Sensitive and specific detection of Cryptosporidium species in PCR-negative samples by loop-mediated isothermal DNA amplification and confirmation of generated LAMP products by sequencing

Strategies for diagnosing Nosema bombycis (Microsporidia: Nosematidae); the agent of pebrine disease

Pebrine disease, caused by Nosema bombycis (N. bombycis), is the most important pathogen known to the silk industry. Historical evidence from several countries shows that the outbreaks of pebrine disease have largely caused the decline of the sericulture industry. Prevention is the first line to combat pebrine as a deadly disease in silkworm; however, no effective treatment has yet been presented to treat the disease. Many different methods have been used for detection of pebrine disease agent. This review focuses on the explanation and comparison of these methods, and describes their advantages and/or disadvantages. Also, it highlights the ongoing advances in diagnostic methods for N. bombycis that could enable efforts to halt this microsporidia infection. The detection methods are categorized as microscopic, immunological and nucleic acid-based approaches, each with priorities over the other methods; however, the suitability of each method depends on the available equipment in the laboratory, the mass of infection, and the speed and sensitivity of detection. The accessibility and economic efficiency are compared as well as the speed and the sensitivity for each method. Although, the light microscopy is the most common method for detection of N. bombycis, qPCR is the most preferred method for large data based on speed and sensitivity as well as early detection ability.

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.

Development of Simplified Recombinase Polymerase Amplification Assay for Rapid and Robust Detection of Citrus Yellow Vein Clearing Virus

Citrus is an economically important fruit crop, belongs to family Rutaceae, cultivated commercially in over 130 countries, which holds a leading profitable position in the international market. The most important citrus varieties are mandarins, oranges, lemons, sweet limes, grapefruits and pomelos. Citrus yellow vein clearing virus (CYVCV) is an important graft transmissible plant pathogen known to reduce productivity of citrus fruits due to its predominant association and widespread occurrence. Requirement of fast, reliable, efficient & economical CYVCV indexing assay is a prerequisite for production of healthy planting material. Currently, nucleic acid isolation and thermal cycler-based assay available for CYVCV indexing is a cumbersome lab intensive method. The present study was undertaken to develop and validate reverse transcription-recombinase polymerase amplification (RT-RPA) assay requiring no tedious RNA isolation, separate cDNA synthesis and costlier instrument like thermo-cycler. Optimized RT-RPA assay was able to amplify CYVCV up to 10-7 dilution (equivalent to 0.1 pg/μl) with the prepared templates of both RNA and crude saps and showed higher sensitivity in detection of CYVCV infection in field samples as compared to the conventional RT-PCR. Developed RT-RPA assay showed high specificity without any cross-reaction with other citrus pathogens (Indian citrus ringspot virus, citrus yellow mosaic virus, citrus tristeza virus, citrus exocortis viroid and huanglongbing). RT-RPA using crude leaf sap as template is quite simple, robust, highly sensitive, time and cost effective; therefore, it can be used in resource constrained laboratories as screening tool, for field surveys and on-site testing programs in farms, nurseries and biosecurity. Present study, first time reports the development, optimization and validation of crude sap-based RT-RPA assay for the detection of CYVCV infection in citrus plants namely; Kinnow mandarin, Mosambi and Grape fruit.

Parallel detection of multiple zoonotic parasites using a real-time fluorogenic loop-mediated isothermal amplification-based quadruple-sample microfluidic chip

Zoonotic parasites pose significant health risks globally. In the present study, we combined a microfluidic chip with loop-mediated isothermal amplification (on-chip LAMP) to detect five zoonotic parasites: Toxoplasma gondii, Cryptosporidium parvum, Cryptosporidium hominis, Clonorchis sinensis, and Taenia solium. This method enabled the simultaneous parallel analysis of five genetic markers from a maximum of four samples per chip. The on-chip LAMP assay was conducted in a highly automated format via the addition (by pipetting) of each sample in a single operation. The reaction was performed in volumes as low as 5 μL at a temperature of 65°C for 60 min, achieving limits of detection ranging from 10-2 to 10-3 pg./μL of recombinant plasmid DNA. All the time-to-positive values were less than 40 min, and almost all the coefficients of variation were less than 10%, even when using limit of detection concentrations for multiple pathogens, indicating robust reproducibility among replicates. The clinical sensitivity and specificity for detecting 135 field samples were 98.08 and 97.59%, respectively, compared with traditional biological methods, indicating good applicability in the detection of field samples. This on-chip LAMP assay allows for low reagent consumption, ease of operation, and multiple analyses of samples and genetic targets, and is applicable for on-site detection and the routine monitoring of multiple zoonotic parasites.

