Establishment and evaluation of a method for extracting exogenous short DNA fragments of Schistosoma japonicum from urine samples / 中国血吸虫病防治杂志

Objective To establish the method for extracting exogenous short DNA fragments of Schistosoma japonicum from urine samples, and to evaluate the efficiency of this method for extraction from urine samples treated with various methods. Methods The S. japonicum SjG28 gene fragment was selected as a target sequence, and the 81 bp short DNA fragment was amplified on the target sequence using PCR assay. Following characterization using sequencing, the short DNA fragment was added into the urine samples as an exogenous short DNA fragment. Primers and probes were designed with SjG28 as a target gene, to establish the real-time fluorescent quantitative PCR (qPCR) assay. The sensitivity of this qPCR assay was evaluated with exogenous short DNA fragments that were diluted at a 1:10 dilution ratio as the DNA template, and the specificity of the qPCR assay was evaluated with the genomic DNA of S. mansoni, S. haematobium, Babesia, Ancyiostoma duodenaie, Cionorchis sinensis, and Paragonimus westermani as DNA templates. Exogenous short DNA fragments were added into artificial and healthy volunteers’ urine samples, followed by pH adjustment, centrifugation and concentration, and the efficiency of extracting exogenous short DNA fragments from urine samples was compared with the QIAmp Viral RNA Mini Kit (Qiagen kit) and BIOG cfDNA easy kit (BIOG kit). Results An 81 bp small DNA fragment of S. japonicum was successfully prepared, and the lowest detection limit of the established qPCR assay was 100 copies/μL of the 81 bp small DNA fragment of S. japonicum. If the genomic DNA of S. japonicum, S. mansoni, S. haematobium, Babesia, A. duodenaie, C. sinensis, and P. westermani served as DNA templates, the qPCR assay only detected fluorescent signals with S. japonicum genomic DNA as the DNA template. If the pH values of artificial urine samples were adjusted to 5, 6, 7 and 8, the recovery rates were (49.12 ± 2.09)%, (84.52 ± 4.96)%, (89.38 ± 3.32)% and (87.82 ± 3.90)% for extracting the exogenous short DNA fragment of S. japonicum with the Qiagen kit, and were (2.30 ± 0.07)%, (8.11% ± 0.26)%, (13.35 ± 0.61)% and (20.82 ± 0.68)% with the BIOG kit, respectively (t = 38.702, 26.955, 39.042 and 29.571; all P values < 0.01). If the Qiagen kit was used for extracting the exogenous short DNA fragment from artificial urine samples, the lowest recovery rate was seen from urine samples with a pH value of 5 (all P values < 0.05), and there were no significant differences in the recovery rate from urine samples with pH values of 6, 7 and 8 (all P values > 0.05). Following centrifugation of artificial [(64.30 ± 1.00)% vs. (58.87 ± 0.26)%; t = 12.033, P < 0.05] and healthy volunteers’ urine samples [(31 165 ± 1 017) copies/μL vs. (28 471 ± 818) copies/μL; t = 23.164, P < 0.05]. In addition, concentration of artificial urine samples with the 10 kDa Centrifugal Filter and concentration of healthy volunteers’ urine samples with the 100 kDa Centrifugal Filter were both effective to increase the recovery of the Qiagen kit for extracting the exogenous short DNA fragment of S. japonicum (both P values < 0.01). Conclusions A method for extracting exogenous short DNA fragments of S. japonicum from urine samples has been successfully established, and the Qiagen kit has a high extraction efficiency. Adjustment of urine pH to 6 to 8 and concentration of healthy volunteers’ urine samples with the 100 kDa Centrifugal Filter are both effective to increase the efficiency of extracting exogenous short DNA fragments of S. japonicum.

First report of invasive Pomacea snails in Shandong Province / 中国血吸虫病防治杂志

Objective To characterize the species of invasive Pomacea snails that were discovered for the first time in Shandong Province. Methods Pomacea snails samples were collected in the field of Jining City, Shandong Province on October 2021 for morphological identification. Pomacea snails were randomly sampled and genomic DNA was extracted from foot muscle tissues of Pomacea snails for multiplex PCR amplification. The PCR amplification product was sequenced. Then, the sequence was aligned and a phylogenetic tree was created using the software MegAlign 7.1.0. In addition, Angiostongylus cantonensis infection was detected in Pomacea snails with the lung microscopy. Results A total of 104 living Pomacea snails were collected, and all were characterized as Pomacea spp. based on morphological features. Of 12 randomly selected adult Pomacea snails, multiplex PCR assay and sequencing identified eleven snails as P. canaliculata and one as P. maculata. No A. cantonensis infection was detected in 104 Pomacea snails. Conclusion This is the first report of invasive Pomacea snails in Shandong Province, where P. canaliculata and P. maculata are found.

