Development and preliminary evaluation of a loop-mediated isothermal amplification procedure for sensitive detection of cryptosporidium oocysts in fecal and water samples

Development of a "Rapid-Crypto Colorimetric LAMP Test" to Detect Cryptosporidiosis in Feces of Newborns Calves

BACKGROUND

Cryptosporidiosis is a disease that causes major intestinal damage in humans and animals. The causative agents of the disease are Cryptosporidium species. In newborn calves, diarrhea can lead to death, resulting in significant economic losses for the farms. Therefore, accurate, rapid, and cost-effective diagnosis of the disease is very important.

MATERIAL AND METHODS

In this study, a novel colorimetric loop-mediated isothermal amplification (LAMP) test named "Rapid-Crypto Colorimetric LAMP test" targeting Cryptosporidium spp. 18S rRNA gene was developed to detect cryptosporidiosis in the feces of newborn calves. The analytical sensitivity of the test was determined by plasmid controls. Clinical sensitivity was determined using the feces of 127 calves collected from farms in İzmir and Manisa provinces. All of the samples were also investigated with Real-Time PCR targeting the Cryptosporidium spp. COWP gene. Cross-reactivity was tested using the DNA of other parasites and bacteria.

RESULTS

According to the results, the analytical sensitivity of the "Rapid-Crypto Colorimetric LAMP test" was found as 1 copy plasmid/reaction. When the results were compared with the Real-Time PCR test, the sensitivity of the "Rapid-Crypto Colorimetric LAMP test" was 100% and the specificity was 97.4%. The test did not cross-react with other parasites and bacteria.   CONCLUSION: The "Rapid-Crypto Colorimetric LAMP test" developed in this study provides an advantage in the diagnosis of Cryptosporidium spp. in calf stool samples since it can be applied in basic laboratories or in the field, does not require experienced personnel, and has high sensitivity. Moreover, diagnosis can be made with the naked eye without using any device.

Rapid detection of Cryptosporidium spp. in diarrheic cattle feces by isothermal recombinase polymerase amplification assays

As a zoonotic parasite, Cryptosporidium spp. could cause severe diarrhea mainly in calves and children globally. Monitoring and prevention of Cryptosporidium spp.'s prevalence is of great significance in both economy and public health aspects. In this study, specific primers and probes were designed within the conserved region of 18S rRNA gene for Cryptosporidium spp. and recombinase polymerase amplification assays based on the fluorescence monitoring (real-time RPA) as well as combined with a lateral flow strip (LFS RPA) were developed. Both of the two RPA assays allowed the exponential amplification of the target fragment within 20 min. After incubation on a metal bath at 42 °C, the LFS RPA results were displayed on the lateral flow strip within 5 min while real-time RPA allowed the real-time observation of the results in Genie III at 39 °C. The RPA assays showed high specificity for Cryptosporidium spp. without any cross-reaction with other tested pathogens causing diarrhea in cattle. With the recombinant plasmid DNA containing the 18S rRNA gene of Cryptosporidium spp. serving as a template, the limit of detection for real-time RPA and LFS RPA assays were 14.6 and 12.7 copies/reaction, respectively. Moreover, the RPA assays were validated by testing diarrheic cattle fecal samples and compared with a real-time PCR. The positive ratio of Cryptosporidium spp. was 24.04 % (44/183) and 26.23 % (48/183) in both RPA assays and real-time PCR assay, respectively, and the kappa coefficient value was 0.942. The diagnostic specificity and diagnostic sensitivity of both RPA assays were 100 % and 91.67 %, respectively. Forty-one of 48 positive samples were successfully sequenced and four Cryptosporidium species were detected, including C. parvum (n = 20), C. andersoni (n = 17), C. bovis (n = 3) and C. ryanae (n = 1). The developed RPA assays are easy to operate and faster to obtain the detection results, and they are suiting for the point-of-care detection and facilitating the prevention and control of Cryptosporidium spp. infections.

Detection of chronic toxoplasmosis in the brain of mice using loop-mediated isothermal amplification (LAMP) and conventional PCR

BACKGROUND

Toxoplasma gondii is a common protozoan parasite that infects approximately one-third of the world's population. It is a disease with multiple manifestations. In immunocompetent individuals, symptoms are mild and flu-like, whereas, in immunocompromised patients, it often results in severe morbidity and mortality. Thus, studies for developing a simple, rapid diagnostic tool for early detection of Toxoplasma are emerging. Molecular diagnosis is highly accurate and helpful in congenitally infected and immunocompromised patients. The loop-mediated isothermal amplification (LAMP) technique was invented to improve nucleic acid amplification efficacy in terms of sensitivity and specificity.

AIM OF THE STUDY

The study aimed to validate a LAMP protocol for detecting Toxoplasma DNA in the brain homogenates from mice experimentally infected with Toxoplasma's ME-49 (cyst-forming type II) strain in comparison to PCR.

METHODS

In this study, the target DNA fragment was the Toxoplasma 529-bp, repeated 200-300 copies/genome. The sensitivity of both LAMP and conventional PCR techniques was estimated in brain homogenates in experimental mice at eight weeks post-infection and compared to the histopathology data.

RESULTS

The LAMP reaction showed positive results in 18 of the 26 examined samples of brain homogenates. PCR showed the characteristic 529-bp band in 15 of the 26 examined samples.

CONCLUSION

The LAMP showed a higher sensitivity over PCR in detecting Toxoplasma infection in brain homogenates of infected mice.

Diagnostic Methods of Common Intestinal Protozoa: Current and Future Immunological and Molecular Methods

Intestinal protozoan infection is a persisting public health problem affecting the populations of developing countries in the tropical and subtropical regions. The diagnosis of intestinal protozoa remains a challenge especially in developing countries due to a shortage of laboratory facilities, limited health funding, and the remoteness of communities. Despite still being widely used, conventional diagnoses using microscopy and staining methods pose important limitations, particularly due to their low sensitivities and specificities. The selection of diagnostic methods needs to be carefully considered based on the objective of examination, availability of resources, and the expected parasite to be found. In this review, we describe various immunodiagnosis and molecular diagnostic methods for intestinal protozoa infection, including their advantages, disadvantages, and suitability for different settings, with a focus on Entamoeba histolytica, Giardia duodenalis, and Cryptosporidium spp.

Development and Preliminary Evaluation of a Nanoparticle-Assisted PCR Assay for the Detection of Cryptosporidium parvum in Calves

C. parvum is an important diarrheal pathogen in humans and animals, especially in young hosts. To accurately and rapidly detect C. parvum infection in calves, we established a nano-PCR assay targeting the cgd3_330 gene for the specific detection of C. parvum. This nano-PCR assay was ten times more sensitive than that of the normal PCR assay by applying the same primers and did not cross-react with C. andersoni, C. bovis, C. ryanae, Balantidium coli, Enterocytozoon bieneusi, Giardia lamblia, and Blastocystis sp. To further test the nano-PCR in clinical settings, a total of 20 faecal samples from calves were examined by using the nano-PCR, the normal PCR, and the nested PCR assays. The positive rates were 30% (6/20), 30% (6/20), and 25% (5/20) for the nano-PCR, the normal PCR, and the nested PCR assays, respectively, indicating that the nano-PCR and the normal PCR assays had the same positive rate (30%). Taken together, the present study could provide a candidate method for the specific detection of C. parvum infection in calves in clinical settings.

