Use of PCR in the field

Simple identification of mitochondrial lineages in contact zones based on lineage-selective primers

A variety of research projects focus on genetic variation among and within maternal lineages as encompassed by mitochondrial DNA (mtDNA). While mtDNA often differs substantially between species, large differences may also be found within species. The evaluation of such divergent lineages, for example in intraspecific contact zones (hybrid zones), commonly involves sequencing numerous individuals. Large-scale sequencing is both expensive and labour-intensive. Based on sequences from 15 individuals, we devised a simple and quick polymerase chain reaction assay for identification of divergent mtDNA lineages in a secondary contact zone of the side-blotched lizard (Uta stansburiana). The application uses lineage-selective primers to amplify a lineage-diagnostic product, and is based on each group of mtDNA haplotypes being a monophyletic assemblage of haplotypes sharing the same maternal ancestry, deeply divergent from the other group. The assay was tested on a larger sample (n = 147) of specimens from the contact zone, confirming its usefulness in quick and reliable identification of mtDNA lineages. This approach can be modified for other species, provided diagnostic lineage variation is available, and may also be performed in simple laboratory settings while conducting fieldwork.

Assessment and monitoring of onchocerciasis in Latin America

Onchocerciasis has historically been one of the leading causes of infectious blindness worldwide. It is endemic to tropical regions both in Africa and Latin America and in the Yemen. In Latin America, it is found in 13 foci located in 6 different countries. The epidemiologically most important focus of onchocerciasis in the Americas is located in a region spanning the border between Guatemala and Mexico. However, the Amazonian focus straddling the border of Venezuela and Brazil is larger in overall area because the Yanomami populations are scattered over a very large geographical region. Onchocerciasis is caused by infection with the filarial parasite Onchocerca volvulus. The infection is spread through the bites of an insect vector, black flies of the genus Simulium. In Africa, the major vectors are members of the S. damnosum complex, while numerous species serve as vectors of the parasite in Latin America. Latin America has had a long history of attempts to control onchocerciasis, stretching back almost 100 years. The earliest programmes used a strategy of surgical removal of the adult parasites from affected individuals. However, because many of the adult parasites lodge in undetectable and inaccessible areas of the body, the overall effect of this strategy on the prevalence of infection was relatively minor. In 1988, a new drug, ivermectin, was introduced that effectively killed the larval stage (microfilaria) of the parasite in infected humans. As the microfilaria is both the stage that is transmitted by the vector fly and the cause of most of the pathologies associated with the infection, ivermectin opened up a new strategy for the control of onchocerciasis. Concurrent with the use of ivermectin for the treatment of onchocerciasis, a number of sensitive new diagnostic tools were developed (both serological and nucleic acid based) that provided the efficiency, sensitivity and specificity necessary to monitor the decline and eventual elimination of onchocerciasis as a result of successful control. As a result of these advances, a strategy for the elimination of onchocerciasis was developed, based upon mass distribution of ivermectin to afflicted communities for periods lasting long enough to ensure that the parasite population was placed on the road to local elimination. This strategy has been applied for the past decade to the foci in Latin America by a programme overseen by the Onchocerciasis Elimination Program for the Americas (OEPA). The efforts spearheaded by OEPA have been very successful, eliminating ocular disease caused by O. volvulus, and eliminating and interrupting transmission of the parasite in 8 of the 13 foci in the region. As onchocerciasis approaches elimination in Latin America, several questions still need to be addressed. These include defining an acceptable upper limit for transmission in areas in which transmission is thought to have been suppressed (e.g. what is the maximum value for the upper bound of the 95% confidence interval for transmission rates in areas where transmission is no longer detectable), how to develop strategies for conducting surveillance for recrudescence of infection in areas in which transmission is thought to be interrupted and how to address the problem in areas where the mass distribution of ivermectin seems to be unable to completely eliminate the infection.

