ORCID Profile
0000-0002-9354-0414
Current Organisation
University of Notre Dame
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Publisher: Cold Spring Harbor Laboratory
Date: 30-12-2022
DOI: 10.1101/2022.12.28.22284015
Abstract: Progress in malaria control has stalled over the recent years. Knowledge on main drivers of transmission explaining small-scale variation in prevalence can inform targeted control measures. We collected finger-prick blood s les from 3061 in iduals irrespective of clinical symptoms in 20 clusters in Busia in western Kenya and screened for Plasmodium falciparum parasites using qPCR and microscopy. Clusters spanned an altitude range of 207 meters (1077-1284 m). We mapped potential mosquito larval habitats and determined their number within 250 m of a household and distances to households using ArcMap. Across all clusters, P. falciparum parasites were detected in 49.8% (1524/3061) of in iduals by qPCR and 19.5% (596/3061) by microscopy. Across the clusters, prevalence ranged from 26% to 70% by qPCR. Three to 34 larval habitats per cluster and 0-17 habitats within a 250m radius around households were observed. Using a generalized linear mixed effect model (GLMM), a 5% decrease in the odds of getting infected per each 10m increase in altitude was observed, while the number of larval habitats and their proximity to households were not statistically significant predictors for prevalence. Kitchen located indoors, open eaves, a lower level of education of the household head, older age, and being male were significantly associated with higher prevalence. Pronounced variation in prevalence at small scales was observed and needs to be taken into account for malaria surveillance and control. Potential larval habitat frequency had no direct impact on prevalence.
Publisher: Cold Spring Harbor Laboratory
Date: 24-04-0005
DOI: 10.1101/306860
Abstract: Longitudinal tracking of in idual Plasmodium falciparum strains in multi-clonal infections is essential for investigating infection dynamics of malaria. The traditional genotyping techniques did not permit tracking changes in in idual clone density during persistent natural infections. Amplicon deep sequencing (Amp-Seq) offers a tool to address this knowledge gap. The sensitivity of Amp-Seq for relative quantification of clones was investigated using three molecular markers, ama1-D2, ama1-D3, and cpmp. Amp-Seq and length-polymorphism based genotyping were compared for their performance in following minority clones in longitudinal s les from Papua New Guinea. Amp-Seq markers were superior to length-polymorphic marker msp2 in detecting minority clones (sensitivity Amp-Seq: 95%, msp2: 85%). Multiplicity of infection (MOI) by Amp-Seq was 2.32 versus 1.73 for msp2. The higher sensitivity had no effect on estimates of force of infection because missed minority clones were detected in preceding or succeeding bleeds. In idual clone densities were tracked longitudinally by Amp-Seq despite MOI , thus providing an additional parameter for investigating malaria infection dynamics. Amp-Seq based genotyping of longitudinal s les improves detection of minority clones and estimates of MOI. Amp-Seq permits tracking of clone density over time to study clone competition or the dynamics of specific, i.e. resistance-associated genotypes.
Publisher: Public Library of Science (PLoS)
Date: 14-11-2013
Publisher: American Society for Microbiology
Date: 09-2011
DOI: 10.1128/AAC.01552-10
Abstract: Plasmodium vivax intervention trials customarily report uncorrected treatment failure rates. Application of recrudescence-reinfection genotyping and drug resistance single-nucleotide polymorphism typing to a 4-arm comparative efficacy trial illustrated that molecular approaches can assist in understanding the relative contributions of true drug resistance (recurrent with same genotype) and new infections to treatment failure. The PCR-corrected adequate clinical and parasitologic response may constitute an informative secondary endpoint in future P. vivax drug trials.
Publisher: Oxford University Press (OUP)
Date: 19-09-2017
Publisher: Public Library of Science (PLoS)
Date: 21-05-2015
Publisher: Public Library of Science (PLoS)
Date: 28-07-2022
DOI: 10.1371/JOURNAL.PGPH.0000828
Abstract: Rapid diagnostic tests (RDTs) are a key tool for the diagnosis of malaria infections among clinical and subclinical in iduals. Low-density infections, and deletions of the P . falciparum hrp2 / 3 genes (encoding the HRP2 and HRP3 proteins detected by many RDTs) present challenges for RDT-based diagnosis. The novel Rapigen Biocredit three-band Plasmodium falciparum HRP2/LDH RDT was evaluated among 444 clinical and 468 subclinical in iduals in a high transmission setting in Burundi. Results were compared to the AccessBio CareStart HRP2 RDT, and qPCR with a sensitivity of .3 parasites/μL blood. Sensitivity compared to qPCR among clinical patients for the Biocredit RDT was 79.9% (250/313, either of HRP2/LDH positive), compared to 73.2% (229/313) for CareStart ( P = 0.048). Specificity of the Biocredit was 82.4% compared to 96.2% for CareStart. Among subclinical infections, sensitivity was 72.3% (162/224) compared to 58.5% (131/224) for CareStart ( P = 0.003), and reached 88.3% (53/60) in children years. Specificity was 84.4% for the Biocredit and 93.4% for the CareStart RDT. No (0/362) hrp2 and 2/366 hrp3 deletions were observed. In conclusion, the novel RDT showed improved sensitivity for the diagnosis of P . falciparum .