Molecular markers based upon whole chloroplast genomes and identifying alpine Gentiana waltonii and G. lhassica (Gentianaceae) / 药学学报

As two original plants of Tibetan herb Jieji, Gentiana waltonii Burk. and Gentiana lhassica Burk. belong to Section Cruciata of Gentiana, Gentianaceae. Here, we report on whole chloroplast genome sequences in the alpine species, respectively, and the features of plastomes were investigated. The plastome of G. waltonii is 148 705 bp long (148 652 bp in G. lhassica) and encodes 112 genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Two pseudogenes, namely ψrps16 and ψinfA, were found in plastomes. In addition, two novel loci were detected, and a species-specific polymerase chain reaction assay was developed for differentiating G. waltonii and G. lhassica from 10 alpine species in Section Cruciata. Gentiana. Our study provides basic data for identifying Tibetan herbs, alpine species conservation and molecular phylogenetic studies of Gentiana and Gentianaceae.

Rapid detection of Respiratory Pathogens using a Multiplex PCR assay among hospitalized children with Acute Respiratory Infection

Background@#Acute respiratory infection (ARI) is a major cause of morbidity and mortality among children worldwide however, local data on the etiologic diagnosis of ARI are limited. @*Objectives@#To determine the prevalence and the most commonly detected respiratory pathogens using a multiplex PCR assay, known as the Respiratory Panel, among hospitalized children with ARI and compare their clinical and laboratory differences. @*Methods@#This is a cross sectional study of children with ARI who were tested with a multiplex PCR assay. Retrospective chart review was done on these patients admitted from January 2018 to February 2020. @*Results@#There were 47 charts reviewed, mean age was 4.2 years old. Out of 47 patients, 36 (76.6%) tested positive for a pathogen. Respiratory syncytial virus (RSV) being the most common followed by Influenza A/H1-2009 and Human metapneumovirus (hMPV). Two patients had viral co-infections and no bacteria were detected on all subjects. 61.7% patients were started on antibiotics on admission. Fever and cough were the most common sign and symptom, respectively. Normal WBC (68% with neutrophilic predominance) and platelet were detected in 72.3% and 70.2% of patients, respectively; 50% of patients had normal CRP and 60.5% had abnormal findings on chest x-ray. Only the presence of chest x-ray findings was found to have a higher probability of yielding a positive Respiratory Panel p=0.27. @*Conclusion@#Among admitted patients with ARI, 76.6% tested positive for a respiratory pathogen. All were caused by viruses presenting as nonspecific manifestations – fever and cough. Clinical manifestations, CBC and CRP showed no association with the Respiratory Panel result while abnormal chest x-ray had a higher probability of yielding a positive Respiratory Panel result.

Application of multiplex PCR assay to study early multiple herpesviruses infection during HSCT / 中华血液学杂志

Objective: To investigate herpesvirus infection in early stage of hematopoietic stem cell transplantation (HSCT) by multiplex polymerase chain reaction (PCR), and to explore the association between multiple herpesviruses infection and clinical characteristics in HSCT patients and its impact on post-transplant complications and prognosis. Methods: A total of 734 peripheral blood samples were collected from 90 patients undergoing HSCT in the Department of Hematology, the First Affiliated Hospital of Soochow University between February 2017 and August 2017. The peripheral blood specimens were obtained before and within 90 days after transplantation at different time points. Lab-Aid824 Nucleic Acid Extraction Mini Reagent was used to extract DNA and multiplex PCR assay was used to simultaneously detect 8 kinds of human herpesviruses from genomic DNA. The incidence of various herpesvirus infections, its correlation with clinical features and effects on post-transplant complications and prognosis were analyzed. Results: The median follow-up time was 192 (range: 35-308) days. Among the 90 patients before transplantation, the incidence of herpes virus infection was 35.6% (32/90), including 12.2% (11/90) with one herpes virus infection and 23.3% (21/90) with multiple viruses infection. The incidence of herpes virus infection after transplantation was 77.8% (70/90), including 20.0% (18/90) with one herpes virus infection and 57.8% (52/90) with multiple herpes virus infection. Among the 52 patients with multiple herpes viruses infection, 30 (57.7%) patients were infected by 2 kinds of viruses, 18 (34.6%) patients by 3 kinds of viruses and 4 (7.7%) patients by 4 kinds of viruses. There was a correlation between HHV-6 and HHV-7 herpesvirus infection (OR=13.880, Q=0.026). EBV infection was related to HHV-7 infection (OR=0.093, Q=0.044). The age of patients was correlated with the incidence of HHV-1 infection before transplantation. There were 24 patients in our study experienced clinical symptoms associated with viral infection. The main manifestations were hemorrhagic cystitis (HC), interstitial pneumonia, enteritis, viral encephalitis and fever of unknown origin. EBV infection was related to HLA incompatibility and the inconsistent of the ABO blood group and grade Ⅱ-Ⅳ aGVHD after transplantation. HLA incompatibility and the unrelated donor and grade Ⅱ-Ⅳ aGVHD were related to multiple viruses infection. Conclusion: Multiple herpesviruses were common in patients undergoing HSCT, which were closely related to HLA mismatch, unrelated donor and grade Ⅱ-Ⅳ aGVHD.

