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Paquette SE, Oduor CI, Gaulke A, Stefan S, Bronk P, Dafonseca V, Barulin N, Lee C, Carley R, Morrison AR, Choi BR, Bailey JA, Plavicki JS. Loss of developmentally derived Irf8+ macrophages promotes hyperinnervation and arrhythmia in the adult zebrafish heart. bioRxiv 2024:2024.04.17.589909. [PMID: 38659956 PMCID: PMC11042273 DOI: 10.1101/2024.04.17.589909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Recent developments in cardiac macrophage biology have broadened our understanding of the critical functions of macrophages in the heart. As a result, there is further interest in understanding the independent contributions of distinct subsets of macrophage to cardiac development and function. Here, we demonstrate that genetic loss of interferon regulatory factor 8 (Irf8)-positive embryonic-derived macrophages significantly disrupts cardiac conduction, chamber function, and innervation in adult zebrafish. At 4 months post-fertilization (mpf), homozygous irf8st96/st96 mutants have significantly shortened atrial action potential duration and significant differential expression of genes involved in cardiac contraction. Functional in vivo assessments via electro- and echocardiograms at 12 mpf reveal that irf8 mutants are arrhythmogenic and exhibit diastolic dysfunction and ventricular stiffening. To identify the molecular drivers of the functional disturbances in irf8 null zebrafish, we perform single cell RNA sequencing and immunohistochemistry, which reveal increased leukocyte infiltration, epicardial activation, mesenchymal gene expression, and fibrosis. Irf8 null hearts are also hyperinnervated and have aberrant axonal patterning, a phenotype not previously assessed in the context of cardiac macrophage loss. Gene ontology analysis supports a novel role for activated epicardial-derived cells (EPDCs) in promoting neurogenesis and neuronal remodeling in vivo. Together, these data uncover significant cardiac abnormalities following embryonic macrophage loss and expand our knowledge of critical macrophage functions in heart physiology and governing homeostatic heart health.
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Popkin-Hall ZR, Seth MD, Madebe RA, Budodo R, Bakari C, Francis F, Pereus D, Giesbrecht DJ, Mandara CI, Mbwambo D, Aaron S, Lusasi A, Lazaro S, Bailey JA, Juliano JJ, Ishengoma DS. Malaria Species Positivity Rates Among Symptomatic Individuals Across Regions of Differing Transmission Intensities in Mainland Tanzania. J Infect Dis 2024; 229:959-968. [PMID: 37992117 PMCID: PMC11011190 DOI: 10.1093/infdis/jiad522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Recent data indicate that non-Plasmodium falciparum species may be more prevalent than thought in sub-Saharan Africa. Although Plasmodium malariae, Plasmodium ovale spp., and Plasmodium vivax are less severe than P. falciparum, treatment and control are more challenging, and their geographic distributions are not well characterized. METHODS We randomly selected 3284 of 12 845 samples collected from cross-sectional surveys in 100 health facilities across 10 regions of Mainland Tanzania and performed quantitative real-time PCR to determine presence and parasitemia of each malaria species. RESULTS P. falciparum was most prevalent, but P. malariae and P. ovale were found in all but 1 region, with high levels (>5%) of P. ovale in 7 regions. The highest P. malariae positivity rate was 4.5% in Mara and 8 regions had positivity rates ≥1%. We only detected 3 P. vivax infections, all in Kilimanjaro. While most nonfalciparum malaria-positive samples were coinfected with P. falciparum, 23.6% (n = 13 of 55) of P. malariae and 14.7% (n = 24 of 163) of P. ovale spp. were monoinfections. CONCLUSIONS P. falciparum remains by far the largest threat, but our data indicate that malaria elimination efforts in Tanzania will require increased surveillance and improved understanding of the biology of nonfalciparum species.
