified by 1% agarose gel electrophoresis, and the brightness of the bands was almost the same;
(3)引物浓度筛选:将停乳链球菌DNA进行连续10倍稀释,浓度分别为1.613×103ng/μL、1.613×102ng/μL、1.613×101ng/μL、1.613×100ng/μL、1.613×102pg/μL、8.065×101pg/μL和4.033×101pg/μL,分别以稀释过的停乳链球菌DNA为模板,采用步骤1所得引物进行PCR反应,通过1%琼脂糖凝胶电泳观察,结果如图3所示,通过1%琼脂糖凝胶电泳检测均能够扩增出目的条带,当DNA浓度低于1.613×102pg/μL时,6条特异性目的条带亮度均减弱。(3) Primer concentration screening: The DNA of Streptococcus dysgalactiae was diluted 10 times in succession to concentrations of 1.613×10 3 ng/μL, 1.613×10 2 ng/μL, 1.613×10 1 ng/μL, 1.613×10 0 ng/μL, 1.613×10 2 pg/μL, 8.065×10 1 pg/μL and 4.033×10 1 pg/μL, respectively. The diluted DNA of Streptococcus dysgalactiae was used as a template and the primers obtained in step 1 were used for PCR reaction. The results were observed by 1% agarose gel electrophoresis. The results are shown in FIG3 . The target bands were all amplified by 1% agarose gel electrophoresis. When the DNA concentration was lower than 1.613×10 2 pg/μL, the brightness of the six specific target bands was weakened.
由此可知,根据停乳链球菌ISP基因设计的6对特异性引物均符合要求。It can be seen that the six pairs of specific primers designed based on the ISP gene of Streptococcus dysgalactiae all meet the requirements.
实施例2RAA-LFD检测方法的建立Example 2 Establishment of RAA-LFD detection method
1、筛选引物:1. Screening primers:
随机选择实施例1中所设计的ISP-F2/ISP-R2为引物,以停乳链球菌DNA为模板,按照表1和表2的反应体系和反应程序进行PCR扩增,将其扩增产物送至生工生物工程(上海)股份有限公司测序,并将测序结果与GenBank中的相应序列进行比对,分析该序列同源性,结果如表3所示;ISP-F2/ISP-R2 designed in Example 1 were randomly selected as primers, and DNA of Streptococcus dysgalactiae was used as a template. PCR amplification was performed according to the reaction system and reaction procedure in Table 1 and Table 2, and the amplified product was sent to Sangon Biotech (Shanghai) Co., Ltd. for sequencing, and the sequencing results were compared with the corresponding sequences in GenBank to analyze the sequence homology. The results are shown in Table 3;
表3用MEGA 7.0和BioEdit进行序列同源性比较Table 3 Sequence homology comparison using MEGA 7.0 and BioEdit
由表3可知,该序列同源性为94.2%~100%,因此选用ISP-F2/ISP-R2用于检测停乳链球菌的ISP基因,在其下游引物5′端标记生物素(Biotin),命名为ISP-RAA-LR;在探针5′端标记羧基荧光素(FAM),3′端标记C3Spacer,在探针30bp处,将碱基T替换为dSpacer,命名为ISP-Probe,用于后续扩增产物的LFD条带检测,如下所示:As shown in Table 3, the sequence homology is 94.2% to 100%, so ISP-F2/ISP-R2 is selected to detect the ISP gene of Streptococcus dysgalactiae, and biotin is labeled at the 5′ end of its downstream primer, named ISP-RAA-LR; carboxyfluorescein (FAM) is labeled at the 5′ end of the probe, and C 3 Spacer is labeled at the 3′ end. At 30 bp of the probe, the base T is replaced by dSpacer, named ISP-Probe, and used for LFD band detection of subsequent amplification products, as shown below:
ISP-RAA-LF:ISP-RAA-LF:
5’-AATGCTCCACATAGGCCGCATAAGTATTAACAGA-3’;5’-AATGCTCCACATAGGCCGCATAAGTATTAACAGA-3’;
ISP-RAA-LR:ISP-RAA-LR:
5’-BiotinGATGTTCTTAATCCTGCAGAGCCTACTCGTCCA-3’;5’-BiotinGATGTTCTTAATCCTGCAGAGCCTACTCGTCCA-3’;
ISP-Probe:ISP-Probe:
5’-FAMTATCTCCAAATTTAAATCAGAGGCAAAAGG/dSpace r/GACCACGGAAGAGGTGT(C3Spacer)-3’。5’-FAMTATCTCCAAATTTAAATCAGAGGCAAAAGG/dSpace r/GACCACGGAAGAGGTGT(C3Spacer)-3’.