Publisher: Elsevier BV
Date: 02-2023
Publisher: Cold Spring Harbor Laboratory
Date: 11-09-2021
DOI: 10.1101/2021.09.08.21263294
Abstract: The five Plasmodium spp. that cause human malaria appear similar under light microscopy, which raises the possibility that misdiagnosis could routinely occur in clinical settings. Assessing the extent of misdiagnosis is of particular importance for monitoring P. knowlesi , which co-circulates with the other Plasmodium spp. We performed a systematic review and meta-analysis of studies comparing the performance of microscopy and PCR for diagnosing malaria in settings with co-circulation of the five Plasmodium spp. We assessed the extent to which co-circulation of Plasmodium parasites affects diagnostic outcomes. We fit a Bayesian hierarchical latent class model to estimate variation in microscopy sensitivity and specificity. Mean sensitivity of microscopy was low, yet highly variable across Plasmodium spp., ranging from 41.7% (95% CI: 22.8 – 64.1%) for P. falciparum and 40.3% (22.0 – 61.5%) for P. vivax to 0.119% (0.0121 – 0.640%) for P. knowlesi , 7.57% (2.66 – 22.0%) for P. malariae , and 0.180% (0.00491 – 1.21%) for P. ovale . Observed PCR prevalence was positively correlated with estimated microscopic sensitivity and negatively correlated with estimated microscopic specificity, though the strength of the associations varied by species. Our analysis suggests that co-circulation of Plasmodium spp. undermines the accuracy of microscopy. Sensitivity was considerably lower for P. knowlesi, P. malariae , and P. ovale . The negative association between specificity and prevalence imply that less frequently encountered species may be misdiagnosed as more frequently encountered species. Together, these results suggest that the burden of P. knowlesi, P. malariae , and P. ovale may be underappreciated in a clinical setting.
Publisher: Springer Science and Business Media LLC
Date: 13-03-2018
Publisher: Springer Science and Business Media LLC
Date: 15-03-2022
DOI: 10.1186/S12936-022-04122-9
Abstract: Molecular and genomic surveillance is becoming increasingly used to track malaria control and elimination efforts. Blood s les can be collected as whole blood and stored at − 20 °C until DNA extraction, or as dried blood spots (DBS), circumventing the need for a cold chain. Despite the wide use of either method, systematic comparisons of how the method of blood s le preservation affects the limit of detection (LOD) of molecular diagnosis and the proportion of DNA recovered for downstream applications are lacking. Extractions based on spin columns, magnetic beads, Tween-Chelex, and direct PCR without prior extraction were compared for whole blood and dried blood spots (DBS) using dilution series of Plasmodium falciparum culture s les. Extracted DNA was quantified by qPCR and droplet digital PCR (ddPCR). DNA recovery was 5- to 10-fold higher for whole blood compared to DBS, resulting in a 2- to 3-fold lower LOD for both extraction methods compared to DBS. For whole blood, a magnetic bead-based method resulted in a DNA recovery rate of 88–98% when extracting from whole blood compared to 17–33% for a spin-column based method. For extractions from DBS, the magnetic bead-based method resulted in 8–20% DNA recovery, while the spin-column based method resulted in only 2% DNA recovery. The Tween-Chelex method was superior to other methods with 15–21% DNA recovery, and even more sensitive than extractions from whole blood s les. The direct PCR method was found to have the lowest LOD overall for both, whole blood and DBS. Pronounced differences in LOD and DNA yield need to be considered when comparing prevalence estimates based on molecular methods and when selecting s ling protocols for other molecular surveillance applications.
Publisher: Public Library of Science (PLoS)
Date: 04-05-2016
Publisher: Public Library of Science (PLoS)
Date: 31-07-2017
Publisher: Public Library of Science (PLoS)
Date: 26-06-2017
Publisher: Springer Science and Business Media LLC
Date: 30-01-2018
Publisher: Public Library of Science (PLoS)
Date: 27-08-2021
DOI: 10.1371/JOURNAL.PNTD.0009672
Abstract: Understanding epidemiological variables affecting gametocyte carriage and density is essential to design interventions that most effectively reduce malaria human-to-mosquito transmission. Plasmodium falciparum and P . vivax parasites and gametocytes were quantified by qPCR and RT-qPCR assays using the same methodologies in 5 cross-sectional surveys involving 16,493 in iduals in Brazil, Thailand, Papua New Guinea, and Solomon Islands. The proportion of infections with detectable gametocytes per survey ranged from 44–94% for P . falciparum and from 23–72% for P . vivax . Blood-stage parasite density was the most important predictor of the probability to detect gametocytes. In moderate transmission settings (prevalence by qPCR %), parasite density decreased with age and the majority of gametocyte carriers were children. In low transmission settings (prevalence %), % of gametocyte carriers were adults. Per survey, 37–100% of all in iduals positive for gametocytes by RT-qPCR were positive by light microscopy for asexual stages or gametocytes (overall: P . falciparum 178/348, P . vivax 235/398). Interventions to reduce human-to-mosquito malaria transmission in moderate-high endemicity settings will have the greatest impact when children are targeted. In contrast, all age groups need to be included in control activities in low endemicity settings to achieve elimination. Detection of infections by light microscopy is a valuable tool to identify asymptomatic blood stage infections that likely contribute most to ongoing transmission at the time of s ling.