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Affiliation(s)
- Zachary R Popkin-Hall
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Misago D Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rule Budodo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Tanga Center, Tanga, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - David J Giesbrecht
- Department of Entomology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | | | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
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Rogier E, Battle N, Bakari C, Seth MD, Nace D, Herman C, Barakoti A, Madebe RA, Mandara CI, Lyimo BM, Giesbrecht DJ, Popkin-Hall ZR, Francis F, Mbwambo D, Garimo I, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey JA, Udhayakumar V, Ishengoma DS. Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions among patients enrolled at 100 health facilities throughout Tanzania: February to July 2021. Sci Rep 2024; 14:8158. [PMID: 38589477 PMCID: PMC11001933 DOI: 10.1038/s41598-024-58455-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/29/2024] [Indexed: 04/10/2024] Open
Abstract
Plasmodium falciparum with the histidine rich protein 2 gene (pfhrp2) deleted from its genome can escape diagnosis by HRP2-based rapid diagnostic tests (HRP2-RDTs). The World Health Organization (WHO) recommends switching to a non-HRP2 RDT for P. falciparum clinical case diagnosis when pfhrp2 deletion prevalence causes ≥ 5% of RDTs to return false negative results. Tanzania is a country of heterogenous P. falciparum transmission, with some regions approaching elimination and others at varying levels of control. In concordance with the current recommended WHO pfhrp2 deletion surveillance strategy, 100 health facilities encompassing 10 regions of Tanzania enrolled malaria-suspected patients between February and July 2021. Of 7863 persons of all ages enrolled and providing RDT result and blood sample, 3777 (48.0%) were positive by the national RDT testing for Plasmodium lactate dehydrogenase (pLDH) and/or HRP2. A second RDT testing specifically for the P. falciparum LDH (Pf-pLDH) antigen found 95 persons (2.5% of all RDT positives) were positive, though negative by the national RDT for HRP2, and were selected for pfhrp2 and pfhrp3 (pfhrp2/3) genotyping. Multiplex antigen detection by laboratory bead assay found 135/7847 (1.7%) of all blood samples positive for Plasmodium antigens but very low or no HRP2, and these were selected for genotyping as well. Of the samples selected for genotyping based on RDT or laboratory multiplex result, 158 were P. falciparum DNA positive, and 140 had sufficient DNA to be genotyped for pfhrp2/3. Most of these (125/140) were found to be pfhrp2+/pfhrp3+, with smaller numbers deleted for only pfhrp2 (n = 9) or only pfhrp3 (n = 6). No dual pfhrp2/3 deleted parasites were observed. This survey found that parasites with these gene deletions are rare in Tanzania, and estimated that 0.24% (95% confidence interval: 0.08% to 0.39%) of false-negative HRP2-RDTs for symptomatic persons were due to pfhrp2 deletions in this 2021 Tanzania survey. These data provide evidence for HRP2-based diagnostics as currently accurate for P. falciparum diagnosis in Tanzania.
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Affiliation(s)
- Eric Rogier
- Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Catherine Bakari
- National Institute for Medical Research, Dar Es Salaam, Tanzania
| | - Misago D Seth
- National Institute for Medical Research, Dar Es Salaam, Tanzania
| | - Douglas Nace
- Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Camelia Herman
- Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Achut Barakoti
- Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
- CDC Foundation, Atlanta, GA, USA
| | - Rashid A Madebe
- National Institute for Medical Research, Dar Es Salaam, Tanzania
| | - Celine I Mandara
- National Institute for Medical Research, Dar Es Salaam, Tanzania
| | - Beatus M Lyimo
- National Institute for Medical Research, Dar Es Salaam, Tanzania
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | | | | | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha Njau
- World Health Organization, Country Office, Dar Es Salaam, Tanzania
| | | | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Deus S Ishengoma
- National Institute for Medical Research, Dar Es Salaam, Tanzania.
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia.
- Harvard T.H Chan School of Public Health, Boston, MA, USA.
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Somé AF, Conrad MD, Kabré Z, Fofana A, Yerbanga RS, Bazié T, Neya C, Somé M, Kagambega TJ, Legac J, Garg S, Bailey JA, Ouédraogo JB, Rosenthal PJ, Cooper RA. Ex vivo drug susceptibility and resistance mediating genetic polymorphisms of Plasmodium falciparum in Bobo-Dioulasso, Burkina Faso. Antimicrob Agents Chemother 2024; 68:e0153423. [PMID: 38411062 PMCID: PMC10989024 DOI: 10.1128/aac.01534-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024] Open
Abstract
Malaria remains a leading cause of morbidity and mortality in Burkina Faso, which utilizes artemether-lumefantrine as the principal therapy to treat uncomplicated malaria and seasonal malaria chemoprevention with monthly sulfadoxine-pyrimethamine plus amodiaquine in children during the transmission season. Monitoring the activities of available antimalarial drugs is a high priority. We assessed the ex vivo susceptibility of Plasmodium falciparum to 11 drugs in isolates from patients presenting with uncomplicated malaria in Bobo-Dioulasso in 2021 and 2022. IC50 values were derived using a standard 72 h growth inhibition assay. Parasite DNA was sequenced to characterize known drug resistance-mediating polymorphisms. Isolates were generally susceptible, with IC50 values in the low-nM range, to chloroquine (median IC5010 nM, IQR 7.9-24), monodesethylamodiaquine (22, 14-46) piperaquine (6.1, 3.6-9.2), pyronaridine (3.0, 1.3-5.5), quinine (50, 30-75), mefloquine (7.1, 3.7-10), lumefantrine (7.1, 4.5-12), dihydroartemisinin (3.7, 2.2-5.5), and atovaquone (0.2, 0.1-0.3) and mostly resistant to cycloguanil (850, 543-1,290) and pyrimethamine (33,200, 18,400-54,200), although a small number of outliers were seen. Considering genetic markers of resistance to aminoquinolines, most samples had wild-type PfCRT K76T (87%) and PfMDR1 N86Y (95%) sequences. For markers of resistance to antifolates, established PfDHFR and PfDHPS mutations were highly prevalent, the PfDHPS A613S mutation was seen in 19% of samples, and key markers of high-level resistance (PfDHFR I164L; PfDHPS K540E) were absent or rare (A581G). Mutations in the PfK13 propeller domain known to mediate artemisinin partial resistance were not detected. Overall, our results suggest excellent susceptibilities to drugs now used to treat malaria and moderate, but stable, resistance to antifolates used to prevent malaria.