Loop-mediated isothermal amplification identifies nematode Leidynema in the hindgut of non-pest cockroach

Cockroach microbiome studies generally focus on pest cockroach species belonging to the Blattidae and Ectobiidae families. There are no reports characterizing the gut microbiome of non-pest cockroach species Blaberus discoidalis (family Blaberidae), which is commonly used as a food source for insectivorous animals. We discovered the parasitic nematode Leidynema appendiculata in the B. discoidalis hindgut during initial work characterizing the gut microbiome of this organism. To determine the proportion of the B. discoidalis colony that was colonized by L. appendiculata, 28 S rDNA was amplified using two Methods: endpoint polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP). B. discoidalis colonies were raised on three diet types (control, high fibre, and high fat and salt) for 21 days before dissection. Each individual was sexed during dissection to identify potential sex-based effects of colonization. Data collected were analysed to determine if diet and sex impacted parasite colonization patterns. LAMP detected a higher proportion of parasite positive samples when compared to endpoint PCR. No sex- or diet-based differences in L. appendiculata colonization were found. This study adds to the limited existing knowledge of the B. discoidalis gut microbiome.

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.

Molecular evaluation of Cryptosporidium spp. among breeding calves of Lorestan province Western Iran

BACKGROUND

Cryptosporidium spp. are opportunistic intestinal protozoans with global distribution and are of great importance as zoonotic protozoans are common to humans and domestic animals, including cattle and calves. Identification and detection of parasite species using precise methods including molecular methods can be an effective step in treating and controlling parasites.

OBJECTIVES

This study aimed to investigate the prevalence of Cryptosporidium among breeding calves of Khorramabad city, Lorestan province, Western Iran, using PCR.

METHODS

The faecal samples were taken from 181 healthy and diarrhoeal calves and after the Ziehl Neelsen Acid-fast staining and microscopic evaluation, the genomic DNA was extracted for molecular evaluations. To detect Cryptosporidium species, specific primers targeting the SAM-1 gene of Cryptosporidium and a commercial master mix were used for PCR.

RESULTS

Out of 181 faecal samples of breeding calves in Khorramabad city, 9 samples (5%) were positive for Cryptosporidium spp. using the PCR method. Statistical analysis of the data showed that there was no significant statistical relationship between Cryptosporidium infection of the calves and variables of age, breed, type of water consumption, clinical signs of diarrhoea, and sampling location, while parasite infection had a significant relationship with calf gender so that all Cryptosporidium positive samples were from male calves (p ≤ 0.05).

CONCLUSIONS

Considering the presence of Cryptosporidium infection, the region's traditional grazing system, and the close relationship between livestock and humans, there is a possibility of human infection in the region. So preventive measures such as periodic animal testing with sensitive and accurate diagnostic techniques including PCR, pharmacological treatment of livestock, water hygiene and the use of industrial grazing instead of traditional grazing to improve the hygiene of food consumed by livestock are recommended.

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.

Optimization of a Loop-Mediated Isothermal Amplification Assay as a Point-of-Care Tool for the Detection of Wuchereria bancrofti in Human Blood in Tana River Delta, Kenya

INTRODUCTION

Accurate detection of filarial parasites in humans and vectors is essential for the implementation and evaluation of Global and National Programs to eliminate lymphatic filariasis. Immunological methods to detect infection are available; however, cross-reactivity issues have been reported in most of them. Nucleic acid-based molecular assays offer high levels of specificity and sensitivity and can be used to detect the infections.

METHODS

In this study, we evaluated loop-mediated isothermal amplification (LAMP) tests to amplify Wuchereria bancrofti DNA in patients' blood. The amplicons were tested by both pH-sensitive dyes for enhanced visual detection and agarose gel electrophoresis. A closed-tube LAMP assay was also evaluated. Cohen's Kappa statistics was used for statistical analysis of the assays. 125 patients consented for blood sampling which were used for clinical analysis of LAMP assays with the PCR method used as the "gold standard."

RESULTS

The sensitivity of the evaluated Wuchereria bancrofti LAMP was 92.3%, with a specificity of 97.3% and kappa statistics value of 0.84, which is in a strong agreement.

CONCLUSION

In this study, LAMP assays coupled with fluorescence dye detection have been found to be suitable for diagnosis and monitoring of Wuchereria bancrofti infections in the Kenyan population.

