Dataset Information

Utility of Plasmodium falciparum DNA from rapid diagnostic test kits for molecular analysis and whole genome amplification.

ABSTRACT:

Background

Rapid diagnostic tests (RDTs) have become the most common diagnostic tool for detection of Plasmodium falciparum malaria, in particular in remote areas. RDT blood spots provide a source of parasite DNA for molecular analysis. In this study, the utility of RDTs for molecular analysis and the performance of different methods for whole genome amplification were investigated.

Methods

Positive P. falciparum RDTs were collected from Kayin, Myanmar from August 2014 to January 2016. The RDT samples were stored for 6 months, 9 months, 20 months, 21 months, and 32 months before DNA extraction and subsequent molecular analysis of P. falciparum kelch 13 (pfkelch13) mutations, P. falciparum multidrug resistance 1 (pfmdr1), and P. falciparum plasmepsin 2 (pfplasmepsin2) gene amplification. In addition, performance of four whole genome amplification (WGA) kits were compared, including REPLI-g^®, MALBAC^TM, PicoPLEX^®, and GenomePlex^®, for which DNA quantity and quality were compared between original DNA and post-WGA products.

Results

The proportion of successful amplification of the different molecular markers was similar between blood spots analysed from RDTs stored for 6, 9, 20, 21, or 32 months. Successful amplification was dependent on the molecular markers fragment length (p value?®, MALBAC^TM, and PicoPLEX^® increased the quantity of DNA 60 to 750-fold, whereas the ratio of parasite DNA amplification over human DNA was most favourable for MALBAC^®. Sequencing results of pfkelch13, P. falciparum chloroquine resistance transporter (pfcrt), P. falciparum dihydrofolate reductase (pfdhfr) and six microsatellite markers assessed from the post-WGA product was the same as from the original DNA.

Conclusions

Blood spots from RDTs are a good source for molecular analysis of P. falciparum, even after storage up to 32 months. WGA of RDT-derived parasite DNA reliably increase DNA quantity with sufficient quality for molecular analysis of resistance markers.

SUBMITTER: Srisutham S

PROVIDER: S-EPMC7251736 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Utility of Plasmodium falciparum DNA from rapid diagnostic test kits for molecular analysis and whole genome amplification.

Srisutham Suttipat S Suwannasin Kanokon K Mathema Vivek Bhakta VB Sriprawat Kanlaya K Smithuis Frank M FM Nosten Francois F White Nicholas J NJ Dondorp Arjen M AM Imwong Mallika M

Malaria journal 20200527 1

<h4>Background</h4>Rapid diagnostic tests (RDTs) have become the most common diagnostic tool for detection of Plasmodium falciparum malaria, in particular in remote areas. RDT blood spots provide a source of parasite DNA for molecular analysis. In this study, the utility of RDTs for molecular analysis and the performance of different methods for whole genome amplification were investigated.<h4>Methods</h4>Positive P. falciparum RDTs were collected from Kayin, Myanmar from August 2014 to January ...[more]

PMID: 32460780

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Project description:BackgroundPlasmodium falciparum strains with mutations/deletions of the genes encoding the histidine-rich proteins 2/3 (pfhrp2/3) have emerged during the last 10 years leading to false-negative results in HRP2-based rapid diagnostic tests (RDTs). This can lead to unrecognized infections in individuals and to setbacks in malaria control in endemic countries where RDTs are the backbone of malaria diagnostics and control.Case descriptionHere the detection of a pfhrp2/3-negative P. falciparum infection acquired in Ethiopia by a 63-year old female traveller is presented. After onset of symptoms during travel, she was first tested negative for malaria, most probably by RDT, at a local hospital in Harar, Ethiopia. Falciparum malaria was finally diagnosed microscopically upon her return to Germany, over 4 weeks after infection. At a parasite density of approximately 5387 parasites/µl, two different high-quality RDTs: Palutop + 4 OPTIMA, NADALRMalaria PF/pan Ag 4 Species, did not respond at their respective P. falciparum test lines. pfhrp2/3 deletion was confirmed by multiplex-PCR. The patient recovered after a complete course of atovaquone and proguanil. According to the travel route, malaria was acquired most likely in the Awash region, Central Ethiopia. This is the first case of imported P. falciparum with confirmed pfhrp2/3 deletion from Ethiopia.ConclusionHRP2-negative P. falciparum strains may not be recognized by the presently available HRP2-based RDTs. When malaria is suspected, confirmation by microscopy and/or qPCR is necessary in order to detect falciparum malaria, which requires immediate treatment. This case of imported P. falciparum, non-reactive to HRP2-based RDT, possibly underlines the necessity for standardized, nationwide investigations in Ethiopia and should alert clinicians from non-endemic countries to the possibility of false-negative RDT results which may increase in returning travellers with potentially life-threatening infections.