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Affiliation(s)
- A. Fabrice Somé
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Melissa D. Conrad
- Department of Medicine, University of California, San Francisco, California, USA
| | - Zachari Kabré
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Aminata Fofana
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - R. Serge Yerbanga
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l’Ouest, Bobo-Dioulasso, Burkina Faso
- Institut des Sciences et Techniques, Bobo-Dioulasso, Burkina Faso
| | - Thomas Bazié
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Catherine Neya
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Myreille Somé
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Tegawinde Josue Kagambega
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Jenny Legac
- Department of Medicine, University of California, San Francisco, California, USA
| | - Shreeya Garg
- Department of Medicine, University of California, San Francisco, California, USA
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | | | - Philip J. Rosenthal
- Department of Medicine, University of California, San Francisco, California, USA
| | - Roland A. Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
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Rosenthal PJ, Asua V, Bailey JA, Conrad MD, Ishengoma DS, Kamya MR, Rasmussen C, Tadesse FG, Uwimana A, Fidock DA. The emergence of artemisinin partial resistance in Africa: how do we respond? Lancet Infect Dis 2024:S1473-3099(24)00141-5. [PMID: 38552654 DOI: 10.1016/s1473-3099(24)00141-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 04/21/2024]
Abstract
Malaria remains one of the most important infectious diseases in the world, with the greatest burden in sub-Saharan Africa, primarily from Plasmodium falciparum infection. The treatment and control of malaria is challenged by resistance to most available drugs, but partial resistance to artemisinins (ART-R), the most important class for the treatment of malaria, was until recently confined to southeast Asia. This situation has changed, with the emergence of ART-R in multiple countries in eastern Africa. ART-R is mediated primarily by single point mutations in the P falciparum kelch13 protein, with several mutations present in African parasites that are now validated resistance mediators based on clinical and laboratory criteria. Major priorities at present are the expansion of genomic surveillance for ART-R mutations across the continent, more frequent testing of the efficacies of artemisinin-based regimens against uncomplicated and severe malaria in trials, more regular assessment of ex-vivo antimalarial drug susceptibilities, consideration of changes in treatment policy to deter the spread of ART-R, and accelerated development of new antimalarial regimens to overcome the impacts of ART-R. The emergence of ART-R in Africa is an urgent concern, and it is essential that we increase efforts to characterise its spread and mitigate its impact.
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Affiliation(s)
- Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, CA, USA.
| | - Victor Asua
- Infectious Diseases Research Collaboration, Kampala, Uganda; University of Tübingen, Tübingen, Germany
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Departments of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Melissa D Conrad
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania; Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania; School of Public Health, Harvard University, Boston, MA, USA
| | - Moses R Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda; Department of Medicine, Makerere University, Kampala, Uganda
| | | | - Fitsum G Tadesse
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia; London School of Hygiene and Tropical Medicine, London, UK
| | - Aline Uwimana
- Rwanda Biomedical Center, Kigali, Rwanda; Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - David A Fidock
- Department of Microbiology and Immunology and Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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Bulger EM, Bixby PJ, Price MA, Villarreal CL, Moreno AN, Herrera-Escobar JP, Bailey JA, Brasel KJ, Cooper ZR, Costantini TW, Gibran NS, Groner JI, Joseph BA, Newgard CD, Stein DM. An Executive Summary of the National Trauma Research Action Plan (NTRAP). J Trauma Acute Care Surg 2024:01586154-990000000-00669. [PMID: 38523118 DOI: 10.1097/ta.0000000000004279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
ABSTRACT The National Trauma Research Action Plan (NTRAP) project successfully engaged multidisciplinary experts to define opportunities to advance trauma research and has fulfilled the recommendations related to trauma research from the National Academies of Sciences, Engineering and Medicine (NASEM) report. These panels identified more than 4,800 gaps in our knowledge regarding injury prevention and the optimal care of injured patients and laid out a priority framework and tools to support researchers to advance this field. Trauma research funding agencies and researchers can use this executive summary and supporting manuscripts to strategically address and close the highest priority research gaps. Given that this is the most significant public health threat facing our children, young adults, and military service personnel, we must do better in prioritizing these research projects for funding and providing grant support to advance this work. Through the Coalition for National Trauma Research (CNTR), the trauma community is committed to a coordinated, collaborative approach to address these critical knowledge gaps and ultimately reduce the burden of morbidity and mortality faced by our patients.
