Real-time Polymerase Chain Reaction Protocol Research Articles

Designing a time-effective TaqMan probe-based real-time polymerase chain reaction protocol for the identification of Yersinia enterocolitica in raw pork meat

The aim of this study was to design a time-effective method comprising a short pre-enrichment step in a non-selective broth in combination with the TaqMan probe applied in the real-time polymerase chain reaction to detectYersinia enterocoliticastrains in raw pork meat. The method enabled to detect 1 colony forming unit per 25 mg ofYersinia enterocoliticain pork meat. The specificity and reliability of the method was not diminished by the company of microflora naturally present in meat. The method was found successful to detect pathogenicYersinia enterocoliticastrains in pork meat. It is advised to be used for assessing the microbial risk and for controlling the microbial quality of meat and meat products.

In <i>Vitro</i> Effects of the Phytocomplex TrichoTech<sup>TM</sup> on Human Fibroblasts: Proliferative Potential and Effects on Gene Expression of FGF-7 and FGF-10

The human hair follicle, a mini-organ formed with neuroectodermal-meso-dermal interaction, is a complex structure, in the active steady state (anagen) the dermal papilla can be considered as a ball of extracellular matrix, surrounding specialized fibroblasts. The cross-talk of dermal papilla with neighbouring matrix cells results in the maintenance of hair fibre production. This study aimed to investigate the proliferative potential of the compound TrichotechTM, a phytocomplex obtained from a mixture of essential oils, on cultured human fibroblasts and its ability to modulate the gene expression of FGF-7 and FGF-10. TrichotechTM was shown to enhance fibroblasts proliferation in concentrations of 0.5% to 2.0%, and also increase the percentage of cells in the S/G2/M phases of the cell cycle. TrichotechTM at both 1.0% and 2.0% induced a statistically significant effect on wound healing assay compared to the untreated control. We examined the interaction between cell survival (PI3K/Akt) and mitogenic (Ras/MAPK) signal transduction pathways after TrichotechTM treatment (1.0% and 2.0%) on the fibroblast cell line. TrichotechTM caused phosphorylation of ERK1/2, as well as greater phosphorylation of MEK in comparison with both the untreated control and ERK1/2. PI3K and AKT, however, were not shown to be significantly more phosphorylated following TrichotechTM exposure. To verify the relative expression of mRNA for FGF-7 and FGF-10 genes, a real-time polymerase chain reaction (qPCR) protocol was used. Results show the increase in mRNA expression by fibroblasts after treatment with TrichotechTM. In both concentrations tested, TrichotechTM was found to increase the expression of FGF-7 and FGF-10. Sirius red staining allows for rapid assessment of collagen content, it showed a significant increase in collagen content in treated fibroblasts. Further investigation concerning TrichotechTM could be helpful towards the development of new bioactive phytocomplexes for dermatological and trichological use.

Development of hydrolysis probe real-time polymerase chain reaction and high-resolution melting analysis protocols for screening of e280k and c.1055del.g mutations in phenylalanine hydroxylase gene

Background: Phenylketonuria (PKU) is one of the most common inborn errors of amino acids metabolism. It is an autosomal recessive disease that is caused by mutations in phenylalanine hydroxylase (PAH) gene. In the North Africa and Eastern Mediterranean region, E280K missense mutation and c.1055del.G frameshift mutation in PAH gene are one of the most common pathogenic mutations seen in PKU patients. Materials and Methods: In this study, we developed molecular protocols for rapid screening of the PKU patients for these two mutations. These protocols are based on hydrolysis probe real-time polymerase chain reaction technique using allele-specific probes labeled with 6-carboxyfluorescein (FAM) for wild-type (WT) and hexachloro-6-carboxyfluorescein (HEX) for mutant genotypes and Black Hole Quencher 1 as a quencher and high-resolution melting analysis using EvaGreen saturating dye. Results: There was complete accordance between the developed protocols in differentiating genotypes and they proved to be rapid, sensitive, and efficient for the detection and differentiation between WT, mutant, and heterozygous genotypes of the E280K and c.1055del.G mutations. Conclusions: These protocols allow easy molecular screening of the mutations studied among the families of affected people, especially for premarital screening.

Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient.

Although vaccines are the best means of protection against influenza, neuraminidase inhibitors are currently the main antiviral treatment available to control severe influenza cases. One of the most frequent substitutions in the neuraminidase (NA) protein of influenza A(H3N2) viruses during or soon after oseltamivir administration is E119V mutation. We describe the emergence of a mixed viral population with the E119E/V mutation in the NA protein sequence in a post-treatment influenza sample collected from an immunocompromised patient in Argentina. This substitution was identified by a real-time reverse transcriptase polymerase chain reaction (RT-PCR) protocol and was confirmed by direct Sanger sequencing of the original sample. In 2014, out of 1140 influenza samples received at the National Influenza Centre, 888 samples (78%) were A(H3N2) strains, 244 (21.3%) were type B strains, and 8 (0.7%) were A(H1N1)pdm09 strains. Out of 888 A(H3N2) samples, 842 were tested for the E119V substitution by quantitative RT-PCR: 841 A(H3N2) samples had the wild-type E119 genotype and in one sample, a mixture of viral E119/ V119 subpopulations was detected. Influenza virus surveillance and antiviral resistance studies can lead to better decisions in health policies and help in medical treatment planning, especially for severe cases and immunocompromised patients.

Development of a SYBR green I real-time PCR assay for specific identification of the fish pathogen Aeromonas salmonicida subspecies salmonicida.

A SYBR Green I real-time polymerase chain reaction protocol for specific detection of the fish pathogen Aeromonas salmonicida subsp. salmonicida was developed and validated for rapid diagnosis of typical furunculosis. The sequence of the aopO gene of A. salmonicida subsp. salmonicida, which encodes for a serine/threonine protein kinase linked to virulence, was chosen for primer design. The selected primers amplified a 119-bp internal fragment of the aopO gene. The specificity test proved that 100% (40/40) of the A. salmonicida subsp. salmonicida strains tested showed a positive amplification with subspecies-specific melting temperatures (Tm) of 80.75±0.35°C. Atypical A. salmonicida subspecies and other non-related bacterial fish pathogens did not amplify or showed unspecific melting profiles, except for one strain of A. salmonicida subsp. achromogenes and one strain of A. salmonicida subsp. smithia. The detection sensitivity was 21fg of purified bacterial DNA per reaction, corresponding to 1-2 bacterial cells and 6-60 bacteria per reaction for seeded kidney and blood. The assay was highly reproducible with low variation coefficient values for intra-run and inter-run assays. The assay also allowed the specific detection of A. salmonicida subsp. salmonicida in tissues of fish naturally and experimentally infected. No amplification was detected when tissues from healthy fish or fish affected by other diseases were tested. The SYBR Green real-time PCR and melt curve analysis developed in this study is a rapid and accurate method for the specific identification of A. salmonicida subsp. salmonicida isolates and its detection on tissues of fish affected by furunculosis.

PRESENCE OF MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS IN ALPACAS (LAMA PACOS) INHABITING THE CHILEAN ALTIPLANO.