Laboratory diagnosis of amebiasis

The detection of Entamoeba histolytica, the causative agent of amebiasis, is an important goal of the clinical microbiology laboratory. To assess the scope of E. histolytica infection, it is necessary to utilize accurate diagnostic tools. As more is discovered about the molecular and cell biology of E. histolytica, there is great potential for further understanding the pathogenesis of amebiasis. Molecular biology-based diagnosis may become the technique of choice in the future because establishment of these protozoa in culture is still not a routine clinical laboratory process. In all cases, combination of serologic tests with detection of the parasite (by antigen detection or PCR) offers the best approach to diagnosis, while PCR techniques remain impractical in many developing country settings. The detection of amebic markers in serum in patients with amebic colitis and liver abscess appears promising but is still only a research tool. On the other hand, stool antigen detection tests offer a practical, sensitive, and specific way for the clinical laboratory to detect intestinal E. histolytica. All the current tests suffer from the fact that the antigens detected are denatured by fixation of the stool specimen, limiting testing to fresh or frozen samples.

A simple and rapid DNA extraction method for the detection of Wuchereria bancrofti infection in the vector mosquito, Culex quinquefasciatus by Ssp I PCR assay

A simple, rapid and inexpensive method for the extraction of DNA from filarial vector, Culex quinquefasciatus, useful in Ssp I PCR assay for xenomonitoring of infection with Wuchereria bancrofti is presented. The DNA extracted by this method was found suitable for PCR detection of W. bancrofti infection in pools of 10-30 mosquitoes. The PCR assay employing the simplified DNA extraction method was evaluated for its sensitivity on field caught Cx. quinquefasciatus, in comparison with the conventional dissection and microscopy technique. When assayed on dissection washings of vector mosquitoes the PCR assay detected 45 pools out of 49 dissection positive pools as positive for infection and hence found to be less sensitive than the conventional technique. The reason for detecting four dissection positive pools as negatives by the PCR assay may be due to the loss of a few numbers of parasites (1-3) present in these pools during the transfer of washings of dissected mosquitoes. The PCR assay detected ten out of 72 dissection negative pools as positives, while it did not detect any of the 62 known negative (laboratory reared, uninfected) mosquito pools as positives. When 38 pools (10 mosquitoes/pool) of intact mosquitoes were assessed for infection by each method, the infection rates obtained by the two methods were almost similar (3.35 and 3.01%, respectively, for conventional method and PCR assay). The results thus show that the DNA extraction method, which is simple, rapid, safe and inexpensive, is efficient to generate DNA from vector mosquitoes useful in PCR assay and hence has potential application in xenomonitoring.

How useful is PCR in the diagnosis of malaria?

Polymerase chain reaction (PCR) assays are the most sensitive and specific method to detect malaria parasites, and have acknowledged value in research settings. However, the time lag between sample collection, transportation and processing, and dissemination of results back to the physician limits the usefulness of PCR in routine clinical practice. Furthermore, in most areas with malaria transmission, factors such as limited financial resources, persistent subclinical parasitaemia, inadequate laboratory infrastructures in the poorer, remote rural areas preclude PCR as a diagnostic method. Even in affluent, non-endemic countries, PCR is not a suitable method for routine use. Nonetheless, PCR could be clinically useful in selected situations.

PCR-based diagnosis of acute and chronic cutaneous leishmaniasis caused by Leishmania (Viannia)