Rapid detection of Galba truncatula in water sources on pasture-land using loop-mediated isothermal amplification for control of trematode infections

BACKGROUND

Fascioliasis caused by the trematodes Fasciola hepatica and F. gigantica, is a global neglected zoonotic disease estimated to cost the livestock industry over €2.5 billion annually. Farm management measures and sustainable use of anthelmintics can, in principle, effectively control trematode infection in livestock and reduce the rate of developing anthelmintic resistance. Previously, we designed an environmental DNA (eDNA) assay to identify a common trematode intermediate host, the freshwater snail Galba truncatula, in water sources to measure specific trematode infection risk areas on pasture-land. To improve this procedure, we now report a loop-mediated isothermal amplification (LAMP) assay to identify G. truncatula eDNA.

METHODS

A LAMP assay was designed and optimised (e.g. temperature, time duration and primer concentration) to identify G. truncatula DNA. The ability of the LAMP assay to target G. truncatula DNA was identified, and LAMP assay limit of detection was investigated in comparison to conventional PCR. In the field, 48 water samples were collected from stream, ditch and water pool habitats in four locations at two Aberystwyth University farms over a seven week period to investigate the applicability of the LAMP assay for use on eDNA samples, in comparison to conventional PCR.

RESULTS

The LAMP assay delivered detectable results in 30 min at 63 °C. The assay discriminated between G. truncatula DNA and non-target DNA, presenting a level of DNA detection comparable to conventional PCR. No significant difference was found between the ability of the LAMP and PCR assay to identify G. truncatula eDNA in water samples. Kappa coefficient analysis revealed a moderate level of agreement between LAMP and PCR assays.

CONCLUSIONS

This study demonstrated that the LAMP assay can detect G. truncatula eDNA in a simple and rapid manner. The LAMP assay may become a valuable tool to determine optimum pasture management for trematode parasite control.

Loop-Mediated Isothermal Amplification (LAMP) Assay to Detect Toxoplasmosis in Schizophrenia Patients

Background

Toxoplasma gondii (T. gondii) causes an important parasitic infection known as toxoplasmosis, which is a globally distributed important zoonosis. One of the major serious characteristics of T. gondii is its ability to manipulate the behavior of intermediate hosts. We performed a cross-sectional study to determine toxoplasmosis in schizophrenic patients, as one of the major neuropsychiatric disorders, using loop-mediated isothermal amplification (LAMP) technic by targeting parasite B1 gene.

Methods

Blood samples were taken from 118 schizophrenic patients hospitalized in tow hospitals including Baharan, Clinic of Psychiatric Ali-ibn-Abi-Talib Hospital (in Zahedan City), and Amir-al Momenin Psychiatric Hospital (in Zabol City), Sistan and Baluchestan Province, southeast Iran in 2016. They were analyzed using LAMP, and compared with the previous data of nested-PCR and serology.

Results

Out of the 118 schizophrenic individuals, 56 patients (47.4%) were found to be infected with T. gondii. The diagnosis of toxoplasmosis was confirmed in 41 patients (34.7%) via the nested-PCR. The seroprevalence of toxoplasmosis in schizophrenic patients was 55.9% (66/118).

Conclusion

We found a high efficiency of LAMP method in identifying toxoplasmosis and its high prevalence among schizophrenic patients. Our findings could provide viable offer implications for the prevention of schizophrenia.

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.

A portable detection assay for Apple stem pitting virus using reverse transcription-recombinase polymerase amplification

A molecular diagnostic assay for the rapid, sensitive and specific detection of Apple stem pitting virus (ASPV) in infected samples, utilizing reverse transcription-recombinase polymerase amplification (RT-RPA) at an isothermal constant temperature of 42 °C and the designed target-specific primers, was developed. The RT-RPA assay was able to be used in ASPV-infected leaves, rootstocks and fruits. Sensitivity tests, using ASPV transcripts, showed that the RT-RPA with the ASPV-specific primers was more sensitive than the conventional RT-PCR, with a detection limit of 1 fg/μL of RNA. In addition, the reaction time for the amplification of ASPV was shortened to as little as 1 min. The assay was highly specific and did not give a positive reaction to other viruses infecting pears. Moreover, the amplified genomic fragment of ASPV produced by the assay could be determined within 4 min using a portable capillary gel electrophoresis system. The entire process, excluding the extraction of total RNA, could be completed in 5 min using portable equipment in the field. This is the first report of utilizing an RT-RPA assay to detect a pear tree virus and the assay could be used both in the laboratory and in the field for ASPV detection.

