通用型基因悬浮芯片检测生物恐怖细菌的方法研究

目的 建立快速、高通量的基因悬浮芯片检测方法,用于生物恐怖病原体的快速筛检.方法 选择保守的细菌16 S rDNA序列,并针对炭疽芽孢杆菌(Bacillus anthracis,B.a)、鼠疫耶尔森菌(Yersinia pestis,Y.p)、布鲁菌属(Brucella spp.,Bru)、土拉弗朗西斯菌(Francisella tularensis,F.t)和类鼻疽伯克霍尔德菌(Burkholderia pseudomallei,B.p)等5种生物恐怖细菌设计种(属)特异性探针,经16 S rDNA通用引物341A、519B扩增基因组DNA,用基因悬浮芯片方法进行检测,并对方法的灵敏度、特异度、重复性、检测能力进行验证.结果 经16 S rDNA通用引物扩增,特异性探针杂交检测,能将样本细菌鉴定到属水平,同属菌出现交叉反应;检出限分别为类鼻疽伯克霍尔德菌1.5 pg/μl,布鲁菌属20 ps/μl,炭疽芽孢杆菌7 pg/μl,土拉弗朗西斯菌0.1 pg/μl,鼠疫耶尔森菌1.1 pg/μl;15次重复检测各探针变异系数(CV)为5.18%～17.88%,具有较好的重复性;方法可正确检出模拟白色粉末样本中炭疽芽孢杆菌和鼠疫耶尔森菌.结论 建立了通用型基因悬浮芯片检测体系快速高通量筛查生物恐怖细菌的方法.     

肝组织中HBV cccDNA荧光定量聚合酶链反应检测法的建立

Objective To establish and optimize a sensitive and specific quantitative realtime polymerase chain reaction(PCR)method for detection of hepatitis B virus covalently closed circular DNA(HBV cccDNA)in liver tissue. Methods Specific primers and probes were designed to detect HBV DNA(tDNA)and cccDNA. A series of plasmids(3.44 × 100-3.44 × 109 copies/μl)containing a full double-stranded copies of HBV genome(genotype C)were used to establish the standard curve of real-time PCR. Liver samples of 33 patients with HBV related hepatocellular carcinoma(HCC), 13 Chronic hepatitis B patients(CHB)and 10 non-HBV patients were collected to verify the sensitivity and specificity of the assay. A fraction of extracted DNA was digested with a Plasmid-Safe ATP-dependent Dnase(PSAD)for HBV cccDNA detection and the remaining was used for tDNA and β-globin detection. The amount(copies/cell)of HBV cccDNA and tDNA were measured by a real-time PCR, using β-globin housekeeping gene as a quantitation standard. Results The standard curves of real-time PCR with a linear range of 3.44 × 100 to 3.44 × 109 copies/μl were established for detecting HBV cccDNA and tDNA, and both of the lowest detection limits of HBV cccDNA and tDNA were 3.44 × 100 copies/μl. The lowest quantitation levels of HBV cccDNA in liver tissues tested in 33 HBV related HCC patients and 13 CHB patients were 0.003 copies/cell and 0.031copies/cell, respectively. HBV cccDNA and tDNA in liver tissue of 10 non-HBV patient appeared to be negative. The true positive rate was increasing through the digestion of HBV DNA by PSAD, and the analytic specificity of cccDNA detection improved by 7.24 × 102 times. Liver tissues of 2 patients were retested 5 times in the PCR for detecting cccDNA and the coefficience of variations on cycle threshold (Ct)were between 0.224%-0.609%. Conclusion A highly sensitive and specific quantitative real time PCR method for the detection of HBV cccDNA in liver tissue was established and could be used for clinical and epidemiological studies.     