We evaluated PCR methods for diagnosis of acute and chronic cutaneous leishmaniasis (CL) in an area of Colombia where Leishmania (Viannia) is endemic. The PCR method specifically amplified whole linearized minicircle kinetoplast DNA (kDNA) of the Leishmania subgenus Viannia from biopsy lysates. PCR products were detected in agarose gels. For 255 acute cases, this PCR method had greater sensitivity (75.7%) than each conventional method, i.e., microscopic examination of Giemsa-stained lesion scraping (46.7%), biopsy culture (55.3%), aspirate culture (46.3%), and the conventional methods combined (70.2%). Among 44 cases of chronic CL, amplification of biopsy DNA was more sensitive (45.5%) than the individual (4.5 to 27.7%) and combined (27.3%) conventional methods. The detection of kDNA in biopsies from chronic lesions was enhanced by a chemiluminescent dot blot hybridization, which produced a sensitivity of 65.8% when alone and 90.9% when in combination with DNA extraction of biopsy lysates (P < 0.001). Three biopsies from 84 skin lesions of other etiologies were falsely positive by PCR (specificity, 96.4%). PCR detected kDNA more frequently in biopsies (detection level, 83.9%) than in aspirates (74.7%) from 103 cases of acute CL. Among aspirates from 53 chronic cases of CL, the alternative methods, DNA extraction and hybridization, increased sensitivity from 41.5 to 56.6% (P > 0.05). This enhanced PCR method in chronic biopsies was so much more sensitive than conventional methods that it should be considered the preferred diagnostic method for chronic CL. These findings support the appropriate incorporation of PCR into diagnostic strategies for cutaneous leishmaniasis.

Future perspectives on veterinary hemoparasite research in the tropics at the start of this century

This paper has two main objectives: (1) to promote discussion about the future of veterinary hemoparasite research at the start of the twenty-first century and the third millennium, and (2) to stimulate young students to start research on parasitology, in particular in the field of veterinary tropical diseases. It is well known that in the twenty-first century human society will be challenged by several major problems resulting from the demographic explosion, since the Earth's population for the year 2020 will reach 8.5 billion, or 10 billion for the year 2050, as long as the birth rate decreases from 2.8 births per woman today to 2.0 by the year 2030 (data released by the U.N. Population Fund, 1998). Since the food production rate, either from plant or animal origin, is lower than the human birth rate, the challenge ahead will be to produce enough food for ten billion people. Consequently, to deal with this problem, especially in developing nations, it is proposed: (1) to give priority status to scientific research in the agriculture and animal fields; (2) to concentrate financial support and efforts for research especially on hemoparasitic diseases (i.e., babesiosis, anaplasmosis, cowdriosis, ehrlichiosis, and trypanosomosis), in particular to apply biotechnology techniques to those animal diseases; and (3) to grant a better role to studies on veterinary and medical parasitology in universities of the Americas and Europe, since in these universities parasitology is currently considered a secondary subject.

Diagnosis of malaria: a review of alternatives to conventional microscopy

Malaria causes significant morbidity and mortality worldwide, including countries with mainly imported malaria. In developing nations, scarce resources lead to inadequate diagnostic procedures. In affluent countries, poor familiarity with malaria may cause clinical and laboratory misdiagnosis. Microscopy of Giemsa-stained thick and thin films remains the current standard for diagnosis. Although it has good sensitivity and allows species identification and parasite counts, it is time consuming, requires microscopical expertise and maintenance of equipment. Microscopy with fluorescent stains (QBC), dipstick antigen detection of HRP2 and pLDH (Parasight-F, ICT Malaria Pf, OptiMAL), polymerase chain reaction assays and some automated blood cell analysers offer new approaches and are reviewed here, with emphasis on clinical relevance and their potential to complement conventional microscopy, especially in countries with imported malaria.

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.

Application of molecular biology in veterinary parasitology

The number of applications of molecular biology in veterinary parasitology is increasing rapidly. The techniques used with eukaryotic cells are generally applicable to the study of parasites and their hosts. The polymerase chain reaction is particularly important for identification and diagnosis of parasites, as well as for many other applications. With species and type specific probes or primers, sensitivities and specificities unheard of with conventional techniques can be achieved. The accumulation of more information on the DNA sequences of parasites will reveal many more unique sequences which can be used for identification, diagnosis, molecular epidemiology, vaccine development and for studying the evolutionary biology and the physiology of parasites and the host-parasite relationship. Similarly, the completion of genome projects on host organisms will greatly assist efforts to select for hosts that are genetically resistant to parasite infection. The study of the molecular biology of antiparasitic drug receptors, potential targets for chemotherapy, and the molecular genetics of drug resistance will allow molecular screens to be used with combinatorial chemistry in the search for new antiparasitic drugs, improvements to existing chemotherapeutic families and better diagnosis and monitoring of drug resistance. While there is a proliferation of molecular biology techniques, the availability of simple kits and of automated techniques and services for sequencing, library construction and oligonucleotide synthesis and other procedures is making it easier for non-specialists to apply many of the common techniques of molecular biology. Molecular biology and the benefits from its application are relevant for veterinary parasitologists in developing countries as well as developed countries and we should introduce aspects of molecular biology to the teaching and training of veterinary parasitologists.

