DNA probe diagnosis of parasitic infections

Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections

Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies.

The development of loop-mediated isothermal amplification targeting alpha-tubulin DNA for the rapid detection of Plasmodium vivax

Background

Malaria that is caused by Plasmodium vivax is the most widely distributed human malaria. Its recent resurgence in many parts of the world, including the Republic of Korea (ROK), emphasizes the importance of improved access to the early and accurate detection of P. vivax to reduce disease burden. In this study, a rapid and efficient loop-mediated isothermal amplification (LAMP)-based method was developed and validated using blood samples from malaria-suspected patients.

Method

A LAMP assay targeting the α-tubulin gene for the detection of P. vivax was developed with six primers that recognize different regions of the target gene. The diagnostic performance of the α-tubulin LAMP assay was compared to three other tests: microscopic examinations, rapid diagnostic tests (RDTs), and nested polymerase chain reactions (PCRs) using 177 whole blood specimens obtained from ROK military personnel from May to December 2011.

Results

The α-tubulin LAMP assay was highly sensitive with a detection limit of 100 copies of P. vivax α-tubulin gene per reaction within 50 min. It specifically amplified the target gene only from P. vivax. Validation of the α-tubulin LAMP assay showed that the assay had the highest sensitivity (P < 0.001 versus microscopy; P = 0.0023 versus RDT) when nested PCR was used as the gold standard and better agreement (concordance: 94.9%, kappa value: 0.865) with nested PCR than RDT and microscopy. A Receiver Operation Characteristics analysis showed that the diagnostic accuracy of the α-tubulin LAMP assay for vivax malaria was higher (Area Under Curve = 0.908) than RDT and microscopy.

Conclusion

This study showed that the P. vivax α-tubulin LAMP assay, which can be used to diagnose early infections of vivax malaria, is an alternative molecular diagnostic tool and a point-of-care test that may help to prevent transmission in endemic areas.

Advances in malaria diagnosis

Malaria is a leading cause of mortality worldwide and accurate diagnostic testing for malaria can potentially save an estimated 100,000 lives annually. New technologies have the potential to circumvent limitations of the traditional diagnostic method, light microscopy, which is labor intensive and requires considerable technician expertise. Immunochromatographic tests, which are easy to use in field conditions and relatively inexpensive, offer a potential solution to the problem of malaria overtreatment in resource-poor endemic countries. Assays based on the PCR are highly sensitive, can be used for unambiguous species identification and, thus, may increasingly complement or even replace light microscopy in developed countries. Experimental diagnostics using flow cytometry and mass spectrometry are currently under investigation for high-throughput screening.

Saving Private Ryan: The Indian Scenario (Rapid Diagnosis of Malaria at Regimental Aid Post)

Immunochromatography test (ICT) (Paracheck Pf) for diagnosis of Plasmodium falciparum (Pf) infection was compared with the conventional smear examination method. A total of 350 specimens of blood from cases of fever were investigated (falciparum malaria 220, vivax malaria 100, controls 30). Paracheck Pf ICT was found to have enormous advantages over smear examination due to its high degree of sensitivity, specificity, speed and ease of performance. Paracheck Pf ICT test kits are stable at room temperature. Regimental medical officers (RMOs) and nursing assistants with minimal training can safely practise Paracheck Pf ICT method. Introduction of this test method in the Armed Forces can facilitate early diagnosis and specific treatment of falciparum malaria even at far flung places. This will have enormous beneficial effect in reducing morbidity due to malaria and saving precious lives. In short as well as long term, it is a viable cost effective option.

Use of PCR in the field

Polymerase chain reaction (PCR) represents a powerful new technology with a variety of field applications. While most of these are still experimental, implementation of PCR-based detection of Onchocerca volvulus in black flies, and subspecific differentiation strongly suggest that potential problems can be overcome. Because of high sensitivity and specificity, PCR provides in some cases the only means to address central parasitological questions, and may well become the 'gold standard' by which other diagnostic techniques are measured. In spite of these advantages, routine implementation of PCR,at present,requires transportation of samples to a central facility for processing, and personnel whose technical competence is high. In addition, reagents are expensive. Robert Barker here weighs up these considerations with regard to the potential utility of PCR assays for some applications.