Publisher: Cold Spring Harbor Laboratory
Date: 10-06-2023
DOI: 10.1101/2023.06.09.544365
Abstract: Malaria cases are frequently recorded in the Ethiopian highlands even at altitudes above 2,000 m. The epidemiology of malaria in the Ethiopian highlands, and in particular the role of importation by human migration from the highly endemic lowlands is not well understood. We characterized the parasite population structure and genetic relatedness by sequencing 159 P. falciparum s les from Gondar and an additional 28 s les from Ziway using a highly multiplexed droplet digital PCR (ddPCR)-based licon deep sequencing method targeting 35 microhaplotypes and drug resistance loci. Diversity was moderate (mean H E : 0.54), and infection complexity was low (74.9% single clone infections). A significant percentage of infections shared genomic haplotypes, even across transmission seasons, indicating persistent local and focal transmission. Multiple clusters of clonal or near-clonal infections were identified, highlighting the overall high genetic relatedness. Frequently, infections from travelers were the earliest observed cases, suggesting that parasites may have been imported and then transmitted locally. We observed population structure between Gondar and Ziway, although some haplotypes were shared between sites. 31.1% of infections carried pfhrp2 deletions and 84.4% pfhrp3 deletions, and 28.7% pfhrp2 / pfhrp3 double deletions. Parasites with pfhrp2/3 deletions and wild-type parasites were genetically distinct. Mutations associated with resistance to sulfadoxine-pyrimethamine and lumefantrine were observed at near-fixation, but no mutations in pfk13 were found. In conclusion, genomic data corroborates local transmission and the importance of intensified control in the Ethiopian highlands.
Publisher: Oxford University Press (OUP)
Date: 29-04-2022
DOI: 10.1093/INTHEALTH/IHAC024
Abstract: Insecticide-treated net (ITN) use is among the most recommended strategies to prevent malaria in pregnancy. We analysed the regional and socio-economic patterns of ITN use among pregnant women in Kenya using data from the 2003, 2008 and 2014 Kenyan Demographic and Health Surveys (KDHSs). Inequality was assessed using four dimensions: economic status, education, place of residence and region. Both relative and absolute summary measures were applied. In addition, simple and complex summary measures, i.e. difference, population attributable fraction, population attributable risk and ratio were considered based on the number of subgroups in each variable. There was overt inequality in the use of ITNs among pregnant women, with greater use among the better-off group in 2003 and 2014. Greater ITN use was also observed among pregnant women with a higher level of education. Pregnant women from urban settings tended to use ITNs (slept under a net the night before the survey) more than their rural counterparts in the 2003 KDHS. There were significant regional variations across the three surveys in all inequality summary measures, except ratio in the 2014 survey. Significant inequality in ITN use among pregnant women was observed at a macro scale.
Publisher: eLife Sciences Publications, Ltd
Date: 02-03-2022
Publisher: Public Library of Science (PLoS)
Date: 05-09-2013
Publisher: JMIR Publications Inc.
Date: 07-10-2020
Abstract: holera poses a significant global health burden. In Bangladesh, cholera is endemic and causes more than 100,000 cases each year. Established environmental reservoirs leave millions at risk of infection through the consumption of contaminated water. The Global Task Force for Cholera Control has called for increased environmental surveillance to detect contaminated water sources prior to human infection in an effort to reduce cases and deaths. The OmniVis rapid cholera detection device uses loop-mediated isothermal lification and particle diffusometry detection methods integrated into a handheld hardware device that attaches to an iPhone 6 to identify and map contaminated water sources. he aim of this study was to evaluate the usability of the OmniVis device with targeted end users to advance the iterative prototyping process and ultimately design a device that easily integrates into users’ workflow. ater quality workers were trained to use the device and subsequently completed an independent device trial and usability questionnaire. Pretraining and posttraining knowledge assessments were administered to ensure training quality did not confound trial and questionnaire evice trials identified common user errors and device malfunctions including incorrect test kit insertion and device powering issues. We did not observe meaningful differences in user errors or device malfunctions accumulated per participant across demographic groups. Over 25 trials, the mean time to complete a test was 47 minutes, a significant reduction compared with laboratory protocols, which take approximately 3 days. Overall, participants found the device easy to use and expressed confidence and comfort in using the device independently. hese results are used to advance the iterative prototyping process of the OmniVis rapid cholera detection device so it can achieve user uptake, workflow integration, and scale to ultimately impact cholera control and elimination strategies. We hope this methodology will promote robust usability evaluations of rapid pathogen detection technologies in device development.
