Detection of pyrimethamine resistance in Plasmodium falciparum by mutation-specific polymerase chain reaction

The point mutation at nucleotide 323 within the dihydrofolate reductase-thymidylate synthase gene of Plasmodium falciparum, which distinguishes pyrimethamine-sensitive from drug-resistant isolates, can be discriminated by the polymerase chain reaction using mutation-specific primers. The technique makes use of the principle that short oligonucleotides with a perfect match at their 3' ends, complementary to the mutation to be detected, will initiate the polymerization by Taq polymerase far more efficiently than primers with a single mismatch in this position. The Asn-108 codon was detected using a primer of 17 nucleotides with an adenosine at its 3' end, the Thr-108 codon with a 14-mer primer ending with a cytosine and the Ser-108 codon with a 16-mer containing guanidine at the critical 3' end. By selecting appropriate counterprimers, the size of the amplification products is either indicative of pyrimethamine-resistant parasites of the 7G8 type, or of pyrimethamine-sensitive parasites of the FCR-3 type or 3D7 type. The fragments obtained can be easily separated in a single lane after agarose gel electrophoresis. Coded P. falciparum DNA samples were typed unambiguously using these primers as were reconstituted parasitized blood samples stored as high salt lysates. Sensitivity, speed and specificity make this assay a realistic alternative to in vitro drug testing to monitor the resistance of P. falciparum to inhibitors of the dihydrofolate reductase.     

Intragenic recombinants of Plasmodium falciparum identified by in situ polymerase chain reaction.

We report an in situ PCR technique for visualising amplified DNA of blood forms of Plasmodium falciparum on microscope slides by fluorescence microscopy. The method is used to assess the changes in frequency of different alleles of the MSP1 gene in cultures of the progeny of a cross. We show that parasites with a recombinant form of this protein possess an initial growth advantage before declining in numbers over the long-term.     

Diagnosis of Toxoplasma parasitemia in patients with AIDS by gene detection after amplification with polymerase chain reaction.

We sought evidence of toxoplasma parasitemia among 37 people with active or dormant Toxoplasma gondii infection or no evidence of infection. DNA was extracted from erythrocyte-free portions of blood samples, and the T. gondii B1 gene was amplified by the polymerase chain reaction. Evidence of T. gondii parasitemia was found in six patients with severe immunosuppression from AIDS and clinical evidence suggestive of or compatible with toxoplasmosis. Results were negative for patients unlikely to have active toxoplasmosis. Gene detection after amplification with the polymerase chain reaction is a promising test for detection of parasitemia, and parasitemia should be tested for in patients with AIDS and unexplained fever or central nervous system abnormalities.     

Malaria attack: a difficult diagnosis in a region of high Plasmodium falciparum endemicity

The diagnosis of malaria attack in regions for highly endemic P. falciparum is difficult. It is more so since the wide use of antimalarials by the infected populations and the spread of drug resistance. A positive test is not evidence for a malarial attack since in certain schools, in both rural regions and in some districts of big towns, over 3/4 of the children attending school are carriers of Plasmodium. On the other hand, true attacks, even severe forms, can occur without evidence of parasitaemia. The parasitic load is thus an important factor but the following must be taken into consideration: age, level of immunity, the extent of transmission and whether if is continuous or not, self medication and the initial systematic treatments, the possibility of drug resistance, ... The difficulties are illustrated by data collected in the Congo.     

Evaluation of the polymerase chain reaction analysis for diagnosis of falciparum malaria in Delhi, India

Plasmodium falciparum infections are frequently fatal if untreated and hence need to be diagnosed and treated early. Malaria diagnosis, with conventional Giemsa staining as a gold standard, has had several limitations. New rapid and accurate methods are needed for diagnosis. In this study, polymerase chain reaction (PCR) analysis specific for diagnosis of P. falciparum was evaluated. For the study, blood samples were collected from 310 patients suspected of having malaria. PCR analysis for P. falciparum from venous blood and at the same time Giemsa staining of thick and thin blood smears was done. A total of 160 (51.6 %) samples were positive for malarial parasite of which 63 (39.4 %) were positive for P. falciparum by Giemsa staining while 61 (38.1 %) were positive for P. falciparum by PCR analysis. Giemsa staining was time consuming, laborious and may give poor results in cases with low parasitaemia. The PCR analysis for P. falciparum was able to detect 3 cases of low parasitaemia missed initially on Giemsa staining, was 96.8 % sensitive, 100% specific but was very costly, needed a lot of practice and standardization and was time consuming. PCR analysis can be used to supplement the conventional Giemsa staining for reliable diagnosis of falciparum malaria especially in cases with low parasitaemia.     

