PCR as a diagnostic and quantitative technique in veterinary parasitology

Molecular identification of Haemonchus contortus in sheep from Upper Egypt

Introduction

Haemonchus spp. are considered the most important strongylid nematodes with a worldwide distribution. The parasite's blood-sucking nature can lead to severe anemia in infected animals. Despite its widespread impact, there is a dearth of comprehensive data on morphological and molecular identification methods for Haemonchus spp. in sheep from Upper Egypt. To address this gap, our current study aimed to assess the prevalence of Haemonchus spp. in 400 sheep fecal samples.

Methods

We employed microscopic examination and molecular techniques, using polymerase chain reaction (PCR) targeting the 18S gene for precise identification. Additionally, the potential risk factors associated with the infection by the parasite in sheep were explored.

Results

The study pointed out that 33.00% (132 of 400) of the examined sheep were infected with Haemonchus spp. Sheep age and seasonal variability were found to be significant factors (p < 0.05) associated with the infection. Notably, sheep under 2 years old exhibited a higher risk, with an infection rate of 43.75% (84 out of 192), than their older counterparts. Furthermore, all reported infections were exclusively observed during the cold season, constituting 58.93% (132 out of 224) of cases. By contrast, no statistically significant association (p > 0.05) was found between the sex of the examined sheep and the occurrence of haemonchosis. Employing molecular methods, we isolated and identified the parasite through PCR analysis of cultured larvae, which were then subsequently confirmed as Haemonchus contortus via phylogenetic analysis.

Discussion

The study concluded that there was a relatively high occurrence of H. contortus among sheep from Upper Egypt. We recommend the implementation of stringent and effective control measures to combat the infection and safeguard livestock health.

Quantitative detection of parasitic ciliate Cryptocaryon irritans in seawater with an optimized sample processing method

The protozoan Cryptocaryon irritans is one of the most important ectoparasites of marine fish, causing 'white spot disease' and mass mortality in aquaculture. To accurately predict disease outbreaks and develop prevention strategies, improved detection methods are required that are sensitive, convenient and rapid. In this study, a pair of specific primers based on the C. irritans 18S rRNA gene was developed and used in a real-time PCR (qPCR) assay. This assay was able to detect five theronts in 1 L of natural seawater. Furthermore, a linear model was established to analyse the log of Ct value and parasite abundance in seawater (y = -2.9623x + 24.2930), and the coefficient of determination (R² ) value was 0.979. A lysis buffer was optimized for theront DNA extraction and used for storage sample. This method was superior to the commercial water DNA kit, and there was no significant degradation of DNA at room temperature for 24-96 hr. A dilution method was developed to manage qPCR inhibitors and used to investigate natural seawater samples in a net cage farm with diseased fish, and the findings were consistent with the actual situation. This study provides a valuable tool for assisting in the early monitoring and control of cryptocaryoniasis in aquaculture.

Molecular detection of Theileria annulata infection in cattle by conventional PCR and quantitative real time PCR in India

Theileria annulata (T. annulata) is a tick-borne apicomplexan parasite that affects bovine. It is endemic in many tropical and subtropics areas, including Odisha, India. The objective of this study is to identify T. annulata infection in the peripheral blood of cattle as a biological sample by conventional PCR (cPCR) and quantitative PCR (qPCR). The phylogenetic analysis was done using the T. annulata merozoite surface antigen (Tams 1) gene. Out of 552 samples of examined blood smears by microscopy, 454 (82.24%) animals were positive for Theileria species. Out of 454 samples, 96 samples were further examined by both cPCR and qPCR, 52 samples (54.16%) were found positive for T. annulata in both PCR methodologies. Phylogenetic analysis revealed that T. annulata Odisha isolate was closely related to T. annulata Uttarakhand, India isolate (KM061799) and Hyderabad, India isolate (MK034702) with Nucleotide sequence identity 95.36%, 95.25%, respectively. This is the first study to detect T. annulata by qPCR in Odisha and supported that both PCR techniques were equally effective for the detection of Tams 1 gene of T. annulata in cattle's blood.

A SYBR green I real-time polymerase chain reaction (PCR) assay for detection and quantification of Trichomonas gallinae

Trichomonas gallinae are parasitic flagellates of importance in wild and domestic birds. The parasite is worldwide distributed, and Columbine birds are its main host. Current research focuses mostly on epidemiological and phylogenetic studies. However, there is still a lack of knowledge regarding parasite-host interaction or therapy development. Real-time PCR is a useful tool for diagnostic and quantification of gene copies in a determined sample. By amplification of a 113-bp region of the 18S small subunit ribosomal RNA gene, a SYBR green-based real-time PCR assay was developed. A standard curve was prepared for quantification analysis. Assay efficiency, linearity, and dissociation analysis were successfully performed. Specificity, sensibility, and reproducibility analysis were tested. This assay could be a useful tool not only for diagnostic purposes but also for future in vivo and in vitro T. gallinae studies.

Nanotechnology and Animal Health

Nanotechnology has been a rapidly expanding area of research with huge potential in many sectors, including animal healthcare. It promises to revolutionize drug and vaccine delivery, diagnostics, and theranostics, which has become an important tool in personalized medicine by integrating therapeutics and diagnostics. Nanotechnology has also been used successfully in animal nutrition. In this review, the application of nanotechnology in animal health will be reviewed with its pros and cons.