Reactivation of cutaneous leishmaniasis after surgery

Cutaneous leishmaniasis (CL) is caused by a parasite from the genus Leishmania. Infection is transmitted to humans from the bite of sandflies. We describe an 85-year-old man who developed CL on his face after recent cutaneous surgery in that site. The case is also unusual because the most likely source of exposure to the infection occurred over 50 years previously. Polymerase chain reaction, slit-skin smear, serology and the leishmanin test were not helpful in diagnosis, which was confirmed by histopathological demonstration of the parasite.

Polymerase chain reaction-based identification of New World Leishmania species complexes by specific kDNA probes

Here we define a new approach for the detection and characterisation of Leishmania complexes by polymerase chain reaction (PCR) and specific hybridisation. The first step consists of PCR amplification of kDNA minicircles using general kinetoplastid primers, which generate a polymorphic multi-banding pattern for all Leishmania species and other Kinetoplastidae. The second step is the identification of the Leishmania species complexes by hybridisation of the PCR products with specific kDNA probes. Polymorphic PCR-products from a genetically diverse set of Leishmania species were analysed by electrophoresis and the banding patterns compared with multi-locus enzyme electrophoresis (MLEE) data. The banding patterns produced by Leishmania species were very heterogeneous, making kDNA-PCR useful for determining closely related strains and for fingerprinting individual strains. The degree of kDNA-PCR and MLEE polymorphism was compared using UPGMA dendrograms. Three complex-specific probes were generated from major PCR bands of reference stocks belonging to the Leishmania mexicana, Leishmania donovani and Leishmania braziliensis complexes, and hybridisation of these probes to membrane-bound PCR products could reliably identify the strain to a complex level. A combination of kDNA-PCR fingerprinting and hybridisation with kDNA probes was found to be useful for both sensitive detection and direct identification of Leishmania species complexes.

Biotin-labeled DNA probe in a PCR-based assay increases detection sensitivity for the equine hemoparasite Babesia caballi

A DNA probe from Babesia caballi (Bc1) was selected by antibody screening of a genomic library. The Bc1 probe hybridized specifically to B. caballi genomic DNA. A polymerase-chain-reaction-based assay for B. caballi DNA was developed from primers deduced from the probe nucleotide sequence. An amplified product of 1.6 kb was detected from as little as 500 fg B. caballi template DNA. Sensitivity increased 1000-fold when the biotin-labeled Bc1 probe was hybridized to the amplicons in a Southern blot.

Detection of Plasmodium ovale malaria parasites by species-specific 18S rRNA gene amplification

A polymerase chain reaction (PCR) assay was developed for the specific detection of Plasmodium ovale, one of the four malaria parasites that infect humans. On the basis of sequence variation of the Plasmodium 18S ribosomal RNA (rRNA) gene, oligonucleotide primers for PCR were designed to amplify various fragments of the P. ovale gene. Using a recombinant plasmid with the complete P. ovale 18S rRNA gene as target, 59 primer combinations were tested so that at least one of the pairs was species-specific while the other primer was either genus conserved or P. ovale species-specific. Three primer pairs yielding DNA fragments at stringent conditions were further tested against genomic DNA of four human malaria species. This approach yielded P. ovale species-specific primer pairs that may be useful for further field testing.

The polymerase chain reaction: applications for the detection of foodborne pathogens

Faster methods for the detection of foodborne microbial pathogens are needed. The polymerase chain reaction (PCR) can amplify specific segments of DNA and is used to detect and identify bacterial genes responsible for causing diseases in humans. The major features and requirements for the PCR are described along with a number of important variations. A considerable number of PCR-based assays have been developed, but they have been applied most often to clinical and environmental samples and more rarely for the detection of foodborne microorganisms. Much of the difficulty in implementing PCR for the analysis of food samples lies in the problems encountered during the preparation of template DNAs from food matrices; a variety of approaches and considerations are examined. PCR methods developed for the detection and identification of particular bacteria, viruses, and parasites found in foods are described and discussed, and the major features of these reactions are summarized.