Publisher: JMIR Publications Inc.
Date: 12-05-2021
DOI: 10.2196/22973
Abstract: Cholera poses a significant global health burden. In Bangladesh, cholera is endemic and causes more than 100,000 cases each year. Established environmental reservoirs leave millions at risk of infection through the consumption of contaminated water. The Global Task Force for Cholera Control has called for increased environmental surveillance to detect contaminated water sources prior to human infection in an effort to reduce cases and deaths. The OmniVis rapid cholera detection device uses loop-mediated isothermal lification and particle diffusometry detection methods integrated into a handheld hardware device that attaches to an iPhone 6 to identify and map contaminated water sources. The aim of this study was to evaluate the usability of the OmniVis device with targeted end users to advance the iterative prototyping process and ultimately design a device that easily integrates into users’ workflow. Water quality workers were trained to use the device and subsequently completed an independent device trial and usability questionnaire. Pretraining and posttraining knowledge assessments were administered to ensure training quality did not confound trial and questionnaire Device trials identified common user errors and device malfunctions including incorrect test kit insertion and device powering issues. We did not observe meaningful differences in user errors or device malfunctions accumulated per participant across demographic groups. Over 25 trials, the mean time to complete a test was 47 minutes, a significant reduction compared with laboratory protocols, which take approximately 3 days. Overall, participants found the device easy to use and expressed confidence and comfort in using the device independently. These results are used to advance the iterative prototyping process of the OmniVis rapid cholera detection device so it can achieve user uptake, workflow integration, and scale to ultimately impact cholera control and elimination strategies. We hope this methodology will promote robust usability evaluations of rapid pathogen detection technologies in device development.
Publisher: Oxford University Press (OUP)
Date: 04-2009
DOI: 10.1086/597303
Abstract: Many antimalarial interventions are accompanied by molecular monitoring of parasite infections, and a number of molecular typing techniques based on different polymorphic marker genes are used. Here, we describe a genotyping technique that provides a fast and precise approach to study Plasmodium vivax infection dynamics during circumstances in which in idual clones must be followed over time. The method was tested with s les from an in vivo drug efficacy study. The sizes of polymerase chain reaction fragments were evaluated by capillary electrophoresis to determine the extent of size polymorphism for 9 potential genetic markers (5 genes of merozoite surface proteins [msp] and 4 microsatellites) in 93-108 P. vivax-positive blood s les from 3 villages in Papua New Guinea. The microsatellites MS16 and Pv3.27 showed the greatest ersity in the study area, with 66 and 31 different alleles, respectively, followed by 2 fragments of msp1 and 2 other microsatellites. msp3alpha, msp4, and msp5 revealed limited polymorphism. Even for the most erse markers, the highest allelic frequencies reached 6% (MS16) or 13% (Pv3.27). To reduce the theoretical probability of superinfection with parasites that have the same haplotype as that detected at baseline, we propose to combine at least 2 markers for genotyping in idual P. vivax infections.
Publisher: Public Library of Science (PLoS)
Date: 14-09-2020
Publisher: Springer Science and Business Media LLC
Date: 10-2012
Publisher: Elsevier BV
Date: 05-2018
Publisher: Informa UK Limited
Date: 18-04-2015
Publisher: Cold Spring Harbor Laboratory
Date: 03-04-2017
DOI: 10.1101/121426
Abstract: Amplicon deep sequencing permits sensitive detection of minority clones and improves discriminatory power for genotyping multi-clone Plasmodium falciparum infections. Such high resolution is needed for molecular monitoring of drug efficacy trials. Targeted sequencing of molecular marker csp and novel marker cpmp was conducted in duplicate on mixtures of parasite culture strains and 37 field s les. A protocol to multiplex up to 384 s les in a single sequencing run was applied. Software “HaplotypR” was developed for data analysis. Cpmp was highly erse (H e =0.96) in contrast to csp (H e =0.57). Minority clones were robustly detected if their frequency was %. False haplotype calls owing to sequencing errors were observed below that threshold. To reliably detect haplotypes at very low frequencies, experiments are best performed in duplicate and should aim for coverage of ’000 reads/ licon. When compared to length polymorphic marker msp2 , highly multiplexed licon sequencing displayed greater sensitivity in detecting minority clones.