Comparison of efficiency of Kato-Katz technique and PCR assay for detecting Clonorchis sinensis infection / 中国血吸虫病防治杂志

Objective To compare the performance of modified Kato-Katz thick smear method (KK method) and PCR assay in field detection of Clonorchis sinensis in human fecal samples, which provides insight into the selection of tools for detecting C. sinensis. Methods Based on the epidemiological investigation of human C. sinensis infections in Tengxian County of Guangxi Zhuang Autonomous Region in 2016, a total of 133 fecal samples were randomly selected and stored at -20 ℃. All fecal samples were detected for C. sinensis infection using KK method and PCR assay, and the detection rate was compared between the two techniques. In addition, Kappa test was used to evaluate the consistency between the two methods. Results Among all fecal samples, the overall detection rate of C. sinensis was 77.44% (103/133), and the detection rate was significantly higher by PCR assay (70.68%, 93/133) than by KK method (57.14%, 76/133) (χ2 = 26.15, P < 0.01). There were 88.16% (67/76) of the microscopy-positive fecal samples positive for PCR assay, and 47.37% (27/57) of the microscopy-negative fecal samples positive for PCR assay. The detection rate of C. sinensis by PCR assay (94.74%, 18/19) was higher in fecal samples with EPG of > 1 000 than in samples with EPG of < 1 000 (85.96%, 49/57) (χ2 = 1.05, P = 0.436). The consistency of the detection rate of C. sinensis was moderate between the KK method and PCR assay (Kappa = 0.73). Conclusions The detection rate of C. sinensis by PCR assay is significantly higher than by KK method. In low-endemic areas of C. sinensis infections, the combination of KK method and PCR assay is suggested, so as to improve the detection rate.

Comparison of efficiency of Kato-Katz technique and PCR assay for detecting Clonorchis sinensis infection / 中国血吸虫病防治杂志

Objective To compare the performance of modified Kato-Katz thick smear method (KK method) and PCR assay in field detection of Clonorchis sinensis in human fecal samples, which provides insight into the selection of tools for detecting C. sinensis. Methods Based on the epidemiological investigation of human C. sinensis infections in Tengxian County of Guangxi Zhuang Autonomous Region in 2016, a total of 133 fecal samples were randomly selected and stored at -20 ℃. All fecal samples were detected for C. sinensis infection using KK method and PCR assay, and the detection rate was compared between the two techniques. In addition, Kappa test was used to evaluate the consistency between the two methods. Results Among all fecal samples, the overall detection rate of C. sinensis was 77.44% (103/133), and the detection rate was significantly higher by PCR assay (70.68%, 93/133) than by KK method (57.14%, 76/133) (χ2 = 26.15, P < 0.01). There were 88.16% (67/76) of the microscopy-positive fecal samples positive for PCR assay, and 47.37% (27/57) of the microscopy-negative fecal samples positive for PCR assay. The detection rate of C. sinensis by PCR assay (94.74%, 18/19) was higher in fecal samples with EPG of > 1 000 than in samples with EPG of < 1 000 (85.96%, 49/57) (χ2 = 1.05, P = 0.436). The consistency of the detection rate of C. sinensis was moderate between the KK method and PCR assay (Kappa = 0.73). Conclusions The detection rate of C. sinensis by PCR assay is significantly higher than by KK method. In low-endemic areas of C. sinensis infections, the combination of KK method and PCR assay is suggested, so as to improve the detection rate.