2、停乳链球菌RAA-LFD检测体系及方法的建立2. Establishment of RAA-LFD detection system and method for Streptococcus dysgalactiae
停乳链球菌RAA-LFD检测体系及方法的建立,由图4所示,具体过程如下:The establishment of the RAA-LFD detection system and method for Streptococcus dysgalactiae is shown in Figure 4, and the specific process is as follows:
(1)将储存于-20℃的试验所需试剂取出融化至室温,在涡旋振荡器混匀,采用掌上离心机瞬时离心;提前将金属水浴锅打开,温度调至39℃,所需试剂如表4所示;(1) Take out the reagents required for the test stored at -20°C and melt them to room temperature, mix them on a vortex oscillator, and centrifuge them instantly using a handheld centrifuge; open the metal water bath in advance and adjust the temperature to 39°C. The required reagents are shown in Table 4;
(2)用步骤(1)准备的所需试剂配置反应预混液,充分混匀并短暂离心,反应预混液的体系如表4所示;(2) Prepare a reaction premix with the required reagents prepared in step (1), mix thoroughly and centrifuge briefly. The system of the reaction premix is shown in Table 4;
(3)将步骤(2)配置的47μL反应预混液转移到装有2.5mg RAA冻干粉的反应管中,使冻干粉充分溶解,并短暂离心;(3) Transfer 47 μL of the reaction premix prepared in step (2) to a reaction tube containing 2.5 mg of RAA lyophilized powder, dissolve the lyophilized powder fully, and centrifuge briefly;
(4)在步骤(3)所得反应管中加入3μL启动剂(乙酸镁溶液),盖紧管盖通过短暂离心使启动剂进入预混液中,混合均匀短暂离心;(4) Add 3 μL of the initiator (magnesium acetate solution) to the reaction tube obtained in step (3), cap the tube tightly and centrifuge briefly to allow the initiator to enter the premixed solution, mix well, and centrifuge briefly;
(5)进行RAA扩增,将步骤(4)所得反应管放入步骤(1)准备的水浴锅中,反应20min;(5) Perform RAA amplification by placing the reaction tube obtained in step (4) into the water bath prepared in step (1) and reacting for 20 min;
(6)反应结束后,将步骤(5)所得扩增产物用PBS缓冲液稀释10倍;(6) After the reaction is completed, the amplified product obtained in step (5) is diluted 10 times with PBS buffer;
(7)取出试验所需数量的LFD试纸条,在LFD试纸条吸收垫上面标好标记;(7) Take out the required number of LFD test strips and mark the absorbent pads of the LFD test strips;
(8)取出相应数量的PCR离心管,标好标记,加入100μL步骤(6)稀释后的反应物到离心管内,吸打混匀;(8) Take out a corresponding number of PCR centrifuge tubes, mark them, add 100 μL of the diluted reactant in step (6) into the centrifuge tubes, and mix by pipetting;
(9)将步骤(7)所得试纸条以样品点向下的方向放入离心管中,静置5~10min;(9) placing the test strip obtained in step (7) into a centrifuge tube with the sample point facing downward and leaving it to stand for 5 to 10 minutes;
(10)在自然光光线充足的地方进行试纸条检测结果的判读,没有条带出现或只出现检测线(T线)视为无效结果;若只出现质控线(C线)则视为阴性结果;若同时出现质控线(C线)和检测线(T线)则视为阳性结果。下述采用RAA-LFD检测都按照上述所建立的方法进行。(10) The test results were interpreted in a place with sufficient natural light. No strips or only the test line (T line) appeared, which was considered an invalid result; if only the quality control line (C line) appeared, it was considered a negative result; if both the quality control line (C line) and the test line (T line) appeared, it was considered a positive result. The following RAA-LFD tests were performed according to the above established method.