Publisher: Springer Science and Business Media LLC
Date: 13-11-2017
Publisher: Springer Science and Business Media LLC
Date: 14-08-2014
Publisher: Springer Science and Business Media LLC
Date: 22-06-2023
DOI: 10.1038/S41467-023-39417-1
Abstract: Zanzibar has made significant progress toward malaria elimination, but recent stagnation requires novel approaches. We developed a highly multiplexed droplet digital PCR (ddPCR)-based licon sequencing method targeting 35 microhaplotypes and drug-resistance loci, and successfully sequenced 290 s les from five districts covering both main islands. Here, we elucidate fine-scale Plasmodium falciparum population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. Despite high genetic ersity, we observe pronounced fine-scale spatial and temporal parasite genetic structure. Clusters of near-clonal infections on Pemba indicate persistent local transmission with limited parasite importation, presenting an opportunity for local elimination efforts. Furthermore, we observe an admixed parasite population on Unguja and detect a substantial fraction (2.9%) of significantly related infection pairs between Zanzibar and the mainland, suggesting recent importation. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and provides actionable insights for prioritizing malaria elimination efforts.
Publisher: Public Library of Science (PLoS)
Date: 20-12-2011
Publisher: Springer Science and Business Media LLC
Date: 24-10-2017
Publisher: Elsevier BV
Date: 09-2023
Publisher: Cold Spring Harbor Laboratory
Date: 06-01-2023
DOI: 10.1101/2023.01.05.522832
Abstract: Over the past 15 years, Zanzibar has made great strides towards malaria elimination yet progress has stalled. Parasite genetic data of Plasmodium falciparum may inform strategies for malaria elimination by helping to identify contributory factors to parasite persistence. Here we elucidate fine-scale parasite population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. We sequenced 518 P. falciparum s les from 5 districts covering both main islands using a novel, highly multiplexed droplet digital PCR (ddPCR)-based licon deep sequencing method targeting 35 microhaplotypes and drug-resistance loci. Despite high genetic ersity, we observe strong fine-scale spatial and temporal structure of local parasite populations, including isolated populations on Pemba Island and genetically admixed populations on Unguja Island, providing evidence of ongoing local transmission. We observe a high proportion of highly related parasites in in iduals living closer together, including between clinical index cases and the mostly asymptomatic cases surrounding them, consistent with isolation-by-distance. We identify a substantial fraction (2.9%) of related parasite pairs between Zanzibar, and mainland Tanzania and Kenya, consistent with recent importation. We identify haplotypes known to confer resistance to known antimalarials in all districts, including multidrug-resistant parasites, but most parasites remain sensitive to current first-line treatments. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and reveals actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination.
Publisher: Springer Science and Business Media LLC
Date: 16-12-2016
DOI: 10.1038/SREP39183
Abstract: Accurate quantification of parasite density in the human host is essential for understanding the biology and pathology of malaria. Semi-quantitative molecular methods are widely applied, but the need for an external standard curve makes it difficult to compare parasite density estimates across studies. Droplet digital PCR (ddPCR) allows direct quantification without the need for a standard curve. ddPCR was used to diagnose and quantify P. falciparum and P. vivax in clinical patients as well as in asymptomatic s les. ddPCR yielded highly reproducible measurements across the range of parasite densities observed in humans, and showed higher sensitivity than qPCR to diagnose P. falciparum , and equal sensitivity for P. vivax . Correspondence in quantification was very high ( .95) between qPCR and ddPCR. Quantification between technical replicates by ddPCR differed 1.5–1.7-fold, compared to 2.4–6.2-fold by qPCR. ddPCR facilitates parasite quantification for studies where absolute densities are required, and will increase comparability of results reported from different laboratories.
Publisher: Public Library of Science (PLoS)
Date: 27-07-2022
DOI: 10.1371/JOURNAL.PGPH.0000454
Abstract: Many Plasmodium spp. infections, both in clinical and asymptomatic patients, are below the limit of detection of light microscopy or rapid diagnostic test (RDT). Molecular diagnosis by qPCR can be valuable for surveillance, but is often h ered by absence of laboratory capacity in endemic countries. To overcome this limitation, we optimized and tested a mobile qPCR laboratory for molecular diagnosis in Ziway, Ethiopia, where transmission intensity is low. Protocols were optimized to achieve high throughput and minimize costs and weight for easy transport. 899 s les from febrile patients and 1021 s les from asymptomatic in iduals were screened by local microscopy, RDT, and qPCR within a period of six weeks. 34/52 clinical Plasmodium falciparum infections were missed by microscopy and RDT. Only 4 asymptomatic infections were detected. No hrp2 deletions were observed among 25 s les typed, but 19/24 s les carried hrp3 deletions. The majority (25/41) of Plasmodium vivax infections (1371 s les screened) were found among asymptomatic in iduals. All asymptomatic P . vivax infections were negative by microscopy and RDT. In conclusion, the mobile laboratory described here can identify hidden parasite reservoirs within a short period of time, and thus inform malaria control activities.