Sensitivity of a polymerase chain reaction-based assay to detect Onchocerca volvulus DNA in skin biopsies

A polymerase chain reaction (PCR) of a 150-bp tandem repeat of Onchocerca volvulus (O-150) combined with Southern-blot hybridization to species-specific DNA probes was employed for DNA detection. O-150 was amplified from parasites originating from Uganda, Benin, Cameroon, Liberia, Ghana, Burkina Faso, Mali, and Zaire and was successfully hybridized to digoxigenin-labeled oligonucleotides. To investigate the sensitivity of the PCR, 2 skin biopsies were taken from each of 227 persons from Uganda with proven O. volvulus infections but with low microfilaria (mf) densities due to ivermectin treatment. One biopsy was tested by PCR and the other was digested using collagenase to assess the total number of mf. The PCR revealed 76.2% of the samples to be positive, and the collagenase method showed that 78.9% were positive, indicating similar sensitivity for the two methods. It is probable that for both techniques the biopsy must contain at least one live mf or fragments of a dead mf. In this study, no free or circulating O. volvulus DNA could be detected in skin biopsies by PCR.

Field diagnosis of onchocerciasis in an area of high versus low endemicity: evaluation of the Dot Blot Assay

Parasitological examination of skin snips is the most widely used diagnostic method for onchocerciasis, but it is associated with inconvenience and low sensitivity. We describe an inexpensive antibody-based dot blot assay (DBA) for the detection of Onchocerca volvulus infection. A field evaluation of this method was performed in the onchocerciasis endemic country Ghana by testing 370 individuals living in a highly onchocerciasis endemic area and 122 in an area of low endemicity. Sera from individuals with other filarial infections were also tested. The DBA was able to detect 95% of the parasitologically confirmed infected individuals in the highly endemic area. Cross-reactivity occurred with a minority of the sera from individuals infected with other filarial worms. The DBA was as good as or superior to presently available diagnostic tests, and it also fulfilled the criteria for a good screening method.

Detection of Plasmodium sporozoites in mosquitoes by polymerase chain reaction and oligonucleotide rDNA probe, without dissection of the salivary glands

Dried Anopheles gambiae mosquito head+thorax portions, infected with Plasmodium falciparum sporozoites, were processed by the polymerase chain reaction. The PCR product was hybridized to an oligonucleotide probe (known as 114R or AW34) diagnostic for Plasmodium. The detection level by autoradiography was ten sporozoites per mosquito. Head+thorax of mosquitoes that contained mature P.falciparum oocysts, without sporozoites, gave no positive signal, indicating that the test detects only infective mosquitoes. This test can be applied to wild mosquito specimens collected, prepared and processed at different time intervals. The technique is convenient, highly sensitive, and could be used with a non-radioactive detection system and specific probes to differentiate Plasmodium spp.

Applications of DNA amplification techniques in veterinary diagnostics

An overview of the principles of the polymerase chain reaction, ligase chain reaction, self-sustained sequence replication and Q beta replicase is given. The application of these methods for the diagnosis of veterinary infectious and hereditary diseases as well as for other diagnostic purposes is discussed and comprehensive tables of reported assays are provided. Specific areas where these DNA-based amplification methods provide substantial advantages over traditional approaches are also highlighted. With regard to PCR-based assays for the detection of viral pathogens, this article is an update of a previous review by Belák and Ballagi-Pordány (1993).