表4RAA反应体系Table 4 RAA reaction system
3.RAA-LFD反应条件优化3. Optimization of RAA-LFD reaction conditions
(1)优化最佳反应温度:以停乳链球菌DNA为模板,采用1中所得ISP-RAA-LF:F和ISP-RAA-LR:R为引物,以ISP-Probe为探针在不同温度下分别进行2中所建立的RAA-LFD检测,设置5组温度梯度,分别为29℃、34℃、39℃、44℃和49℃,阴性反应加入等量的ddH2O替换,作为阴性对照,结果如图5所示,其中NC为阴性对照;(1) Optimization of the optimal reaction temperature: Using Streptococcus dysgalactiae DNA as a template, using ISP-RAA-LF: F and ISP-RAA-LR: R obtained in 1 as primers, and using ISP-Probe as a probe, the RAA-LFD detection established in 2 was performed at different temperatures. Five groups of temperature gradients were set, namely 29°C, 34°C, 39°C, 44°C and 49°C. An equal amount of ddH 2 O was added to replace the negative reaction as a negative control. The results are shown in Figure 5, where NC is a negative control.
由图5A可知,在39℃~44℃温度范围内,RAA扩增产物均被试纸条检测到,且试纸条检测线T线上的条带亮度随着温度的增加呈现先增加后减少的趋势,当温度低于39℃或高于44℃时,试纸条T线上的条带亮度不明显;如图5B可知,使用ImageJ软件分析T线灰度值无显著差异(P>0.05),为使检测温度更接近环境温度,选择39℃作为最佳反应温度;As shown in Figure 5A, within the temperature range of 39°C to 44°C, the RAA amplification products were all detected by the test strips, and the brightness of the band on the test strip detection line T line showed a trend of first increasing and then decreasing with the increase of temperature. When the temperature was lower than 39°C or higher than 44°C, the brightness of the band on the test strip T line was not obvious; as shown in Figure 5B, there was no significant difference in the gray value of the T line analyzed by ImageJ software (P>0.05). In order to make the detection temperature closer to the ambient temperature, 39°C was selected as the optimal reaction temperature;
(2)优化最佳反应时间:以停乳链球菌DNA为模板,采用1中所得ISP-RAA-LF:F和ISP-RAA-LR:R为引物,以ISP-Probe为探针在温度39℃的基础上优化反应时间,分别在5min、10min、15min、20min、25min和30min进行RAA-LFD检测,阴性反应加入等量的ddH2O替换,作为阴性对照,反应进行5min后观察实验结果,实验结果如图5C所示;(2) Optimizing the best reaction time: Using Streptococcus dysgalactiae DNA as a template, using ISP-RAA-LF: F and ISP-RAA-LR: R obtained in 1 as primers, and using ISP-Probe as a probe, the reaction time was optimized at 39°C. RAA-LFD detection was performed at 5 min, 10 min, 15 min, 20 min, 25 min and 30 min, respectively. An equal amount of ddH 2 O was added to replace the negative reaction as a negative control. The experimental results were observed after the reaction was carried out for 5 min. The experimental results are shown in Figure 5C;
由图5C可知,试纸条检测线T线开始呈现一条较弱的亮带,随着反应时间的增加,检测线逐渐增亮;由图5D可知,当反应时间分别为15min、20min、25min和30min时,T线灰度值无显著差异(P>0.05),为保证实验的快速性,选择15min为RAA最佳反应时间。As shown in Figure 5C, the test strip detection line T line initially showed a weak bright band, and as the reaction time increased, the detection line gradually brightened; as shown in Figure 5D, when the reaction time was 15min, 20min, 25min and 30min, respectively, there was no significant difference in the gray value of the T line (P>0.05). In order to ensure the rapidity of the experiment, 15min was selected as the optimal reaction time for RAA.