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Popkin-Hall ZR, Seth MD, Madebe RA, Budodo R, Bakari C, Francis F, Pereus D, Giesbrecht DJ, Mandara CI, Mbwambo D, Aaron S, Lusasi A, Lazaro S, Bailey JA, Juliano JJ, Gutman JR, Ishengoma DS. Prevalence of non-falciparum malaria infections among asymptomatic individuals in four regions of Mainland Tanzania. Parasit Vectors 2024; 17:153. [PMID: 38519992 PMCID: PMC10960463 DOI: 10.1186/s13071-024-06242-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Recent studies point to the need to incorporate the detection of non-falciparum species into malaria surveillance activities in sub-Saharan Africa, where 95% of the world's malaria cases occur. Although malaria caused by infection with Plasmodium falciparum is typically more severe than malaria caused by the non-falciparum Plasmodium species P. malariae, P. ovale spp. and P. vivax, the latter may be more challenging to diagnose, treat, control and ultimately eliminate. The prevalence of non-falciparum species throughout sub-Saharan Africa is poorly defined. Tanzania has geographical heterogeneity in transmission levels but an overall high malaria burden. METHODS To estimate the prevalence of malaria species in Mainland Tanzania, we randomly selected 1428 samples from 6005 asymptomatic isolates collected in previous cross-sectional community surveys across four regions and analyzed these by quantitative PCR to detect and identify the Plasmodium species. RESULTS Plasmodium falciparum was the most prevalent species in all samples, with P. malariae and P. ovale spp. detected at a lower prevalence (< 5%) in all four regions; P. vivax was not detected in any sample. CONCLUSIONS The results of this study indicate that malaria elimination efforts in Tanzania will need to account for and enhance surveillance of these non-falciparum species.
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Affiliation(s)
- Zachary R Popkin-Hall
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA.
| | - Misago D Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rule Budodo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Tanga Center, Tanga, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | | | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Julie R Gutman
- Malaria Branch, National Center for Emerging and Zoonotic Infectious Diseases, US Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
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Ishengoma DS, Mandara CI, Madebe RA, Warsame M, Ngasala B, Kabanywanyi AM, Mahende MK, Kamugisha E, Kavishe RA, Muro F, Mandike R, Mkude S, Chacky F, Njau R, Martin T, Mohamed A, Bailey JA, Fola AA. Microsatellites reveal high polymorphism and high potential for use in anti-malarial efficacy studies in areas with different transmission intensities in mainland Tanzania. Malar J 2024; 23:79. [PMID: 38491359 PMCID: PMC10943981 DOI: 10.1186/s12936-024-04901-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Tanzania is currently implementing therapeutic efficacy studies (TES) in areas of varying malaria transmission intensities as per the World Health Organization (WHO) recommendations. In TES, distinguishing reinfection from recrudescence is critical for the determination of anti-malarial efficacy. Recently, the WHO recommended genotyping polymorphic coding genes, merozoite surface proteins 1 and 2 (msp1 and msp2), and replacing the glutamate-rich protein (glurp) gene with one of the highly polymorphic microsatellites in Plasmodium falciparum to adjust the efficacy of antimalarials in TES. This study assessed the polymorphisms of six neutral microsatellite markers and their potential use in TES, which is routinely performed in Tanzania. METHODS Plasmodium falciparum samples were obtained from four TES sentinel sites, Kibaha (Pwani), Mkuzi (Tanga), Mlimba (Morogoro) and Ujiji (Kigoma), between April and September 2016. Parasite genomic DNA was extracted from dried blood spots on filter papers using commercial kits. Genotyping was done using six microsatellites (Poly-α, PfPK2, TA1, C3M69, C2M34 and M2490) by capillary method, and the data were analysed to determine the extent of their polymorphisms and genetic diversity at the four sites. RESULTS Overall, 83 (88.3%) of the 94 samples were successfully genotyped (with positive results for ≥ 50.0% of the markers), and > 50.0% of the samples (range = 47.6-59.1%) were polyclonal, with a mean multiplicity of infection (MOI) ranging from 1.68 to 1.88 among the four sites. There was high genetic diversity but limited variability among the four sites based on mean allelic richness (RS = 7.48, range = 7.27-8.03, for an adjusted minimum sample size of 18 per site) and mean expected heterozygosity (He = 0.83, range = 0.80-0.85). Cluster analysis of haplotypes using STRUCTURE, principal component analysis, and pairwise genetic differentiation (FST) did not reveal population structure or clustering of parasites according to geographic origin. Of the six markers, Poly-α was the most polymorphic, followed by C2M34, TA1 and C3M69, while M2490 was the least polymorphic. CONCLUSION Microsatellite genotyping revealed high polyclonality and genetic diversity but no significant population structure. Poly-α, C2M34, TA1 and C3M69 were the most polymorphic markers, and Poly-α alone or with any of the other three markers could be adopted for use in TES in Tanzania.
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Affiliation(s)
- Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania.
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia.