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of paratuberculosis. The organism causes disease in both domestically managed and wild ruminant species. South American camelids have a long, shared history with indigenous people in the Andes. Over the last few decades, increasing numbers of alpacas were exported to numerous countries outside South America. No paratuberculosis surveillance has been reported for these source herds. In this study, individual fecal samples from 85 adult alpacas were collected from six separate herds in the Chilean Altiplano. A ParaTB mycobacterial growth indicator tube (MGIT) liquid culture of each individual fecal sample, followed by real-time polymerase chain reaction (PCR) protocol was used for confirmation. DNA extracts from a subset of confirmed MAP isolates were subjected to mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing. Fifteen alpaca were fecal culture test-positive. Five false-positive culture samples were negative on PCR analysis for Mycobacterium avium subsp. avium (MAA), Mycobacterium bovis (M. bovis), and the 16 S rDNA gene. Three MAP isolates subset-tested belonged to the same MIRU-VNTR type, showing four repeats for TR292 (locus 1) in contrast to the three repeats typical of the MAP reference strain K10. The number of repeats found in the remaining loci was identical to that of the K10 strain. It is not known how nor when MAP was introduced into the alpaca population in the Chilean Altiplano. The most plausible hypothesis to explain the presence of MAP in these indigenous populations is transmission by contact with infected domestic small ruminant species that may on occasion share pastures or range with alpacas. Isolation of this mycobacterial pathogen from such a remote region suggests that MAP has found its way beyond the confines of intensively managed domestic agriculture premises.

Role of cytomegalovirus on the maturation and function of monocyte derived dendritic cells of liver transplant patients.

To study the impact of association between cytomegalovirus (CMV) pathogenesis with dendritic cell (DC) maturation and function was evaluated in CMV reactivated liver transplanted patients in comparing with non-reactivated ones, and healthy controls. Monocyte derived dendritic cells (MoDCs) was generated from collected ethylenediaminetetraacetic acid-treated blood samples from patient groups and controls. In these groups, expression rates and mean fluorescent intensity of DC markers were evaluated using flowcytometry technique. Secretion of cytokines including: interleukin (IL)-6, IL-12 and IL-23 were determined using enzyme-linked immunosorbent assay methods. The gene expression of toll-like receptor 2 (TLR2), TLR4 and IL-23 were analyzed using in-house real-time polymerase chain reaction protocols. Results have been shown significant decreases in: Expression rates of MoDC markers including CD83, CD1a and human leukocyte antigen DR (HLA-DR), the mean fluorescence intensitys for CD1a and HLA-DR, and secretion of IL-12 in CMV reactivated compared with non-reactivated liver transplanted patients. On the other hand, significant increases have been shown in the secretions of IL-6 and IL-23 and gene expression levels of TLR2, TLR4 and IL-23 from MoDCs in CMV reactivated compared with non-reactivated liver transplanted recipients. DC functional defects in CMV reactivated recipients, such as decrease in expression of DC maturation markers, increase in secretion of proinflammatory cytokines, and TLRs can emphasize on the importance of CMV infectivity in development of liver rejection in transplanted patients.

Real-Time PCR for Detection and Identification of Anguina funesta, A. agrostis, A. tritici, and A. pacificae.

A number of seed, leaf, and stem gall nematodes are of significance to the forage and landscape grass and livestock industries. In North America, the bentgrass nematode, Anguina agrostis, reduces seed production on Agrostis tenuis and several other grass species. Anguina funesta is a seed-gall nematode that is most significant for its association with the toxigenic bacteria Rathayibacter toxicus. The wheat seed gall nematode A. tritici causes significant damage to wheat and other cereals; although it has been found in many countries worldwide, it has not been detected in the United States since 1975. Molecular methods based upon sequence variation in the ribosomal internal spacer region are useful for accurate identification of Anguina spp. Described herein are new species-specific primers and TaqMan probes for real-time polymerase chain reaction (PCR) identification of A. agrostis, A. funesta, A. tritici, and A. pacificae. Primer and probe combinations were each specific for the intended species and were sensitive enough to detect as few as 1.25 copies of nematode ribosomal DNA. PCR was also specific and sensitive in duplex assays that included genus-specific internal control primers as well as species-specific primers and probes. These standardized real-time PCR protocols should facilitate fast and accurate identification of Anguina spp. by diagnostic laboratories.

Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization.