Project description:BackgroundThe first pillar of the UNAIDS 90-90-90 goal seeks to accurately identify persons living with HIV (PLHIV), a process that is predicated on facilities having the necessary HIV tests available to perform the task. In many rural settings, the identification of PLHIV is accomplished through a two-step process involving the sequential use of 2 separate rapid diagnostic tests (RDTs). Inadequate inventory of either test has ramifications for the success of HIV-related programs. The purpose of this study was to evaluate the inventory levels of HIV RDT kits at specific healthcare facilities in Zambézia province, Mozambique.MethodsUsing facility-level pharmacy stock surveillance data from October 2015 through September 2016, we assessed the inventory levels of HIV RDTs at 75 health facilities in 8 districts within Zambézia province, Mozambique. Using programmatically established categories (good, sufficient, threatened, or stockout), defined in conjunction with the provincial health authorities, descriptive statistics were performed to determine inventory control of HIV RDTs at the district and health facility levels. Monthly proportions of adequate (good + sufficient) inventory were calculated for each district to identify inventory trends over the evaluation period. To assess whether the proportion of inadequate stocks differed between RDT, a mixed-effects logistic regression was conducted, with inadequate inventory status as the outcome of interest.ResultsWhen viewed as a whole, the inventory of each test kit was reported as being at adequate levels more than 89% of the time across the 75 facilities. However, disaggregated analysis revealed significant variability in the inventory levels of HIV RDTs at the district level. Specifically, the districts of Inhassunge, Namacurra, and Pebane reported inadequate inventory levels (threatened + stockout), of one or both test kits, for more than 10% of the study period. In addition, a disparity between inventory levels of each test kit was identified, with the odds of reporting inadequate inventory levels of the confirmatory test (Uni-Gold™) being approximately 1.8-fold greater than the initial test (Determine™) (odds ratio: 1.82, 95% CI: 1.40-2.38).ConclusionAs Test and Treat programs evolve, a significant emphasis should be placed on the "test" component of the strategy, beginning with assurances that health facilities have the adequate inventory of RDT necessary to meet the needs of their community. As national policy-makers rely predominantly on data from the upstream arm of the supply chain, it is unlikely the disparity between inventory levels of HIV RDTs identified at individual districts and specific health facilities would have been recognized. Moving forward, our findings point to a need for (1) renewed efforts reinforcing appropriate downstream forecasting of essential medicines and diagnostic tests in general and for Uni-Gold™ test kits specifically, and (2) simple metrics that may be routinely collected at all health facilities and which may then easily and quickly flow upstream so that policy-makers may optimally allocate resources.

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Project description:BackgroundThe need for new malaria surveillance tools and strategies is critical, given improved global malaria control and regional elimination efforts. High quality Plasmodium falciparum DNA can reliably be extracted from malaria rapid diagnostic tests (RDTs). Together with highly sensitive molecular assays, wide scale collection of used RDTs may serve as a modern tool for improved malaria case detection and drug resistance surveillance. However, comparative studies of DNA extraction efficiency from RDTs and the field applicability are lacking. The aim of this study was to compare and evaluate different methods of DNA extraction from RDTs and to test the field applicability for the purpose of molecular epidemiological investigations.MethodsDNA was extracted from two RDT devices (Paracheck-Pf® and SD Bioline Malaria Pf/Pan®), seeded in vitro with 10-fold dilutions of cultured 3D7 P. falciparum parasites diluted in malaria negative whole blood. The level of P. falciparum detection was determined for each extraction method and RDT device with multiple nested-PCR and real-time PCR assays. The field applicability was tested on 855 paired RDT (Paracheck-Pf) and filter paper (Whatman® 3MM) blood samples (734 RDT negative and 121 RDT positive samples) collected from febrile patients in Zanzibar 2010. RDT positive samples were genotyped at four key single nucleotide polymorphisms (SNPs) in pfmdr1 and pfcrt as well as for pfmdr1 copy number, all associated with anti-malarial drug resistance.ResultsThe P. falciparum DNA detection limit varied with RDT device and extraction method. Chelex-100 extraction performed best for all extraction matrixes. There was no statistically significant difference in PCR detection rates in DNA extracted from RDTs and filter paper field samples. Similarly there were no significant differences in the PCR success rates and genotyping outcomes for the respective SNPs in the 121 RDT positive samples.ConclusionsThe results support RDTs as a valuable source of parasite DNA and provide evidence for RDT-DNA extraction for improved malaria case detection, molecular drug resistance surveillance, and RDT quality control.

Dataset Information

Utility of Plasmodium falciparum DNA from rapid diagnostic test kits for molecular analysis and whole genome amplification.

Background

Methods

Results

Conclusions

Publications

Utility of Plasmodium falciparum DNA from rapid diagnostic test kits for molecular analysis and whole genome amplification.

Similar Datasets

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