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.

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.

Development of a rapid loop-mediated isothermal amplification assay for diagnosis and assessment of cure of Leishmania infection

Background

Leishmaniasis is a spectrum of diseases with great relevance to public health. Conventional diagnostic methods are time consuming, needing trained personnel. A robust, rapid and cost effective diagnostic test is warranted for on-time diagnosis and field application.

Methods

We have developed a loop mediated isothermal amplification (LAMP) assay with primers (n = 6) based on Leishmania donovani kDNA for detection of Leishmania infection, using a closed tube to prevent cross-contamination. The assay was used to detect Leishmania infection in biological samples obtained from patients of visceral leishmaniasis (VL), post kala-azar dermal leishmaniasis (PKDL) and cutaneous leishmaniasis (CL).

Results

The assay was positive for L. donovani, L. tropica and L. major parasites, with the highest sensitivity towards L. donovani (1 fg DNA). The high sensitivity of the assay for detection of L. donovani was reflected in its ability to detect parasite DNA within 30 min of amplification time with a threshold detection limit of ≥25 copies per reaction. The assay detected parasite in 64 of 66 VL blood samples (sensitivity, 96.9%; 95% CI: 89.6-99.2%), 15 of 15 VL bone marrow aspirate samples (sensitivity, 100%; 95% CI:79.6-100%), 65 of 67 PKDL tissue biopsy samples (sensitivity, 97%; 95% CI:89.7-99.2%). The assay was evaluated in a few cases of CL wherein it was found positive in 8 of 10 tissue biopsies (sensitivity, 80%; 95% CI: 49-94.3%). The assay was negative in all control blood (n = 76) and tissue biopsy (n = 24) samples (specificity, 100%; 95% CI: 96.3-100%). Further, the assay was evaluated for its utility in assessment of cure in treated VL and PKDL patients. The assay detected parasite DNA in 2 of 20VL blood samples and 2 of 21 PKDL tissue samples. Out of 4 cases that were positive for parasite DNA at post treatment stage, 2 patients (1VL and 1 PKDL) returned with relapse.

Conclusions

The study demonstrated a Leishmania genus specific closed tube LAMP assay for reliable and rapid molecular diagnosis of VL and PKDL with potential for application in assessment of cure.

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.

Contribution of environmental media to cryptosporidiosis and giardiasis prevalence in Tehran: a focus on surface waters

The occurrences of Cryptosporidium and Giardia in surface sources of drinking water in Tehran were monitored, using US EPA method 1623.1. The prevalence ratios (PR) of positive samples among other media (animal's stools, vegetables, and human's stools) were also estimated from literature data. The density of Giardia and Cryptosporidium in water samples were 0.129 ± 0.069 cysts/L and 0.005 ± 0.002 oocysts/L, respectively. Estimated PR in vegetables, animal stools, surface waters, and human stools were 6.65, 20.42, 21.05, and 4.28 % for Cryptosporidium and 6.46, 17.13, 73.68, and 15.65 % for Giardia, respectively. These reveal the importance of surface waters' and animal stools' roles in the prevalence of cryptosporidiosis and giardiasis in Tehran's population. Giardia's prevalence in untreated surface waters in Tehran was found 3.5 times as much as Cryptosporidium while this found 2.3 times on a global scale. Moreover, the prevalence of giardiasis to cryptosporidiosis infections in Tehran's human population was 3.65. These values could be a clue to attribute the infections to the occurrence of parasites in surface waters. Significant (p < 0.05) associations were observed between rainfalls and presence of Giardia (r = 0.62) and Cryptosporidium (r = 0.60) in surface waters. In autumn, rainfalls can increase the parasites occurrences in surface waters. Significant (p < 0.05) difference on the density of parasites was found between some seasons using Kruskal-Wallis and multiple comparison tests. A significant correlation (r = 0.86) between Giardia and Cryptosporidium densities also confirms the common sources of pollution in surface waters. Findings suggest that untreated surface waters in Tehran may be a potential route of human exposure to protozoan parasites.