肝组织中HBV cccDNA荧光定量聚合酶链反应检测法的建立

Objective To establish and optimize a sensitive and specific quantitative realtime polymerase chain reaction(PCR)method for detection of hepatitis B virus covalently closed circular DNA(HBV cccDNA)in liver tissue. Methods Specific primers and probes were designed to detect HBV DNA(tDNA)and cccDNA. A series of plasmids(3.44 × 100-3.44 × 109 copies/μl)containing a full double-stranded copies of HBV genome(genotype C)were used to establish the standard curve of real-time PCR. Liver samples of 33 patients with HBV related hepatocellular carcinoma(HCC), 13 Chronic hepatitis B patients(CHB)and 10 non-HBV patients were collected to verify the sensitivity and specificity of the assay. A fraction of extracted DNA was digested with a Plasmid-Safe ATP-dependent Dnase(PSAD)for HBV cccDNA detection and the remaining was used for tDNA and β-globin detection. The amount(copies/cell)of HBV cccDNA and tDNA were measured by a real-time PCR, using β-globin housekeeping gene as a quantitation standard. Results The standard curves of real-time PCR with a linear range of 3.44 × 100 to 3.44 × 109 copies/μl were established for detecting HBV cccDNA and tDNA, and both of the lowest detection limits of HBV cccDNA and tDNA were 3.44 × 100 copies/μl. The lowest quantitation levels of HBV cccDNA in liver tissues tested in 33 HBV related HCC patients and 13 CHB patients were 0.003 copies/cell and 0.031copies/cell, respectively. HBV cccDNA and tDNA in liver tissue of 10 non-HBV patient appeared to be negative. The true positive rate was increasing through the digestion of HBV DNA by PSAD, and the analytic specificity of cccDNA detection improved by 7.24 × 102 times. Liver tissues of 2 patients were retested 5 times in the PCR for detecting cccDNA and the coefficience of variations on cycle threshold (Ct)were between 0.224%-0.609%. Conclusion A highly sensitive and specific quantitative real time PCR method for the detection of HBV cccDNA in liver tissue was established and could be used for clinical and epidemiological studies.     

嗜水气单胞菌TaqMan实时PCR检测方法的建立

Objective To develop a TaqMan real-time PCR for the detection of aeromonas hydrophila. Methods The conserved region of major adhesion gene of aeromonas hydrophila (aha) was used to design primers and TaqMan probe. A total of six concentration gradients for forward and reverse primers ranging from 200 -700 nmol/L were chosen, and four concentration gradients for probe ranging from I00 -400 nmol/L were chosen. And then the concentration of primers and probe were optimized by ANOVA of completely randomized design respectively. The specificity of the established method was evaluated by using bacteria as contrast, including 45 strains Vibrio cholerae,20 strains Vibrio parahemolyticus, 10 strains Vibrio fluvialis,4 strains Vibrio mimicus,5 strains Vibrio vulnificus, 1 strain Vibrio aiginoayticns, 1 strain Vibrio furnissii, 5 strains Salmonella, 10 strains Shigella and 2 strains Piesiomonas shigelloides. The sensitivity, bacterial sensitivity and DNA sensitivity included,were evaluated. The stool of healthy people was contaminated by aeromonas hydrephila artificially, and the ability of the established TaqMan real-time PCR system for detection of aeromonas hydrophila was also evaluated. Results The cycle threshold (Ct) value deserved from 6 groups of primers concentration gradient was (x±s) :20.69±0.33,20.72±0.21,20.81±0. 12,20.74±0.12,20.51±0. 16 and 20.69±0. 11, respectively, and the concentration of forward primer and reverse primer was determined to be 200 nmol/L (F=1.33, P=0. 28). The Ct value deserved from 4 groups of probe concentration gradient was (x±s) : 20.56±0. 08,20.82±0.05,20. 82±0. 11 and 20.93±0.09,respectively,and the concentration of probe was determined to be 100 nmol/L(F =5.26,P =O. 01 ). The bacterial sensitivity and DNA sensitivity were 80 CFU/ml and 100 fg/μl respectively,and the sensitivity to detect aeromonas hydrophila from stool was 8 × 103 CFU/ml, which might be 8 CFU/ml after 8 hours' enrichment. No amplification was observed in the templates of other bacterial. Conclusion The TaqMan real-time PCR method targeting the aha gene of aeromonas hydrophila had a high sensitivity and specificity and might be used to detect aeromonas hydrophila from pure bacterial and stool rapidly.     