Publisher: Public Library of Science (PLoS)
Date: 23-04-2021
DOI: 10.1371/JOURNAL.PMED.1003576
Abstract: Glucose-6-phosphate dehydrogenase (G6PD) activity is dependent upon G6PD genotype and age of the red blood cell (RBC) population, with younger RBCs having higher activity. Peripheral parasitemia with Plasmodium spp. induces hemolysis, replacing older RBCs with younger cells with higher G6PD activity. This study aimed to assess whether G6PD activity varies between in iduals with and without malaria or a history of malaria. In iduals living in the Chittagong Hill Tracts of Bangladesh were enrolled into 3 complementary studies: (i) a prospective, single-arm clinical efficacy trial of patients ( n = 175) with uncomplicated malaria done between 2014 and 2015, (ii) a cross-sectional survey done between 2015 and 2016 ( n = 999), and (iii) a matched case–control study of aparasitemic in iduals with and without a history of malaria done in 2020 ( n = 506). G6PD activity was compared between in iduals with and without malaria diagnosed by microscopy, rapid diagnostic test (RDT), or polymerase chain reaction (PCR), and in aparasitemic participants with and without a history of malaria. In the cross-sectional survey and clinical trial, 15.5% (182/1,174) of participants had peripheral parasitemia detected by microscopy or RDT, 3.1% (36/1,174) were positive by PCR only, and 81.4% (956/1,174) were aparasitemic. Aparasitemic in iduals had significantly lower G6PD activity (median 6.9 U/g Hb, IQR 5.2–8.6) than those with peripheral parasitemia detected by microscopy or RDT (7.9 U/g Hb, IQR 6.6–9.8, p 0.001), but G6PD activity similar to those with parasitemia detected by PCR alone (submicroscopic parasitemia) (6.1 U/g Hb, IQR 4.8–8.6, p = 0.312). In total, 7.7% (14/182) of patients with malaria had G6PD activity 70% compared to 25.0% (248/992) of participants with submicroscopic or no parasitemia (odds ratio [OR] 0.25, 95% CI 0.14–0.44, p 0.001). In the case–control study, the median G6PD activity was 10.3 U/g Hb (IQR 8.8–12.2) in 253 patients with a history of malaria and 10.2 U/g Hb (IQR 8.7–11.8) in 253 in iduals without a history of malaria ( p = 0.323). The proportion of in iduals with G6PD activity 70% was 11.5% (29/253) in the cases and 15.4% (39/253) in the controls (OR 0.7, 95% CI 0.41–1.23, p = 0.192). Limitations of the study included the non-contemporaneous nature of the clinical trial and cross-sectional survey. Patients with acute malaria had significantly higher G6PD activity than in iduals without malaria, and this could not be accounted for by a protective effect of G6PD deficiency. G6PD-deficient patients with malaria may have higher than expected G6PD enzyme activity and an attenuated risk of primaquine-induced hemolysis compared to the risk when not infected.
Publisher: Springer Science and Business Media LLC
Date: 23-09-2020
DOI: 10.1186/S12936-020-03418-Y
Abstract: Surveillance of low-density infections and of exposure to vectors is crucial to understand where malaria elimination might be feasible, and where the risk of outbreaks is high. Archived rapid diagnostic tests (RDTs), used by national malaria control and elimination programs for clinical diagnosis, present a valuable, yet rarely used resource for in-depth studies on malaria epidemiology. 1022 RDTs from two sub-Districts in Bangladesh (Alikadam and Kamalganj) were screened by qPCR for low-density Plasmodium falciparum and Plasmodium vivax infections, and by ELISA for Anopheles salivary gland antibodies as a marker for exposure to vectors. Concordance between RDT and qPCR was moderate. qPCR detected 31/1022 infections compared to 36/1022 diagnosed by RDT. Exposure to Anopheles was significantly higher in Kamalganj despite low transmission, which could be explained by low bed net use. Archived RDTs present a valuable source of antibodies for serological studies on exposure to vectors. In contrast, the benefit of screening archived RDTs to obtain a better estimate of clinical case numbers is moderate. Kamalganj could be prone to outbreaks.