Validation of Romanowsky staining as a novel screening test for the detection of faecal cryptosporidial oocysts

Cryptosporidiosis is an emerging waterborne protozoan disease and one of the major causes of neonatal diarrhea in humans and animals. But the disease remains under diagnosed due to lack of availability of special stains in majority of laboratories at primary health centers. Therefore, it requires a rapid screening test for routine diagnosis in conventional laboratory set up. In this pursuit, the present study was planned. During this study, fecal samples from 100 representative animals randomly selected from 17 out breaks of bovine calf diarrhea, were stained with modified Ziehl Neelsen staining (mZN) and Leishman's stain to demonstrate cryptosporidial oocysts and for routine fecal examination, respectively. By mZN staining, 25 cases confirmed the presence of cryptosporidial oocysts. However, examination of Leishman's stained fecal smears revealed round hollow unstained bodies resembling cryptosporidia in 20 cases. Therefore, a comparative morphometric analysis was made between the two techniques to determine their relative efficacy in demonstrating cryptosporidia in the feces of affected animals. The analyses showed that the Leishman's stain can be effective in making a presumptive diagnosis of cryptosporidiosis with a little experience. Confirmation of cryptosporidiosis was done by histopathological examination of intestinal sections of calves died during these out breaks. The findings appear to have great clinical value for routine laboratory screening of fecal samples for cryptosporidiosis as conventional Romanowsky stains are readily available and used for multipurpose examination in most of the laboratories at grass root level. Perusal of literature proved this to be the first attempt at easy diagnostics for cryptosporidiosis.

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.

Cryptosporidium genotypes in children and calves living at the wildlife or livestock interface of the Kruger National Park, South Africa

Cryptosporidium infection is one of the most common causes of parasitic diarrhoea worldwide in cattle and humans. In developing countries, human cryptosporidiosis is most prevalent during early childhood and links between zoonotic infection and animal related activities have been demonstrated. This study investigated the prevalence and species/genotype distribution of Cryptosporidium among children (< 5 years) and calves (< 6 months) living in a rural farming area adjacent to the Kruger National Park in South Africa, where interactions between humans and wild and domestic animals are known to occur. Cryptosporidium oocysts were detected in 8/143 stool samples of children recruited within the hospital system (5.6%; 95% CI 2.4%, 10.7%) and in 2/352 faecal samples of calves (0.6%; 95% CI 0.1%, 2.0%) using the modified Ziehl–Neelsen (MZN) staining technique. Microscopy positive samples from children were further analysed by PCR targeting the 18S rRNA gene and identified as Cryptosporidium hominis (3/4) and Cryptosporidium meleagridis (1/4). Regardless of the microscopy outcome, randomly selected samples (n = 36) from calves 0–4 months of age were amplified and sequenced at the 18S rRNA gene using nested PCR. Two calves tested positive (5.6%; 95% CI 1.7%, 18.7%), and revealed the presence of Cryptosporidium parvum and Cryptosporidium bovis. The detection of only two zoonotic species (C. parvum in one calf and C. meleagridis in one child) suggests that zoonotic cryptosporidiosis is not currently widespread in our study area; however, the potential exists for amplification of transmission in an immunocompromised population.

Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics

BACKGROUND

Plant viruses in the genus Begomovirus, family Geminiviridae often cause substantial crop losses. These viruses have been emerging in many locations throughout the tropics and subtropics. Like many plant viruses, they are often not recognized by plant diagnostic clinics due in large part to the lack of rapid and cost effective assays. An isothermal amplification assay, Recombinase polymerase amplification (RPA), was evaluated for its ability to detect three begomoviruses and for its suitability for use in plant diagnostic clinics. Methods for DNA extraction and separation of amplicons from proteins used in the assay were modified and compared to RPA manufacturer's protocols. The modified RPA assays were compared to PCR assays for sensitivity, use in downstream applications, cost, and speed.

RESULTS

Recombinase polymerase amplification (RPA) assays for the detection of Bean golden yellow mosaic virus, Tomato mottle virus and Tomato yellow leaf curl virus (TYLCV) were specific, only amplifying the target viruses in three different host species. RPA was able to detect the target virus when the template was in a crude extract generated using a simple inexpensive extraction method, while PCR was not. Separation of RPA-generated amplicons from DNA-binding proteins could be accomplished by several methods, all of which were faster and less expensive than that recommended by the manufacturer. Use of these modifications resulted in an RPA assay that was faster than PCR but with a similar reagent cost. This modified RPA was the more cost effective assay when labor is added to the cost since RPA can be performed much faster than PCR. RPA had a sensitivity approximate to that of ELISA when crude extract was used as template. RPA-generated amplicons could be used in downstream applications (TA cloning, digestion with a restriction endonuclease, direct sequencing) similar to PCR but unlike some other isothermal reactions.