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Billy Ngasala
- Department of Parasitology, School of Public Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | | | | | - Erasmus Kamugisha
- Bugando Medical Centre, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Reginald A Kavishe
- Kilimanjaro Christian Medical Centre, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Florida Muro
- Kilimanjaro Christian Medical Centre, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Renata Mandike
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Sigsbert Mkude
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Ritha Njau
- Malariologist and Public Health Specialist, Dar es Salaam, Tanzania
| | - Troy Martin
- HIV Vaccine Trials Network, Fred Hutch Cancer Research Centre, Seattle, WA, USA
| | - Ally Mohamed
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Abebe A Fola
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
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de Cesare M, Mwenda M, Jeffreys AE, Chirwa J, Drakeley C, Schneider K, Mambwe B, Glanz K, Ntalla C, Carrasquilla M, Portugal S, Verity RJ, Bailey JA, Ghinai I, Busby GB, Hamainza B, Hawela M, Bridges DJ, Hendry JA. Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing. Nat Commun 2024; 15:1413. [PMID: 38360754 PMCID: PMC10869361 DOI: 10.1038/s41467-024-45688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum complicates the development of genomic methods, while resource constraints in malaria endemic regions can limit their deployment. Here, we demonstrate an approach for targeted nanopore sequencing of P. falciparum from dried blood spots (DBS) that enables cost-effective genomic surveillance of malaria in low-resource settings. We release software that facilitates flexible design of amplicon sequencing panels and use this software to design two target panels for P. falciparum. The panels generate 3-4 kbp reads for eight and sixteen targets respectively, covering key drug-resistance associated genes, diagnostic test antigens, polymorphic markers and the vaccine target csp. We validate our approach on mock and field samples, demonstrating robust sequencing coverage, accurate variant calls within coding sequences, the ability to explore P. falciparum within-sample diversity and to detect deletions underlying rapid diagnostic test failure.
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Affiliation(s)
- Mariateresa de Cesare
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | | | - Anna E Jeffreys
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - Jacob Chirwa
- National Malaria Elimination Centre, Chainama, Lusaka, Zambia
| | | | | | | | - Karolina Glanz
- Max Planck Institute for Infection Biology, Berlin, Germany
| | | | | | | | | | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Isaac Ghinai
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - George B Busby
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - Busiku Hamainza
- National Malaria Elimination Centre, Chainama, Lusaka, Zambia
| | - Moonga Hawela
- National Malaria Elimination Centre, Chainama, Lusaka, Zambia
| | | | - Jason A Hendry
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK.
- Max Planck Institute for Infection Biology, Berlin, Germany.
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10
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Connelly SV, Brazeau NF, Msellem M, Ngasala BE, Aydemir Ö, Goel V, Niaré K, Giesbrecht DJ, Popkin-Hall ZR, Hennelly CM, Park Z, Moormann AM, Ong'echa JM, Verity R, Mohammed S, Shija SJ, Mhamilawa LE, Morris U, Mårtensson A, Lin JT, Björkman A, Juliano JJ, Bailey JA. Strong isolation by distance and evidence of population microstructure reflect ongoing Plasmodium falciparum transmission in Zanzibar. medRxiv 2024:2023.02.15.23285960. [PMID: 36865135 PMCID: PMC9980253 DOI: 10.1101/2023.02.15.23285960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Zanzibar archipelago of Tanzania has become a low-transmission area for Plasmodium falciparum. Despite being considered an area of pre-elimination for years, achieving elimination has been difficult, likely due to a combination of imported infections from mainland Tanzania, and continued local transmission. To shed light on these sources of transmission, we applied highly multiplexed genotyping utilizing molecular inversion probes to characterize the genetic relatedness of 282 P. falciparum isolates collected across Zanzibar and in Bagamoyo District on the coastal mainland from 2016-2018. Overall, parasite populations on the coastal mainland and Zanzibar archipelago remain highly related. However, parasite isolates from Zanzibar exhibit population microstructure due to rapid decay of parasite relatedness over very short distances. This, along with highly related pairs within shehias, suggests ongoing low level local transmission. We also identified highly related parasites across shehias that reflect human mobility on the main island of Unguja and identified a cluster of highly related parasites, suggestive of an outbreak, in the Micheweni district on Pemba island. Parasites in asymptomatic infections demonstrated higher complexity of infection than those in symptomatic infections, but have similar core genomes. Our data support importation as a main source of genetic diversity and contribution to the parasite population on Zanzibar, but they also show local outbreak clusters where targeted interventions are essential to block local transmission. These results highlight the need for preventive measures against imported malaria and enhanced control measures in areas that remain receptive for malaria reemergence due to susceptible hosts and competent vectors.