Publisher: Cold Spring Harbor Laboratory
Date: 31-01-2021
DOI: 10.1101/2021.01.28.21250689
Abstract: Plasmodium vivax relapses caused by reactivating hypnozoites are a major barrier for elimination and control of this form of malaria. Radical cure is a form of therapy capable of addressing this problem. Recent clinical trials of radical cure have yielded efficacy estimates ranging from 65% to 94%, with substantial variation across trial sites. We performed an analysis of simulated trial data using a transmission model to demonstrate that variation in efficacy estimates across trial sites can arise from differences in the conditions under which trials are conducted. Our analysis revealed that differences in transmission intensity, heterogeneous exposure, and relapse rate can yield efficacy estimates ranging as wide as 12-78%, despite simulating trial data under the uniform assumption that treatment had a 75% chance of clearing hypnozoites. A longer duration of prophylaxis leads to a greater measured efficacy, particularly at higher transmission intensities, making the comparison of the protection of different radical cure treatment regimens against relapse more challenging. We show that vector control and parasite genotyping offer two potential means to yield more standardized efficacy estimates that better reflect protection against relapse. We predict that site-specific biases are likely to contribute to variation in efficacy estimates both within and across phase-III clinical trials. Future clinical trials can reduce site-specific biases by conducting trials in low-transmission settings where reinfections from mosquito biting are less common, by preventing reinfections using vector control measures, or by identifying and excluding likely reinfections that occur during follow-up using parasite genotyping methods. Radical cure holds promise as a strategy for Plasmodium vivax malaria control by clearing the parasites known as hypnozoites that latently infect the liver and cause relapsing infections. The efficacy of radical cure treatment regimens is evaluated in phase-III clinical trials. Recent trial results have noted substantial variation in efficacy estimates across trial sites, complicating the interpretation of the benefit of radical cure. However, P. vivax infections identified during the course of the clinical trial could include reinfections from mosquito biting that do not directly reflect the effect of the therapeutic being trialed, potentially biasing efficacy estimates. In this study, we simulated clinical trials to identify the causes and solutions of these site-specific biases. We found that features of both the trial location, such as the transmission intensity, and the trial design, such as the duration of follow-up, lead to an underestimate of the effect of radical cure against hypnozoites. We then demonstrated that vector control and parasite genotyping are two possible strategies to reduce these biases. These insights can be leveraged to aid in the interpretation of past trial results and to help design future clinical trials that minimize site-specific biases.
Publisher: Public Library of Science (PLoS)
Date: 16-10-2017
Publisher: Public Library of Science (PLoS)
Date: 15-04-2015
Publisher: Public Library of Science (PLoS)
Date: 28-04-2011
Publisher: Springer Science and Business Media LLC
Date: 09-01-2021
DOI: 10.1186/S12879-020-05761-6
Abstract: Transmission stemming from asymptomatic infections is increasingly being recognized as a threat to malaria elimination. In many regions, malaria transmission is seasonal. It is not well understood whether Plasmodium falciparum modulates its investment in transmission to coincide with seasonal vector abundance. We s led 1116 asymptomatic in iduals in the wet season, when vectors are abundant, and 1743 in the dry season, in two sites in western Kenya, representing different transmission intensities (Chulaimbo, moderate transmission, and Homa Bay, low transmission). Blood s les were screened for P. falciparum by qPCR, and gametocytes by pfs25 RT-qPCR. Parasite prevalence by qPCR was 27.1% (Chulaimbo, dry), 48.2% (Chulaimbo, wet), 9.4% (Homabay, dry), and 7.8% (Homabay, wet). Mean parasite densities did not differ between seasons ( P = 0.562). pfs25 transcripts were detected in 119/456 (26.1%) of infections. In the wet season, fewer infections harbored detectable gametocytes (22.3% vs. 33.8%, P = 0.009), but densities were 3-fold higher (wet: 3.46 transcripts/uL, dry: 1.05 transcripts/uL, P 0.001). In the dry season, 4.0% of infections carried gametocytes at moderate-to-high densities likely infective ( 1 gametocyte per 2 uL blood), compared to 7.9% in the wet season. Children aged 5–15 years harbored 76.7% of infections with gametocytes at moderate-to-high densities. Parasites increase their investment in transmission in the wet season, reflected by higher gametocyte densities. Despite increased gametocyte densities, parasite density remained similar across seasons and were often below the limit of detection of microscopy or rapid diagnostic test, thus a large proportion of infective infections would escape population screening in the wet season. Seasonal changes of gametocytemia in asymptomatic infections need to be considered when designing malaria control measures.
Publisher: Public Library of Science (PLoS)
Date: 26-01-2018
Publisher: Cold Spring Harbor Laboratory
Date: 07-06-2017
DOI: 10.1101/145250
Abstract: Plasmodium vivax is the key obstacle to malaria elimination in Asia and Latin America, largely attributed to its ability to form resilient hypnozoites (sleeper-cells) in the host liver that escape treatment and cause relapsing infections. The decision to form hypnozoites is made early in the liver infection and may already be set in sporozoites prior to invasion. To better understand these early stages of infection, we undertook a comprehensive transcriptomic and histone epigenetic characterization of P. vivax sporozoites. The salivary-gland sporozoite transcriptome is heavily composed of transcripts associated with functions needed for early infection of the vertebrate host and development within hepatocytes. Through comparisons to recently published proteome data for the P. vivax sporozoite, our study finds that although highly transcribed, these transcripts are not detectable as proteins and may be regulated through translational repression a finding we test for a small subset of transcripts and proteins through immunofluorescent microscopy of sporozoites and liver stages in humanized mice. We identify differential transcription between the sporozoite and published transcriptomes of asexual blood-stages and mixed versus hypnozoite-enriched liver stages. These comparisons point to multiple layers of transcriptional, post-transcriptional and post-translational control that appear active in sporozoites and to a lesser extent hypnozoites, but largely absent in replicating liver schizonts or mixed blood-stages. Common transcripts up-regulated in sporozoites and hypnozoites compared to mixed (i.e., schizont) liver-stages identify genes linked to dormancy ersistence in bacteria, amoebae and plants. We also characterise histone epigenetic modifications in the P. vivax sporozoite and explore their role in regulating transcription. Collectively, these data support the hypothesis that the sporozoite as a tightly programmed stage primed to infect the human host and identifies potential mechanisms for hypnozoite-formation that may be further explored in liver stage models.