PurposeInfluenza A viruses, human coronaviruses (hCoV) and human bocavirus (hBoV) are emerging respiratory viruses. This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses.MethodologyPublished sequences for the 15 human coronaviruses were used to design a consensus PCR targeting the replicase open reading frame 1b. A previously published PCR targeting the NS1 Gene of all known human bocavirus strains was also utilized. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. Association between co-infection and disease outcome was assessed using logistic regression.ResultsThe limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. A total of 12 hCoV and 17 hBoV were identified in the 217 influenza A positive samples. A higher proportion (61.5 %; 8/13) of SeasFluA/hBoV co-infections were identified in patients that were admitted either to a general ward or the intensive care unit compared to 44.3 % (66/149) of single SeasFlu A virus infections (OR 2.5 95 % CI 0.67–9.34, p = 0.17). In a stratified analysis, there was a trend towards higher association between FluA, hCoV and hBoV with increasing age (especially in patients aged 24–45 years and >65 year old).ConclusionOur hCoV RT-PCR protocol appeared to be of adequate analytical sensitivity for diagnosis. More and larger studies are needed to confirm the role of hCoV, hBoV in causing severe disease when they co-infect with influenza A viruses.

Clinical Characteristics and Cost Burden of Children Hospitalized with Pandemic Influenza A (H1N1-2009) in a Tertiary Care Center in İstanbul.

Dear Editor, After the detection of the first case in April 2009, pandemic H1N1 influenza caused infection in more than 214 countries, resulting in at least 18,449 deaths. A multicenter study in Turkey revealed that 821 children were hospitalized with pandemic H1N1 influenza (1). The economic burden of pandemic H1N1 influenza has been estimated for many countries (2–4). We aimed to evaluate the clinical features and direct medical costs of children hospitalized with pandemic H1N1 influenza in comparison with H1N1 negative patients. Charts of children admitted to a single center with suspicion of pandemic H1N1 influenza were reviewed. Patients with clinical findings compatible with the criteria defined by the World Health Organization or a history of contact with a person with influenza-like illness (ILI) who had undergone microbiologic testing were included. The “in-house” real-time polymerase chain reaction protocol provided by the Centers for Disease Control and Prevention was used for the detection of pandemic H1N1 influenza. Underlying risk factors, clinical features, and total costs were determined. Total costs included bed stay, diagnostics, pharmacy, and charges for medical services. The present retrospective study was approved by the Institutional Ethics Committee and written informed consent was taken from all parents or legal guardians. Among 90 patients hospitalized during November 2009 and January 2010, 32 were laboratory confirmed cases of pandemic H1N1 influenza. 43.8% had an underlying risk factor, with neuromuscular disorders (18.8%) and chronic respiratory diseases (15.5%) being the most common. 31.2% had thrombocytopenia (platelets 11×103/mL), 37% had elevated aspartate amino-transferase (>35 IU/L) and 18% had elevated alanine aminotransferase levels (>46 IU/L). Fever (100% versus 84%) and lethargy (28.1% versus 8.6%) were more prevalent in H1N1 positive patients in comparison to H1N1 negative cases. Only one patient with pandemic H1N1 influenza and neuromuscular disease died on the 11th day of admission. The median cost of hospitalization for pandemic H1N1 influenza was $254 USD per case (Table 1). TABLE 1 Demographic, clinical and cost data of H1N1 positive and H1N1 negative patients Our study provides the first evidence that pandemic H1N1 influenza resulted in a substantial cost burden related to hospitalized children in Turkey. In comparison with H1N1 negative patients, the direct cost was slightly higher in the H1N1 positive group, but the difference was not significant since the majority of patients had received antiviral and antibiotic treatment due to heightened concern of physicians. The clinical features of the two groups were similar, except for a higher prevalence of fever and lethargy in the H1N1 positive patients. A similar study conducted in an adult population of Turkey revealed that altered mental status, fever ≥38°C, and tachypnea were significantly higher in patients with confirmed influenza (5). The mean hospital charges incurred for the 61 hospitalized children during the spring 2009 pandemic influenza epidemic in Wisconsin was $14,687 USD (2). Total direct health care costs were determined to be $510 USD per patient hospitalized with pandemic H1N1 influenza in Malaysia (3). Zarogoulidis et al. (4) reported that health care costs were higher for pandemic H1N1 influenza compared with non-H1N1 respiratory infections, mainly due to the protection measures used and the increased duration of hospitalization in the intensive care unit.