Application of multiplex PCR assay to study early multiple herpesviruses infection during HSCT / 中华血液学杂志

Objective@#To investigate herpesvirus infection in early stage of hematopoietic stem cell transplantation (HSCT) by multiplex polymerase chain reaction (PCR), and to explore the association between multiple herpesviruses infection and clinical characteristics in HSCT patients and its impact on post-transplant complications and prognosis.@*Methods@#A total of 734 peripheral blood samples were collected from 90 patients undergoing HSCT in the Department of Hematology, the First Affiliated Hospital of Soochow University between February 2017 and August 2017. The peripheral blood specimens were obtained before and within 90 days after transplantation at different time points. Lab-Aid824 Nucleic Acid Extraction Mini Reagent was used to extract DNA and multiplex PCR assay was used to simultaneously detect 8 kinds of human herpesviruses from genomic DNA. The incidence of various herpesvirus infections, its correlation with clinical features and effects on post-transplant complications and prognosis were analyzed.@*Results@#The median follow-up time was 192 (range: 35-308) days. Among the 90 patients before transplantation, the incidence of herpes virus infection was 35.6% (32/90), including 12.2% (11/90) with one herpes virus infection and 23.3% (21/90) with multiple viruses infection. The incidence of herpes virus infection after transplantation was 77.8% (70/90), including 20.0% (18/90) with one herpes virus infection and 57.8% (52/90) with multiple herpes virus infection. Among the 52 patients with multiple herpes viruses infection, 30 (57.7%) patients were infected by 2 kinds of viruses, 18 (34.6%) patients by 3 kinds of viruses and 4 (7.7%) patients by 4 kinds of viruses. There was a correlation between HHV-6 and HHV-7 herpesvirus infection (OR=13.880, Q=0.026). EBV infection was related to HHV-7 infection (OR=0.093, Q=0.044). The age of patients was correlated with the incidence of HHV-1 infection before transplantation. There were 24 patients in our study experienced clinical symptoms associated with viral infection. The main manifestations were hemorrhagic cystitis (HC), interstitial pneumonia, enteritis, viral encephalitis and fever of unknown origin. EBV infection was related to HLA incompatibility and the inconsistent of the ABO blood group and grade Ⅱ-Ⅳ aGVHD after transplantation. HLA incompatibility and the unrelated donor and grade Ⅱ-Ⅳ aGVHD were related to multiple viruses infection.@*Conclusion@#Multiple herpesviruses were common in patients undergoing HSCT, which were closely related to HLA mismatch, unrelated donor and grade Ⅱ-Ⅳ aGVHD.

Benznidazole therapy for Chagas disease in asymptomatic Trypanosoma cruzi -seropositive former blood donors: evaluation of the efficacy of different treatment regimens

Abstract: INTRODUCTION: Chagas disease currently affects 5.7 million people in Latin America and is emerging in non-endemic countries. There is no consensus concerning the efficacy of trypanocidal therapy for patients with the chronic form of the disease. We evaluated cardiac function and sociodemographic, clinical, and serologic characteristics of a group of asymptomatic Trypanosoma cruzi-seropositive former blood donors, and compared the effects of benznidazole treatment applied for different lengths of time. METHODS: Blood donors who screened positive for T. cruzi between 1998 and 2002 were recruited 10 years later for follow-up (n = 244); 46 individuals had received treatment. Three subjects had terminated treatment prematurely. The remaining 43 individuals were divided into two groups: individuals who had received benznidazole therapy for 50-60 days (n = 28; BT ≤60 group) or more than 60 days (n = 15; BT >60). Serologic assays, biochemical tests, electrocardiographic, echocardiographic, and clinical examinations were performed on all participants. Parasite loads were determined by qualitative and quantitative polymerase chain reaction. RESULTS: Parasitemia was significantly reduced in the BT ≤60 and BT >60 groups compared with the untreated group. There were no differences in epidemiologic profiles or clinical, biochemical, electrocardiographic, or echocardiographic data between any of the groups. CONCLUSIONS: Despite elimination or significant reduction in parasitemia in patients with chronic Chagas disease who received benznidazole, there was no clinical difference between those who were treated for >60 days and those treated for a shorter duration. Furthermore, the adverse effects of benznidazole appear to be less severe than previous reports would suggest.

Establishment and preliminary application of an assay for the detection of porcine parvovirus in cells used for production / 中华微生物学和免疫学杂志