4、RAA-LFD法检测停乳链球菌的敏感性和特异性分析4. Analysis of sensitivity and specificity of RAA-LFD method for detecting Streptococcus dysgalactiae
(1)RAA-LFD法检测停乳链球菌的敏感性分析:以不同浓度的停乳链球菌DNA为模板,选择ISP-F2/ISP-R2引物分别进行PCR扩增,反应程序与反应体系如表1和表2所示;采用1中所得ISP-RAA-LF和ISP-RAA-LR为引物分别进行RAA-LFD检测,结果如图6所示,其中M为DNA分子质量标准;NC为阴性对照;1为1.002×103ng/μL;2为1.002×102ng/μL;3为1.002×101ng/μL;4为1.002×100ng/μL;5为1.002×102pg/μL;6为1.002×101pg/μL;7为1.002×100pg/μL;a为停乳链球菌;b为无乳链球菌;c为海豚链球菌;d为金黄色葡萄球菌;e为拟态弧菌;f为嗜水气单胞菌;g为爱德华氏菌;(1) Analysis of the sensitivity of RAA-LFD method for detecting Streptococcus dysgalactiae: Using different concentrations of Streptococcus dysgalactiae DNA as template, ISP-F2/ISP-R2 primers were selected for PCR amplification, and the reaction procedures and reaction systems are shown in Tables 1 and 2; ISP-RAA-LF and ISP-RAA-LR obtained in 1 were used as primers for RAA-LFD detection, and the results are shown in Figure 6, where M is the DNA molecular mass standard; NC is the negative control; 1 is 1.002×10 3 ng/μL; 2 is 1.002×10 2 ng/μL; 3 is 1.002×10 1 ng/μL; 4 is 1.002×10 0 ng/μL; 5 is 1.002×10 2 pg/μL; 6 is 1.002×10 1 pg/μL; 7 is 1.002×10 0 pg/μL; a is Streptococcus dysgalactiae; b is Streptococcus agalactiae; c is Streptococcus iniae; d is Staphylococcus aureus; e is Vibrio mimicus; f is Aeromonas hydrophila; g is Edwardsiella;
由图6A可知,当停乳链球菌DNA浓度为1.002×103ng/μL~1.002×100ng/μL时,目的条带明亮,表明采用PCR扩增,最低检测限为1.002×100ng/μL;由图6B可知,当停乳链球菌DNA浓度降低时,试纸条T线的亮度逐渐变弱,当停乳链球菌DNA浓度低于1.002×102pg/μL时,T线上的条带亮度不明显;由图6C可知,使用ImageJ软件分析的T线灰度值无显著差异(P>0.05),因此,RAA-LFD法对停乳链球菌的最低检测限为1.002×102pg/μL,采用RAA-LFD法检测的基因组灵敏度比传统PCR法的基因组灵敏度高;As shown in Figure 6A, when the DNA concentration of Streptococcus dysgalactiae is 1.002×10 3 ng/μL~1.002×10 0 ng/μL, the target band is bright, indicating that the minimum detection limit of PCR amplification is 1.002×10 0 ng/μL; as shown in Figure 6B, when the DNA concentration of Streptococcus dysgalactiae decreases, the brightness of the T line of the test strip gradually weakens. When the DNA concentration of Streptococcus dysgalactiae is lower than 1.002×10 2 pg/μL, the brightness of the band on the T line is not obvious; as shown in Figure 6C, there is no significant difference in the gray value of the T line analyzed by ImageJ software (P>0.05). Therefore, the minimum detection limit of RAA-LFD method for Streptococcus dysgalactiae is 1.002×10 2 pg/μL, and the genome sensitivity detected by RAA-LFD method is higher than that of traditional PCR method.