嗜水气单胞菌TaqMan实时PCR检测方法的建立

Objective To develop a TaqMan real-time PCR for the detection of aeromonas hydrophila. Methods The conserved region of major adhesion gene of aeromonas hydrophila (aha) was used to design primers and TaqMan probe. A total of six concentration gradients for forward and reverse primers ranging from 200 -700 nmol/L were chosen, and four concentration gradients for probe ranging from I00 -400 nmol/L were chosen. And then the concentration of primers and probe were optimized by ANOVA of completely randomized design respectively. The specificity of the established method was evaluated by using bacteria as contrast, including 45 strains Vibrio cholerae,20 strains Vibrio parahemolyticus, 10 strains Vibrio fluvialis,4 strains Vibrio mimicus,5 strains Vibrio vulnificus, 1 strain Vibrio aiginoayticns, 1 strain Vibrio furnissii, 5 strains Salmonella, 10 strains Shigella and 2 strains Piesiomonas shigelloides. The sensitivity, bacterial sensitivity and DNA sensitivity included,were evaluated. The stool of healthy people was contaminated by aeromonas hydrephila artificially, and the ability of the established TaqMan real-time PCR system for detection of aeromonas hydrophila was also evaluated. Results The cycle threshold (Ct) value deserved from 6 groups of primers concentration gradient was (x±s) :20.69±0.33,20.72±0.21,20.81±0. 12,20.74±0.12,20.51±0. 16 and 20.69±0. 11, respectively, and the concentration of forward primer and reverse primer was determined to be 200 nmol/L (F=1.33, P=0. 28). The Ct value deserved from 4 groups of probe concentration gradient was (x±s) : 20.56±0. 08,20.82±0.05,20. 82±0. 11 and 20.93±0.09,respectively,and the concentration of probe was determined to be 100 nmol/L(F =5.26,P =O. 01 ). The bacterial sensitivity and DNA sensitivity were 80 CFU/ml and 100 fg/μl respectively,and the sensitivity to detect aeromonas hydrophila from stool was 8 × 103 CFU/ml, which might be 8 CFU/ml after 8 hours' enrichment. No amplification was observed in the templates of other bacterial. Conclusion The TaqMan real-time PCR method targeting the aha gene of aeromonas hydrophila had a high sensitivity and specificity and might be used to detect aeromonas hydrophila from pure bacterial and stool rapidly.     

嗜水气单胞菌TaqMan实时PCR检测方法的建立

Objective To develop a TaqMan real-time PCR for the detection of aeromonas hydrophila. Methods The conserved region of major adhesion gene of aeromonas hydrophila (aha) was used to design primers and TaqMan probe. A total of six concentration gradients for forward and reverse primers ranging from 200 -700 nmol/L were chosen, and four concentration gradients for probe ranging from I00 -400 nmol/L were chosen. And then the concentration of primers and probe were optimized by ANOVA of completely randomized design respectively. The specificity of the established method was evaluated by using bacteria as contrast, including 45 strains Vibrio cholerae,20 strains Vibrio parahemolyticus, 10 strains Vibrio fluvialis,4 strains Vibrio mimicus,5 strains Vibrio vulnificus, 1 strain Vibrio aiginoayticns, 1 strain Vibrio furnissii, 5 strains Salmonella, 10 strains Shigella and 2 strains Piesiomonas shigelloides. The sensitivity, bacterial sensitivity and DNA sensitivity included,were evaluated. The stool of healthy people was contaminated by aeromonas hydrephila artificially, and the ability of the established TaqMan real-time PCR system for detection of aeromonas hydrophila was also evaluated. Results The cycle threshold (Ct) value deserved from 6 groups of primers concentration gradient was (x±s) :20.69±0.33,20.72±0.21,20.81±0. 12,20.74±0.12,20.51±0. 16 and 20.69±0. 11, respectively, and the concentration of forward primer and reverse primer was determined to be 200 nmol/L (F=1.33, P=0. 28). The Ct value deserved from 4 groups of probe concentration gradient was (x±s) : 20.56±0. 08,20.82±0.05,20. 82±0. 11 and 20.93±0.09,respectively,and the concentration of probe was determined to be 100 nmol/L(F =5.26,P =O. 01 ). The bacterial sensitivity and DNA sensitivity were 80 CFU/ml and 100 fg/μl respectively,and the sensitivity to detect aeromonas hydrophila from stool was 8 × 103 CFU/ml, which might be 8 CFU/ml after 8 hours' enrichment. No amplification was observed in the templates of other bacterial. Conclusion The TaqMan real-time PCR method targeting the aha gene of aeromonas hydrophila had a high sensitivity and specificity and might be used to detect aeromonas hydrophila from pure bacterial and stool rapidly.     