Visceral leishmaniasis: a practical strategy for quantitative molecular diagnosis in naturally infected dogs

The diagnosis of canine visceral leishmaniasis (CVL) has been a problem for public health services due to the variety of clinical signs similar to other diseases and low sensitivity and specificity of available tests. In this sense, our main objective was to develop a simple, rapid, and accurate quantitative real-time PCR (qPCR) diagnosis for CVL. Thus, low-invasive samples from bone marrow (BM), popliteal lymph nodes (PLN), and conjunctival swabs (CS) were selected from negative and VL-positive dogs, using as gold standard, immunological and parasitological tests performed with different tissues. Oligonucleotides for Leishmania infantum kDNA were designed and the limit of quantification and amplification efficiency of the qPCR were determined using tissue-specific standards produced with DNA from those different tissues, mixed with DNA from a known amount of L. infantum promastigotes. Endogenous control was used to validate a comparative Ct method, and tissue parasite concentrations were estimated by comparison with tissue-specific reference standard samples. The overall analysis of the qPCR data suggests the following ranking for tissue choice: PLN > BM > CS. Finally, we have concluded that this molecular approach simplifies and accelerates the quantitative diagnostic process because it is easy to perform, requiring no DNA dosing or standard curve application, and it shows good diagnostic parameters, especially when using popliteal lymph node samples.

A Mistaken Diagnosis of Secondary Glioblastoma as Parasitosis

Background: Glioblastoma is a malignant brain tumor with poor prognosis requiring early diagnosis. Secondary glioblastoma refers to cases that progressed from low-grade glioma. Evidence shows that timely resection correlates with increased survival.

Case presentation: We describe a case of a patient with secondary glioblastoma who was mistakenly diagnosed with Angiostrongylus cantonensis infection until 7 years after disease onset. The patient presented with non-specific clinical manifestations at disease onset. A conventional magnetic resonance imaging (MRI) in the primary survey provided insufficient information, and thus failed to identify the malignancy. During follow-up, unfortunately, clinicians were misled by the patient's raw food diet, a positive serum parasite antibody and a result of low glucose metabolism on Fluorodeoxyglucose-positron emission tomography-computed tomography (FDG-PET-CT). The patient was diagnosed with parasitosis. However, his condition kept getting worse under antiparasitic treatment. Preoperative magnetic resonance spectroscopy (MRS) and diffusion tensor imaging (DTI) failed to reverse the mistaken impression. Final diagnosis was confirmed until intraoperative and postoperative pathological findings indicated glioblastoma.

Conclusion: We ascribe the incorrect diagnosis to insufficient understanding on imaging manifestations of brain neoplasm as well as clinical features of parasitosis. Thus, we review the MRI, FDG-PET-CT, MRS, and DTI data of this case according to the timeline, refer to relevant studies, and point out the pitfalls. With a long course of slowly progressing, this was a rare case of secondary glioblastoma with the absence of isocitrate dehydrogenase 1 (IDH1) gene mutation.

A morphological and molecular comparison of Eimeria bovis-like oocysts (Apicomplexa: Eimeriidae) from European bison, Bison bonasus L., and cattle, Bos taurus L., and the development of two multiplex PCR assays for their identification

The European bison, Bison bonasus is the largest terrestrial mammal in Europe; it is also on the red list, being recognized as vulnerable to extinction by the International Union for Conservation of Nature. The species suffers from low genetic variability, rendering it vulnerable to various environmental and biological threats. This study presents the first molecular confirmation of Eimeria bovis infection in European bison, and details a 1708 bp nucleotide sequence of the 18S rRNA gene in European bison-derived E. bovis (GenBank: MK691697). It also describes two multiplex PCR assays based on 18S rRNA gene for identifying Eimeria bovis oocysts and developmental stages in European bison and cattle. These yielded DNA banding patterns common for those of Eimeria spp. (250 bp for the first assay and 305 bp for the second assay) and species-specific E. bovis DNA in positive samples (344 bp and 586 bp, respectively). Both multiplex PCRs yielded bands characteristic of Eimeria spp. and E. bovis in samples containing DNA of oocysts from both bison and cattle. Moreover, convergent results were obtained for the DNA of the wall of colon in both assays, indicating the presence of developmental stages of Eimeria spp. other than E. bovis. Despite displaying the same sporulation time (four days), and similar general morphological features, the E. bovis oocysts derived from European bison were significantly narrower than those obtained from cattle (t = -6.19, p < 0.001), with a significantly higher shape index (length/width ratio) (t = 3.94, p <  0.001). The result provides further evidence for infection of European bison with a highly-pathogenic bovine protozoan, E. bovis.

Real-time PCR diagnosis of Schistosoma japonicum in low transmission areas of China

Background

Schistosomiasis in the People’s Republic of China (PRC) can be traced back to antiquity. In the past 60 years, the Chinese government has made great efforts to control this persistent disease with elimination slated by 2020 through the implementation of a comprehensive control strategy. This strategy aims to reduce the role of bovines and humans as sources of infection as a pre-requisite for elimination through transmission interruption. The goal of elimination will be achievable only by the implementation of a sustainable surveillance and control system, with sensitive diagnosis a key feature so that the true disease burden is not underestimated. Currently used diagnostics lack the necessary sensitivity to accurately determine the prevalence of Schistosoma japonicum infection in areas with low infection intensities. It is of critical importance to find and treat people and to identify animals with low-level infections if the National Control Programme for China is to achieve schistosomiasis elimination.

Methods

We evaluated a real-time polymerase chain reaction (qPCR) assay using 633 human stool samples collected from five villages in Hunan, Anhui, Hubei, and Jiangxi provinces, and 182 bovine (70 cattle and 112 buffalo) stool samples obtained from four villages in Hunan, Anhui, and Jiangxi provinces in the PRC. All stool samples were subjected to the miracidium hatching test (MHT, a diagnostic procedure used in the National Schistosomiasis Control Programme) and the qPCR assay. Samples positive by MHT were subjected to either the Kato-Katz technique for humans, or the formalin-ethyl acetate sedimentation-digestion (FEA-SD) procedure for bovines, to determine infection intensities.

Results

The qPCR assay exhibited a high level of sensitivity in the detection of S. japonicum infections. With both the human and bovine samples, a significantly higher prevalence was determined using the qPCR assay (11.06% humans, 24.73% bovines) than with the MHT (0.93% humans, 7.69% bovines). The animal contamination index (calculated using data obtained with the qPCR technique) for all positive bovines was 27 618 000 eggs per day, indicating a considerable amount of environmental egg contamination that would be underestimated using less sensitive diagnostic procedures.

Conclusions

The qPCR assay we have evaluated will be applicable as a future field diagnostic and surveillance tool in low-transmission zones where schistosomiasis elimination is targeted and for monitoring post-intervention areas to verify that elimination has been maintained.

Electronic supplementary material

The online version of this article (10.1186/s40249-018-0390-y) contains supplementary material, which is available to authorized users.

A Quantitative PCR Protocol for Detection of Oxyspirura petrowi in Northern Bobwhites (Colinus virginianus)

Oxyspirura petrowi is a parasitic nematode that infects wild birds. This parasite has a broad host range, but has recently been reported in high prevalences from native Galliformes species in the United States. In order to better understand the impact O. petrowi has on wild bird populations, we developed a quantitative PCR protocol to detect infections in wild northern bobwhites (Colinus virginianus). We used paired fecal and cloacal swab samples from wild caught and experimentally infected northern bobwhites and matching fecal float data from experimentally infected birds to validate our assay. Overall we detected more positive birds from fecal samples than the paired cloacal swabs and there was strong agreement between the qPCR results from fecal samples and from fecal flotation (84%; κ = 0.69 [0.53-0.84 95% CI]). We also detected O. petrowi DNA in ten replicates of samples spiked with one O. petrowi egg. This qPCR assay is an effective assay to detect O. petrowi infections in wild birds. Our results suggest that fecal samples are the most appropriate sample for detecting infections; although, cloacal swabs can be useful for determining if O. petrowi is circulating in a population.

A standardised faecal collection protocol for intestinal helminth egg counts in Asian elephants, Elephas maximus

The quantitative assessment of parasite infection is necessary to measure, manage and reduce infection risk in both wild and captive animal populations. Traditional faecal flotation methods which aim to quantify parasite burden, such as the McMaster egg counting technique, are widely used in veterinary medicine, agricultural management and wildlife parasitology. Although many modifications to the McMaster method exist, few account for systematic variation in parasite egg output which may lead to inaccurate estimations of infection intensity through faecal egg counts (FEC). To adapt the McMaster method for use in sampling Asian elephants (Elephas maximus), we tested a number of possible sources of error regarding faecal sampling, focussing on helminth eggs and using a population of over 120 semi-captive elephants distributed across northern Myanmar. These included time of day of defecation, effects of storage in 10% formalin and 10% formol saline and variation in egg distribution between and within faecal boluses. We found no significant difference in the distribution of helminth eggs within faecal matter or for different defecation times, however, storage in formol saline and formalin significantly decreased egg recovery. This is the first study to analyse several collection and storage aspects of a widely-used traditional parasitology method for helminth parasites of E. maximus using known host individuals. We suggest that for the modified McMaster technique, a minimum of one fresh sample per elephant collected from any freshly produced bolus in the total faecal matter and at any point within a 7.5 h time period (7.30am-2.55 pm) will consistently represent parasite load. This study defines a protocol which may be used to test pre-analytic factors and effectively determine infection load in species which produce large quantities of vegetative faeces, such as non-ruminant megaherbivores.

Polymerase Chain Reaction: A Better Method for Diagnosing Chronic Schistosoma mansoni Infections

For more effective diagnosis of the acute and chronic stages of Schistosoma mansoni infection in humans, the polymerase chain reaction (PCR) technique was compared with the Kato-Katz method. A total of 150 stool samples were collected from inpatient and outpatient clinics at the Department of Tropical Medicine, Minia University Hospital, Egypt. Three groups of patients, 50 with acute intestinal schistosomiasis, 70 with chronic intestinal schistosomiasis and 30 normal healthy controls were studied. Stool samples were analyzed by PCR and the Kato-Katz method. The mean number of eggs per gram of feces was 4.6 when estimated by the Kato-Katz method in positive stool samples from acute schistosomiasis cases but only 1.7 in chronic cases. In acute intestinal schistosomiasis, 15 and 45 out of 50 cases were positive by Kato-Katz and PCR, respectively. In the chronic intestinal schistosomiasis cases, 6 and 68 out of 70 cases were positive by the Kato-Katz and PCR methods, respectively. We conclude that PCR appears to be an effective diagnostic technique for S. mansoni infection, especially where a low worm burden exists, such as in chronic cases.

Report of Theileria luwenshuni and Theileria sp. RSR from cervids in Gansu, China