(2)RAA-LFD法检测停乳链球菌的特异性分析:分别以停乳链球菌、无乳链球菌、海豚链球菌、金黄色葡萄球菌、拟态弧菌、嗜水气单胞菌和爱德华氏菌的DNA为模板,采用1中所得ISP-RAA-LF:F和ISP-RAA-LR:R:为引物分别进行RAA-LFD检测,验证该方法检测停乳链球菌的特异性,结果如图6D所示;(2) Analysis of the specificity of RAA-LFD method for detecting Streptococcus dysgalactiae: DNA of Streptococcus dysgalactiae, Streptococcus agalactiae, Streptococcus iniae, Staphylococcus aureus, Vibrio mimicus, Aeromonas hydrophila and Edwardsiella pneumoniae were used as templates, and ISP-RAA-LF:F and ISP-RAA-LR:R: obtained in 1 were used as primers to perform RAA-LFD detection, respectively, to verify the specificity of this method for detecting Streptococcus dysgalactiae. The results are shown in FIG6D .
由图6D可知,停乳链球菌在试纸条T线上具有明亮的阳性条带,而其他6种病原菌在试纸条T线上无阳性条带,因此,RAA-LFD法对停乳链球菌的特异性强,不受水产品中其他的致病菌影响。As shown in Figure 6D, Streptococcus dysgalactiae has a bright positive band on the T line of the test strip, while the other six pathogens have no positive bands on the T line of the test strip. Therefore, the RAA-LFD method has a strong specificity for Streptococcus dysgalactiae and is not affected by other pathogenic bacteria in aquatic products.
实施例3Example 3
采用PCR检测方法以及RAA-LFD检测方法分别检测50尾斑马鱼评估停乳链球菌RAA-LFD检测方法的性能,将两种方法进行比较,结果如表5和图7~9所示。50 zebrafish were tested by PCR and RAA-LFD respectively to evaluate the performance of RAA-LFD detection method for Streptococcus dysgalactiae. The two methods were compared and the results are shown in Table 5 and Figures 7-9.
表5RAA-LFD与传统PCR在试验样本中的比较Table 5 Comparison of RAA-LFD and traditional PCR in experimental samples
由表5可知,两种方法的阳性符合率为97.6%,阴性符合率为90.0%,总符合率为98.0%。As shown in Table 5, the positive coincidence rate of the two methods is 97.6%, the negative coincidence rate is 90.0%, and the total coincidence rate is 98.0%.
由图7可知,RAA-LFD方法检测到41个阳性样本和9个阴性样本,阳性率为82.0%,阴性率为18.0%;由图8可知,传统PCR检测到40份阳性样本和10份阴性样本,阳性率为80.0%,阴性率为20.0%;由图9可知,两条线相较于高的属于RAA组,低的属于PCR组,与传统PCR相比,RAA-LFD的AUC为0.950,敏感性为100%,特异性为90%,实际样品检测结果表明,RAA-LFD法具有较高的检测准确性,实际应用效果较好。As shown in Figure 7, the RAA-LFD method detected 41 positive samples and 9 negative samples, with a positive rate of 82.0% and a negative rate of 18.0%; as shown in Figure 8, the traditional PCR detected 40 positive samples and 10 negative samples, with a positive rate of 80.0% and a negative rate of 20.0%; as shown in Figure 9, the two lines belong to the RAA group and the low line belongs to the PCR group. Compared with the traditional PCR, the AUC of RAA-LFD is 0.950, the sensitivity is 100%, and the specificity is 90%. The actual sample detection results show that the RAA-LFD method has a higher detection accuracy and a better practical application effect.
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