CONCLUSIONS

RPA could prove useful for the cost effective detection of plant viruses by plant diagnostic clinics. It can be performed in one hour or less with a reagent cost similar to that of PCR but with a lower labor cost, and with an acceptable level of sensitivity and specificity.

Loop-mediated isothermal amplification assay targeting the blaCTX-M9 gene for detection of extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae

Extended-spectrum β-lactamases (ESBLs) produced by Enterobacteriaceae are one of the resistance mechanisms to most β-lactam antibiotics. ESBLs are currently a major problem in both hospitals and community settings worldwide. Rapid and reliable means of detecting ESBL-producing bacteria is necessary for identification, prevention and treatment. Loop-mediated isothermal amplification (LAMP) is a technique that rapidly amplifies DNA with high specificity and sensitivity under isothermal conditions. This study was aimed to develop a convenient, accurate and inexpensive method for detecting ESBL-producing bacteria by a LAMP technique. ESBLs-producing Escherichia coli and Klebsiella pneumoniae were isolated from a tertiary hospital in Bangkok, Thailand and reconfirmed by double-disk synergy test. A set of four specific oligonucleotide primers of LAMP for detection of bla(CTX-M9) gene was designed based on bla(CTX-M9) from E. coli (GenBank Accession No. AJ416345). The LAMP reaction was amplified under isothermal temperature at 63°C for 60 min. Ladder-like patterns of band sizes from 226 bp of the bla(CTX-M9) DNA target was observed. The LAMP product was further analyzed by restriction digestion with MboI and TaqI endonucleases. The fragments generated were approximately 168, 177 and 250 bp in size for MboI digestion and 165, 193, 229, 281 and 314 bp for TaqI digestion, which is in agreement with the predicted sizes. The sensitivity of the LAMP technique to bla(CTX-M9) was greater than that of the PCR method by at least 10,000-fold. These results showed that the LAMP primers specifically amplified only the bla(CTX-M9) gene. Moreover, the presence of LAMP amplicon was simply determined by adding SYBR Green I in the reaction. In conclusion, this technique for detection of ESBLs is convenient, reliable and easy to perform routinely in hospitals or laboratory units in developing countries.

Reverse transcription loop-mediated isothermal amplification for rapid and quantitative assay of covert mortality nodavirus in shrimp

A disease known as covert mortality disease has become an increasing problem in the shrimp farming industry in recent years in China and several countries of Southeast Asia, leading to serious losses in production. Litopenaeus vannamei (also known as Pacific white shrimp) is affected by this disease that leads to a range of clinical symptoms including hepatopancreas atrophy and necrosis, soft shell, slow growth, and abdominal muscle whitening and necrosis in the acute stage of disease. A new nodavirus, termed covert mortality nodavirus (CMNV), has been shown to be the etiological agent. In this study, we report a sensitive and specific real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid and quantitative detection of CMNV. The optimal conditions for this newly developed RT-LAMP reaction were found to be 6mM MgCl₂ and 1.6mM dNTPs, an incubation temperature of 65°C and a reaction time of 50min. The analytical sensitivity of the RT-LAMP assay was estimated to be 6.3pg total RNA of CMNV-infected shrimp and 27 copies of the target plasmid. The diagnostic sensitivity and specificity of the newly developed assay versus the standard nested reverse transcription PCR (RT-PCR) assay was 96.4% and 94.4%, respectively. The reaction products were detected by visual inspection after staining with an in-tube DNA fluorescent dye, a measure taken to eliminate the risk of contamination. The quantitative RT-LAMP assay for CMNV showed high correlation coefficient (r²=0.9953) when the initial templates were above 1000 copies, however the correlation coefficient decreased when the initial templates were lower than 1000 copies. Test of viral load in shrimp indicated that the viral loads varied from 1.5×10² to 6.7×10⁶ copies per mg of cephalothorax tissue. Thus, the CMNV RT-LAMP assay is a sensitive and specific new tool for the field detection and quantification of CMNV in the diagnosis and surveillance of covert mortality disease.

Gastritis, Enteritis, and Colitis in Horses

The gastrointestinal system of horses is affected by a large variety of inflammatory infectious and noninfectious conditions. The most prevalent form of gastritis is associated with ulceration of the pars esophagea. Although the diagnostic techniques for alimentary diseases of horses have improved significantly over the past few years, difficulties still exist in establishing the causes of a significant number of enteric diseases in this species. This problem is compounded by several agents of enteric disease also being found in the intestine of clinically normal horses, which questions the validity of the mere detection of these agents in the intestine.