Developing a time and effort-effective, highly sensitive TaqMan probe-based real-time polymerase chain reaction protocol for the detection of Salmonella in milk, yoghurt, and cheese

A time- and effort-effective, highly sensitive method combining brief pre-enrichment for only 4 h in a non-selective broth and TaqMan probe-based real-time PCR was developed for the detection of different concentrations of a cocktail of 8 Salmonella Typhimurium strains in milk and dairy products. As few as 1 cfu 25 mL−1 of Salmonella in milk was detectable, and sensitivity was not influenced by the presence of contaminating microflora or using milk containing different combinations of fat and solids-not-fat. The method could be also successfully used for detecting Salmonella during the preparation and cold storage of yoghurt and soft cheese. It was able to detect injured cells in cheese prepared from 10% and 12% salted milk after 3 months of cold storage. Given that the method generates quantitative data related to the numbers of the pathogen in these products, it is recommended for use in microbial risk assessments, and hazard analysis critical control point (HACCP) plans.

The use of real-time PCR to study Penicillium chrysogenum growth kinetics on solid food at different water activities

Fungal growth on solid foods can make them unfit for human consumption, but certain specialty foods require fungi to produce their characteristic properties. In either case, a reliable way of measuring biomass is needed to study how various factors (e.g. water activity) affect fungal growth rates on these substrates. Biochemical markers such as chitin, glucosamine or ergosterol have been used to estimate fungal growth, but they cannot distinguish between individual species in mixed culture. In this study, a real-time polymerase chain reaction (rt-PCR) protocol specific for a target fungal species was used to quantify its DNA while growing on solid food. The measured amount of DNA was then related to the biomass present using an experimentally determined DNA-to-biomass ratio. The highly sensitive rt-PCR biomass assay was found to have a wide range, able to quantify the target DNA within a six orders-of-magnitude difference. The method was used to monitor germination and growth of Penicillium chrysogenum spores on a model porous food (cooked wheat flour) at 25°C and different water activities of 0.973, 0.936, and 0.843. No growth was observed at 0.843, but lag, exponential and stationary phases were identified in the growth curves for the higher water activities. The calculated specific growth rates (μ) during the exponential phase were almost identical, at 0.075/h and 0.076/h for aw=0.973 and 0.936, respectively. The specificity of the method was demonstrated by measuring the biomass of P. chrysogenum while growing together with Aspergillus niger on solid media at aw=0.973.

Validation of real-time PCR for detection of six major pathogens in seafood products