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Affiliation(s)
- Sean V Connelly
- MD-PhD Program, University of North Carolina, Chapel Hill, NC 27599
| | | | - Mwinyi Msellem
- Research Division, Ministry of Health, Zanzibar, Tanzania
| | - Billy E Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Global Health and Migration Unit, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Özkan Aydemir
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Varun Goel
- Carolina Population Center, University of North Carolina, Chapel Hill, NC 27599
| | - Karamoko Niaré
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912 USA
| | - David J Giesbrecht
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912 USA
| | - Zachary R Popkin-Hall
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Christopher M Hennelly
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Zackary Park
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | | | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London
| | - Safia Mohammed
- Zanzibar Malaria Elimination Program (ZAMEP), Zanzibar, Tanzania
| | - Shija J Shija
- Zanzibar Malaria Elimination Program (ZAMEP), Zanzibar, Tanzania
| | - Lwidiko E Mhamilawa
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Global Health and Migration Unit, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Ulrika Morris
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Andreas Mårtensson
- Global Health and Migration Unit, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Jessica T Lin
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Anders Björkman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan J Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, 27599 USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912 USA
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11
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Meier-Scherling CPG, Watson OJ, Asua V, Ghinai I, Katairo T, Garg S, Conrad M, Rosenthal PJ, Okell LC, Bailey JA. Selection of artemisinin partial resistance Kelch13 mutations in Uganda in 2016-22 was at a rate comparable to that seen previously in South-East Asia. medRxiv 2024:2024.02.03.24302209. [PMID: 38352505 PMCID: PMC10862983 DOI: 10.1101/2024.02.03.24302209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Background Artemisinin partial resistance, mediated by mutations in the Plasmodium falciparum Kelch13 protein (K13), rapidly spread in South-East Asia (SEA), undermining antimalarial efficacies of artemisinin-based combination therapies (ACT). Validated K13 mutations have recently arisen in Africa, but rates of increase are not well characterized. Methods We investigated K13 mutation prevalence at 16 sites in Uganda (2016-2022, 6586 samples), and five sites in SEA (2003-2018, 5465 samples) by calculating selection coefficients using Bayesian mixed-effect linear models. We then tested whether SEA K13 mutation prevalence could have been forecast accurately using up to the first five years of available data and forecast future K13 mutation prevalence in Uganda. Findings The selection coefficient for the prevalence of relevant K13 mutations (441L, 469F/Y, 561H, 675V) was estimated at s=0·383 (95% CrI: 0·247 - 0·528) per year, a 38% relative prevalence increase. Selection coefficients across Uganda were s=0·968 (0·463 - 1·569) for 441L, s=0·153 (-0·445 - 0·727) for 469F, s=0·222 (-0·011 - 0·398) for 469Y, and s=0·152 (-0·023 - 0·312) for 675V. In SEA, the selection coefficient was s=-0·005 (-0·852 - 0·814) for 539T, s=0·574 (-0·092 - 1·201) for 580Y, and s=0·308 (0·089 - 0·536) for all validated K13 mutations. Forecast prevalences for Uganda assuming constant selection neared fixation (>95% prevalence) within a decade (2028-2033) for combined K13 mutations. Interpretation The selection of K13 mutations in Uganda was at a comparable rate to that observed in SEA, suggesting K13 mutations may continue to increase quickly in Uganda. Funding NIH R01AI156267, R01AI075045, and R01AI089674.
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Affiliation(s)
| | - Oliver J Watson
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Victor Asua
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Thomas Katairo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Shreeya Garg
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Melissa Conrad
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Philip J. Rosenthal
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lucy C Okell
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Jeffrey A. Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, RI, USA
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12
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Tebit DM, Nickel G, Gibson R, Rodriguez M, Hathaway NJ, Bain K, Reyes-Rodriguez AL, Ondoa P, Heeney JL, Li Y, Bongorno J, Canaday D, McDonald D, Bailey JA, Arts EJ. Replicative fitness and pathogenicity of primate lentiviruses in lymphoid tissue, primary human and chimpanzee cells: relation to possible jumps to humans. EBioMedicine 2024; 100:104965. [PMID: 38215691 PMCID: PMC10827413 DOI: 10.1016/j.ebiom.2023.104965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Simian immunodeficiency viruses (SIV) have been jumping between non-human primates in West/Central Africa for thousands of years and yet, the HIV-1 epidemic only originated from a primate lentivirus over 100 years ago. METHODS This study examined the replicative fitness, transmission, restriction, and cytopathogenicity of 22 primate lentiviruses in primary human lymphoid tissue and both primary human and chimpanzee peripheral blood mononuclear cells. FINDINGS Pairwise competitions revealed that SIV from chimpanzees (cpz) had the highest replicative fitness in human or chimpanzee peripheral blood mononuclear cells, even higher fitness than HIV-1 group M strains responsible for worldwide epidemic. The SIV strains belonging to the "HIV-2 lineage" (including SIVsmm, SIVmac, SIVagm) had the lowest replicative fitness. SIVcpz strains were less inhibited by human restriction factors than the "HIV-2 lineage" strains. SIVcpz efficiently replicated in human tonsillar tissue but did not deplete CD4+ T-cells, consistent with the slow or nonpathogenic disease observed in most chimpanzees. In contrast, HIV-1 isolates and SIV of the HIV-2 lineage were pathogenic to the human tonsillar tissue, almost independent of the level of virus replication. INTERPRETATION Of all primate lentiviruses, SIV from chimpanzees appears most capable of infecting and replicating in humans, establishing HIV-1. SIV from other Old World monkeys, e.g. the progenitor of HIV-2, replicate slowly in humans due in part to restriction factors. Nonetheless, many of these SIV strains were more pathogenic than SIVcpz. Either SIVcpz evolved into a more pathogenic virus while in humans or a rare SIVcpz, possibly extinct in chimpanzees, was pathogenic immediately following the jump into human. FUNDING Support for this study to E.J.A. was provided by the NIH/NIAID R01 AI49170 and CIHR project grant 385787. Infrastructure support was provided by the NIH CFAR AI36219 and Canadian CFI/Ontario ORF 36287. Efforts of J.A.B. and N.J.H. was provided by NIH AI099473 and for D.H.C., by VA and NIH AI AI080313.