Challenging loop-mediated isothermal amplification (LAMP) technique for molecular detection of Toxoplasma gondii

Objective

To compare analytical sensitivity and specificity of a newly described DNA amplification technique, LAMP and nested PCR assay targeting the RE and B1 genes for the detection of Toxoplasma gondii (T. gondii) DNA.

Methods

The analytical sensitivity of LAMP and nested-PCR was obtained against10-fold serial dilutions of T. gondii DNA ranging from 1 ng to 0.01 fg. DNA samples of other parasites and human chromosomal DNA were used to determine the specificity of molecular assays.

Results

After testing LAMP and nested-PCR in duplicate, the detection limit of RE-LAMP, B1-LAMP, RE-nested PCR and B1-nested PCR assays was one fg, 100 fg, 1 pg and 10 pg of T. gondii DNA respectively. All the LAMP assays and nested PCRs were 100% specific. The RE-LAMP assay revealed the most sensitivity for the detection of T. gondii DNA.

Conclusions

The obtained results demonstrate that the LAMP technique has a greater sensitivity for detection of T. gondii. Furthermore, these findings indicate that primers based on the RE are more suitable than those based on the B1 gene. However, the B1-LAMP assay has potential as a diagnostic tool for detection of T. gondii.

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.

[Cryptosporidium and Giardia as water contaminant pathogens in Hungary]

INTRODUCTION

Many species of Cryptosporidium, and two assemlages of Giardia duodenalis cause typically acute diaorrhoea in human. The oocysts and cysts of these parasites excreted in faeces are capable of infecting other hosts and those are environmentally stable.

AIM

The aims of the study were to evaluate the prevalence and genotypes of Cryptosporidium and Giardia species from different water sources as well as to monitor and characterize the (oo)cyst contamination sources in watersheds. In addition, an epidemiological study was performed in three selected settlements.

METHOD

Wide range of modern epidemiological and molecular detection methods have been applied.

RESULTS

(Oo)cysts densities were associated with water receiving effluents of sewage treatment plants or originating from a forest environment. It was confirmed, that cattle can be a source of Cryptosporidium oocysts at watersheds and aquatic birds can play a role in the environmental dissemination of these protozoa. The epidemiological study demonstrated a specific epidemiological situation, giving essential evidence about giardiasis in asymptomatic carriers. The applied novel detection technology was found to be cost effective and simple procedure for screening catchments to identify those that require further treatment and more detailed microscopic counts.

CONCLUSIONS

The presented results contribute to a better understanding the epidemiology and relevance of waterborne parasites, their surveillance and performance of future control measures to prevent waterborne infections in Hungary.

Detection of Cryptosporidium and Giardia (oo)cysts by IFA, PCR and LAMP in surface water from Rasht, Iran

BACKGROUND

Cryptosporidium and Giardia in water supplies is acknowledged as a public health problem. In the present study, we applied immunofluorescence assay (IFA), PCR and loop-mediated isothermal amplification (LAMP) for the detection of the two protozoa.

METHODS

Over a period of 12 months, surface water samples were collected from two rivers in the north of Iran, and filtrated by 142 mm membrane filters. At each sampling point 10 L water were used for IFT and the10 L were analysed using molecular methods.

RESULTS

In 15/40 samples, (oo)cysts were detected by one of the IFA, PCR or LAMP methods. Five samples that were Cryptosporidium-negative by IFA were positive by LAMP. A total of 10 out of 13 samples that were Giardia-positive by IFA were also positive by PCR. IFA revealed high levels of Giardia, with 1-1800 cysts and 1-16 Cryptosporidium oocysts detected per 10 L.

CONCLUSION

The study reveals that the investigated water supplies were contaminated by Cryptosporidium and Giardia. The LAMP assay has advantages for detection and screening of these protozoa at relatively low concentration in water samples. The three assays applied are complimentary but no single one will give the true prevalence of these parasites in surface water samples. However, each method has its own advantages and disadvantages dependent of the aim and the study design; a combination of detection methods should be applied to discover whether water is, or is not, contaminated with (oo)cysts. This is the first report on the occurrence of (oo)cysts in Iranian surface waters to compare the results of parasite detection obtained with the different methods.