Detection of SARS-CoV-2 in Different Human Biofluids Using the Loop-Mediated Isothermal Amplification Assay: A Prospective Diagnostic Study in Fortaleza, Brazil

We adopted the reverse‐transcriptase‐loop‐mediated isothermal amplification (RT‐LAMP) to detect severe acute respiratory syndrome coronavirus 2 (SARS‐Cov‐2) in patient samples. Two primer sets for genes N and Orf1ab were designed to detect SARS‐CoV‐2, and one primer set was designed to detect the human gene Actin. We collected prospective 138 nasopharyngeal swabs, 70 oropharyngeal swabs, 69 salivae, and 68 mouth saline wash samples from patients suspected to have severe acute respiratory syndrome (SARS) caused by SARS‐CoV‐2 to test the RT‐LAMP in comparison with the gold standard technique reverse‐transcription quantitative polymerase chain reaction  (RT‐qPCR). The accuracy of diagnosis using both primers, N5 and Orf9, was evaluated. Sensitivity and specificity for diagnosis were 96% (95% confidence interval [CI]: 87–99) and 85% (95% CI: 76–91) in 138 samples, respectively. Accurate diagnosis results were obtained only in nasopharyngeal swabs processed via extraction kit. Accurate and rapid diagnosis could aid coronavirus disease 2019 (COVID‐19) pandemic management by identifying, isolating, and treating patients rapidly.

Development of a New LAMP Assay for the Detection of Ancylostoma caninum DNA (Copro-LAMPAc) in Dog Fecal Samples

Ancylostoma caninum is a zoonotic nematode which is able to affect animals and humans. Diagnosis in the definitive host and environmental detection are key to prevent its dissemination and achieve control. Herein, a new coprological LAMP method for the detection of A. caninum (Copro-LAMPAc) DNA was developed. DNA extraction was performed using a low-cost method and a fragment of the cox-1 gene was used for primer design. The analytical sensitivity, evaluated with serial dilutions of genomic DNA from A. caninum adult worms, was 100 fg. A specificity of 100% was obtained using genomic DNA from the host and other pathogens. The Copro-LAMPAc was evaluated using environmental canine fecal samples. When compared with gold standard optical microscopy in epidemiological studies, it proved to be more sensitive. This new LAMP assay can provide an alternative protocol for screening and identification of A. caninum for epidemiological studies in endemic areas.

Omics-Based Analytical Approaches for Assessing Chicken Species and Breeds in Food Authentication

Chicken is known to be the most common meat type involved in food mislabeling and adulteration. Establishing a method to authenticate chicken content precisely and identifying chicken breeds as declared in processed food is crucial for protecting consumers' rights. Categorizing the authentication method into their respective omics disciplines, such as genomics, transcriptomics, proteomics, lipidomics, metabolomics, and glycomics, and the implementation of bioinformatics or chemometrics in data analysis can assist the researcher in improving the currently available techniques. Designing a vast range of instruments and analytical methods at the molecular level is vital for overcoming the technical drawback in discriminating chicken from other species and even within its breed. This review aims to provide insight and highlight previous and current approaches suitable for countering different circumstances in chicken authentication.

Development of a low-cost copro-LAMP assay for simultaneous copro-detection of Toxocara canis and Toxocara cati

Toxocariasis is a zoonotic disease caused mainly by Toxocara canis and Toxocara cati and diagnosis in dogs and cats is an important tool for its control. For this reason, a new coprological loop-mediated isothermal amplification (LAMP) assay was developed for the simultaneous detection of these species. The primer set was designed on a region of the mitochondrial cox-1 gene. Amplification conditions were evaluated using a temperature gradient (52°C to 68°C), different incubation times (15–120 min), and different concentrations of malachite green dye (0.004–0.4% w/v). The analytical sensitivity was evaluated with serial dilutions of genomic DNA from T. canis and T. cati adult worms, and with serial dilutions of DNA extracted from feces using a low-cost in-house method. The specificity was evaluated using genomic DNA from Canis lupus familiaris, Felis catus, Escherichia coli, Toxascaris leonina, Ancylostoma caninum, Echinococcus granulosus sensu stricto and Taenia hydatigena. The LAMP assay applied to environmental fecal samples from an endemic area showed an analytical sensitivity of 10–100 fg of genomic DNA and 10−5 serial dilutions of DNA extracted from feces using the low-cost in-house method; with a specificity of 100%. Additionally, the total development of the assay was carried out in a basic laboratory and per-reaction reagent cost decreased by ~80%. This new, low-cost tool can help identify the most common agents of toxocariasis in endemic areas in order to manage prevention strategies without having to rely on a laboratory with sophisticated equipment.

Development of a Loop-mediated isothermal amplification (LAMP) technique for specific and early detection of Mycobacterium leprae in clinical samples

Leprosy, a progressive, mutilating and highly stigmatized disease caused by Mycobacterium leprae (ML), continues to prevail in the developing world. This is due to the absence of rapid, specific and sensitive diagnostic tools for its early detection since the disease gets notified only with the advent of physical scarring in patients. This study reports the development of a Loop-mediated isothermal amplification (LAMP) technique for fast, sensitive and specific amplification of 16S rRNA gene of ML DNA for early detection of leprosy in resource-limited areas. Various parameters were optimized to obtain robust and reliable amplification of ML DNA. Blind clinical validation studies were performed which showed that this technique had complete concurrence with conventional techniques. Total absence of amplification of negative control DNA confirmed the specificity of this test. Various visual detection methods viz. colorimetric, turbidity differentiation and bridge flocculation were standardized to establish easy-to-read and rapid diagnosis. This technique eliminates the lack of accuracy and sensitivity in skin smear tests in patients and the requirement for expensive lab equipments and trained technicians. The technique holds promise for further expansion and has the potential to cater to the unmet needs of society for a cheap, highly-sensitive and robust rapid diagnosis of ML.

Optimization and validation of a loop-mediated isothermal amplification (LAMP) assay for detection of Giardia duodenalis in leafy greens

Giardia duodenalis is one of the most common food and water-borne intestinal parasites of humans and animals worldwide. Fresh, ready-to-eat produce such as leafy greens and salad mixes are considered potential transmission vehicles for Giardia infection in humans. Therefore, a specific, sensitive, and reliable method for Giardia detection in leafy greens is needed. We optimized washing procedures for the recovery of Giardia cysts from leafy greens and adapted and validated an existing EF1α LAMP assay for the detection of Giardia DNA to support routine diagnostic surveillance and disease outbreak investigations. Four leafy green types (35 ± 1 g) were spiked with 100 Giardia cysts and we compared washing by shaking with 1 M glycine (n = 20) or 0.1% Alconox (n = 20). DNA was extracted from washes, tested by LAMP and melt curve analysis, and time to positive (TTP) values compared. The detection limit was determined by spiking 10 (n = 40) Giardia cysts onto these same types of leafy greens and processing as above with 0.1% Alconox. Method robustness was assessed by subjecting spring mix (n = 45 total) to aging (1, 3 or 7 days) and washes to aging and freezing conditions prior to testing. Assay repeatability and specificity were evaluated, and an artificial positive control (APC) distinguishable by melt temperature (Tm) from DNA of Giardia spiked on leafy greens was designed to rule out cross-contamination from the control. Giardia detection rates were higher and TTP was lower (P < 0.05) for 0.1% Alconox (19/20, 8.85 ± 0.3 min) compared with 1 M glycine (15/20, 14.53 ± 7.2 min). The LAMP assay detected 10 Giardia cysts spiked on leafy greens in 13–34 min in 14/40 samples tested. Robustness assessment showed that TTP was higher (P < 0.0001) when spiked produce was stored for 7 days (13.09 ± 1.14 min) compared to fresh (9.72 ± 0.43 min). No unspiked samples were positive by LAMP, and the Tm for DNA of Giardia spiked on leafy greens was higher (P < 0.0001, 87.43 ± 0.05 °C) than the APC (86.43 ± 0.12 °C). Within-assay repeatability co-efficient of variation (CV) for TTP was 5.4% and no cross-contamination occurred when spiked and un-spiked samples were processed in alternate order. The optimized sample processing procedure combined with the EF1α LAMP assay is a sensitive, specific, labour-saving, and rapid method for the detection of Giardia cysts in leafy greens.

•

We adapted and validated EF1α LAMP assay for detection of Giardia in leafy greens.

•

Giardia LAMP is sensitive, specific and has a faster turnaround time than nPCR.

•

The assay performs well on aged and deteriorated produce samples.

•

Giardia LAMP has been implemented in our lab for routine surveillance testing.

An innovative and user-friendly smartphone-assisted molecular diagnostic approach for rapid detection of canine vector-borne diseases

Present-day diagnostic tools and technologies for canine diseases and other vector-borne parasitic diseases hardly meet the requirements of an efficient and rapid diagnostic tool, which can be suitable for use at the point-of-care in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been always a method of choice in the development and validation of quick, precise, and sensitive diagnostic assays for pathogen detection and to reorganize point-of-care (POC) molecular diagnostics. In this study, we have demonstrated an efficient detection system for parasitic vector-borne pathogens like Ehrlichia canis and Hepatozoon canis by linking the LAMP assay to a smartphone via a simple, inexpensive, and a portable “LAMP box,” All the components of the LAMP box were connected to each other wirelessly. This LAMP box was made up of an isothermal heating pad mounted below an aluminum base which served as a platform for the reaction tubes and LAMP assay. The entire setup could be connected to a smartphone via an inbuilt Wi-Fi that allowed the user to establish the connection to control the LAMP box. A 5 V USB power source was used as a power supply. The sensitivity of the LAMP assay was estimated to be up to 10⁻⁶ dilution limit using the amplified, purified, and quantified specific DNA templates. It can also serve as an efficient diagnostic platform for many other veterinary infectious or parasitic diseases of zoonotic origin majorly towards field-based diagnostics.

Critical review of methods for isothermal amplification of nucleic acids for environmental analysis

The past 30 years have seen the emergence and proliferation of isothermal amplification methods (IAMs) for rapid, sensitive detection and quantification of nucleic acids in a variety of sample types. These methods share dependence on primers and probes with quantitative PCR, but they differ in the specific enzymes and instruments employed, and are frequently conducted in a binary, rather than quantitative format. IAMs typically rely on simpler instruments than PCR analyses due to the maintenance of a single temperature throughout the amplification reaction, which could facilitate deployment of IAMs in a variety of environmental and field settings. This review summarizes the mechanisms of the most common IAM methods and their use in studies of pathogens, harmful algae and fecal indicators in environmental waters, feces, wastewater, reclaimed water, and tissues of aquatic animals. Performance metrics of sensitivity, specificity and limit of detection are highlighted, and the potential for use in monitoring and regulatory contexts is discussed.

Human intestinal parasitic infection: a narrative review on global prevalence and epidemiological insights on preventive, therapeutic and diagnostic strategies for future perspectives

INTRODUCTION

Intestinal parasitic infection (IPI) is a global health concern among socioeconomically deprived communities in many developing countries. Many preventative strategies have been deployed to control IPI, however, there is a lack in standards on the techniques used to diagnose and monitor the prevalence of IPI.

AREAS COVERED

The present article will review the diseases associated with IPI and discuss the current IPI control strategies such as the water, sanitation, and hygiene (WASH) interventions, community-led total sanitation (CLTS) approach, and regular anthelminthic treatments. For the first time, this review will also evaluate all currently practised diagnostic techniques for the detection of intestinal parasites and provide insights on future IPI control strategies.

EXPERT OPINION

Advanced and improved diagnostic methods such as qPCR coupled with a high-resolution melting curve, aptamers, biosensors, and detection of extracellular vesicles can be used for detection of IPI. Vaccination against intestinal parasites can be made available to increase antibodies to interfere with the blood-feeding process by the parasites, which subsequently reduces the reproductive rates of the parasites. These methods collectively can serve as future management strategies for intestinal parasitic infections.

Development of a convenient detection method for Trichomonas vaginalis based on loop-mediated isothermal amplification targeting adhesion protein 65

Background

Trichomoniasis resulting from Trichomonas vaginalis (T. vaginalis) has been considered as a commonly seen disease with the transmission way of sex. At present, the detection methods of T. vaginalis mainly include wet mount microscopy, culture, PCR, immunofluorescence and ELISA. However, all of these detection methods exist shortcomings.

Methods

In this study, a loop-mediated isothermal amplification (LAMP) assay that targeted the species-specific sequence of adhesion protein 65 (AP65) gene had been conducted to detect T. vaginalis. The optimum reaction system and conditions were optimized in this rapid detection method.

Results

The results of sensitivity analysis showed that the LAMP assay targeting the AP65 gene was 1000 times more sensitive than the nested PCR targeting the actin gene commonly used for detection of T. vaginalis, and the detecting limitation of the former was 10 trichomonad. Moreover, the amplification of the target gene AP65 by LAMP assay exhibited high specificity and the product was exclusively from T. vaginalis. The detection technique of LAMP did not exhibit cross-reactivity with the common pathogens of Trichinella spiralis, Toxoplasma gondii, Escherichia coli, Candida albicans, Staphylococcus aureus, Haemophilus.

Conclusions

According to the present study, the LAMP assay with the target of AP65 gene, was suitable for the early diagnosis of T. vaginalis infections. Consequently, the LAMP assay was proposed by the current study as a point-of-care examination and an alternative molecular tool which exhibited the potential value in the treatment, control and prevention of trichomoniasis transmission and relevant complication.

Clinical, Molecular and Serological Diagnosis of Canine Leishmaniosis: An Integrated Approach

Canine leishmaniosis (CanL) is caused by protozoans of the genus Leishmania and characterized by a broad spectrum of clinical signs in dogs. Early diagnosis is of great importance in order to perform an appropriate therapy and to prevent progression towards severe disease. The aim of this study was to compare a point-of-care molecular technique, i.e., the loop-mediated isothermal amplification (LAMP), with a real-time polymerase chain reaction (Rt-PCR), and three serological techniques, i.e., immunofluorescence antibody test (IFAT), enzyme-linked immunosorbent assay (ELISA), and a rapid SNAP Leishmania test, to develop an integrated approach for the diagnosis of CanL. Sixty dogs were chosen after physical examination and collection of blood and sera samples, fine-needle aspiration of lymph nodes, and conjunctival swabs were performed. Lymphadenopathy (82.3%), as well as clinicopathological alterations of total proteins (70.6%), were the most frequent signs. Forty-one (68.3%) samples resulted positive at least to one technique. IFAT resulted in the best serological diagnostic method (specificity = 100%, sensitivity = 97.2%), detecting a higher number of positive samples than those revealed by other techniques. Among the samples used for molecular analysis, fine-needle aspiration of lymph nodes was revealed as the best sample source. LAMP showed a substantial agreement (κ = 0.80; p <0.0001) with Rt-PCR; therefore, it could be promising for the rapid diagnosis of CanL. Nevertheless, further studies should be performed to confirm these findings.

Loop mediated isothermal amplification (LAMP) of Toxoplasma DNA from dried blood spots

INTRODUCTION

The cosmopolitan protozoan Toxoplasma gondii is a major parasite of warm-blooded animals including man. Early and accurate diagnosis is a must for proper treatment that prevents life threatening sequels. Loop-mediated isothermal amplification (LAMP) is a novel technique that can amplify DNA with high sensitivity and specificity under isothermal conditions.

AIM OF THE STUDY

To validate a LAMP-specific protocol for detection of Toxoplasma DNA using dried blood spots (DBS) from mice experimentally infected with the cystogenic Toxoplasma ME-49 strain.

METHODS

In this study, the target DNA fragment was the Toxoplasma 529-bp repeat element that exists in 200-300 copies per T. gondii genome. The sensitivity of both LAMP and conventional PCR techniques was estimated in DBS samples from experimental mice at 1-week and 8-weeks post-infection.

RESULTS

Out of 20 blood samples gathered on Whatman filter paper from mice at 1-week post-infection, 18 and 16 were positive by LAMP and conventional PCR, respectively. Neither techniques detected parasite DNA in blood at 8th week of infection.

CONCLUSION

Dried blood spots are easy source of material for molecular studies. LAMP assay proved higher sensitivity than the conventional PCR in detecting parasitemia in early infection with the cystogenic Toxoplasma strain.

Development of a copro-LAMP assay for detection of several species of Echinococcus granulosus sensu lato complex

Cystic echinococcosis represents a significant problem in human and animal health and constitutes one of the most severe Neglected Tropical Diseases prioritized by the World Health Organization. The etiological agent is the complex Echinococcus granulosus sensu lato (s. l.), composed of several species/genotypes. Diagnosis in the definitive host and molecular epidemiology studies are important points for cystic echinococcosis control. Here we developed a new copro-LAMP assay, LAMP EGSL, for diagnosis in the definitive host for simultaneous detection of Echinococcus granulosus sensu stricto (s. s.), Echinococcus ortleppi, and Echinococcus canadensis species. Also, the analytical sensitivity, specificity and plausibility of performance in a rural context of a previously reported species-specific LAMP reaction, was evaluated. Both reactions showed high analytical sensitivity values (10 fg-100 fg DNA) and did not show cross reaction with DNA from host or other helminthic parasites. LAMP EGSL was performed with samples from an endemic area. In addition, the alkaline hydrolysis of one E. granulosus s. s. adult parasite followed by specific LAMP to E. granulosus s. s. was performed in a laboratory with low resources from another cystic echinococcosis endemic area. The results obtained suggest that LAMP EGSL represents a potential tool for canine diagnosis that could be useful for cystic echinococcosis control programs. In addition, we showed that LAMP reaction for E. granulous s. s., E. ortleppi and E. canadensis specific detection, could be useful for molecular epidemiology studies applicable to the definitive host. Both reactions were performed in endemic, rural areas without sophisticated equipment.

Particle Diffusometry: An Optical Detection Method for Vibrio cholerae Presence in Environmental Water Samples

There is a need for a rapid, robust, and sensitive biosensor to identify low concentrations of pathogens in their native sample matrix without enrichment or purification. Nucleic acid-based detection methods are widely accepted as the gold standard in diagnostics, but robust detection of low concentrations of pathogens remains challenging. Amplified nucleic acids produce more viscous solutions, which can be measured by combining these products with fluorescent particles and measuring the change in the particle diffusion coefficient using a technique known as particle diffusometry. Here, we utilize Vibrio cholerae (V. cholerae) as a proof-of-concept for our detection system due to its inherently low concentration in environmental water samples. We demonstrate that particle diffusometry can be used to detect down to 1 V. cholerae cell in molecular-grade water in 20 minutes and 10 V. cholerae cells in pond water in just 35 minutes in 25 µL reaction volumes. The detection limit in pond water is environmentally relevant and does not require any enrichment or sample preparation steps. Particle diffusometry is 10-fold more sensitive than current gold standard fluorescence detection of nucleic acid amplification. Therefore, this novel measurement technique is a promising approach to detect low levels of pathogens in their native environments.

Diagnosis and control of chicken coccidiosis: a recent update

Coccidiosis is a deadly disease that hampers chicken's productivity and welfare. Thus, the disease is a major menace to the global poultry industry. Coccidiosis which is caused by the apicomplexan parasite of the genus Eimeria has seven known species which affect the different parts of the intestinal tract of chickens. The disease which occurs by ingestion of sporulated oocyst has been associated with poor poultry management system. Mixed infection among the species of this parasite contributes to both pathogenicity and misdiagnosis of the disease. A progress in identification and diagnosis approach which cuts across pathological, morphological and molecular has been reported for this parasite. Control measures which include anticoccidial drugs, vaccines and natural products have dominated literature for this disease. However, the emergence of genetic and antigenic diversity with implication on resistance to anticoccidials among different strains of Eimeria parasite has generated concerns on the effectiveness of the current anticoccidial vaccines. A new look on the control strategy therefore becomes imperative. This study reviews the current trends on the identification and control of chicken coccidiosis with focus on (1) Avian coccidiosis (2) Epidemiology of chicken coccidiosis (3) Eimeria parasite and distribution in poultry (4) Diagnosis of Eimeria parasite (5) Control measures of coccidiosis (6) Threats posed by genetic and antigenic diversity of Eimeria parasite on coccidiosis control. Genomic study on diversity of Eimeria parasite becomes imperative for effective vaccine design against coccidiosis.

Development of loop-mediated isothermal amplification (LAMP) assay for detection of Hepatozoon canis infection in dogs

The laboratory diagnosis of canine hepatozoonosis, caused by Hepatozoon canis is tedious, especially in chronic and latent infections. In the present investigation, a loop mediated isothermal amplification (LAMP) assay was developed and standardized targeting the partial 18S rRNA gene (GenBank accession no. KU096058). The LAMP primers specifically amplified H. canis DNA, whereas no amplification was detected in DNA samples from dogs infected with Babesia vogeli, B. gibsoni, Ehrlichia canis and Trypanosoma evansi, and no amplification was observed in DNA samples from H. canis-free dogs. The threshold sensitivity level of the assay was determined to be 15 fg of genomic DNA of H. canis. Furthermore, evaluation of blood samples collected from 250 dogs presented at Small Animal Clinics, Teaching Veterinary Clinical Complex, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab (India) was carried out for the presence of H. canis by microscopy, 18S PCR assay and LAMP assay. Of the total samples subjected to these tests, LAMP detected H. canis in 75 samples, while 18S PCR and microscopy detected H. canis in 28 and 9 samples, respectively. The present investigation has developed, for the first time, a highly sensitive, specific and rapid LAMP assay for the detection of H. canis, which has practical applications for the screening of field samples.

Validation of SYBR green I based closed tube loop mediated isothermal amplification (LAMP) assay and simplified direct-blood-lysis (DBL)-LAMP assay for diagnosis of visceral leishmaniasis (VL)

Background

The World Health Organization has targeted elimination of visceral leishmaniasis (VL) in the Indian subcontinent (ISC) by 2020. Despite distinctive decline seen in the number of VL cases in ISC, there is still a quest for development of a diagnostic test which has the utility for detection of active infection and relapse cases and as a test of cure. The present study validated the sensitivity and specificity of SYBR Green I based closed tube LAMP assay reported by us for diagnosis of VL.

Methodology

The validation study was carried out at two endemic sites in India, located at Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna and Institute of Medical Sciences (IMS), Banaras Hindu University (BHU), Varanasi. Standard operating protocols were provided at the two sites for applying LAMP assay on confirmed VL cases. The diagnostic accuracy of LAMP assay was evaluated by Receiver operator curve (ROC) analysis. Furthermore, a simplified LAMP assay based on direct blood lysis, DBL-LAMP, was developed and verified for its diagnostic accuracy.

Principal findings

A total of 267 eligible participants were included in the study which comprised of 179 VL cases and 88 controls. Sensitivity and specificity of the LAMP assay were 98.32% (95% C.I– 95.2–99.7%) and 96.59% (95% C.I.-90.4–99.3%), respectively. ROC curve analysis depicted no significant difference between area under curve (AUC_ROC) for LAMP assay and rK39 RDT, indicative of LAMP as an excellent diagnostic test. DBL-LAMP assay, performed on 67 VL and 100 control samples, yielded a sensitivity of 93.05% (95% C.I- 84.75–97%) and specificity of 100% (95% C.I.- 96.30–100%).

Conclusions/Significance

The validated closed tube LAMP for diagnosis of VL will provide impetus to the ongoing VL elimination programme in ISC. The assay based on direct blood lysis promotes its scope for application in field settings by further reducing time and cost.

Definitive diagnosis of visceral leishmaniasis(VL) by demonstration of amastigotes by microscopy is invasive and risky. Serology based diagnosis using rK39 rapid diagnostic test(RDT) has excellent sensitivity of~97% when combined with clinical symptoms but is inconclusive for detection of active infection and relapses due to persistence of anti-leishmanial antibodies. The developed SYBR Green I based closed tube LAMP assay overcomes these constraints and further, direct blood lysis (DBL)-LAMP, makes it more suitable for field application. The study involved validation of LAMP assay at two endemic sites in India, on a total of 179 VL patients confirmed by rK39 RDT and/ or microscopy and 88 controls. The assay was highly sensitive (98.32%) and specific (96.59%). Further, DBL-LAMP assay yielded a sensitivity and specificity of 93.05% and 100%, respectively. In conclusion, the study has validated the field potential of LAMP assay for diagnosis of VL which will provide momentum to ongoing VL elimination in the Indian subcontinent (ISC).

Molecular surveillance of Cryptosporidium and Giardia duodenalis in sludge and spent filter backwash water of a water treatment plant

The purpose of this study was to monitor the presence of Cryptosporidium spp. and Giardia duodenalis in a water treatment plant (WTP) using settling sludge and backwash water (BW) samples in previous and post the deflocculation of polyaluminium chloride (PAC) flacks. Eleven collections were performed. BW and settling sludge (SSF) were concentrated by calcium carbonate flocculation, and another aliquot of settling sludge (SSC) by centrifugation. The samples were divided as follows: Group A, containing 33 samples without degradation of PAC flakes, and Group B, with degradation by alkalinization with 10 M NaOH. Sample DNA was extracted with a commercial kit, and nested polymerase chain reaction (PCR) was used to detect Cryptosporidium and G. duodenalis. All samples from Group A were negative for Cryptosporidium spp., and 6.1% (2/33) were positive for G. duodenalis in SSC samples. While the absence of Cryptosporidium may be due to a low contamination level of the water resource, the presence of G. duodenalis indicates contamination of the raw water. The detection of G. duodenalis in SSC samples indicates that this detection method was the most effective. The 33 samples from Group B were negative for both protozoa, probably due to the presence of aluminium and humic substances.

Methods for the detection of Cryptosporidium and Giardia: From microscopy to nucleic acid based tools in clinical and environmental regimes

The detection and characterization of genotypes and sub genotypes of Cryptosporidium and Giardia is essential for their enumeration, surveillance, prevention, and control. Different diagnostic methods are available for the analysis of Cryptosporidium and Giardia including conventional phenotypic tools that face major limitations in the specific diagnosis of these protozoan parasites. The substantial advancement in the development of genetic signature based molecular tools for the quantification, diagnosis and genetic variation analysis has increased the understanding of the epidemiology and preventive measures of related infections. The conventional methods such as microscopy, antibody and enzyme based approaches, offer better detection results when combined with advanced molecular methods. Gene based approaches increase the precision of identification, for example, many signatures detected in environmental matrices represent species/genotype that are not infectious to humans. This review summarizes the available methods and the advantages and limitations of advance detection techniques like nucleic acid-based approaches for the detection of viable oocysts and cysts of Cryptosporidium and Giardia along with the conventional and widely accepted detection techniques like microscopy, antibody and enzyme based ones. This technical article also encourages the wide application of molecular methods in genetic characterization of distinct species of Cryptosporidium and Giardia, to adopt necessary preventive measures with reliable identification and mapping the source of contamination.

Comparison of current methods used to detect Cryptosporidium oocysts in stools

In this review all of the methods that are currently in use for the investigation of Cryptosporidium in stool material are highlighted and critically discussed. It appears that more qualifications and background knowledge in this field regarding the diagnosis of the Cryptosporidium parasite is required. Furthermore, there is no standardization for the protocols that are commonly used to either detect oocysts in faeces or to diagnose the Cryptosporidium infection. It is therefore necessary to initiate further education and research that will assist in improving the accuracy of the diagnosis of Cryptosporidium oocysts in the faecal micro-cosmos. Where ambient concentrations of oocysts are low in stool material, detection becomes a formidable task. Procedures for ring tests and the standardization of multi-laboratory testing are recommended. It is also necessary to enhance the routine surveillance capacity of cryptosporidiosis and to improve the safety against it, considering the fact that this disease is under diagnosed and under reported. This review is intended to stimulate research that could lead to future improvements and further developments in monitoring the diagnostic methodologies that will assist in harmonizing Cryptosporidium oocysts in stool diagnosis.

Lateral Flow Loop-Mediated Isothermal Amplification Test with Stem Primers: Detection of Cryptosporidium Species in Kenyan Children Presenting with Diarrhea

Background. Cryptosporidium is a protozoan parasite and a major cause of diarrhea in children and immunocompromised patients. Current diagnostic methods for cryptosporidiosis such as microscopy have low sensitivity while techniques such as PCR indicate higher sensitivity levels but are seldom used in developing countries due to their associated cost. A loop-mediated isothermal amplification (LAMP) technique, a method with shorter time to result and with equal or higher sensitivity compared to PCR, has been developed and applied in the detection of Cryptosporidium species. The test has a detection limit of 10 pg/µl (~100 oocysts/ml) indicating a need for more sensitive diagnostic tools. This study developed a more sensitive lateral flow dipstick (LFD) LAMP test based on SAM-1 gene and with the addition of a second set of reaction accelerating primers (stem primers). Results. The stem LFD LAMP test showed analytical sensitivity of 10 oocysts/ml compared to 100 oocysts/ml (10 pg/ul) for each of the SAM-1 LAMP test and nested PCR. The stem LFD LAMP and nested PCR detected 29/39 and 25/39 positive samples of previously identified C. parvum and C. hominis DNA, respectively. The SAM-1 LAMP detected 27/39. On detection of Cryptosporidium DNA in 67 clinical samples, the stem LFD LAMP detected 16 samples and SAM-2 LAMP 14 and nested PCR identified 11. Preheating the templates increased detection by stem LFD LAMP to 19 samples. Time to results from master mix preparation step took ~80 minutes. The test was specific, and no cross-amplification was recorded with nontarget DNA. Conclusion. The developed stem LFD LAMP test is an appropriate method for the detection of C. hominis, C. parvum, and C. meleagridis DNA in human stool samples. It can be used in algorithm with other diagnostic tests and may offer promise as an effective diagnostic tool in the control of cryptosporidiosis.

An overview of methods/techniques for the detection of Cryptosporidium in food samples

Cryptosporidium is one of the most important parasitic protozoa of concern within the food production industry, worldwide. This review describes the evolution and its development, and it monitors the methodology that has been used for Cryptosporidium in food material since 1984, when the first publication appeared regarding the detection of Cryptosporidium parvum in food materials. The methods that are currently being used for the detection of Cryptosporidium oocysts in food material (mainly vegetables) and all of the other available published methods are discussed in this review. Generating more consistent and reliable data should lead to a better understanding of the occurrence, transport and fate of the oocysts in food material. Improvements in monitoring and developing effective methodology, along with food security, offer more practical possibilities for both the developed and developing worlds.

Advancements in Parasite Diagnosis and Challenges in the Management of Parasitic Infections: A Mini Review

Intestinal parasitic infections (IPIs) remain a widespread public health concern causing severe implications in both developed and developing countries. Globally, numerous studies have been carried out ranging from various communities to schoolchildren as well as indigenous communities. The infections are commonly caused by helminths (e.g. Ascaris lumbricoides, Trichuris trichiura and hookworm) and protozoa (e.g. Blastocystis hominis, Cryptosporidium sp., Entamoeba histolytica and Giardia duodenalis). Poor sanitation and poverty are some of the factors associated with IPIs. With the ever-increasing impact of IPIs, newer detection approaches have been developed and studied. The efficacy of diagnostic method is crucial to give an accurate identification of these parasites. Recent developments of diagnostic tools such as serology- and molecular-based assays are assisting the conventional method of microscopy in detecting and further confirming current or past infections and the specific species of parasites. Ongoing investigations in parasitic infections using these advanced tools will provide useful information that will enable the evaluation of the effectiveness of the current control program and thus, assist future planning for improved strategies in eradicating these parasitic infections.

Laboratory diagnosis of cryptosporidiosis

Cryptosporidiosis is a major etiology of persistent and chronic diarrhea in children and immunocompromised patients. In addition, it is also one of the important pathogens causing zoonotic or waterborne outbreaks. A number of conventional and molecular tests are available, but each test is riddled with few limitations. Further, there is a need to develop point of care tests and multiplexed tests for simultaneous detection of multiple pathogens.

An advanced uracil DNA glycosylase-supplemented loop-mediated isothermal amplification (UDG-LAMP) technique used in the sensitive and specific detection of Cryptosporidium parvum, Cryptosporidium hominis, and Cryptosporidium meleagridis in AIDS patients

The rapid and accurate detection of Cryptosporidium spp. is critically important for the prevention and timely treatment of cryptosporidiosis in AIDS patients (APs). This study was conducted to examine a UDG-LAMP technique for the first time to diagnose cryptosporidiosis in APs. After collecting demographic and clinical data, three stool samples were collected from the participants (120 volunteering APs). The microscopic examination of stained smears using the acid-fast method and the UDG-LAMP assay were performed for each sample. 10% of APs were infected with Cryptosporidium spp. The number of detected cryptosporidiosis cases using the acid-fast staining and UDG-LAMP methods were significantly different (P < 0.001). Diarrhea and weight loss were found to be significantly associated with cryptosporidiosis in patients (P < 0.05). The pretreatment of LAMP reagents with UDG successfully eliminated the likelihood of product re-amplification remaining from previous reactions. The UDG-LAMP technique could detect cryptosporidiosis in APs with high sensitivity and rapidity without carryover contamination.