嗜水气单胞菌TaqMan实时PCR检测方法的建立

Objective To develop a TaqMan real-time PCR for the detection of aeromonas hydrophila. Methods The conserved region of major adhesion gene of aeromonas hydrophila (aha) was used to design primers and TaqMan probe. A total of six concentration gradients for forward and reverse primers ranging from 200 -700 nmol/L were chosen, and four concentration gradients for probe ranging from I00 -400 nmol/L were chosen. And then the concentration of primers and probe were optimized by ANOVA of completely randomized design respectively. The specificity of the established method was evaluated by using bacteria as contrast, including 45 strains Vibrio cholerae,20 strains Vibrio parahemolyticus, 10 strains Vibrio fluvialis,4 strains Vibrio mimicus,5 strains Vibrio vulnificus, 1 strain Vibrio aiginoayticns, 1 strain Vibrio furnissii, 5 strains Salmonella, 10 strains Shigella and 2 strains Piesiomonas shigelloides. The sensitivity, bacterial sensitivity and DNA sensitivity included,were evaluated. The stool of healthy people was contaminated by aeromonas hydrephila artificially, and the ability of the established TaqMan real-time PCR system for detection of aeromonas hydrophila was also evaluated. Results The cycle threshold (Ct) value deserved from 6 groups of primers concentration gradient was (x±s) :20.69±0.33,20.72±0.21,20.81±0. 12,20.74±0.12,20.51±0. 16 and 20.69±0. 11, respectively, and the concentration of forward primer and reverse primer was determined to be 200 nmol/L (F=1.33, P=0. 28). The Ct value deserved from 4 groups of probe concentration gradient was (x±s) : 20.56±0. 08,20.82±0.05,20. 82±0. 11 and 20.93±0.09,respectively,and the concentration of probe was determined to be 100 nmol/L(F =5.26,P =O. 01 ). The bacterial sensitivity and DNA sensitivity were 80 CFU/ml and 100 fg/μl respectively,and the sensitivity to detect aeromonas hydrophila from stool was 8 × 103 CFU/ml, which might be 8 CFU/ml after 8 hours' enrichment. No amplification was observed in the templates of other bacterial. Conclusion The TaqMan real-time PCR method targeting the aha gene of aeromonas hydrophila had a high sensitivity and specificity and might be used to detect aeromonas hydrophila from pure bacterial and stool rapidly.     

嗜水气单胞菌TaqMan实时PCR检测方法的建立

Objective To develop a TaqMan real-time PCR for the detection of aeromonas hydrophila. Methods The conserved region of major adhesion gene of aeromonas hydrophila (aha) was used to design primers and TaqMan probe. A total of six concentration gradients for forward and reverse primers ranging from 200 -700 nmol/L were chosen, and four concentration gradients for probe ranging from I00 -400 nmol/L were chosen. And then the concentration of primers and probe were optimized by ANOVA of completely randomized design respectively. The specificity of the established method was evaluated by using bacteria as contrast, including 45 strains Vibrio cholerae,20 strains Vibrio parahemolyticus, 10 strains Vibrio fluvialis,4 strains Vibrio mimicus,5 strains Vibrio vulnificus, 1 strain Vibrio aiginoayticns, 1 strain Vibrio furnissii, 5 strains Salmonella, 10 strains Shigella and 2 strains Piesiomonas shigelloides. The sensitivity, bacterial sensitivity and DNA sensitivity included,were evaluated. The stool of healthy people was contaminated by aeromonas hydrephila artificially, and the ability of the established TaqMan real-time PCR system for detection of aeromonas hydrophila was also evaluated. Results The cycle threshold (Ct) value deserved from 6 groups of primers concentration gradient was (x±s) :20.69±0.33,20.72±0.21,20.81±0. 12,20.74±0.12,20.51±0. 16 and 20.69±0. 11, respectively, and the concentration of forward primer and reverse primer was determined to be 200 nmol/L (F=1.33, P=0. 28). The Ct value deserved from 4 groups of probe concentration gradient was (x±s) : 20.56±0. 08,20.82±0.05,20. 82±0. 11 and 20.93±0.09,respectively,and the concentration of probe was determined to be 100 nmol/L(F =5.26,P =O. 01 ). The bacterial sensitivity and DNA sensitivity were 80 CFU/ml and 100 fg/μl respectively,and the sensitivity to detect aeromonas hydrophila from stool was 8 × 103 CFU/ml, which might be 8 CFU/ml after 8 hours' enrichment. No amplification was observed in the templates of other bacterial. Conclusion The TaqMan real-time PCR method targeting the aha gene of aeromonas hydrophila had a high sensitivity and specificity and might be used to detect aeromonas hydrophila from pure bacterial and stool rapidly.     