Theileria parasites are important tick-borne pathogens of animals and cause huge economic losses worldwide. Here, we undertook to assess the prevalence of Theileria spp. in cervids in Gansu, China, based on PCR analysis and sequencing of the 18S rRNA genes. Molecular survey showed that Theileria luwenshuni and Theileria sp. RSR were frequently found in Gansu cervids, and the prevalence of T. luwenshuni was 66.7% (n = 9, 6/9) in roe deer in Zhengning County, 58.3% (n = 12, 7/12) in sika deer in Ningxian County, 50% (n = 10, 5/10) in sika deer and 42.9% (n = 14, 6/14) in red deer in Weiyuan County. The prevalence of Theileria sp. RSR was 77.8% (n = 9, 7/9) in roe deer in Zhengning County, 75% (n = 12, 9/12) in sika deer in Ningxian County, 60.0% (n = 10, 6/10) in sika deer, and 50.0% (n = 14, 7/14) in red deer in Weiyuan County. The co-prevalence of the two T. luwenshuni and Theileria sp. RSR was 55.6% (n = 5, 5/9) in roe deer in Zhengning County, 50% (n = 12, 6/12) in sika deer in Ningxian county, 50% (n = 10, 5/10) in sika deer and 35.7% (n = 14, 5/14) in red deer in Weiyuan County, respectively. No other Theileria species was found in these samples. T. luwenshuni and Theileria sp. RSR were detected for the first time in cervids in Gansu, China. Animal experiments showed that four sheep were inoculated with roe deer blood from Zhengning, sika deer blood from Ningxian, sika deer blood, and red deer blood from Weiyuan, respectively, and the Theileria isolated from these inoculated sheep was identified as T. luwenshuni, but Theileria sp. RSR was not detected in these sheep. Our results extend our understanding of the epidemiology of cervine theileriosis in Gansu, China, and will facilitate the implementation of measures to control theileriosis in cervids and small ruminants. This was the first report to demonstrate the occurrence of T. luwenshuni from roe deer, sika deer, and red deer worldwide.

Advances in the diagnosis of key gastrointestinal nematode infections of livestock, with an emphasis on small ruminants

Parasitic nematodes (roundworms) of livestock have major economic impact globally. In spite of the diseases caused by these nematodes and some advances in the design of new therapeutic agents (anthelmintics) and attempts to develop vaccines against some of them, there has been limited progress in the establishment of practical diagnostic techniques. The specific and sensitive diagnosis of gastrointestinal nematode infections of livestock underpins effective disease control, which is highly relevant now that anthelmintic resistance (AR) is a major problem. Traditional diagnostic techniques have major constraints, in terms of sensitivity and specificity. The purpose of this article is to provide a brief background on gastrointestinal nematodes (Strongylida) of livestock and their control; to summarize conventional methods used for the diagnosis and discuss their constraints; to review key molecular-diagnostic methods and recent progress in the development of advanced amplification-based and sequencing technologies, and their implications for epidemiological investigations and the control of parasitic diseases.

Evaluation of a real-time PCR test for the detection and discrimination of theileria species in the African buffalo (Syncerus caffer)

A quantitative real-time PCR (qPCR) assay based on the cox III gene was evaluated for the simultaneous detection and discrimination of Theileria species in buffalo and cattle blood samples from South Africa and Mozambique using melting curve analysis. The results obtained were compared to those of the reverse line blot (RLB) hybridization assay for the simultaneous detection and differentiation of Theileria spp. in mixed infections, and to the 18S rRNA qPCR assay results for the specific detection of Theileria parva.

Theileria parva, Theileria sp. (buffalo), Theileria taurotragi, Theileria buffeli and Theileria mutans were detected by the cox III assay. Theileria velifera was not detected from any of the samples analysed. Seventeen percent of the samples had non-species specific melting peaks and 4.5% of the samples were negative or below the detection limit of the assay. The cox III assay identified more T. parva and Theileria sp. (buffalo) positive samples than the RLB assay, and also detected more T. parva infections than the 18S assay. However, only a small number of samples were positive for the benign Theileria spp. To our knowledge T. taurotragi has never been identified from the African buffalo, its identification in some samples by the qPCR assay was unexpected.

Because of these discrepancies in the results, cox III qPCR products were cloned and sequenced. Sequence analysis indicated extensive inter- and intra-species variations in the probe target regions of the cox III gene sequences of the benign Theileria spp. and therefore explains their low detection. The cox III assay is specific for the detection of T. parva infections in cattle and buffalo. Sequence data generated from this study can be used for the development of a more inclusive assay for detection and differentiation of all variants of the mildly pathogenic and benign Theileria spp. of buffalo and cattle.

An epidemiological survey of Theileria infections in small ruminants in central China

Here, we conducted an epidemiological study in five regions in central China to assess the impact of theileriosis on small ruminants. PCR analysis and microscopic evaluations of blood smears to detect ovine and caprine theileriosis was conducted, in which 256 blood samples and 250 ticks were collected from sheep and goats, and tested for Theileria uilenbergi, T. luwenshuni, and T. ovis. The 18S rRNA gene sequences were deduced from positive samples and used for phylogenetic analysis. The results showed that T. luwenshuni was found most frequently in the five investigated regions and the prevalence of T. luwenshuni was found to be very high by PCR analysis. In contrast, T. uilenbergi and T. ovis infections were not detected in these regions. Phylogenetic tree analysis showed that all of the newly isolated Theileria spp. was in the same clade as T. luwenshuni. Haemaphysalis longicornis, which can transmit T. luwenshuni, was also detected in the sampled sheep and goats in these regions. Our results provide important data to increase the understanding of the epidemiology of ovine and caprine theileriosis, and will aid in the implementation of measures to control theileriosis transmission to small ruminants in central China.

Next-generation molecular-diagnostic tools for gastrointestinal nematodes of livestock, with an emphasis on small ruminants: a turning point?

Parasitic nematodes of livestock have major economic impact worldwide. Despite the diseases caused by these nematodes, some advances towards the development of new therapeutic agents and attempts to develop effective vaccines against some of them, there has been limited progress in the development of practical diagnostic methods. The specific and sensitive diagnosis of parasitic nematode infections of livestock underpins effective disease control, which is now particularly important given the problems associated with anthelmintic resistance in parasite populations. Traditional diagnostic methods have major limitations, in terms of sensitivity and specificity. This chapter provides an account of the significance of parasitic nematodes (order Strongylida), reviews conventional diagnostic techniques that are presently used routinely and describes advances in polymerase chain reaction (PCR)-based methods for the specific diagnosis of nematode infections. A particular emphasis is placed on the recent development of a robotic PCR-based platform for high-throughput diagnosis, and its significance and implications for epidemiological investigations and for use in control programmes.