Abstract] Objective To establish an assay for the detection of porcine parvovirus ( PPV) and to verify its application for monitoring cells used for production.Methods A pair of primers and one probe were designed according to the conserved sequence encoding non-structural protein 1 (NS1).Based on the designed primers, a real-time fluorescent quantitative PCR assay for the detection of PPV was developed. Several parameters including the linearity, precision, minimum detection limit and anti-interference of the established assay were evaluated.A stock of PPV strains was prepared by infecting swine testicle ( ST) cells with PPV strains.An assay for the detection of PPV infection was developed by using ST cells as sensitive cells.A combined ST cell infection-PCR test was developed by combining the ST cell infection assay with the real-time fluorescent quantitative PCR assay.The sensitivity of ST cell infection-PCR test was analyzed.The cell samples used for production of biological products were detected by using the established assay.Results The real-time fluorescent quantitative PCR assay was specific for the detection of PPV without cross-reaction to other species of parvovirus virus, SV40 virus and other porcine viruses.The linear range of the assay was 1×109-1×104 copies/μl with a R2 value more than 0.98.The sensitivity of the real-time quantitative PCR assay was 1×104 copies/μl.Both of the intra-and inter-coefficient of variation (CV) were less than 5%in Ct values.The intra-and inter-CV in copies of detection were 5%-15% and 30%-40% respectively.The minimum detection limit of the real-time fluorescent quantitative PCR assay was 1CCID50/ml.The PPV strains were detected in cell samples with no interference.The sensitivity of ST cells infection-PCR test was 0.01CCID50/ml.All of the 22 cell samples were negative for PPV by using the real-time fluorescent quanti-tative PCR assay.Conclusion The real-time fluorescent quantitative PCR and the ST cell infection-PCR test for the detection of PPV in cells were established successfully.The application of the two assays was conducive to further enhance the safety of using cells for production and therapy.

Development of a nested PCR assay for detection of Helicobacter bilis / 中国人兽共患病学报

In this study ,the objective is to establish a nested‐PCR assay for the detection of H .bilis with high sensitivity and specificity .The nested primers were designed based on sequences of 16S rRNA gene of seventeen subtypes of H .bilis .Af‐ter optimizing reaction condition ,the sensitivity and specificity of the assay were examined via the detection of feces simulated samples ,mice infection model samples and clinic patients’ samples .The detection sensitivity of H .bilis strain for feces simu‐lated samples was 10 CFU/100 μL .H .bilis was successfully detected in the liver ,caecum and feces of experimentally infected mice .Moreover ,H .bilis was successfully detected in the bile ,cholecyst mucous membrane and feces samples from two of ten patients with cholelithiasis .Due to the PCR assay’s high sensitivity and specificity ,the method may be used to detect the infec‐tion of H .bilis .

COMPARISON BETWEEN AUTOMATED SYSTEM AND PCR-BASED METHOD FOR IDENTIFICATION AND ANTIMICROBIAL SUSCEPTIBILITY PROFILE OF CLINICAL Enterococcus spp / Comparação entre o sistema automatizado e PCR na identificação e susceptibilidade de isolados clínicos de Enterococcus spp

Enterococci are increasingly responsible for nosocomial infections worldwide. This study was undertaken to compare the identification and susceptibility profile using an automated MicrosScan system, PCR-based assay and disk diffusion assay of Enterococcus spp. We evaluated 30 clinical isolates of Enterococcus spp. Isolates were identified by MicrosScan system and PCR-based assay. The detection of antibiotic resistance genes (vancomycin, gentamicin, tetracycline and erythromycin) was also determined by PCR. Antimicrobial susceptibilities to vancomycin (30 µg), gentamicin (120 µg), tetracycline (30 µg) and erythromycin (15 µg) were tested by the automated system and disk diffusion method, and were interpreted according to the criteria recommended in CLSI guidelines. Concerning Enterococcus identification the general agreement between data obtained by the PCR method and by the automatic system was 90.0% (27/30). For all isolates of E. faecium and E. faecalis we observed 100% agreement. Resistance frequencies were higher in E. faecium than E. faecalis. The resistance rates obtained were higher for erythromycin (86.7%), vancomycin (80.0%), tetracycline (43.35) and gentamicin (33.3%). The correlation between disk diffusion and automation revealed an agreement for the majority of the antibiotics with category agreement rates of > 80%. The PCR-based assay, the van(A) gene was detected in 100% of vancomycin resistant enterococci. This assay is simple to conduct and reliable in the identification of clinically relevant enterococci. The data obtained reinforced the need for an improvement of the automated system to identify some enterococci.