Abstract Seafood can pose a public health concern to consumers. It is often consumed raw and may be contaminated with several foodborne pathogens. In order to guarantee the safety of seafood, real-time polymerase chain reaction (PCR) protocols may be used as these enable results to be provided within 24 h. The first goal of our work was to develop real-time PCR protocols enabling the detection of six foodborne pathogens that may be present in seafood products ( Campylobacter jejuni , Campylobacter coli , enterohemorrhagic Escherichia coli , Salmonella spp., Vibrio parahaemolyticus , and Vibrio vulnificus ). The corresponding gene targets were: 50S/VS1 , rfbE , ttr , tlh , and vvp . A multiplex PCR was also developed to detect the virulence genes of V. parahaemolyticus : tdh and trh . A total of 420 bacterial strains belonging to four different genera/strains were used in this study. Sensitivity and specificity were always 100%, except in the case of Salmonella spp., where three strains were not detected by our PCR protocols. The second objective of our work was to assess the detection limit of our real-time PCR protocols on artificially contaminated seafood products (raw shrimps, cooked shrimps, and raw mussels), purchased in public stores. Six different levels of contamination were assayed in four replicates for each matrix. The real-time PCR protocols enabled a better level of detection than the ISO methods, except for Salmonella in raw shrimps and for V. vulnificus in shrimps (raw and cooked). The estimated level of detection was between 1 and 47 cfu/25 g sample for the ISO norms and between 1 and 315 cfu/25 g sample for the real-time PCR protocols tailored in our work. The real-time PCRs developed in our work allowed for good selectivity, sensitivity, and specificity. The sensitivity on seafood products was estimated at a level of 100%, except for Salmonella (97%). In the spiking assays, the levels of detection were lower with the real-time PCR protocol than those obtained with the ISO method. This was not the case for V. vulnificus in raw and cooked shrimps and for Salmonella in raw shrimps. These real-time PCR protocols appear to be good alternative methods for surveillance of seafood products to ensure the absence of foodborne pathogens. One additional conclusion is that laboratories have to use enrichment media that are compatible with those recommended by ISO standards. This may facilitate the isolation of the pathogen if the real-time PCR protocol gives a suspect positive signal during the first step of the seafood analysis.

Is aceticlastic methanogen composition in full-scale anaerobic processes related to acetate utilization capacity?

In this study, biomass samples were obtained from six municipal and nine industrial full-scale anaerobic processes to investigate whether the aceticlastic methanogen population composition is related to acetate utilization capacity and the nature of the wastewater treated, i.e. municipal sludge or industrial wastewater. Batch serum bottle tests were used to determine the specific acetate utilization rate (AUR), and a quantitative real-time polymerase chain reaction protocol was used to enumerate the acetate-utilizing Methanosaeta and Methanosarcina populations in the biomass samples. Methanosaeta was the dominant aceticlastic methanogen in all samples, except for one industrial wastewater-treating anaerobic process. However, Methanosarcina density in industrial biomass samples was higher than the Methanosarcina density in the municipal samples. The average AUR values of municipal and industrial wastewater treatment plant biomass samples were 10.49 and 10.65mg CH3COO(-)/log(aceticlastic methanogen gene copy).d, respectively. One-way ANOVA test and principle component analysis showed that the acetate utilization capacities and aceticlastic methanogen community composition did not show statistically significant correlation among the municipal digesters and industrial wastewater-treating processes investigated.

PCR protocol for detection of Vibrio ordalii by amplification of the vohB (hemolysin) gene

Vibrio ordalii is the causative agent of atypical vibriosis and has the potential to cause severe losses in salmonid aquaculture. To prevent and control outbreaks, a rapid, reproducible, sensitive, and effective diagnostic method is needed. We evaluated a new conventional polymerase chain reaction (PCR) and real-time PCR (qPCR) protocol using a primer set (VohB_Fw-VohB_Rv) designed to amplify a 112 bp fragment flanking the vohB gene (coding for hemolysin production), against 24 V. ordalii strains isolated from different fish species, the V. ordalii type strain, and 42 representative related and unrelated bacterial species. The primer set was species-specific, recognizing all V. ordalii strains evaluated, with no cross-reaction with the other bacterial species. A sensitivity of 103 copies of the vohB gene was obtained with a standard curve. When the VohB_Fw-VohB_Rv qPCR protocol was applied to Atlantic salmon seeded tissues (kidney, liver, spleen, and muscle), the detection limit ranged from 5.27 × 102 to 4.13 × 103 V. ordalii CFU ml-1, i.e. 62 to 145 copies of the vohB gene, using the previously calculated standard curve. The conventional PCR also detected V. ordalii, but the total reaction time was 1 h longer. When the qPCR protocol was applied to naturally infected cage-cultured Atlantic salmon samples, 5 of 8 fish tested positive for V. ordalii, but only one of them was diagnosed as positive by direct cultivation on agar. We conclude that the PCR protocol evaluated is fast, specific, and sensitive enough to detect V. ordalii in infected tissues and is an important tool for secure diagnosis of atypical vibriosis, and is therefore helpful for the control of the disease through the prompt detection within fish populations.