Direct and indirect costs of co-infection in the wild: Linking gastrointestinal parasite communities, host hematology, and immune function

Most animals are concurrently infected with multiple parasites, and interactions among these parasites may influence both disease dynamics and host fitness. However, the sublethal costs of parasite infections are difficult to measure and the effects of concomitant infections with multiple parasite species on individual physiology and fitness are poorly described for wild hosts. To understand the direct and indirect physiological costs of co-infection, we investigated the relationships among gastrointestinal parasite richness, species identity, and abundance and host hematological parameters, body condition, and investment in lymphocyte defenses. Using aggregate-scale parasite data from African buffalo (Syncerus caffer), we found few direct or indirect associations between infection and hematology in male hosts, and no significant associations were observed in female hosts or with respect to body condition in either sex. These results suggest that only strong physiological effects are detectable with aggregate-scale parasite data, and that hematological variables may be more sensitive to changes in condition than standard body fat condition indices. Analyses accounting for parasite species identity in female buffalo revealed that different parasites show distinct relationships with host hematology, body condition, and immune investment. However, four of six species-specific associations were obscured when parasites were considered in combination. Overall, fitness-related physiological mediators such as hematological indices may provide assessments of direct and indirect effects of parasite infection, particularly when parasite species identity and community composition are considered.

Rapid detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini eggs in human fecal samples using a duplex real-time fluorescence resonance energy transfer PCR and melting curve analysis

We developed a single step duplex real-time fluorescence resonance energy transfer (FRET) PCR merged with melting curve analysis for the fast detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini eggs in human fecal samples. Two species of mitochondrial NADH dehydrogenase subunit 2 (nad2) DNA elements, the 165-bp nad2 product of C. sinensis and the 209-bp nad2 product of O. viverrini, were amplified by species-specific primers, and the fluorescence melting curve analyses were generated from hybrid of amplicons and two pairs of species-specific fluorophore-labeled probes. By their different fluorescence channels and melting temperatures, both C. sinensis and O. viverrini eggs in infected human fecal samples were detected and differentiated with high (100%) sensitivity and specificity. Detection limit was as little as a single C. sinensis egg and two O. viverrini eggs in 100 mg of fecal sample. The assay could distinguish the DNA of both parasites from the DNA of negative fecal samples and fecal samples with other parasitosis, as well as from the well-defined genomic DNA of human leukocytes and other parasites. It can reduce labor time of microscopic examination and is not prone to carry over contamination of agarose electrophoresis. Our duplex real-time FRET PCR method would be useful to determine the accurate range of endemic areas and/or to discover the co-endemic areas of two liver flukes, C. sinensis and O. viverrini, in Asia. This method also would be helpful for the differential diagnosis of the suspected cases of liver fluke infections among travelers who had visited the endemic countries of those parasites.

Differential detection of Trichinella papuae, T. spiralis and T. pseudospiralis by real-time fluorescence resonance energy transfer PCR and melting curve analysis

Trichinellosis caused by nematodes of Trichinella spp. is a zoonotic foodborne disease. Three Trichinella species of the parasite including Trichinella spiralis, Trichinella papuae and Trichinella pseudospiralis, have been etiologic agents of human trichinellosis in Thailand. Definite diagnosis of this helminthiasis is based on a finding of the Trichinella larva (e) in a muscle biopsy. The parasite species or genotype can be determined using molecular methods, e.g., polymerase chain reaction (PCR). This study has utilized real-time fluorescence resonance energy transfer PCR (real-time FRET PCR) and a melting curve analysis for the differential diagnosis of trichinellosis. Three common Trichinella species in Thailand were studied using one set of primers and fluorophore-labeled hybridization probes specific for the small subunit of the mitochondrial ribosomal RNA gene. Using fewer than 35 cycles as the cut-off for positivity and using different melting temperatures (T(m)), this assay detected T. spiralis, T. papuae and T. pseudospiralis in muscle tissue and found the mean T(m) ± SD values to be 51.79 ± 0.06, 66.09 ± 0.46 and 51.46 ± 0.09, respectively. The analytical sensitivity of the technique enabled the detection of a single Trichinella larva of each species, and the detection limit for the target DNA sequence was 16 copies of positive control plasmid. A test of the technique's analytical specificity showed no fluorescence signal for a panel of 19 non-Trichinella parasites or for human and mouse genomic DNA. Due to the sensitivity and specificity of the detection of these Trichinella species, as well as the fast and high-throughput nature of these tools, this method has application potential in differentiating non-encapsulated larvae of T. papuae from T. spiralis and T. pseudospiralis in tissues of infected humans and animals.

Gene Expression Profiling via Multigene Concatemers

We established a novel method, Gene Expression Profiling via Multigene Concatemers (MgC-GEP), to study multigene expression patterns simultaneously. This method consists of the following steps: (1) cDNA was obtained using specific reverse primers containing an adaptor. (2) During the initial 1-3 cycles of polymerase chain reaction (PCR), the products containing universal adaptors with digestion sites at both termini were amplified using specific forward and reverse primers containing the adaptors. (3) In the subsequent 4-28 cycles, the universal adaptors were used as primers to yield products. (4) The products were digested and ligated to produce concatemers. (5) The concatemers were cloned into the vector and sequenced. Then, the occurrence of each gene tag was determined. To validate MgC-GEP, we analyzed 20 genes in Saccharomyces cerevisiae induced by weak acid using MgC-GEP combined with real-time reverse transcription (RT)-PCR. Compared with the results of real-time RT-PCR and the previous reports of microarray analysis, MgC-GEP can precisely determine the transcript levels of multigenes simultaneously. Importantly, MgC-GEP is a cost effective strategy that can be widely used in most laboratories without specific equipment. MgC-GEP is a potentially powerful tool for multigene expression profiling, particularly for moderate-throughput analysis.

Extremophiles and their application to veterinary medicine

Extremophiles can be defined as organisms that can survive in extreme environments that cannot support mammalian life. They include microorganisms that can tolerate temperature extremes, extremes of pH, salinity, hydrostatic pressure and ionizing radiation, as well as low oxygen tension, desiccation and the presence of heavy metals. Psychrophilic organisms also include fish in polar waters and animals that withstand freezing. Rare examples of thermophilic pathogens exist, and the main category of extremophilic animal pathogens comprises psychrophilic and psychrotrophic microorganisms that cause fish diseases, e.g. Flavobacterium psychrophilum, Moritella viscosa, Aliivibrio wodanis and Aliivibrio salmonicida. The most widely known application of an extremophile product in veterinary medicine is DNA polymerase from thermophiles, which is a mainstay of PCR-based diagnostics for an extensive range of animal pathogens. DNA polymerases and other extremophile enzymes are also used in many molecular biology applications and animal genomics. Other extremophile products may find application in veterinary medicine in the future. These include enzymes in biosensors, compatible solutes in skin care products, drug excipients, treatments for respiratory disease, radioprotectants, peptide antibiotics, archaeal lipids for drug delivery and anti-cancer therapeutics.

Diagnosis of parasitic diseases: old and new approaches

Methods for the diagnosis of infectious diseases have stagnated in the last 20–30 years. Few major advances in clinical diagnostic testing have been made since the introduction of PCR, although new technologies are being investigated. Many tests that form the backbone of the “modern” microbiology laboratory are based on very old and labour-intensive technologies such as microscopy for malaria. Pressing needs include more rapid tests without sacrificing sensitivity, value-added tests, and point-of-care tests for both high- and low-resource settings. In recent years, research has been focused on alternative methods to improve the diagnosis of parasitic diseases. These include immunoassays, molecular-based approaches, and proteomics using mass spectrometry platforms technology. This review summarizes the progress in new approaches in parasite diagnosis and discusses some of the merits and disadvantages of these tests.

Real-time fluorescence resonance energy transfer PCR with melting curve analysis for the detection of Opisthorchis viverrini in fish intermediate hosts

A real-time fluorescence resonance energy transfer (FRET) PCR combined with a melting curve analysis was developed for the detection of Opisthorchis viverrini in its fish intermediate host, cyprinoid fishes. Real-time FRET PCR is based on a fluorescence melting curve analysis of a hybrid between an amplicon generated from a family of repeated DNA elements, the pOV-A6 specific probe sequence (Genbank Accession No. S80278), a 162 bp repeated sequence specific to O. viverrini, and specific fluorophore-labeled probes. The real-time FRET PCR could detect as little as a single metacercaria artificially inoculated in 30 fish samples. The O. viverrini infected fishes were distinguished from non-infected fishes and from the genomic DNA of other parasites by their melting temperature. Sensitivity and specificity of this method were both 100% in the laboratory setting and it outperformed the microscopic method on field-collected samples as well. Melting curve analysis is a rapid, accurate, and sensitive alternative for the specific detection of O. viverrini infected fishes. It allows a high throughput and can be performed on small samples. The assay has not only great potential for epidemiological surveys of fish intermediate hosts but it could also be adapted as screening tool for a range of foodborne parasites in freshwater fishes.

Detection of Opisthorchis viverrini in infected bithynid snails by real-time fluorescence resonance energy transfer PCR-based method and melting curve analysis

A real-time fluorescence resonance energy transfer (FRET) PCR combined with melting curve analysis was developed for the detection of Opisthorchis viverrini in experimentally infected bithynid snails, its first intermediate hosts. The test is based on the fluorescence melting curve analysis of a hybrid between an amplicon from the pOV-A6-specific probe sequence, a 162-bp repeated sequence specific to O. viverrini and specific fluorophore-labeled probes. The real-time FRET PCR could detect as little as a single cercaria artificially introduced in a pool of 30 non-infected snails. The O. viverrini-infected snails were discriminated from non-infected snails and from genomic DNA of other parasite DNAs by their melting temperatures. Sensitivity and specificity of this method were both 100%. Melting curve analysis is a sensitive alternative for the specific detection of O. viverrini-infected snails; it is rapid, allows a high throughput, and can be done on small samples. The assay not only has a high potential for epidemiological surveys of O. viverrini-infected bithynid snails, but also for the detection of cercariae infestations of natural waterways when monitoring transmission sites.

Detection and semi-quantification of Strongylus vulgaris DNA in equine faeces by real-time quantitative PCR

Strongylus vulgaris is an important strongyle nematode with high pathogenic potential infecting horses world-wide. Several decades of intensive anthelmintic use has virtually eliminated clinical disease caused by S. vulgaris, but has also caused high levels of anthelmintic resistance in equine small strongyle (cyathostomin) nematodes. Recommendations aimed at limiting the development of anthelmintic resistance by reducing treatment intensity raises a simultaneous demand for reliable and accurate diagnostic tools for detecting important parasitic pathogens. Presently, the only means available to differentiate among strongyle species in a faecal sample is by identifying individual L3 larvae following a two week coproculture procedure. The aim of the present study is to overcome this diagnostic obstacle by developing a fluorescence-based quantitative PCR assay capable of identifying S. vulgaris eggs in faecal samples from horses. Species-specific primers and a TaqMan probe were designed by alignment of published ribosomal DNA sequences of the second internal transcribed spacer of cyathostomin and Strongylus spp. nematodes. The assay was tested for specificity and optimized using genomic DNA extracted from identified male worms of Strongylus and cyathostomin species. In addition, eggs were collected from adult female worms and used to evaluate the quantitative potential of the assay. Statistically significant linear relationships were found between egg numbers and cycle of threshold (Ct) values. PCR results were unaffected by the presence of cyathostomin DNA in the sample and there was no indication of PCR inhibition by faecal sources. A field evaluation on faecal samples obtained from four Danish horse farms revealed a good agreement with the traditional larval culture (kappa-value=0.78), but with a significantly higher performance of the PCR assay. An association between Ct values and S. vulgaris larval counts was statistically significant. The present assay can reliably and semi-quantitatively detect minute quantities of S. vulgaris eggs in faecal samples.

Real-time PCR for detection of low intensity Schistosoma japonicum infections in a pig model

Decades of successful Schistosoma japonicum control have increased the interest in how to diagnose low intensity infections. A real-time PCR assay targeting the mitochondrial NADH dehydrogenase I gene in S. japonicum was evaluated in infected pigs with very low egg output. Six out of 12 S. japonicum infected pigs were treated with praziquantel 8 weeks after infection and all pigs were followed for 16 weeks post-infection. One commercial and one non-commercial extraction method were evaluated in combination with PCR on faecal samples. PCR with either extraction method were equally sensitive as the DBL-filtration/sedimentation technique in the acute, productive stage. PCR recovered slightly more positive samples in the chronic stage, but most faecal samples were negative for both PCR and microscopy from week 9 post-infection irrespective of treatment. IgG antibody titers against soluble egg antigen IgG remained high throughout the study in both the treated and non-treated group. PCR was consistently negative in serum and urine samples and negative in most of the caecal biopsies. We conclude that the S. japonicum faecal PCR is a highly sensitive test. However, in clinical samples when faecal egg output almost reaches nil in the chronic stage despite persistent worm burdens, both the faecal PCR and microscopy results were negative. Real-time PCR is less labour intensive than most microscopy methods, but has a higher material cost per sample.

A multiplex PCR that discriminates between Trypanosoma brucei brucei and zoonotic T. b. rhodesiense

Two subspecies of Trypanosoma brucei s.l. co-exist within the animal populations of Eastern Africa; T. b. brucei a parasite which only infects livestock and wildlife and T. b. rhodesiense a zoonotic parasite which infects domestic livestock, wildlife, and which in humans, results in the disease known as Human African Trypanosomiasis (HAT) or sleeping sickness. In order to assess the risk posed to humans from HAT it is necessary to identify animals harbouring potentially human infective parasites. The multiplex PCR method described here permits differentiation of human and non-human infective parasites T. b. rhodesiense and T. b. brucei based on the presence or absence of the SRA gene (specific for East African T. b. rhodesiense), inclusion of GPI-PLC as an internal control indicates whether sufficient genomic material is present for detection of a single copy T. brucei gene in the PCR reaction.

A trypanosome species isolated from naturally infected Haemaphysalis hystricis ticks in Kagoshima Prefecture, Japan

Common arthropod vectors for trypanosomes are flies, fleas and bugs. This study reports on an unknown trypanosome species isolated from naturally infected Haemaphysalis hystricis ticks, hereby, referred to as Trypanosoma KG1 isolate. The parasite has been successfully cultured in vitro with L929 or HEK 293T cell line as feeder cells. This trypanosome cannot survive in vitro without feeder cells. Following experimental infections of ticks, the trypomastigote-like and the epimastigote-like forms of this trypanosome could be detected by Giemsa-stained smears of the midgut and salivary glands of Ornithodoros moubata ticks which were made to feed on a culturing medium containing Trypanosoma KG1 isolate through an artificial membrane. Trypanosoma KG1 isolate could also be detected from Giemsa-stained smears of the haemolymph up to 30 days post-inoculation into the O. moubata haemocoel. Trypanosoma KG1 isolate cannot be propagated in laboratory animals including mice, rats, rabbits and sheep. A phylogenetic tree constructed with the 18S rRNA gene indicates that Trypanosoma KG1 is a member of the stercorarian trypanosomes.

The use of multiplex PCR to detect and differentiate food- and beverage-associated microorganisms: a review

Regarding food safety, rapid detection of microbial species is crucial to develop effective preventive and/or adjustment measures. Classical methods for determining the presence of certain species are time-consuming and labor-intensive, hence, molecular methods, which offer speed, sensitivity and specificity, have been developed to address this problem. Multiplex PCR (MPCR) is widely applied in the various fields of microbiology for the rapid differentiation of microbial species without compromising accuracy. This paper describes the method and reports on the state-of-the-art application of this technique to the identification of microorganisms vehiculated with foods and beverages. The identification of both pathogens and probiotics and the species important for food fermentation or deterioration will be discussed. Applications of MPCR in combination with other techniques are also reviewed. Potentials, pitfalls, limitations and future prospects are summarised.

Detection of the Pinewood Nematode, Bursaphelenchus xylophilus, Using a Real-Time Polymerase Chain Reaction Assay

ABSTRACT The pinewood nematode, Bursaphelenchus xylophilus, has caused significant damage to pine plantations both in East Asia and North America and is an important quarantine organism. A real-time polymerase chain reaction (PCR) assay was developed to detect B. xylophilus. A set of primers and probe specific for B. xylophilus was designed to target the ribosomal DNA internal transcribed spacer region. Optimal primer concentration, Mg(2+) concentration, and extension temperature were 400 nM, 3.0 mM, and 60 degrees C, respectively. The assay was highly specific and sensitive, detecting as little as 0.01 ng of B. xylophilus DNA. The real-time PCR assay also successfully detected B. xylophilus in field samples, and it should be very useful for quarantine purposes.