Os enterococos são cada vez mais responsáveis por infecções hospitalares em todo o mundo. Este estudo foi realizado para comparar a identificação e perfil de suscetibilidade entre o sistema automatizado MicrosScan e a técnica molecular de PCR em espécies de Enterococcus spp. Foram avaliados 30 isolados clínicos de Enterococcus spp. Os isolados foram identificados pelo sistema MicrosScan® e pela técnica de PCR. A detecção de genes de resistência a antibióticos (vancomicina, gentamicina, tetraciclina e eritromicina) foi determinada por PCR. Suscetibilidades antimicrobianas à vancomicina (30 µg), gentamicina (120 µg), tetraciclina (30 µg) e eritromicina (15 µg), foram testados pelos métodos automatizados e pelo disco difusão, de acordo com as orientações do CLSI. No que diz respeito à identificação de Enterococcus em geral entre os dados obtidos pelo método de PCR e pelo sistema automático foi de 90,0% (27/30). Para todos os isolados de E. faecium e E. faecalis observamos concordância de 100%. Freqüências de resistência foi maior em E. faecium do que em E. faecalis. As taxas de resistência obtidas foi maior para eritromicina (86,7%), vancomicina (80,0%), tetraciclina (43,35%) e gentamicina (33,3%). A correlação entre a técnica de disco difusão e automação revelou-se de acordo para maioria dos antibióticos com taxas > 80%. O gene van(A) foi detectado em 100% dos Enterococcus resistentes á vancomicina. O ensaio baseado em PCR é de simples realização e de confiança para identificação de enterococos clinicamente relevantes. Os dados obtidos reforçam a necessidade de melhoria no sistema automatizado para identificar alguns enterococos.

Antibiotic resistance in lactic acid bacteria isolated from some pharmaceutical and dairy products

A total of 244 lactic acid bacteria (LAB) strains were isolated from 180 dairy and pharmaceutical products that were collected from different areas in Minia governorate, Egypt. LAB were identified phenotypically on basis of morphological, physiological and biochemical characteristics. Lactobacillus isolates were further confirmed using PCR-based assay. By combination of phenotypic with molecular identification Lactobacillus spp. were found to be the dominant genus (138, 76.7%) followed by Streptococcus spp. (65, 36.1%) and Lactococcus spp. (27, 15%). Some contaminant organisms such as (Staphylococcus spp., Escherichia coli, Salmonella spp., mould and yeast) were isolated from the collected dairy samples but pharmaceutical products were free of such contaminants. Susceptibility of LAB isolates to antibiotics representing all major classes was tested by agar dilution method. Generally, LAB were highly susceptible to Beta-lactams except penicillin. Lactobacilli were resistant to vancomycin, however lactococci and streptococci proved to be very susceptible. Most strains were susceptible to tetracycline and showed a wide range of streptomycin MICs. The MICs of erythromycin and clindamycin for most of the LAB were within the normal range of susceptibility. Sixteen Lactobacillus,8 Lactococcus and 8 Streptococcus isolates including all tetracycline and/or erythromycin resistant strains were tested for the presence of tetracycline and/or erythromycin resistant genes [tet(M) and/or erm(B)]. PCR assays shows that some resistant strains harbor tet(M) and/or erm(B) resistance genes.

Incidence and multiplex PCR based detection of trichothecene chemotypes of Fusarium culmorum isolates collected from freshly harvested Maize kernels in Southern India

Hundred Fusarium culmorum strains, isolated from freshly harvested maize grain samples from Southern parts of India, were incubated in czapek-dox medium and analyzed for trichothecene (DON/NIV) production. The mPCR assay was standardized targeting trichothecene metabolic pathway genes viz., Tri6, Tri7, Tri13 for detection of trichothecene (DON/NIV) chemotypes and rDNA gene for specific detection of F. culmorum species. Primers for targeted genes were designed and used to predict whether these isolates could produce deoxynivalenol/nivalenol, 94 isolates were able to produce DON/NIV by mPCR assay. Chemical analysis of DON/NIV was carried out for mPCR positive isolates by high performance-thin layer chromatography (HPTLC). To check the practical usefulness of developed mPCR assay, 150 field samples of maize were evaluated and results were compared with conventional HPTLC method. Out of 150 samples, 34% samples stayed as a positive for NIV contamination whereas 44% were found to have deoxynivalenol contamination. Moreover, mPCR results are equivocally matched with the HPTLC chemical analysis for field samples. Chemotyping of F. culmorum isolates were reported for the first time from India, and highlights the important potential of F. culmorum to contaminate maize with DON/NIV.

Inhibition of EV71 replication in vitro by polysaccharides from Selaginella tamaritcina / 国际药学研究杂志