Development of conventional and real-time PCR protocols for specific and sensitive detection of Colletotrichum capsici in chilli (Capsicum annuum L.)

Anthracnose, caused by Colletotrichum capsici, is a major disease of chilli (Capsicum annuum L.) affecting both fruit and seed quality. The pathogen is both internally and externally seedborne. However, a rapid and sensitive method for detection of this pathogen in seeds is currently limited. In this study, a polymerase chain reaction (PCR) method based on sequence characterized amplified region (SCAR) marker was developed for specific and sensitive detection of C. capsici in chilli seeds and fruits. The developed SCAR primers were highly specific to C. capsici and resulted in the amplification of an expected 250-bp fragment from genomic DNA of all seven of the C. capsici isolates tested. No amplification occurred when the SCAR primers were tested with genomic DNA from three other fungal isolates and four other Colletotrichum species. The SCAR primers successfully amplified similar sized fragments from DNA derived from C. capsici-infected chilli fruits. The molecular detection sensitivity of C. capsici was 1 pg of purified C. capsici DNA template and 25 ng of DNA from C. capsici-infected chilli fruits. A real-time PCR assay was also developed using SYBR Green chemistry for detection of C. capsici in chilli fruits and seeds. The standard curve obtained showed a linear correlation between copy number of the cloned target DNA sequence of C. capsici and cycle threshold (Ct) values, with R2 of 0.98. These PCR-based assays may be highly useful in detection of this important pathogen in chilli seeds and fruits in plant quarantine laboratories.

Relationship Between Fusarium virguliforme and Heterodera glycines in Commercial Soybean Fields in Wisconsin

Fusarium virguliforme (syn. Fusarium solani f. sp. glycines), the causal agent of sudden death syndrome, and Heterodera glycines, soybean cyst nematode (SCN), are economically important pathogens of soybean (Glycine max) in the Midwestern United States, including Wisconsin. In 2011 and 2012, samples submitted to a SCN detection program were assayed for SCN using a sieving/centrifugation method and for F. virguliforme using a real-time quantitative polymerase chain reaction (RT-qPCR) protocol. In 2011, 135 soil samples were submitted and H. glycines was detected in 56 samples, while 10 samples were positive for F. virguliforme. In 2012, 64 of 318 samples tested positive for H. glycines and 13 tested positive for F. virguliforme. The relationship between the occurrence of H. glycines and F. virguliforme was examined further for samples that were positive for H. glycines and/or F. virguliforme. Kendall's tau rank correlation coefficient was −0.59 (P < 0.01), indicating a negative association. Furthermore, the best-fitting logistic regression model that described the probability of detecting H. glycines in a soil sample based on detecting F. virguliforme confirmed the negative correlation. This result suggests that SCN and F. virguliforme do not rely on each other to colonize fields, indicating that fields heavily infested with SCN are not necessarily at greater risk of F. virguliforme colonization. Accepted for publication 24 October 2013. Published 28 January 2014.