嗜水气单胞菌TaqMan实时PCR检测方法的建立

Objective To develop a TaqMan real-time PCR for the detection of aeromonas hydrophila. Methods The conserved region of major adhesion gene of aeromonas hydrophila (aha) was used to design primers and TaqMan probe. A total of six concentration gradients for forward and reverse primers ranging from 200 -700 nmol/L were chosen, and four concentration gradients for probe ranging from I00 -400 nmol/L were chosen. And then the concentration of primers and probe were optimized by ANOVA of completely randomized design respectively. The specificity of the established method was evaluated by using bacteria as contrast, including 45 strains Vibrio cholerae,20 strains Vibrio parahemolyticus, 10 strains Vibrio fluvialis,4 strains Vibrio mimicus,5 strains Vibrio vulnificus, 1 strain Vibrio aiginoayticns, 1 strain Vibrio furnissii, 5 strains Salmonella, 10 strains Shigella and 2 strains Piesiomonas shigelloides. The sensitivity, bacterial sensitivity and DNA sensitivity included,were evaluated. The stool of healthy people was contaminated by aeromonas hydrephila artificially, and the ability of the established TaqMan real-time PCR system for detection of aeromonas hydrophila was also evaluated. Results The cycle threshold (Ct) value deserved from 6 groups of primers concentration gradient was (x±s) :20.69±0.33,20.72±0.21,20.81±0. 12,20.74±0.12,20.51±0. 16 and 20.69±0. 11, respectively, and the concentration of forward primer and reverse primer was determined to be 200 nmol/L (F=1.33, P=0. 28). The Ct value deserved from 4 groups of probe concentration gradient was (x±s) : 20.56±0. 08,20.82±0.05,20. 82±0. 11 and 20.93±0.09,respectively,and the concentration of probe was determined to be 100 nmol/L(F =5.26,P =O. 01 ). The bacterial sensitivity and DNA sensitivity were 80 CFU/ml and 100 fg/μl respectively,and the sensitivity to detect aeromonas hydrophila from stool was 8 × 103 CFU/ml, which might be 8 CFU/ml after 8 hours' enrichment. No amplification was observed in the templates of other bacterial. Conclusion The TaqMan real-time PCR method targeting the aha gene of aeromonas hydrophila had a high sensitivity and specificity and might be used to detect aeromonas hydrophila from pure bacterial and stool rapidly.     

嗜水气单胞菌TaqMan实时PCR检测方法的建立

Objective To develop a TaqMan real-time PCR for the detection of aeromonas hydrophila. Methods The conserved region of major adhesion gene of aeromonas hydrophila (aha) was used to design primers and TaqMan probe. A total of six concentration gradients for forward and reverse primers ranging from 200 -700 nmol/L were chosen, and four concentration gradients for probe ranging from I00 -400 nmol/L were chosen. And then the concentration of primers and probe were optimized by ANOVA of completely randomized design respectively. The specificity of the established method was evaluated by using bacteria as contrast, including 45 strains Vibrio cholerae,20 strains Vibrio parahemolyticus, 10 strains Vibrio fluvialis,4 strains Vibrio mimicus,5 strains Vibrio vulnificus, 1 strain Vibrio aiginoayticns, 1 strain Vibrio furnissii, 5 strains Salmonella, 10 strains Shigella and 2 strains Piesiomonas shigelloides. The sensitivity, bacterial sensitivity and DNA sensitivity included,were evaluated. The stool of healthy people was contaminated by aeromonas hydrephila artificially, and the ability of the established TaqMan real-time PCR system for detection of aeromonas hydrophila was also evaluated. Results The cycle threshold (Ct) value deserved from 6 groups of primers concentration gradient was (x±s) :20.69±0.33,20.72±0.21,20.81±0. 12,20.74±0.12,20.51±0. 16 and 20.69±0. 11, respectively, and the concentration of forward primer and reverse primer was determined to be 200 nmol/L (F=1.33, P=0. 28). The Ct value deserved from 4 groups of probe concentration gradient was (x±s) : 20.56±0. 08,20.82±0.05,20. 82±0. 11 and 20.93±0.09,respectively,and the concentration of probe was determined to be 100 nmol/L(F =5.26,P =O. 01 ). The bacterial sensitivity and DNA sensitivity were 80 CFU/ml and 100 fg/μl respectively,and the sensitivity to detect aeromonas hydrophila from stool was 8 × 103 CFU/ml, which might be 8 CFU/ml after 8 hours' enrichment. No amplification was observed in the templates of other bacterial. Conclusion The TaqMan real-time PCR method targeting the aha gene of aeromonas hydrophila had a high sensitivity and specificity and might be used to detect aeromonas hydrophila from pure bacterial and stool rapidly.