Improved specificity of Trypanosoma cruzi identification by polymerase chain reaction using an oligonucleotide derived from the amino-terminal sequence of a Tc24 protein

In the present study, the diagnostic value of Trypanosoma cruzi recombinant protein (Tc24) was examined. Although antibodies against Tc24 were detected during natural and experimental T. cruzi infections, specificity studies revealed that sera from T. rangeli-infected mice also recognized to some extent Tc24 protein. In addition, sera from Tc24-immunized mice reacted against a 21 kDa polypeptide in T. rangeli extracts. Detailed analysis of the antibody response against 20-40 peptide localized in the Tc24 amino-terminal domain suggests that this sequence is not expressed by T. rangeli 21 kDa antigen. Therefore, the PCR reaction using oligonucleotides corresponding to a 20-26 peptide clearly demonstrated the specificity of the oligoprobes for T. cruzi identification. Positive signals were also found when using blood samples from T. cruzi-infected mice. Taken together, these results suggest that the PCR-based 20-26 assay may be useful in the specific diagnosis of Chagas' disease.

Epidemiology, diagnosis and control of leishmaniasis in the Mediterranean region

The leishmaniases are a widespread and medically important group of parasitic diseases, some of which pose a serious health threat in communities throughout the Mediterranean basin. In 1993, a joint, collaborative study of the Mediterranean leishmaniases was initiated by scientists from Israel, Turkey, Portugal and the Netherlands. The aim of this project was the development of a multi-component approach to the successful control of all forms of leishmaniasis, with special emphasis on the more severe, visceral leishmaniasis (VL). The need for highly sensitive and accurate new tools to facilitate diagnosis and epidemiological surveys of endemic areas and for studies on the immunology of VL in laboratory models (dogs and mice) was soon recognized. It is anticipated that the development of these tools and the associated technology will provide a better understanding of the disease and improve its control.

Identification and epidemiological typing of Naegleria fowleri with DNA probes

Naegleria fowleri is a small free-living amoeboflagellate found in warm water habitats worldwide. The organism is pathogenic to humans, causing fatal primary amoebic meningoencephalitis. When monitoring the environment for the presence of N. fowleri, it is important to reliably differentiate the organism from other closely related but nonpathogenic species. To this end, we have developed species-specific DNA probes for use in the rapid identification of N. fowleri from the environment. Samples were taken from the thermal springs in Bath, England, and cultured for amoebae. Of 84 isolates of thermophilic Naegleria spp., 10 were identified as N. fowleri by probe hybridization. The identity of these isolates was subsequently confirmed by their specific whole-cell DNA restriction fragment length polymorphisms (RFLPs). One DNA clone was found to contain a repeated element that detected chromosomal RFLPs that were not directly visible on agarose gels. This enabled the further differentiation of strains within geographically defined whole-cell DNA RFLP groups. N. fowleri DNA probes represent a specific and potentially rapid method for the identification of the organism soon after primary isolation from the environment.

DNA probes and PCR for diagnosis of parasitic infections

DNA probe and PCR-based assays to identify and detect parasites are technically complex; however, they have high sensitivity, directly detect parasites independent of the immunocompetence or previous clinical history of the patient, and can distinguish between organisms that are morphologically similar. Diagnosis of parasites is often based on direct detection by microscopy, which is insensitive and laborious and can lack specificity. Most PCR-based assays were more sensitive than DNA probe assays. The development of PCR-based diagnostic assays requires multiple steps following the initial selection of oligonucleotide primers and reporter probe. Generally, the ability to detect the DNA of one parasite was attained by PCR; however, advances in the preparation of samples for PCR (extraction of DNA while removing PCR inhibitors) will be required to achieve that sensitivity with human specimens. Preliminary PCR systems have been developed for many different parasites, yet few have been evaluated with a large number of clinical specimens and/or under field conditions. Those evaluations are essential for determination of clinical and field utility and performance and of the most appropriate application of the assay. Several situations in which PCR-based diagnosis will result in epidemiologic, medical, or public health advances have been identified.