Objective To evaluate the inhibitory effect of polysaccharides from Selaginella tamariscina on Enterovirus 71 (EV71) replication in vitro. Methods For detecting the cytotoxicity, series of doses of polysaccharides from Selaginella tamariscina were added in RD cells, cell survival rates were evaluated by observing the cytopathic effect (CPE) and using cell counting Kit-8 (CCK8) assay, then the half toxic concentration(CC50) of the drugs were calculated. For studying the antiviral activity, the cellular model was established by infecting RD cells with EV71. Several groups were set in the experiments: normal control group, virus-infected group, positive drug treated EV71 -infected group(ribavirin 3. 2 mg/L) and series of doses of polysaccharides treated EV71 -infected groups. The CPE inhibitions were determined by using CCK8 assay and the half inhibitory concentrations of drugs(IC50) were calculated. The inhibitiory effect of polysaccharides on EV71 RNA were determined by using real-time RT-PCR methods for detecting the virus RNA levels in cell cultures. Results The CC50 of 30% and 50% alcohol precipitated polysaccharides from Selaginella tamariscina on RD cells were 396 and 142 mg/L, respectively; the IC50 calculated according to the CPE inhibitory rates were respectively 40. 8 and 26. 2 mg/L. Additionally, these two polysaccharides significantly reduced viral RNA copies in EV71-infected RD cells. Conclusion Selaginella tamariscina together with its 30% and 50% alcohol precipitated polysaccharides can be developed as potential new anti - E V 71 drugs.

Diagnostic Utility of a Clonality Test for Lymphoproliferative Diseases in Koreans Using the BIOMED-2 PCR Assay

BACKGROUND: A clonality test for immunoglobulin (IG) and T cell receptor (TCR) is a useful adjunctive method for the diagnosis of lymphoproliferative diseases (LPDs). Recently, the BIOMED-2 multiplex polymerase chain reaction (PCR) assay has been established as a standard method for assessing the clonality of LPDs. We tested clonality in LPDs in Koreans using the BIOMED-2 multiplex PCR and compared the results with those obtained in European, Taiwanese, and Thai participants. We also evaluated the usefulness of the test as an ancillary method for diagnosing LPDs. METHODS: Two hundred and nineteen specimens embedded in paraffin, including 78 B cell lymphomas, 80 T cell lymphomas and 61 cases of reactive lymphadenitis, were used for the clonality test. RESULTS: Mature B cell malignancies showed 95.7% clonality for IG, 2.9% co-existing clonality, and 4.3% polyclonality. Mature T cell malignancies exhibited 83.8% clonality for TCR, 8.1% co-existing clonality, and 16.2% polyclonality. Reactive lymphadenitis showed 93.4% polyclonality for IG and TCR. The majority of our results were similar to those obtained in Europeans. However, the clonality for IGK of B cell malignancies and TCRG of T cell malignancies was lower in Koreans than Europeans. CONCLUSIONS: The BIOMED-2 multiplex PCR assay was a useful adjunctive method for diagnosing LPDs.

Evaluation of the BD GeneOhm MRSA Real-time PCR Assay for Detection of Nasal Colonization by MRSA / 대한임상미생물학회지

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a major nasocomial pathogen. The active surveillance of MRSA is essential to limit its transmission. The BD GeneOhm MRSA real-time PCR assay (Becton Dickinson Diagnostics, San Diego, USA) has been recently developed and used for same-day MRSA detection directly from nasal swab specimens. The authors of the present study compared GeneOhm MRSA PCR with culture methods to evaluate its diagnostic performance for MRSA active surveillance. METHODS: The present study was conducted on patients admitted to the ICU for six months. A total of 371 nasal swab specimens were obtained from patients at admission day and at the seven-day follow-up. The swab was streaked onto culture media, and presumptive S. aureus colonies were confirmed as MRSA using the BD Phoenix automated microbiology system (Becton Dickinson Diagnostic Systems, Sparks, USA). In addition, GeneOhm MRSA PCR was performed. For discrepant results between Gene-Ohm MRSA PCR and culture, the enrichment broth culture method was performed. RESULTS: There were 34 samples with discrepant results between the GeneOhm MRSA PCR and culture. The overall agreement was 90.7%. For the detection of MRSA, the GeneOhm MRSA PCR was 96.8% sensitive and 86.3% specific, with positive and negative predictive values of 83.9% and 97.3%, respectively. CONCLUSION: Identification of MRSA-colonized patients was achieved in as little as two hours, and the high negative predictive value of GeneOhm MRSA PCR suggests that the assay is a rapid method for the identification of persons who are not colonized with MRSA. However, due to the low positive predictive value, GeneOhm MRSA PCR combined with enrichment culture in cases of positive GeneOhm MRSA PCR is potentially useful for active MRSA surveillance activities.

A RT-PCR assay for the detection of encephalomycarditis virus infections in pigs

Encephalomyocarditis virus (EMCV) infections can cause losses in pig farms all over the world. Rapid, sensitive and unequivocal detection of this virus is therefore essential for the diagnosis and control of the disease. An RT-PCR assay was developed, optimized and evaluated for encephalomyocarditis virus detection in organ based on a pair of primers that amplifies a 165 bp DNA fragment from a highly conserved nucleotide region of the viral 3D glycoprotein. PCR products of the expected size were obtained from Cuban EMCV 744/03 strain. Non-specific reactions were not observed when other porcine RNA genome viruses and uninfected cells were used. The analytical sensitivity of the test was estimated to be 2 TCID50/50 mL. The analysis of tissue homogenate samples from naturally infected animals proved the potential usefulness of the method for a rapid disease diagnosis from field cases.

Development of a polymerase chain reaction assay for the detection of pseudorabies virus in clinical samples / Desenvolvimento de um ensaio de reação de polimerase em cadeia para detecção do vírus da pseudo-raiva em amostras clínicas

Aujeszky's disease, also known as pseudorabies causes severe economic losses in swine industry and affects the pig husbandry all over the world. The conventional diagnostic procedure is time-consuming and false-negative results may occur in submissions from latently infected animals. The development, optimization and evaluation of a polymerase chain reaction (PCR) assay are presented for the diagnosis of pseudorabies infection. This assay was based on the amplification of a highly conserved viral gD gene fragment. PCR products of the expected size were obtained from PRV strains. Non-specific reactions were not observed when a related herpesvirus, other porcine DNA genome viruses and uninfected cells were used to assess PCR. The analytical sensitivity of the test was estimated to be 1.34 TCID50/50 uL. The analysis of tissue homogenate samples from naturally infected animals proved the potential usefulness of the method for a rapid disease diagnosis from field cases. A rapid, sensitive and specific PCR-based diagnostic assay to detect pseudorabies virus in clinical samples is provided.

A doença de Aujeszky, também conhecida como pseudo-raiva, causa perdas econômicas graves na indústria suína e afeta a criação de suínos em todo o mundo. O procedimento de diagnóstico convencional é demorado, podendo ocorrer resultados falso-negativos em animais infectados de forma latente. Este estudo apresenta o desenvolvimento, otimização e avaliação de um ensaio de Reação de Polimerase em Cadeia para o diagnóstico da pseudo-raiva. O ensaio baseou-se na amplificação do fragmento genético viral gD altamente conservado. Os produtos da PCR de tamanho esperado foram obtidos a partir de isolados de PRV. Não foram observadas reações inespecíficas quando foram testados herpes-vírus relacionados, outros vírus DNA de suínos e células não infectadas. A sensibilidade analítica estimada do teste foi 1,34 TCID50/50 uL. A análise de homogenatos feitos com tecidos de animais naturalmente infectados mostrou que o método é útil para o diagnóstico rápido da doença no campo, sendo um ensaio rápido, sensível e específico para detectar o vírus da pseudo-raiva em amostras clinicas.

Development of a polymerase chain reaction assay for the detection of pseudorabies virus in clinical samples

Aujeszky's disease, also known as pseudorabies causes severe economic losses in swine industry and affects the pig husbandry all over the world. The conventional diagnostic procedure is time-consuming and false-negative results may occur in submissions from latently infected animals. The development, optimization and evaluation of a polymerase chain reaction (PCR) assay are presented for the diagnosis of pseudorabies infection. This assay was based on the amplification of a highly conserved viral gD gene fragment. PCR products of the expected size were obtained from PRV strains. Non-specific reactions were not observed when a related herpesvirus, other porcine DNA genome viruses and uninfected cells were used to assess PCR. The analytical sensitivity of the test was estimated to be 1.34 TCID50/50 uL. The analysis of tissue homogenate samples from naturally infected animals proved the potential usefulness of the method for a rapid disease diagnosis from field cases. A rapid, sensitive and specific PCR-based diagnostic assay to detect pseudorabies virus in clinical samples is provided.

A doença de Aujeszky, também conhecida como pseudo-raiva, causa perdas econômicas graves na indústria suína e afeta a criação de suínos em todo o mundo. O procedimento de diagnóstico convencional é demorado, podendo ocorrer resultados falso-negativos em animais infectados de forma latente. Este estudo apresenta o desenvolvimento, otimização e avaliação de um ensaio de Reação de Polimerase em Cadeia para o diagnóstico da pseudo-raiva. O ensaio baseou-se na amplificação do fragmento genético viral gD altamente conservado. Os produtos da PCR de tamanho esperado foram obtidos a partir de isolados de PRV. Não foram observadas reações inespecíficas quando foram testados herpes-vírus relacionados, outros vírus DNA de suínos e células não infectadas. A sensibilidade analítica estimada do teste foi 1,34 TCID50/50 uL. A análise de homogenatos feitos com tecidos de animais naturalmente infectados mostrou que o método é útil para o diagnóstico rápido da doença no campo, sendo um ensaio rápido, sensível e específico para detectar o vírus da pseudo-raiva em amostras clinicas.