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Affiliation(s)
- Denis M Tebit
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Global Biomed Scientific, LLC, P.O. Box 2368, Forest, VA, USA
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard Gibson
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Myriam Rodriguez
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Nicolas J Hathaway
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Katie Bain
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Angel L Reyes-Rodriguez
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pascal Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia; Department of Global Health, Institute of Global Health and Development, University of Amsterdam, Amsterdam, the Netherlands
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Yue Li
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Jennifer Bongorno
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - David Canaday
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David McDonald
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Eric J Arts
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Microbiology and Immunology, Western University, Ontario, Canada.
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13
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Bailey JA, Morton AJ, Jones J, Chapman CJ, Oliver S, Morling JR, Patel H, Humes DJ, Banerjea A. 'Low' faecal immunochemical test (FIT) colorectal cancer: a 4-year comparison of the Nottingham '4F' protocol with FIT10 in symptomatic patients. Colorectal Dis 2024; 26:309-316. [PMID: 38173125 DOI: 10.1111/codi.16848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
AIM The aim of this work was to evaluate colorectal cancer (CRC) outcomes after 'low' (sub-threshold) faecal immunochemical test (FIT) results in symptomatic patients tested in primary care. METHOD This work comprised a retrospective audit of 35 289 patients with FIT results who had consulted their general practitioner with lower gastrointestinal symptoms and had subsequent CRC diagnoses. The Rapid Colorectal Cancer Diagnosis pathway was introduced in November 2017 to allow incorporation of FIT into clinical practice. The local '4F' protocol combined FIT results with blood tests and digital rectal examination (DRE): FIT, full blood count, ferritin and finger [DRE]. The outcome used was detection rates of CRC, missed CRC and time to diagnosis in local 4F protocols for patients with a subthreshold faecal haemoglobin (fHb) result compared with thresholds of 10 and 20 μg Hb/g faeces. RESULTS A single threshold of 10 μg Hb/g faeces identifies a population in whom the risk of CRC is 0.2%, but this would have missed 63 (10.5%) of 599 CRCs in this population. The Nottingham 4F protocol would have missed fewer CRCs [42 of 599 (7%)] despite using a threshold of 20 μg Hb/g faeces for patients with normal blood tests. Subthreshold FIT results in patients subsequently diagnosed with a palpable rectal tumour yielded the longest delays in diagnosis. CONCLUSION A combination of FIT with blood results and DRE (the 4F protocol) reduced the risk of missed or delayed diagnosis. Further studies on the impact of such protocols on the diagnostic accuracy of FIT are expected. The value of adding blood tests to FIT may be restricted to specific parts of the fHb results spectrum.
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Affiliation(s)
- J A Bailey
- Nottingham Colorectal Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queens Medical Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - A J Morton
- Nottingham Colorectal Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queens Medical Centre, School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - J Jones
- Nottingham Colorectal Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - C J Chapman
- Eastern Hub, Bowel Cancer Screening Programme, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - S Oliver
- NHS Nottingham and Nottinghamshire Integrated Care Board, Nottingham, UK
| | - J R Morling
- NHS Nottingham and Nottinghamshire Integrated Care Board, Nottingham, UK
- Lifespan and Population Health, School of Medicine, University of Nottingham, City Hospital, Nottingham, UK
| | - H Patel
- NHS Nottingham and Nottinghamshire Integrated Care Board, Nottingham, UK
| | - D J Humes
- Nottingham Colorectal Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre (BRC), Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - A Banerjea
- Nottingham Colorectal Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
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Ishengoma DS, Mandara CI, Bakari C, Fola AA, Madebe RA, Seth MD, Francis F, Buguzi C, Moshi R, Garimo I, Lazaro S, Lusasi A, Aaron S, Chacky F, Mohamed A, Njau RJA, Kitau J, Rasmussen C, Bailey JA, Juliano JJ, Warsame M. Evidence of artemisinin partial resistance in North-western Tanzania: clinical and drug resistance markers study. medRxiv 2024:2024.01.31.24301954. [PMID: 38352311 PMCID: PMC10863006 DOI: 10.1101/2024.01.31.24301954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Background Artemisinin-based combination therapies (ACTs) are the recommended antimalarial drugs for the treatment of uncomplicated malaria. The recent emergence of artemisinin partial resistance (ART-R) in Rwanda, Uganda and Eritrea is of great concern. In Tanzania, a nationwide molecular malaria surveillance in 2021 showed a high prevalence of the Kelch13 (K13) 561H mutation in Plasmodium falciparum from the north-western region, close to the border with Rwanda and Uganda. This study was conducted in 2022 to evaluate the efficacy of artemether-lumefantrine (AL) and artesunate-amodiaquine (ASAQ) for the treatment of uncomplicated falciparum malaria and to confirm the presence of ART-R in Tanzania. Methods This single-arm study evaluated the efficacy of AL and ASAQ in eligible children aged six months to 10 years at Bukangara Dispensary in Karagwe District, Kagera Region. Clinical and parasitological responses were monitored for 28 days according to standard WHO protocol. Mutations in K13 gene and extended haplotypes with these mutations were analysed using Sanger and whole genome sequencing data, respectively. Findings 176 children (88 in each AL and ASAQ group) were enrolled and all achieved the defined outcomes. PCR-corrected adequate clinical and parasitological response (ACPR) was 98.3% (95% CI: 90.8-100) and 100.0% (95% CI: 95.8-100) for AL and ASAQ, respectively. Parasitaemia on day 3 was observed in 11/88 (12.5%) and 17/88 (19.3%) in the AL and ASAQ groups, respectively. The half-life of parasitaemia was significantly higher (>6.5 hrs) in patients with parasitaemia on day 3 and/or mutations in K13 gene at enrolment. Most patients with parasitaemia on day 3 (8/11 = 72.7% in the AL group and 10/17 = 58.8% in the ASAQ group) had 561H mutation at enrolment. The parasites with K13 mutations were not similar to those from south-east Asia and Rwanda, but had the same core haplotype of a new 561H haplotype reported in Kagera in 2021. Interpretation These findings confirm the presence of ART-R in Tanzania. A context-specific strategy to respond to artemisinin partial resistance is urgently needed. Although both AL and ASAQ showed high efficacy, increased vigilance for reduced efficacy of these ACTs and detection of ART-R in other parts of the country is critical.