Detection of Theileria sergenti infection in cattle by polymerase chain reaction amplification of parasite-specific DNA

A pair of synthetic oligonucleotide primers, designed from the gene encoding a 32-kDa intraerythrocytic piroplasm surface protein of Theileria sergenti, were used to amplify parasite DNA from the blood of T. sergenti-infected cattle by means of the polymerase chain reaction (PCR). PCR-amplified DNA was examined by electrophoresis and by dot blot or microplate hybridization using a parasite-specific cDNA probe. PCR was specific for T. sergenti, since no amplification was detected with DNA from Anaplasma centrale, Babesia ovata, uninfected erythrocytes, and leukocytes. This method was sensitive enough to detect about 4.5 parasites per microliters of blood with a 10-microliters sample volume. Moreover, of 66 specimens from grazing cattle, 40 were microscopically positive, whereas PCR revealed that 54 samples were positive. Therefore, PCR provides a useful diagnostic tool for detecting T. sergenti-infected cattle, and it is significantly more sensitive than the current methods.

Detection of Echinococcus multilocularis DNA in fox faeces using DNA amplification

In order to identify Echinococcus multilocularis DNA in fox faeces for epidemiological purposes, we have developed a new method to prepare DNA suitable for PCR amplification. DNA isolation from fox excrement was performed according to a novel procedure involving lysis in KOH, phenol-chloroform extraction and a purification step on a matrix (Prep-A-Gene). The target sequence for amplification was the E. multilocularis U1 snRNA gene. PCR products were indistinguishable for 32 different E. multilocularis isolates and no signal was observed after ethidium bromide staining with DNAs from other tapeworm species, including E. granulosus. The sensitivity of amplification was monitored by the addition of E. multilocularis DNA or eggs to faeces free of E. multilocularis and was estimated to be 1 egg per 4 g of faeces. PCR products were blotted onto nylon membranes and hybridized with an internal oligonucleotide probe in order to confirm the results. Twenty nine faecal samples from foxes shot in Franche-Comté (East France) were tested. Out of 10 samples from foxes in which no E. multilocularis adult worms could be observed after necropsy, 7 were PCR positive, showing that the PCR test is more sensitive than microscopical examination. Out of 19 samples from foxes harbouring E. multilocularis adult worms, 18 were PCR positive. The remaining PCR-negative sample could be due either to the misidentification of the species of adult worm (E. granulosus and E. multilocularis), or to DNA variation between different isolates of E. multilocularis. Further work in the field should be initiated in order to confirm these results.

Flow cytometric screening of blood samples for malaria parasites

An automated method for the detection and estimation of malaria parasites in blood samples using flow cytometry is presented. In a single-step procedure 50 microliters of blood sample was collected in 1 ml of lysis solution containing formaldehyde, causing red blood cells to lyse while parasites and white blood cells are preserved. Thus prepared, samples could be transported and remained stored in lysis solution until flow cytometric analysis was performed. The cells were stained for DNA with the fluorescent dye Hoechst 33258 and subsequently analyzed by a FACStar flow cytometer. Parasites and white blood cells were distinguished and counted based on blue Hoechst fluorescence and forward scattering. Since red blood cells were lysed, parasite numbers were given related to the number of white blood cells similar to what is done in microscopic examination of thick blood smears. In dilution experiments with animal and human material, parasite counts by flow cytometry correlated very well with the theoretically calculated numbers (regression coefficients of > 0.94). In human material parasitemias of approximately 0.005% were detected. In a pilot study, 700 samples were collected in Thailand and screened by microscopic examination of thick smears and by flow cytometry; 29 were found positive by combining both methods, 2 were missed by flow cytometry, and 20 were missed by microscopists in the field. After microscopic reexamination in the central laboratory, 15 of these 20 were found positive, 5 remained unconfirmed.