The concentration of Cryptosporidium and Giardia in water--the role and importance of recovery efficiency

The concentration of Cryptosporidium and of Giardia in surface water is a subject of importance to public health and public water supply. The term concentration is a fundamental property of any water quality parameter having a classical definition as used in chemistry and biology. Analytical methods for measuring the occurrence of Cryptosporidium and Giardia in water find only a fraction of the organisms actually present. This paper collects recently available data to examine the role and importance of recovery efficiency measurement to description of the concentrations of these organisms. Data from Australian sources graphically illustrate the variability of recovery efficiency at individual sites over relatively short time scales. Additional data on replicated recovery measurements establish their reproducibility. The recently released USEPA LT2 data along with those from Australia illustrate the independent variation of Cryptosporidium and Giardia occurrence and recovery efficiency at individual sampling locations. Calculation of concentration from paired raw numbers and recovery efficiency measurements clearly shows the magnitude and importance of taking recovery into account in expressing the concentration of these organisms.

Looking for Cryptosporidium: the application of advances in detection and diagnosis

The protozoan Cryptosporidium is a major public and animal health concern. Young children, immunocompromised people, and pre-weaning animals are especially vulnerable, but treatment options are limited and there is no vaccine. A laboratory diagnosis is required to confirm cases of cryptosporidiosis, and species and genotype determination is essential in distinguishing human from non-human sources, understanding transmission, and strengthening the epidemiological evidence for causative links in outbreaks. However, testing is not consistent, as demonstrated by investigation of a significant increase in cases in some European countries during 2012. Many methods employed are laborious and time-consuming; recent advances, translated into diagnostic assays, can improve testing and facilitate typing to support clinical and environmental investigations.

Loop-mediated isothermal amplification method for a differential identification of human Taenia tapeworms

Loop-mediated isothermal amplification (LAMP), which employs a Bst DNA polymerase with strand-displacement activity and four primers (two inner primers and two outer primers) recognizing six distinct regions on the target DNA, is a highly sensitive, specific, simple, and rapid nucleotide amplification method. Moreover, because the Bst DNA polymerase resists much DNA polymerase inhibitors present in biological specimens, the LAMP method is suitable for the detection of infectious agents from clinical material such as fecal samples. Here, we describe the LAMP method which can differentially detect and identify human Taenia tapeworms, Taenia solium, T. saginata, and T. asiatica, using DNA specimens prepared from parasite tissue and human fecal sample.

Detection of Cryptosporidium species in the sea and tap water samples of Black Sea, Turkey

The aim of this study was to evaluate Cryptosporidium spp. contamination of sea and tap water samples from Sinop and Ordu Provinces, Black Sea, Turkey. The samples (10 L) were collected in spring, summer, autumn, and winter in 2011. A total of 128 water samples was analyzed using an immunofluorescence test (IFT), as well as loop-mediated isothermal amplification (LAMP) and nested polymerase chain reaction (PCR). Cryptosporidium spp. oocysts were detected by IFT in 43 of the 70 samples (61.4%; 1-40 oocysts per 0.5 L) and 35 of the 58 samples (60.3%; 1-23 oocysts per 0.5 L) in the sea water samples from Ordu and Sinop, respectively. The highest number of oocysts by IFT were detected in spring and winter in Ordu and Sinop, respectively. The results of the S-adenosylmethionine synthetase (SAM) gene LAMP assays were 65.5% positive for Cryptosporidium parvum , Cryptosporidium hominis , and Cryptosporidium meleagridis in all examined samples, while the SSUrRNA gene nested PCR assay was 31.0% positive. Six C. parvum nested PCR products from all positive samples were successfully sequenced.

Comparison of nested PCR and microscopy for the detection of cryptosporidiosis in bovine calves

The comparative efficacies of different conventional parasitological methods and nested PCR for diagnosis of bovine cryptosporidiosis in faecal samples were evaluated. Among the 100 samples collected from calves in and around Ludhiana Direct faecal smear staining technique revealed 25.0 % positivity for the oocysts of Cryptosporidium spp. with sensitivity and specificity of 68.12 and 92.98 %, respectively. Zinc sulphate solution floatation and saturated sugar solution floatation staining techniques showed sensitivity and specificity of 83.92 and 96.36; 81.03 and 98.14 %, respectively. Products of the primary PCR of Cryptosporidium spp. directed against small subunit (18S) ribosomal RNA when employed as template in nested PCR produced the amplicons of desired size (834 bp) in 47.0 % of the samples. Amplification of 834 bp fragment was also observed in positive control, while no amplification was observed in negative control. Results indicated PCR assays as highly sensitive and specific techniques for the screening of the samples for Cryptosporidium spp. but in developing countries and under field conditions where limited resources do not allow the application of PCR assays, concentration staining methods are recommended.