Comparison of a conventional polymerase chain reaction with real-time polymerase chain reaction for the detection of neurotropic viruses in cerebrospinal fluid samples

Purpose: To compare a conventional polymerase chain reaction (PCR) and real-time PCR for the detection of neurotropic DNA viruses. Materials and Methods: A total of 147 cerebrospinal fluid (CSF) samples was collected from patients attending a tertiary care hospital in South India for a period from 2005 to 2008. All these samples were tested using a conventional multiplex/uniplex PCR and a real-time multiplex/uniplex PCR. This technique was used to detect a large number of herpes viruses responsible for central nervous system infections, including HSV-1, HSV-2, VZV, CMV and EBV and the polyoma virus JCV. Results: Overall, in the entire set of samples, the real-time PCR yielded 88 (59.9%) positives and conventional PCR had six (4.1%) positives. Conclusion: Our results suggest that the real-time PCR assay was more sensitive compared with the conventional PCR. The advantage of real-time PCR is that it can be performed much faster than conventional PCR. Real-time PCR is less time-consuming, less labour-intensive and also reduces the chance of contamination as there is no post-amplification procedure. In the entire study population, the major viruses detected using real-time PCR were EBV (34%), HSV-2 (10.8%) and VZV (6.8%).     

Method of polymerase chain reaction in toxoplasmosis diagnosis

Since introduction of polymerase chain reaction for the detection of DNA Toxoplasma gondii 398 biological samples from 301 patients were examined from 2000 to 2003. Positive finding of toxoplasmosis DNA we noted in 23 cases. Polymerase chain reaction enables exact and fast diagnosis of the actual parasitemia Toxoplasma gondii, which is important especially in the pregnant patients, new-born with suspicion on congenital toxoplasmosis and in the patients with immunosupression.     

Devices for rapid diagnosis of Malaria: evaluation of prototype assays that detect Plasmodium falciparum histidine-rich protein 2 and a Plasmodium vivax-specific antigen

The ParaSight F test was developed as a pioneer industry effort in the large-scale, process-controlled production of a device for the rapid diagnosis of malaria. This device performed well in field settings but was limited to the detection of a single malaria species, Plasmodium falciparum. The ParaSight F+V assay advanced upon the ParaSight F test format by incorporating a monoclonal antibody directed against a proprietary Plasmodium vivax-specific antigen, in addition to the antibody directed against P. falciparum histidine-rich protein 2, which was used in the ParaSight F assay. The modified assay was developed to add the capability to detect P. falciparum and P. vivax in a single-test-strip format. The present study evaluated three distinct ParaSight F+V prototypes with samples from symptomatic patients in regions of Thailand and Peru where malaria is endemic. Over a 2-year enrollment period (1998 and 1999), a total of 4,894 patients consented to participation in the study. Compared with the results for duplicate microscopic examinations of Giemsa-stained blood smears as the reference diagnostic standard, each successive prototype showed substantial improvement in performance. The final ParaSight F+V prototype, evaluated in 1999, had an overall sensitivity for detection of asexual P. falciparum parasites of 98%. The sensitivity of the device was 100% for P. falciparum densities of >500 parasites/ micro l, with a sensitivity of 83% for parasite densities of 5,000/ micro l, 92% for parasite densities of 1,001 to 5,000/ micro l, 94% for parasite densities of 501 to 1,000/ micro l, and 55% for parasite densities of 1 to 500/ micro l. The specificity for the exclusion of P. vivax was 87%. The areas under the receiver operating characteristic curves for the diagnostic performance of the assay for the detection of P. falciparum and P. vivax were 0.8907 and 0.8522, respectively. These findings indicate that assays for rapid diagnosis have the potential to enhance diagnostic capabilities in those instances in which skilled microscopy is not readily available.     

Development of the polymerase chain reaction for diagnosis of chancroid.

The published nucleotide sequences of the 16S rRNA gene of Haemophilus ducreyi were used to develop primer sets and probes for the diagnosis of chancroid by polymerase chain reaction (PCR) DNA amplification. One set of broad specificity primers yielded a 303-bp PCR product from all bacteria tested. Two 16-base probes internal to this sequence were species specific for H. ducreyi when tested with 12 species of the families Pasteurellaceae and Enterobacteriaceae. The two probes in combination with the broad specificity primers were 100% sensitive with 51 strains of H. ducreyi isolated from six continents over a 15-year period. The direct detection of H. ducreyi from 100 clinical specimens by PCR showed a sensitivity of 83 to 98% and a specificity of 51 to 67%, depending on the number of amplification cycles.     

Silicon inhibition effects on the polymerase chain reaction: a real-time detection approach

In the miniaturization of biochemical analysis systems, biocompatibility of the microfabricated material is a key feature to be considered. A clear insight into interactions between biological reagents and microchip materials will help to build more robust functional bio-microelectromechanical systems (BioMEMS). In the present work, a real-time polymerase chain reaction (PCR) assay was used to study the inhibition effects of silicon and native silicon oxide particles on Hepatitis B Virus (HBV) DNA PCR amplification. Silicon nanoparticles with different surface oxides were added into the PCR mixture to activate possible interactions between the silicon-related materials and the PCR reagents. Ratios of silicon nanoparticle surface area to PCR mixture volume (surface to volume ratio) varied from 4.7 to 235.5 mm2/microL. Using high speed centrifugation, the nanoparticles were pelleted to tube inner surfaces. Supernatant extracts were then used in subsequent PCR experiments. To test whether silicon materials participated in amplifications directly, in some cases, entire PCR mixture containing silicon nanoparticles were used in amplification. Fluorescence histories of PCR amplifications indicated that with the increase in surface to volume ratio, amplification efficiency decreased considerably, and within the studied ranges, the higher the particle surface oxidation, the stronger the silicon inhibition effects on PCR. Adsorption of Taq polymerase (not nucleic acid) on the silicon-related material surface was the primary cause of the inhibition phenomena and silicon did not participate in the amplification process directly.     

Comparison of different PCR protocols for the detection and diagnosis of Plasmodium falciparum

An assessment of differing PCR protocols for the diagnosis of Plasmodium falciparum infection was performed on samples from an area of holoendemic malaria transmission in western Burkina Faso. The PCR protocols had generally high sensitivities (>92%) and specificities (>69%), but the negative predictive values (NPV) were moderate and differed widely among the PCR protocols tested. These PCR protocols that amplified either the P. falciparum pfcrt gene or the small subunit ribosomal DNA were the most reliable diagnostic tools. However, the moderate NPV imply that more than one PCR protocol should be used for diagnosis in holoendemic areas.N. Oster and I.Z. Abdel-Aziz have contributed equally to this work.     

Typing of Plasmodium falciparum DNA from 2 years old Giemsa-stained dried blood spots using nested polymerase chain reaction assay

A panel of 129 Giemsa-stained thick blood spots (TBS) confirmed for Plasmodium falciparum infection having different levels of parasite density were collected from a malaria endemic area. DNA was extracted and nested polymerase chain reaction (PCR) assay was performed to amplify P. falciparum DNA. Nested PCR assay successfully amplified P. falciparum DNA at a very low parasitaemia of ~10 parasites/μl of blood. Current PCR assay is very simple and can be used retrospectively to monitor the invasion and prevalence of different Plasmodium species in endemic areas.     

Plasmodium falciparum Malaria: reduction of endothelial cell apoptosis in vitro

Organ failure in Plasmodium falciparum malaria is associated with neutrophil activation and endothelial damage. This study investigates whether neutrophil-induced endothelial damage involves apoptosis and whether it can be prevented by neutralization of neutrophil secretory products. Endothelial cells from human umbilical veins were coincubated with neutrophils from healthy donors and with sera from eight patients with P. falciparum malaria, three patients with P. vivax malaria, and three healthy controls. Endothelial apoptosis was demonstrated by terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) and annexin V staining. The rate of apoptosis of cells was markedly increased after incubation with patient serum compared to that with control serum. Apoptosis was most pronounced after incubation with sera from two patients with fatal cases of P. falciparum malaria, followed by sera of survivors with severe P. falciparum malaria and, finally, by sera of patients with mild P. falciparum and P. vivax malaria. Ascorbic acid, tocopherol, and ulinastatin reduced the apoptosis rate, but gabexate mesilate and pentoxifylline did not. Furthermore, in fatal P. falciparum malaria, apoptotic endothelial cells were identified in renal and pulmonary tissue by TUNEL staining. These findings show that apoptosis caused by neutrophil secretory products plays a major role in endothelial cell damage in malaria. The antioxidants ascorbic acid and tocopherol and the protease inhibitor ulinastatin can reduce malaria-associated endothelial apoptosis in vitro.     

The polymerase chain reaction in the human immunodeficiency virus diagnosis

The PCR technique detects HIV1 and HIV2 DNA and RNA sequences in mononuclear cells with high sensitivity. It allows therefore to analyse the mother to child HIV1 transmission. Moreover, in the near future, the quantification of the PCR products could allow the follow-up of the patients treated for HIV infection.