Evolution of the retrotransposons TRS/ingi and of the tubulin genes in trypanosomes

The African trypanosomes have genomes of high plasticity, as demonstrated for instance by their ability to shuffle their genes around, coding for variant-specific surface glycoproteins (VSGs). Another indication of their genome plasticity is the presence of multiple retro-elements. The retrotransposon-like element TRS/ingi is present in many copies in the genome of trypanosomes. One particular derivative of TRS/ingi, called TUBIS, had previously been found to interrupt a tubulin gene in a particular strain of T. brucei. Here both TRS/ingi and TUBIS were studied by hybridizing genomic DNA of various strains and species of trypanosomes with suitable probes in order to elucidate the evolution of this family of retro-elements. The TSR/ingi elements are highly repeated and have very long open reading frames, while TUBIS clearly is a truncated, inactivated form of this element, found in only one particular chromosomal location. Both elements were shown to be present in several strains and species of the subgenus Trypanozoon, in particular in T. brucei brucei, T. gambiense, T. rhodesiense, T. equiperdum and T. evansi. They could not be detected in species of other subgenera, in particular in T. congolense and T. cruzi. These findings suggest that the retrotransposon TRS/ingi was acquired by trypanosomes only after divergence of present day subgenera. The TUBIS element was found in exactly the same chromosomal location (at the 3' end of the tubulin gene cluster) in many different strains and species of the subgenus Trypanozoon. This shows that the element was transposed to this location before speciation of the subgenus. Although, TRS/ingi is unlikely to be involved directly in VSG switching, it may have contributed to the genome plasticity of trypanosomes.

[Molecular biological techniques in the diagnosis of tropical parasitic diseases]

Recent advances in the development of molecular biological techniques have resulted in their supplementary application for improved diagnosis of tropical parasitic diseases. The main areas of interest are the production of recombinant antigens for immunodiagnosis, and the detection of parasites by hybridization of nucleic acids and by DNA amplification (PCR) in vitro.

Sequence analysis of small subunit ribosomal RNA genes and its use for detection and identification of Leishmania parasites

The sequence of the most variable part of the small subunit ribosomal RNA (SSU rRNA) gene, comprising 800 bases, was analysed for 9 Leishmania taxa and compared with those of Trypanosoma brucei, Trypanosoma cruzi and Crithidia fasciculata. Considerable differences were observed between the sequence of the Leishmania taxa on the one hand and those of Crithidia and Trypanosoma on the other. Amongst the Leishmania taxa only a few point mutations were found, all located within 2 sequence blocks in the central part of the SSU rRNA gene, which are unique for Kinetoplastida. These unique sequences were used for the development of kinetoplastid-specific probes and a Leishmania-specific PCR assay of high sensitivity (less than 10 parasites could be detected). Based on the observed point-mutations an identification of the Leishmania parasites, according to complex, could be achieved by direct sequencing, restriction fragment analysis or single-stranded conformation polymorphism of the PCR-generated fragments.

Development of genomic probes to Sarcocystis cruzi (Apicomplexa)

A genomic library of Sarcocystis cruzi sporozoite DNA was constructed in bacteriophage lambda gt10. Recombinant phages containing insert DNA were selected by growth on Escherichia coli strain C600 hflA150. Of 14 clones examined, 11 contained DNA inserts ranging in size from approximately 1.45 kilobase (kb) to 6.18 kb. Insert DNA from four of these clones specifically hybridized to 32P-labelled S. cruzi merozoite DNA. One of these insert DNA, clone SL41, was selected and labelled with 32P. This probe did not hybridize with the other ten DNA inserts nor with bovine cellular DNA, but it hybridized with sporozoite, merozoite and bradyzoite DNA preparations. The SL41 probe could detect merozoite DNA in as little as 17 ng total DNA. Genomic probes detecting developmental stages of Sarcocystis spp. could provide an improved means is diagnosis of acute bovine sarcocystosis.