DNA detection of Trypanosoma evansi: Diagnostic validity of a new assay based on loop-mediated isothermal amplification (LAMP)

Trypanosoma evansi (T. evansi) is the most widely spread pathogenic trypanosome in the world. The control of trypanosomiasis depends on accurate diagnosis and effective treatment. Focusing on the presence of T. evansi in Asia, we developed a detection assay based on tracing phosphate ions (Pi) generated during LAMP targeting the variant surface glycoprotein (VSG) gene of Rode Trypanozoon antigenic type 1.2 (RoTat 1.2 VSG). The diagnostic potential as well as the use of the assay as a test-of-cure method after berenil treatment, was assessed in mice at different time points of infection. In addition, 67 buffalo blood collected from Tongling county, Anhui province, as well as 42 cattle sera from the Shanghai area, were used to evaluate the diagnostic validity of the test. The detection limit of the novel LAMP assay was determined to be as low as 1 fg of T. evansi DNA, while the reaction time for the test was only 30min. Hence it outperforms both microscopy and PCR. In the test-of-cure assessment, successful berenil mediated cure could be confirmed within 48h after treatment. This offers a tremendous advantage over conventional antibody-based diagnostic tools in which successful cure only can be confirmed after months. In the cattle and buffalo screening, the LAMP was able to detect a false-negative determined sample, wrongly classified in a conventional microscopy and PCR screening. Finally, no cross-reactivity was observed with other zoonotic parasites, such as T. evansi type B, T. congolense, T. brucei, Schistosoma japonicum, Plasmodium falciparum, Leishmania donovani, Toxoplasma gondii and Angiostrongylus cantonensis. We conclude that the novel LAMP assay is sensitive, specific and convenient for field use, particularly in areas where infection incidence has become extremely low. The LAMP assay could be used as a tool for trypanosomiasis control and elimination strategies in areas where T. evansi Type A infections are causing a threat to livestock farming.

A loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Enterococcus spp. in water

Faecal pollution of water and the resulting potential presence of human enteric pathogens is a predominant threat to public health. Microbiological water quality can be assessed by the detection of standard faecal indicator bacteria (SFIB) such as E. coli or certain Enterococcus species. In recent years, isothermal amplification methods have become a useful alternative to polymerase chain reaction (PCR), allowing molecular diagnostics with simple or no instrumentation. In this study, a novel screening method for the molecular detection of Enterococcus spp. by loop-mediated isothermal amplification (LAMP) is described. A set of six specific LAMP primers was designed to amplify a diagnostic fragment of the Enterococcus 23S rRNA gene, which is present in several enterococcal species targeted by quantitative PCR (qPCR), which is the standard technique recommended by the US Environmental Protection Agency. Sensitivity and specificity tests were performed using a set of 30 Enterococcus and non-target bacterial reference strains. It is shown that LAMP is equally sensitive and even more specific than the qPCR assay. A dilution series of Enterococcus faecalis DNA revealed that the LAMP method can reliably detect 130 DNA target copies per reaction within 45 min. Additionally, enterococci isolated from Austrian surface waterbodies, as well as a set of DNA extracts from environmental waters, were tested. Contingency analysis demonstrated a highly significant correlation between the results of the developed LAMP assay and the reference qPCR method. Furthermore, a simple staining procedure with a fluorescence dye demonstrated the identification of amplified products by eye. In conclusion, this method is an important component for the efficient screening and testing of water samples in low-resource settings lacking sophisticated laboratory equipment and highly trained personnel, requiring only a simple heating block.

Improvement and Evaluation of Loop-Mediated Isothermal Amplification for Rapid Detection of Toxoplasma gondii Infection in Human Blood Samples

Loop-mediated isothermal amplification (LAMP), an attractive DNA amplification method, was developed as a valuable tool for the rapid detection of Toxoplasma gondii. In this study, species-specific LAMP primers were designed by targeting the AF146527 sequence, which was a conserved sequence of 200- to 300-fold repetitive 529 bp fragment of T.gondii. LAMP reaction system was optimized so that it could detect the minimal DNA sample such as a single tachyzoite or 10 copies of recombinant plasmid. No cross-reactivity was found when using DNA from other parasites as templates. Subsequently, a total of 200 human blood samples were directly investigated by two diagnostic methods, LAMP and conventional PCR. Fourteen of 200 (7%) samples were positive for Toxoplasma by LAMP (the primers developed in this study), whereas only 5 of 200 (2.5%) were proved positive by conventional PCR. The procedure of the LAMP assay was very simple, as the reaction would be carried out in a single tube under isothermal conditions at 64°C and the result would be read out with 1 h (as early as 35 min with loop primers). Thus, this method has the advantages of rapid amplification, simple operation, and easy detection and would be useful for rapid and reliable clinical diagnosis of acute toxoplasmosis, especially in developing countries.

Genotyping of Cryptosporidium spp. in environmental water in Turkey

This research was undertaken to study the molecular detection and characterization of Cryptosporidium spp. in environmental water sources at Samsun and Giresun Provinces of The Black Sea in Turkey. Two-hundred forty and one-hundred eighty environmental samples were collected from a total of twenty and twenty-five sampling sites of Giresun and Samsun Provinces. One hundred twenty untreated drinking water samples were also detected for Cryptosporidium spp. in both investigated areas. 101 (%42), 92 (%38.3) of 240 and 74 (41.1%), 70 (38.8%) of 180 environmental samples have been found positive for Cryptosporidium spp. by Loop mediated isothermal amplification (LAMP) targeting the S-adenosyl-L-methionine synthetase (SAM) gene and nested PCR targeting small subunit (SSU)rRNA gene in Samsun and Giresun Provinces, respectively. Of the tested untreated drinking water samples collected from the investigated area, one sample was positive for Cryptosporidium spp. Six and twelve samples were clearly sequenced for the Cryptosporidium (SSU)rRNA gene among the highest positive samples selected from each of the twenty and twenty-five sampling sites of Giresun and Samsun Provinces, respectively. Genetic characterization of Cryptosporidium isolates from water samples represented Cryptosporidium bovis for five samples, Cryptosporidium parvum for six samples and one sample for Cryptosporidium felis in Samsun Province, where C. parvum for five samples and C. bovis for one sample were sequenced in Giresun Province. According to accessible information sources, this is the first research about genotyping of Cryptosporidium spp. in water samples collected from Samsun and Giresun Provinces of Turkey.

Development of a Loop Mediated Isothermal Amplification for Diagnosis of Ascaris lumbricoides in Fecal Samples

Ascaris lumbricoides is a nematode parasite that causes the common tropical infection ascariasis in humans. It is also considered among the neglected tropical diseases. Diagnosis relies mainly on microscopy-based methods which are laborious, are limited by low sensitivity, and require high expertise. We have developed a loop mediated isothermal amplification (LAMP) for diagnosis of ascariasis in fecal samples, based on the first internal transcribed (ITS-1) spacer region of the ribosomal DNA. We used Primer Explorer V4 software to design primers. Ascaris adult and ova were obtained from naturally infected school children, whose parents/guardians gave consent for their participation in the study. Genomic DNA was extracted using alkaline lysis method and amplified by LAMP at 63°C for 45 minutes. LAMP products were visualized by naked eyes after adding SYBR Green dye and also on agarose gel. LAMP successfully and reliably detected Ascaris DNA from a single egg and in fecal samples. The assay specifically detected Ascaris DNA without amplifying DNA from ova of other parasites which commonly coexist with A. lumbricoides in feces. The developed LAMP assay has great potential for use in ascariasis diagnosis at the point of care and in low infection intensity situation that characterize control and elimination campaigns.

Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods

Eukaryotes are an important component of the human gut, and their relationship with the human host varies from parasitic to commensal. Understanding the diversity of human intestinal eukaryotes has important significance for human health. In the past few decades, most of the multitudes of techniques that are involved in the diagnosis of the eukaryotic population in the human intestinal tract were confined to pathological and parasitological aspects that mainly rely on traditionally based methods. However, development of culture-independent molecular techniques comprised of direct DNA extraction from faeces followed by sequencing, offer new opportunities to estimate the occurrence of eukaryotes in the human gut by providing data on the entire eukaryotic community, particularly not-yet-cultured or fastidious organisms. Further broad surveys of the eukaryotic communities in the gut based on high throughput tools such as next generation sequencing might lead to uncovering the real diversity of these ubiquitous organisms in the human intestinal tract and discovering the unrecognized roles of these eukaryotes in modulating the host immune system and inducing changes in host gut physiology and ecosystem.

Giardia and Cryptosporidium spp. dissemination during wastewater treatment and comparative detection via immunofluorescence assay (IFA), nested polymerase chain reaction (nested PCR) and loop mediated isothermal amplification (LAMP)

Environmental water samples from the Lower Rhine area in Germany were investigated via immunofluorescence assays (IFAs), nested polymerase chain reaction (nested PCR) and loop-mediated isothermal amplification (LAMP) to detect the presence of Giardia spp. (n=185) and Cryptosporidium spp. (n=227). The samples were concentrated through filtration or flocculation, and oocysts were purified via centrifugation through a sucrose density gradient. For all samples, IFA was performed first, followed by DNA extraction for the nested PCR and LAMP assays. Giardia cysts were detected in 105 samples (56.8%) by IFA, 62 samples (33.5%) by nested PCR and 79 samples (42.7%) by LAMP. Cryptosporidium spp. were detected in 69 samples (30.4%) by IFA, 95 samples (41.9%) by nested PCR and 99 samples (43.6%) by LAMP. According to these results, the three detection methods are complementary for monitoring Giardia and Cryptosporidium in environmental waters.

Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9

Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures.

Loop-mediated isothermal amplification (LAMP) assays for the species-specific detection of Eimeria that infect chickens

Eimeria species parasites, protozoa which cause the enteric disease coccidiosis, pose a serious threat to the production and welfare of chickens. In the absence of effective control clinical coccidiosis can be devastating. Resistance to the chemoprophylactics frequently used to control Eimeria is common and sub-clinical infection is widespread, influencing feed conversion ratios and susceptibility to other pathogens such as Clostridium perfringens. Despite the availability of polymerase chain reaction (PCR)-based tools, diagnosis of Eimeria infection still relies almost entirely on traditional approaches such as lesion scoring and oocyst morphology, but neither is straightforward. Limitations of the existing molecular tools include the requirement for specialist equipment and difficulties accessing DNA as template. In response a simple field DNA preparation protocol and a panel of species-specific loop-mediated isothermal amplification (LAMP) assays have been developed for the seven Eimeria recognised to infect the chicken. We now provide a detailed protocol describing the preparation of genomic DNA from intestinal tissue collected post-mortem, followed by setup and readout of the LAMP assays. Eimeria species-specific LAMP can be used to monitor parasite occurrence, assessing the efficacy of a farm's anticoccidial strategy, and to diagnose sub-clinical infection or clinical disease with particular value when expert surveillance is unavailable.

Development of loop-mediated isothermal amplification (LAMP) for detection of Babesia gibsoni infection in dogs

Diagnosis of canine babesiosis, caused by Babesia gibsoni is difficult, especially in chronically infected dogs. A loop mediated isothermal amplification (LAMP) assay was developed and standardized by using four oligonucleotide primers targeting the hypervariable region of 18S rRNA gene (GenBank Acc. no. KC461261). The primers specifically amplified B. gibsoni DNA, while no amplification was detected with DNA from non-infected dogs as well as from dogs infected with Babesia canis vogeli, Hepatozoon canis, Ehrlichia canis and Trypanosoma evansi. The assay could detect 1.35 × 10(-7) parasitaemia and 10(-4) dilution of recombinant plasmid, equivalent to 12 pg of target DNA. All the samples were tested by nested PCR as well as LAMP assay. LAMP was found to be 10 times more sensitive than nested PCR targeting the same gene. Out of 75 suspected field samples, collected from different parts of the country, LAMP could detect B. gibsoni in 43 samples, while nested PCR and microscopy could detect 37 and 23 samples, respectively. High sensitivity, specificity and rapidity of LAMP assay may be exploited for screening large number of samples in a field setting.

Diagnosis of Parasitic Infections

Methods for the diagnosis of parasitic infections have stagnated in the past three decades. Labor-intensive methods such as microscopy still remain the mainstay of several diagnostic laboratories. There is a need for more rapid tests that do not sacrifice sensitivity and that can be used in both clinical settings as well as in poor resource field settings. The fields of diagnostic medical parasitology, treatment, and vaccines are undergoing dramatic change. In recent years, there has been tremendous effort to focus research on the development of newer diagnostic methods focusing on serological, molecular, and proteomic approaches. This article examines the various diagnostic tools that are being used in clinical laboratories, optimized in reference laboratories, and employed in mass screening programs.

Molecular diagnosis of infectious diarrhea: focus on enteric protozoa

Robust detection of enteric protozoa is a critical step toward determining the etiology of diarrhea. Widespread use of conventional microscopy, culturing and antigen detection in both industrial and developing countries is limited by relatively low sensitivity and specificity. Refinements of these conventional approaches that reduce turnaround time and instrumentation have yielded strong alternatives for clinical and research use. However, advances in molecular diagnostics for protozoal, bacterial, viral and helminth infections offer significant advantages in studies seeking to understand pathogenesis, transmission and long-term consequences of infectious diarrhea. Quantitation of enteropathogen burden and highly multiplexed platforms for molecular detection dramatically improve predictive power in emerging models of diarrheal etiology, while eliminating the expense of multiple tests.

Techniques for the diagnosis of Fasciola infections in animals: room for improvement

The common liver fluke, Fasciola hepatica, causes fascioliasis, a significant disease in mammals, including livestock, wildlife and humans, with a major socioeconomic impact worldwide. In spite of its impact, and some advances towards the development of vaccines and new therapeutic agents, limited attention has been paid to the need for practical and reliable methods for the diagnosis of infection or disease. Accurate diagnosis is central to effective control, particularly given an emerging problem with drug resistance in F. hepatica. Traditional coprological techniques have been widely used, but are often unreliable. Although there have been some advances in establishing immunologic techniques, these tools can suffer from a lack of diagnostic specificity and/or sensitivity. Nonetheless, antigen detection tests seem to have considerable potential, but have not yet been adequately evaluated in the field. Moreover, advanced nucleic acid-based methods appear to offer the most promise for the diagnosis of current infection. This chapter (i) provides a brief account of the biology and significance of F. hepatica/fascioliasis, (ii) describes key techniques currently in use, (iii) compares their advantages/disadvantages and (iv) reviews polymerase chain reaction-based methods for specific diagnosis and/or the genetic characterization of Fasciola species.