Fluorescence based strategies for genetic analysis

Synthetic chemistry has been central to the design of modern methods of genetic analysis. In this article, we discuss the underlying chemistry and biophysical principles that have been used in the development of robust methods for the analysis of DNA in the diagnostic laboratory.

Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples

Unique DNA sequences are present in all species and can be used as biomarkers for the detection of cells from that species. These DNA sequences can most easily be detected using the polymerase chain reaction (PCR), which allows very small quantities of target DNA sequence to be amplified even when the target is mixed with large amounts of nontarget DNA. PCR amplification of DNA markers that are present in a wide range of species has proven very useful for studies of species diversity in environmental samples. The taxonomic range of species to be identified from environmental samples may often need to be restricted to simplify downstream analyses and to ensure that less abundant sequences are amplified. Group-specific PCR primer sets are one means of specifying the range of taxa that produce an amplicon in a PCR. We have developed a range of group-specific PCR primers for studying the prey diversity found in predator stomach contents and scats. These primers, their design and their application to studying prey diversity and identity in predator diet are described.

Sex ratio variation in gastrointestinal nematodes of Svalbard reindeer; density dependence and implications for estimates of species composition

Estimates of the intensity and abundance of species provide essential data for ecological, evolutionary and epidemiological studies of gastrointestinal nematode communities. These estimates are typically derived from the species composition of adult males when only males have readily scorable species-specific morphological traits. Such estimation assumes that all species in the community have the same adult sex ratio. We evaluated this assumption for the trichostrongyle nematodes Ostertagia gruehneri and Marshallagia marshalli in infracommunities in Svalbard reindeer by identifying to species adult females using a polymerase chain reaction assay. The proportion of males was found to be slightly higher in O. gruehneri than in M. marshalli. Evidence for seasonal variation and density dependence in the adult sex ratio was only found for O. gruehneri. Possible demographic mechanisms for such sex ratio variation are discussed, and stochastic models that generate density-dependent sex ratios proposed. Sex ratio variation caused substantial bias in some male-based estimates of intensity of infection, while substantial and consistent bias in estimates of abundances was only evident in late winter samples. Our results suggest that estimating sex ratios can be particularly important in individual host level studies of nematode species of low abundance.

Rapid detection of Wuchereria bancrofti in mosquitoes by LightCycler polymerase chain reaction and melting curve analysis

A LightCycler real-time polymerase chain reaction (PCR) assay was developed to detect Wuchereria bancrofti DNA in blood-fed mosquitoes. The assay is based on fluorescence melting curve analysis of the PCR product generated from a family of repeated DNA elements: the 182 bp SspI repeat, specific to the genus Wuchereria. According to the melting temperature, W. bancrofti infected-mosquitoes were differentiated from Brugia malayi-infected and non-infected mosquitoes as well as from genomic DNA of Dirofilaria immitis and human DNA. The method proved to be 100% sensitive in all W. bancrofti-infected mosquitoes. Melting curve analysis offers a rapid alternative for the specific detection of W. bancrofti in mosquitoes. It is very accurate and sensitive, allows a high throughput and can be performed on very small samples. The method therefore has great potential for application in epidemiological studies.

A real-time PCR assay for quantifying Plasmodium falciparum infections in the mosquito vector

Transmission-blocking vaccines prevent the development of Plasmodium parasite within the mosquito vector, thereby thwarting the spread of malaria through a community. The gold standard for determining the efficacy of a transmission-blocking vaccine is the standard membrane feeding assay. This assay requires the dissection of mosquitoes and microscopic counting of oocysts present on the mosquito mid-gut, typically at 7-10 days p.i. Here we describe a real-time quantitative PCR assay that is rapid, target-specific and robust, with a sensitive detection threshold and which may be employed earlier p.i. than the standard membrane feeding assay and is applicable to preserved material. The real-time PCR assay utilises the LightCycler platform and SYBR Green I detection system to amplify 180 bp of the asexual form of the Plasmodium falciparum rRNA gene. It has a quantitative range of greater than four orders of magnitude and a detection threshold of 10 parasites. Validation experiments using a monoclonal antibody of known blocking activity revealed the real-time PCR assay to give equivalent results to the standard membrane feeding assay. In addition, the PCR assay can establish the effect of such a monoclonal antibody on the parasites' development within the oocyst and on the sporozoite (the transmissible stage) yield, providing a more pertinent assessment of transmission blocking activity than is possible by the standard membrane feeding assay. This assay may also be employed to monitor the sporogonic development of P. falciparum parasites within the mosquito vector.

Molecular cloning and expression of the full-length tropomyosin gene from Trichinella spiralis

A clone, designated as TsTM, was selected from the cDNA library of newborn larvae (NBL) of Trichinella spiralis through immunoscreening against infected sera. The clone contained a cDNA transcript of 855 bp in length with a single open reading frame, which encoded 285-amino acids (33 kDa in the estimated molecular weight). A sequence analysis revealed that the clone TsTM encoded the full-length of tropomyosin gene. The phylogenetic analysis of the tropomyosin gene was in good agreement with the classical taxonomical position of T. spiralis. The fusion proteins encoded by the clone TsTM were produced in an Escherichia coli expression system and affinity purified, and the antibody was raised against the protein for the following studies. The antibody against the fusion protein positively bound to the hypodermal muscle layer in immunolocalization analysis, and the 35 kDa band in crude extracts of muscle larvae but not in excretory and secretory (ES) products on Western blots. The antigenicity of the clone TsTM was recognized by host mice but exhibited little species specificity.