English

Trichomonas vaginalis is a protozoan parasite that infects the human urogenital tract. This study determined the prevalence and risk factors of T. vaginalis infection amongst human immunodeficiency virus (HIV) infected patients in Limpopo Province using urine-based real time polymerase chain reaction (RT-PCR). Urine samples were collected from 155 patients attending three public hospitals and one private clinic in the Vhembe region. Demographic data, clinical and socioeconomic status were collected from the patients using a structured questionnaire. Total genomic DNA was isolated from urine samples using the Qiagen Blood Mini Kit and RT-PCR protocol was used for the detection of T. vaginalis. The overall prevalence of T. vaginalis in our study population was 21%. The prevalence was higher among patients less than 25 years compared to older patients. Patients who were taking antibiotics at the time of sample collection had less infection compared to patients who were not on antibiotics (24% vs. 7%; p=0.042). Low CD4 counts and early age of sexual debut appeared to be important risk factors. The high recovery rate obtained in this study demonstrates the importance of employing real-time PCR techniques in the diagnosis of the trichomoniasis in this population. Key words: Trichomonas vaginalis, opportunistic infection, sexually transmitted disease, urine, real-time polymerase chain reaction, prevalence, Limpopo province.

A Comparison of Real-Time PCR Protocols for the Quantitative Monitoring of Asymptomatic Olive Infections by Verticillium dahliae Pathotypes

Early, specific, and accurate in planta detection and quantification of Verticillium dahliae are essential to prevent the spread of Verticillium wilt in olive using certified pathogen-free planting material and development of resistance. We comparatively assessed the accuracy, specificity, and efficiency of eight real-time quantitative polymerase chain reaction protocols published since 2002 for the specific detection and quantification of V. dahliae in various host plant species and in soil, using a background of DNAs extracted from olive roots, stems, and leaves. Results showed that some of those protocols were not specific for V. dahliae or were inhibited when using backgrounds other than water. Ranking of protocols according to a weighted score system placed protocols TAQ (based on intergenic spacer ribosomal DNA target gene) and SYBR-4 (based on the β-tubulin 2 target gene) first in sensitivity and efficiency for the quantification of V. dahliae DNA in small amounts and different types of olive tissues (root and stem) tested. Use of TAQ and SYBR-4 protocols allowed accurate quantification of V. dahliae DNA regardless of the background DNA, with a detection limit being fixed at a cycle threshold of 36 (≈18 fg for SYBR-4 and 15 fg for TAQ) of V. dahliae. The amount of DNA from defoliating (D) and nondefoliating (ND) V. dahliae pathotypes was monitored in Verticillium wilt-resistant 'Frantoio' olive using the TAQ and SYBR-4 protocols. In the infection bioassay, higher amounts of D V. dahliae DNA were measured in olive stems, whereas the average amount of fungal DNA in roots was higher for ND-infected plants than D-infected ones. Overall, V. dahliae DNA amounts in all olive tissues tested tended to slightly decrease or remain stable by the end of the experiment (35 days after inoculation). The SYBR-4 and TAQ protocols further enabled detection of V. dahliae in tissues of symptomless plants, suggesting that both techniques can be useful for implementing certification schemes of pathogen-free planting material as well as helpful tools in breeding resistance to V. dahliae in olive.

Comparison of the direct fluorescence assay and real-time polymerase chain reaction for the detection of influenza virus A and B in immunocompromised patients

OBJECTIVE:This study evaluated the diagnostic performance of two methods for the detection of influenza virus in immunocompromised transplant patients.METHODS:A total of 475 respiratory samples, 236 from patients in a hematopoietic stem cell transplantation program and 239 from kidney transplant patients, were analyzed by a direct fluorescence assay and the Centers for Disease Control real-time polymerase chain reaction protocol for influenza A and B detection.RESULTS:Influenza detection using either method was 7.6% in the hematopoietic stem cell transplant group and 30.5% in the kidney transplant patient group. Influenza detection by real-time polymerase chain reaction yielded a higher positive rate compared with fluorescence than that reported by other studies, and this difference was more pronounced for influenza A. The fluorescence assay sensitivity, specificity, positive and negative predictive values, and kappa coefficient were 17.6%, 100%, 1, 0.83, and 0.256, respectively, and lower detection rates occurred in the kidney transplant patients.CONCLUSIONS:The real-time polymerase chain reaction performance and the associated turnaround time for a large number of samples support the choice of this method for use in different routine diagnostic settings and influenza surveillance in high-risk patients.