Publisher: Elsevier BV
Date: 12-2017
Publisher: Springer Science and Business Media LLC
Date: 09-10-2015
Publisher: Public Library of Science (PLoS)
Date: 21-05-2015
Publisher: eLife Sciences Publications, Ltd
Date: 28-06-2022
DOI: 10.7554/ELIFE.72083
Abstract: Most rapid diagnostic tests for Plasmodium falciparum malaria target the Histidine-Rich Proteins 2 and 3 (HRP2 and HRP3). Deletions of the hrp2 and hrp3 genes result in false-negative tests and are a threat for malaria control. A novel assay for molecular surveillance of hrp2 / hrp3 deletions was developed based on droplet digital PCR (ddPCR). The assay quantifies hrp2 , hrp3 , and a control gene with very high accuracy. The theoretical limit of detection was 0.33 parasites/µl. The deletion was reliably detected in mixed infections with wild-type and hrp2 -deleted parasites at a density of parasites/reaction. For a side-by-side comparison with the conventional nested PCR (nPCR) assay, 248 s les were screened in triplicate by ddPCR and nPCR. No deletions were observed by ddPCR, while by nPCR hrp2 deletion was observed in 8% of s les. The ddPCR assay was applied to screen 830 s les from Kenya, Zanzibar/Tanzania, Ghana, Ethiopia, Brazil, and Ecuador. Pronounced differences in the prevalence of deletions were observed among sites, with more hrp3 than hrp2 deletions. In conclusion, the novel ddPCR assay minimizes the risk of false-negative results (i.e., hrp2 deletion observed when the s le is wild type), increases sensitivity, and greatly reduces the number of reactions that need to be run.
Publisher: Public Library of Science (PLoS)
Date: 17-04-2023
DOI: 10.1371/JOURNAL.PGPH.0001505
Abstract: Progress in malaria control has stalled over the recent years. Knowledge on main drivers of transmission explaining small-scale variation in prevalence can inform targeted control measures. We collected finger-prick blood s les from 3061 in iduals irrespective of clinical symptoms in 20 clusters in Busia in western Kenya and screened for Plasmodium falciparum parasites using qPCR and microscopy. Clusters spanned an altitude range of 207 meters (1077–1284 m). We mapped potential mosquito larval habitats and determined their number within 250 m of a household and distances to households using ArcMap. Across all clusters, P . falciparum parasites were detected in 49.8% (1524/3061) of in iduals by qPCR and 19.5% (596/3061) by microscopy. Across the clusters, prevalence ranged from 26% to 70% by qPCR. Three to 34 larval habitats per cluster and 0–17 habitats within a 250m radius around households were observed. Using a generalized linear mixed effect model (GLMM), a 5% decrease in the odds of getting infected per each 10m increase in altitude was observed, while the number of larval habitats and their proximity to households were not statistically significant predictors for prevalence. Kitchen located indoors, open eaves, a lower level of education of the household head, older age, and being male were significantly associated with higher prevalence. Pronounced variation in prevalence at small scales was observed and needs to be taken into account for malaria surveillance and control. Potential larval habitat frequency had no direct impact on prevalence.
Publisher: Public Library of Science (PLoS)
Date: 29-08-2012
Publisher: Cold Spring Harbor Laboratory
Date: 16-04-2022
DOI: 10.1101/2022.04.13.22273827
Abstract: Many Plasmodium spp. infections, both in clinical and asymptomatic patients, are below the limit of detection of light microscopy or rapid diagnostic test (RDT). Molecular diagnosis by qPCR can be valuable for surveillance, but is often h ered by absence of laboratory capacity in endemic countries. To overcome this limitation, we optimized and tested a mobile qPCR laboratory for molecular diagnosis in Ziway, Ethiopia, where transmission intensity is low. Protocols were optimized to achieve high throughput and minimize costs and weight for easy transport. 899 s les from febrile patients and 1021 s les from asymptomatic in iduals were screened by local microscopy, RDT, and qPCR within a period of six weeks. 34/52 clinical Plasmodium falciparum infections were missed by microscopy and RDT. Only 4 asymptomatic infections were detected. No hrp2 deletions were observed among 25 s les typed, but 19/24 s les carried hrp3 deletions. The majority (25/41) of Plasmodium vivax infections (1371 s les screened) were found among asymptomatic in iduals. All asymptomatic P. vivax infections were negative by microscopy and RDT. In conclusion, the mobile laboratory described here can identify hidden parasite reservoirs within a short period of time, and thus inform malaria control activities.
Location: Australia
No related grants have been discovered for Cristian Koepfli.