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Affiliation(s)
- Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, VIC, Australia
- Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania
| | | | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Abebe A. Fola
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Creyton Buguzi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Issa Garimo
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Samwel Lazaro
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | | | - Sijenunu Aaron
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Ritha J. A. Njau
- Malariologist and Public Health Specialist, Muhimbili University of Health and Allied Sciences, School of Public Health and Social Sciences Dar es Salaam, Tanzania
| | - Jovin Kitau
- World Health Organization Country Office, Dar es Salaam, Tanzania
| | | | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | | | - Marian Warsame
- Gothenburg University, Gothenburg, Sweden
- Benadir University, Mogadishu, Somalia
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15
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Lyimo BM, Bakari C, Popkin-Hall ZR, Giesbrecht DJ, Seth MD, Pereus D, Moshi R, Boniface R, Mandara CI, Madebe R, Juliano JJ, Bailey JA, Ishengoma DS. Genetic polymorphism and evidence of signatures of selection in the Plasmodium falciparum circumsporozoite protein gene in Tanzanian regions with different malaria endemicity. medRxiv 2024:2024.01.23.24301587. [PMID: 38343796 PMCID: PMC10854334 DOI: 10.1101/2024.01.23.24301587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Background In 2021 and 2023, the World Health Organization approved RTS, S/AS01 and R21/Matrix M malaria vaccines, respectively, for routine immunization of children in African countries with moderate to high transmission. These vaccines are made of Plasmodium falciparum circumsporozoite protein (Pfcsp) but polymorphisms in this gene raises concerns regarding strain-specific responses and the long-term efficacy of these vaccines. This study assessed the Pfcsp genetic diversity, population structure and signatures of selection among parasites from areas of different malaria transmission in mainland Tanzania, to generate baseline data before the introduction of the malaria vaccines in the country. Methods The analysis involved 589 whole genome sequences generated by and as part of the MalariaGEN Community Project. The samples were collected between 2013 and January 2015 from five regions of mainland Tanzania: Morogoro and Tanga (Muheza) (moderate transmission areas), and Kagera (Muleba), Lindi (Nachingwea), and Kigoma (Ujiji) (high transmission areas). Wright's inbreeding coefficient (Fws), Wright's fixation index (FST), principal component analysis, nucleotide diversity, and Tajima's D were used to assess within-host parasite diversity, population structure and natural selection. Results Based on Fws (< 0.95), there was high polyclonality (ranged from 69.23% in Nachingwea to 56.9% in Muheza). No population structure was detected in the Pfcsp gene in the five regions (mean FST= 0.0068). The average nucleotide diversity (π), nucleotide differentiation (K) and haplotype diversity (Hd) in the five regions were 4.19, 0.973 and 0.0035, respectively. The C-terminal region of Pfcsp showed high nucleotide diversity at Th2R and Th3R regions. Positive values for the Tajima's D were observed in the Th2R and Th3R regions consistent with balancing selection. The Pfcsp C-terminal sequences had 50 different haplotypes (H_1 to H_50) and only 2% of sequences matched the 3D7 strain haplotype (H_50). Conclusions The findings demonstrate high diversity of the Pfcsp gene with limited population differentiation. The Pfcsp gene showed positive Tajima's D values for parasite populations, consistent with balancing selection for variants within Th2R and Th3R regions. This data is consistent with other studies conducted across Africa and worldwide, which demonstrate low 3D7 haplotypes and little population structure. Therefore, additional research is warranted, incorporating other regions and more recent data to comprehensively assess trends in genetic diversity within this important gene. Such insights will inform the choice of alleles to be included in the future vaccines.
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Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ruth Boniface
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Rashid Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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16
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Gaither C, Morgan C, Kirby R, Karema C, Gashema P, White SJ, Topazian HM, Geibrecht D, Thwai K, Boyter K, Munyaneza T, Muvunyi CM, De Dieu Butera J, