A5059518162- Malaria Research and Control
- Mosquito-borne diseases and control
- Vector-borne infectious diseases
- Travel-related health issues
- Livestock and Poultry Management
- Hemoglobinopathies and Related Disorders
- Evolution and Genetic Dynamics
- Gene expression and cancer classification
- Aquaculture disease management and microbiota
- vaccines and immunoinformatics approaches
- Urinary Tract Infections Management
- Parasite Biology and Host Interactions
- Data Analysis with R
- Virology and Viral Diseases
- HIV Research and Treatment
- Vibrio bacteria research studies
- COVID-19 epidemiological studies
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Medical History and Research
- Resilience and Mental Health
- Bayesian Methods and Mixture Models
- SARS-CoV-2 and COVID-19 Research
- Poxvirus research and outbreaks
- HIV/AIDS Research and Interventions
University of California, San Francisco
1960-2024
University of California, Berkeley
2018-2024
Center for Global Health
2019
Scottish National Blood Transfusion Service
1997
University of California, Los Angeles
1978
Saint Louis University
1978
Eye Cancer Foundation
1960
The National Trust
1960
The growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat human health. Detection low abundance pathogen sequences remains challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), next-generation CRISPR/Cas9 diagnostic method that takes advantage the efficiency, specificity and flexibility Cas9 enrich programmed set sequences. FLASH-NGS achieves up 5 orders...
Anopheles stephensi, an Asian malaria vector, continues to expand across Africa. The vector is now firmly established in urban settings the Horn of Its presence areas where resurged suggested a possible role causing outbreaks. Here, using prospective case-control design, we investigated An. stephensi transmission following outbreak Dire Dawa, Ethiopia April-July 2022. Screening contacts patients with and febrile controls revealed spatial clustering Plasmodium falciparum infections around...
As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising understanding transmission and spread disease, but a high prevalence multi-clone or polygenomic infections can render estimation even basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to...
Sensitive field-deployable diagnostic tests can assist malaria programs in achieving elimination. The performance of a new Alere™ Malaria Ag P.f Ultra rapid test (uRDT) was compared with the currently available SD Bioline RDT blood specimens from asymptomatic individuals Nagongera, Uganda, and Karen Village, Myanmar, representative high- low-transmission areas, respectively, as well pretreatment study participants four Plasmodium falciparum-induced blood-stage (IBSM) studies. A quantitative...
Local and cross-border importation remain major challenges to malaria elimination are difficult measure using traditional surveillance data. To address this challenge, we systematically collected parasite genetic data travel history from thousands of cases across northeastern Namibia estimated human mobility mobile phone We observed strong fine-scale spatial structure in local populations, providing positive evidence that the majority were due transmission. This result was largely consistent...
The performance of Plasmodium falciparum-specific histidine-rich protein 2-based rapid diagnostic tests (RDTs) to evaluate suspected malaria in low-endemicity settings has not been well characterized.Using dried blood spot samples from patients with at 37 health facilities 2012 2014 the country Swaziland, we investigated accuracy RDTs using qualitative polymerase chain reaction (PCR) (nested PCR targeting cytochrome b gene) and quantitative as reference standards. To explore reasons for...
Abstract Background To better understand transmission dynamics, we characterized Plasmodium falciparum genetic diversity in Eswatini, where is low and sustained by importation. Methods Twenty-six P. microsatellites were genotyped 66% of confirmed cases (2014–2016; N = 582). Population within-host used to characterize differences between imported locally acquired infections. Logistic regression was assess the added value metrics classify local infections beyond epidemiology data alone....
Abstract Background Targeted next-generation sequencing offers the potential for consistent, deep coverage of information-rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods identify and sequence these are currently limited. Methods A bioinformatic pipeline multiplex were developed simultaneously 100 targets applied dried blood spot (DBS) controls field isolates from Mozambique. For comparison, whole-genome data generated same controls. Results...
Malaria parasite genetic data can provide insight into phenotypes, evolution, and transmission. However, estimating key parameters such as allele frequencies, multiplicity of infection (MOI), within-host relatedness from is challenging, particularly in the presence multiple related coinfecting strains. Existing methods often rely on single nucleotide polymorphism (SNP) do not account for relatedness.
Major advances in Plasmodium sequencing approaches, bioinformatic pipelines, and data analysis tools have provided valuable insights into malaria epidemiology from parasite genomic data. However, translating genetic actionable information for decision-makers remains a challenge. Significant barriers limit the integration of these functional ecosystem that produces standardized, interpretable results use by national control programs. The Genomic Epidemiology (PlasmoGenEpi) network convened 18...
The discovery of the life-threatening zoonotic infection Plasmodium knowlesi has added to challenges prompt and accurate malaria diagnosis surveillance. In this study from Aceh Province, Indonesia, a elimination setting where P. endemicity was not previously known, we report laboratory investigation difficulties encountered when using molecular detection methods for quality assurance microscopically identified clinical cases. From 2014 2015, 20 (49%) falciparum, 16 (39%) vivax, 3 (7%)...
Malaria rapid diagnostic tests (RDTs) primarily detect Plasmodium falciparum antigen histidine-rich protein 2 (HRP2) and the malaria-conserved lactate dehydrogenase (LDH) for P. vivax other malaria species. The performance of RDTs their utility is dependent on circulating concentration distributions in infected individuals a population which endemic limit detection RDT antigens.
Reactive case detection (RACD) is a widely practiced malaria elimination intervention whereby close contacts of index cases receive testing to inform treatment and other interventions. However, the optimal diagnostic operational approaches for this resource-intensive strategy are not clear.We conducted 3-year prospective national evaluation RACD in Eswatini, setting. Loop-mediated isothermal amplification (LAMP) was compared traditional rapid (RDT) improved infections hotspots (RACD events...
Subpatent malaria infections, or low-density infections below the detection threshold of microscopy standard rapid diagnostic testing (RDT), can perpetuate persistent transmission and, therefore, may be a barrier for countries like Namibia that are pursuing elimination. This potential burden in has not been well characterized. Using two-stage cluster sampling, cross-sectional design, subjects all age were enrolled during end 2015 season Zambezi region, located northeast Namibia. Malaria RDTs...
Malaria parasite genetic data can provide insight into phenotypes, evolution, and transmission. However, estimating key parameters such as allele frequencies, multiplicity of infection (MOI), within-host relatedness from has been challenging, particularly in the presence multiple related coinfecting strains. Existing methods often rely on single nucleotide polymorphism (SNP) do not account for relatedness. In this study, we introduce a Bayesian approach called MOIRE (Multiplicity Of...
We evaluated whether multiplex polymerase chain reaction (M-PCR) detects viable micro-organisms by comparing micro-organism identification with standard urine culture (SUC) and expanded quantitative (EQUC). Of the 395 organisms detected M-PCR, EQUC 89.1% (p = 0.10), whereas SUC 27.3% < 0.0001 vs. M-PCR p vs EQUC). identified 260 nonfastidious bacteria, 96.5% 0.68), 41.5% 0.0001). Common bacteria missed included Escherichia coli (72.5% detected), Klebsiella pneumoniae (66.7% Enterococcus...
Southern Province, Zambia has experienced a dramatic decline in Plasmodium falciparum malaria transmission the past decade and is targeted for elimination. Zambia's National Malaria Elimination Program recommends reactive case detection (RCD) within 140 m of index households to enhance surveillance eliminate remaining foci.To evaluate whether RCD captures local transmission, we genotyped 26 microsatellites from 106 samples collected (n = 27) secondary 79) cases detected through Macha...
Malaria antigen detection through rapid diagnostic tests (RDTs) is widely used to diagnose malaria and estimate prevalence. To support more sensitive next-generation RDT development screen asymptomatic malaria, we developed evaluated the Q-Plex™ Human Array (Quansys Biosciences, Logan, UT), which quantifies antigens commonly in RDTs—Plasmodium falciparum–specific histidine-rich protein 2 (HRP2), P. falciparum-specific lactate dehydrogenase (Pf LDH), Plasmodium vivax–specific LDH (Pv Pan (Pan...
Abstract Background Current methods to classify local and imported malaria infections depend primarily on patient travel history, which can have limited accuracy. Genotyping has been investigated as a complementary approach track the spread of identify origin infections. Methods An extended panel 26 microsatellites (16 new microsatellites) for Plasmodium falciparum was evaluated in 602 from sub-Saharan African countries Jiangsu Province People’s Republic China. The potential microsatellite...
Abstract The development of vaccines against malaria and serodiagnostic tests for detecting recent exposure requires tools antigen discovery suitable animal models. protein microarray is a high‐throughput, sample sparing technique, with applications in infectious disease research, clinical diagnostics, epidemiology, vaccine development. We recently demonstrated Qdot‐based indirect immunofluorescence together portable optical imager ArrayCAM using single isotype detection could replicate data...
The World Health Organization recommendation on the use of a single low dose primaquine (SLD-PQ) to reduce Plasmodium falciparum malaria transmission requires more safety data. We conducted an open-label, nonrandomized, dose-adjustment trial 3 doses in glucose-6-phosphate dehydrogenase (G6PD)-deficient adult males Mali, followed by assessment G6PD-deficient boys aged 11–17 years and those 5–10 years, including G6PD-normal control groups. primary outcome was greatest within-person percentage...
The detection of submicroscopic infections in low prevalence settings has become an increasingly important challenge for malaria elimination strategies. current field rapid diagnostic tests (RDTs) Plasmodium falciparum are inadequate to detect low-density infections. Therefore, there is a need develop more sensitive tools. In parallel, highly laboratory reference assay will be essential evaluate new Recently, the Alere™ Malaria Ag P.f ELISA (HS ELISA) was developed P. histidine-rich protein...
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Accurately identifying and targeting the human reservoir of malaria parasitemia is critical for control, requires a reliable sensitive diagnostic method. Loop-mediated isothermal amplification (LAMP) increasingly used to diagnose submicroscopic parasitemia. Although most published studies report sensitivity LAMP compared with nested polymerase chain reaction (PCR) as ≥ 80%, they have failed use consistent, comparator. We cross-sectional samples from children adults in Tororo, Uganda, region...