Differentiating Plasmodium falciparum alleles by transforming Cartesian X,Y data to polar coordinates

<p>Abstract</p> <p>Background</p> <p>Diagnosis of infectious diseases now benefits from advancing technology to perform multiplex analysis of a growing number of variables. These advances enable simultaneous surveillance of markers characterizing species and strain complexity, mutations associated with drug susceptibility, and antigen-based polymorphisms in relation to evaluation of vaccine effectiveness. We have recently developed assays detecting single nucleotide polymorphisms (SNPs) in the <it>P. falciparum </it>genome that take advantage of post-PCR ligation detection reaction and fluorescent microsphere labeling strategies. Data from these assays produce a spectrum of outcomes showing that infections result from single to multiple strains. Traditional methods for distinguishing true positive signal from background can cause false positive diagnoses leading to incorrect interpretation of outcomes associated with disease treatment.</p> <p>Results</p> <p>Following analysis of <it>Plasmodium falciparum </it>dihydrofolate reductase SNPs associated with resistance to a commonly used antimalarial drug, Fansidar (Sulfadoxine/pyrimethamine), and presumably neutral SNPs for parasite strain differentiation, we first evaluated our data after setting a background signal based on the mean plus three standard deviations for known negative control samples. Our analysis of single allelic controls suggested that background for the absent allele increased as the concentration of the target allele increased. To address this problem, we introduced a simple change of variables from customary (<it>X,Y</it>) (Cartesian) coordinates to planar polar coordinates (<it>X </it>= <it>r</it>cos(<it>θ</it>), <it>Y </it>= <it>r</it>sin(<it>θ</it>)). Classification of multidimensional fluorescence signals based on histograms of angular and radial data distributions proved more effective than classification based on Cartesian thresholds. Comparison with known diallelic dilution controls suggests that histogram-based classification is effective for major:minor allele concentration ratios as high as 10:1.</p> <p>Conclusion</p> <p>We have observed that the diallelic SNP data resulting from analysis of <it>P. falciparum </it>mutations is more accurately diagnosed when a simple polar transform of the (<it>X,Y</it>) data into (<it>r,θ</it>) is used. The development of high through-put methods for genotyping <it>P. falciparum </it>SNPs and the refinement of analytical approaches for evaluating these molecular diagnostic results significantly advance the evaluation of parasite population diversity and antimalarial drug resistance.</p

Application of a Polymerase Chain Reaction-ELISA to Detect Wuchereria bancrofti in Pools of Wild-Caught Anopheles punctualatus in a Filariasis Control Area in Papua New Guinea

Chemotherapy-based eradication programs are aimed at stopping transmission of Wuchereria bancroftiby its obligatory mosquito vector. This study compares one year post-treatment W. bancrofti infection rates of Anopheles punctulatus, the main vector of lymphatic filariasis in Papua New Guinea, using traditional dissection techniques and a polymerase chain reaction (PCR)-based ELISA of a parasite-specific Ssp I repeat. A total of 633 mosquitoes in 35 batches were dissected. Six batches contained W. bancrofti-infected mosquitoes, giving a minimum infection rate of 0.9%. This value was not different than the actual infection rate, which was 9 (1.4%) of 633 mosquitoes (P� 0.48). The DNA was extracted from 47 pools containing a mean of 13.2 mosquitoes per pool. A total of 621 mosquitoes were processed for the PCR-ELISA, including 486 caught by human bait and 135 by light trap, which included both dead and live mosquitoes. Of 23 pools of alcohol-preserved human-bait mosquitoes, seven were positive by the PCR-ELISA, giving an infection rate identical to that obtained by dissection of individual mosquitoes (1.4%). The minimum infection rates for pools of light-trap mosquitoes found dead and alive were 2.7% (2 of 74) and 4.9% (3 of 61), respectively. These values did not differ from each other (P � 0.84), but the overall infection rate of light- trap mosquitoes was greater than that of mosquitoes captured by human bait (3.7% versus 1.4%; P � 0.09). These data indicate that the PCR-ELISA of a W. bancrofti Ssp I repeat using pools of mosquitoes is comparable to traditional dissection techniques for monitoring transmission intensity following introduction of mass chemotherapy. This approach may also be useful for rapid and cost-effective assessment of transmission in endemic areas where the frequency of overt lymphatic pathology is low

A new high-throughput method for simultaneous detection of drug resistance associated mutations in Plasmodium vivax dhfr, dhps and mdr1 genes

<p>Abstract</p> <p>Background</p> <p>Reports of severe cases and increasing levels of drug resistance highlight the importance of improved <it>Plasmodium vivax </it>case management. Whereas monitoring <it>P. vivax </it>resistance to anti-malarial drug by <it>in vivo </it>and <it>in vitro </it>tests remain challenging, molecular markers of resistance represent a valuable tool for high-scale analysis and surveillance studies. A new high-throughput assay for detecting the most relevant markers related to <it>P. vivax </it>drug resistance was developed and assessed on Papua New Guinea (PNG) patient isolates.</p> <p>Methods</p> <p><it>Pvdhfr, pvdhps </it>and <it>pvmdr1 </it>fragments were amplified by multiplex nested PCR. Then, PCR products were processed through an LDR-FMA (ligase detection reaction - fluorescent microsphere assay). 23 SNPs, including <it>pvdhfr </it>57-58-61 and 173, <it>pvdhps </it>382-383, 553, 647 and <it>pvmdr1 </it>976, were simultaneously screened in 366 PNG <it>P. vivax </it>samples.</p> <p>Results</p> <p>Genotyping was successful in 95.4% of the samples for at least one gene. The coexistence of multiple distinct haplotypes in the parasite population necessitated the introduction of a computer-assisted approach to data analysis. Whereas 73.1% of patients were infected with at least one wild-type genotype at codons 57, 58 and 61 of <it>pvdhfr</it>, a triple mutant genotype was detected in 65.6% of the patients, often associated with the 117T mutation. Only one patient carried the 173L mutation. The mutant 647P <it>pvdhps </it>genotype allele was approaching genetic fixation (99.3%), whereas 35.1% of patients were infected with parasites carrying the <it>pvmdr1 </it>976F mutant allele.</p> <p>Conclusions</p> <p>The LDR-FMA described here allows a discriminant genotyping of resistance alleles in the <it>pvdhfr</it>, <it>pvdhps</it>, and <it>pvmdr1 </it>genes and can be used in large-scale surveillance studies.</p

Significant geographical differences in prevalence of mutations associated with Plasmodium falciparum and Plasmodium vivax drug resistance in two regions from Papua New Guinea

Drug resistance remains a major obstacle to malaria treatment and control. It can arise and spread rapidly, and vary substantially even at sub-national level. National malaria programmes require cost-effective and timely ways of characterizing drug-resistance at multiple sites within their countries.; An improved multiplexed post-PCR ligase detection reaction-fluorescent microsphere assay (LDR-FMA) was used to simultaneously determine the presence of mutations in chloroquine resistance transporter (crt), multidrug resistance 1 (mdr1), dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) genes in Plasmodium falciparum (n = 727) and Plasmodium vivax (n = 574) isolates collected in 2006 from cross-sectional community population surveys in two geographically distinct regions (Madang and East Sepik) of Papua New Guinea (PNG) where strong regional differences in in vivo aminoquinoline and antifolate therapeutic efficacy had previously been observed. Data were compared to those of a follow-up survey conducted in 2010.; Despite some very low parasite densities, the assay successfully amplified all P. falciparum and P. vivax loci in 77 and 69 % of samples, respectively. In 2006, prevalences of pfdhfr (59R-108 N) double mutation/wild type pfdhps haplotype, pfcrt SVMNT haplotype (72S-76T double mutation), and 86Y pfmdr1 mutation all exceeded 90 %. For P. vivax, 65 % carried at least two pvdhfr mutations, 97 % the 647P pvdhps mutation and 54 % the 976F pvmdr1 mutation. Prevalence of mutant haplotypes was higher in Madang than East Sepik for pfcrt SVMNT (97.4 vs 83.3 %, p = 0.001), pfdhfr (59R-108 N) (100 vs 90.6 %, p = 0.001), pvdhfr haplotypes (75.8 vs 47.6 %, p = 0.001) and pvmdr1 976F (71.2 vs 26.2 %, p &lt; 0.001). Data from a subsequent Madang survey in 2010 showed that the prevalence of pfdhps mutations increased significantly from &lt;5 % to &gt;30 % (p &lt; 0.001) as did the prevalence of pvdhfr mutant haplotypes (from 75.8 to 97.4 %, p = 0.012).; This LDR-FMA multiplex platform shows feasibility for low-cost, high-throughput, rapid characterization of a broad range of drug-resistance markers in low parasitaemia infections. Significant geographical differences in mutation prevalence correlate with previous genotyping surveys and in vivo trials and may reflect variable drug pressure and differences in health-care access in these two PNG populations

Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing

Understanding mosquito host choice is important for assessing vector competence or identifying disease reservoirs. Unfortunately, the availability of an unbiased method for comprehensively evaluating the composition of insect blood meals is very limited, as most current molecular assays only test for the presence of a few pre-selected species. These approaches also have limited ability to identify the presence of multiple mammalian hosts in a single blood meal. Here, we describe a novel high-throughput sequencing method that enables analysis of 96 mosquitoes simultaneously and provides a comprehensive and quantitative perspective on the composition of each blood meal. We validated in silico that universal primers targeting the mammalian mitochondrial 16S ribosomal RNA genes (16S rRNA) should amplify more than 95% of the mammalian 16S rRNA sequences present in the NCBI nucleotide database. We applied this method to 442 female Anopheles punctulatus s. l. mosquitoes collected in Papua New Guinea (PNG). While human (52.9%), dog (15.8%) and pig (29.2%) were the most common hosts identified in our study, we also detected DNA from mice, one marsupial species and two bat species. Our analyses also revealed that 16.3% of the mosquitoes fed on more than one host. Analysis of the human mitochondrial hypervariable region I in 102 human blood meals showed that 5 (4.9%) of the mosquitoes unambiguously fed on more than one person. Overall, analysis of PNG mosquitoes illustrates the potential of this approach to identify unsuspected hosts and characterize mixed blood meals, and shows how this approach can be adapted to evaluate inter-individual variations among human blood meals. Furthermore, this approach can be applied to any disease-transmitting arthropod and can be easily customized to investigate non-mammalian host sources

Performance Across Worldview-2 and RapidEye for Reproducible Seagrass Mapping

Satellite remote sensing offers an effective remedy to challenges in ground-based and aerial mapping that have previously impeded quantitative assessments of global seagrass extent. Commercial satellite platforms offer fine spatial resolution, an important consideration in patchy seagrass ecosystems. Currently, no consistent protocol exists for image processing of commercial data, limiting reproducibility and comparison across space and time. Additionally, the radiometric performance of commercial satellite sensors has not been assessed against the dark and variable targets characteristic of coastal waters. This study compared data products derived from two commercial satellites: DigitalGlobe\u27s WorldView-2 and Planet\u27s RapidEye. A single scene from each platform was obtained at St. Joseph Bay in Florida, USA, corresponding to a November 2010 field campaign. A reproducible processing regime was developed to transform imagery from basic products, as delivered from each company, into analysis-ready data usable for various scientific applications. Satellite-derived surface reflectances were compared against field measurements. WorldView-2 imagery exhibited high disagreement in the coastal blue and blue spectral bands, chronically overpredicting. RapidEye exhibited better agreement than WorldView-2, but overpredicted slightly across all spectral bands. A deep convolutional neural network was used to classify imagery into deep water, land, submerged sand, seagrass, and intertidal classes. Classification results were compared to seagrass maps derived from photointerpreted aerial imagery. This study offers the first radiometric assessment of WorldView-2 and RapidEye over a coastal system, revealing inherent calibration issues in shorter wavelengths of WorldView-2. Both platforms demonstrated as much as 97% agreement with aerial estimates, despite differing resolutions. Thus, calibration issues in WorldView-2 did not appear to interfere with classification accuracy, but could be problematic if estimating biomass. The image processing routine developed here offers a reproducible workflow for WorldView-2 and RapidEye imagery, which was tested in two additional coastal systems. This approach may become platform independent as more sensors become available

A polymerase chain reaction/ligase detection reaction fluorescent microsphere assay to determine Plasmodium falciparum MSP-119 haplotypes

The merozoite surface protein-1 (MSP-1) is a blood stage antigen currently being tested as a vaccine against Plasmodium falciparum malaria. Determining the MSP-1(19) haplotype(s) present during infection is essential for assessments of MSP-1 vaccine efficacy and studies of protective immunity in human populations. The C-terminal fragment (MSP-1(19)) has four predominant haplotypes based on point mutations resulting in non-synonymous amino acid changes: E-TSR (PNG-MAD20 type), E-KNG (Uganda-PA type), Q-KNG (Wellcome type), and Q-TSR (Indo type). Current techniques using direct DNA sequencing are laborious and expensive. We present an MSP-1(19) allele-specific polymerase chain reaction (PCR)/ligase detection reaction-fluorescent microsphere assay (LDR-FMA) that allows simultaneous detection of the four predominant MSP-1(19) haplotypes with a sensitivity and specificity comparable with other molecular methods and a semi-quantitative determination of haplotype contribution in mixed infections. Application of this method is an inexpensive, accurate, and high-throughput alternative to distinguish the predominant MSP-1(19) haplotypes in epidemiologic studies

Enhanced detection of gametocytes by magnetic deposition microscopy predicts higher potential for Plasmodium falciparum transmission

<p>Abstract</p> <p>Background</p> <p>Aggregated haemozoin crystals within malaria-infected erythrocytes confer susceptibility of parasitized cells to a magnetic field. Here the utility of this method for diagnosis of human malaria is evaluated in a malaria-endemic region of Papua New Guinea (PNG).</p> <p>Methods and findings</p> <p>Individuals with <it>Plasmodium falciparum </it>malaria symptoms (n = 55) provided samples for conventional blood smear (CBS) and magnetic deposition microscopy (MDM) diagnosis. Standard Giemsa staining and light microscopy was performed to evaluate all preparations. <it>Plasmodium falciparum </it>parasitaemia observed on MDM slides was consistently higher than parasitaemia observed by (CBS) for ring (CBS = 2.6 vs. MDM = 3.4%; t-test P-value = 0.13), trophozoite (CBS = 0.5 vs. MDM = 1.6%; t-test P-value = 0.01), schizont (CBS = 0.003 vs. MDM = 0.1%; t-test P-value = 0.08) and gametocyte (CBS = 0.001 vs. MDM = 0.4%; t-test P-value = 0.0002) parasitaemias. Gametocyte prevalence determined by CBS compared to MDM increased from 7.3% to 45%, respectively.</p> <p>Conclusion</p> <p>MDM increased detection sensitivity of <it>P. falciparum</it>-infected, haemozoin-containing erythrocytes from infected humans while maintaining detection of ring-stage parasites. Gametocyte prevalence five-fold higher than observed by CBS suggests higher malaria transmission potential in PNG endemic sites compared to previous estimates.</p