Polymerase chain reaction amplification of Trypanosoma cruzi kinetoplast minicircle DNA isolated from whole blood lysates: diagnosis of chronic Chagas' disease

A 6 M guanidine-HCl/0.2 M EDTA solution was used to lyse and store whole blood specimens. DNA stored in guanidine-EDTA-blood (GEB) lysate was found to be undegraded after incubation at 37 degrees C for 1 month, suggesting that this represents an appropriate reagent for transport of blood samples from the field to a laboratory for analysis. Trypanosoma cruzi kinetoplast DNA in GEB lysate can be cleaved using the chemical nuclease, 1,10-phenanthroline-copper ion (OP-Cu2+). This procedure liberates linearized minicircle molecules from network catenation, distributing them throughout the lysate, and allowing a small aliquot of the original lysate to be analyzed by PCR amplification. This increases the sensitivity of the method dramatically for the detection of small numbers of trypanosomes in a large volume of blood. DNAs isolated from aliquots of T. cruzi-positive GEB lysates were polymerase chain reaction (PCR)-amplified with 3 sets of T. cruzi-specific kDNA minicircle primers, yielding the 83-bp and 122-bp conserved region fragments and the 330-bp variable region fragments. The PCR products were analyzed by gel electrophoresis and/or hybridization. Results indicate that a single T. cruzi cell in 20 ml of blood can be detected by this method. Blood samples from several chronic chagasic patients were tested. Amplification of T. cruzi kDNA minicircle sequences was obtained in al cases, even when xenodiagnosis was negative. This PCR-based test should prove useful as a replacement or complement for xenodiagnosis or serology in clinical and epidemiological studies of chronic Chagas' disease.

Detection and identification of Leishmania parasites by in situ hybridization with total and recombinant DNA probes

In situ hybridization on cultured promastigotes and sandfly smears were performed with nonradioactively labeled total DNA and recombinant DNA probes containing minicircle kinetoplast DNA (kDNA) or nuclear DNA inserts. Total DNA probes lack specificity whereas recombinant nuclear DNA probes work only if they contain repetitive sequences. Minicircle kDNAs of five Leishmania isolates, representative of five Leishmania taxa found in Kenya, were sequenced. Comparison of the sequences showed a 150-bp region with around 80% homology, whereas the rest of the minicircles had about 50% homology. Nevertheless, application of these probes in in situ hybridization assays as tested on Leishmania promastigotes in the vector gave good specificity and hybridization signal. Two types of labeling were tested: incorporation of biotin-labeled dUTP or directly horseradish peroxidase (HRP)-labeled nucleotides. Both techniques provided good sensitivity and signal-to-noise ratio on cultured promastigotes. Hybridization with HRP-labeled kDNA probes gave a superior signal-to-noise ratio if tested on sandfly preparations. This method provided a reliable and fast identification and facilitated the detection of promastigotes in sandflies. The technique presented here may be helpful in rapid identification of Leishmania promastigotes, and thus make epidemiological studies easier and less time consuming.

Leishmaniasis in a domestic goat in Kenya

The pathological and electron-microscopic features of the first case of autochthonous leishmaniasis affecting a domestic goat in Kenya are described. They are similar to what have been described in man and other animals. Using a short amino-acid sequence common to all the species of leishmania as primers for kDNA synthesis, the intervening sequence of 120 bases was amplified in the goat's tissues by polymerase chain reaction (PCR). The leishmania kinetoplast DNA sequence was detected in all the different infected tissues of the goat examined. The sensitivity and specificity of this assay are discussed. The result of the assay used was consistent with the parasite being either L. major or L. aethiopica as the infecting agent. The isoenzyme studies were consistent with L. aethiopica as the strain responsible for this goat's infection. The control of leishmaniasis and its vector must take into account the potential role of animal reservoirs in the environment. Even though Kenya and other East African countries are endemic for kala-azar, the presence of kala-azar in goats is of considerable veterinary public health importance in Africa. Efforts must not be spared to identify and detect other possible animal reservoirs in the subregion. Using DNA amplification techniques, which are sensitive and specific, such as the one described in this paper, sera and other biological fluids and tissues from different animal species should be utilized for detecting additional reservoirs for leishmania parasites particularly in known endemic areas of the world.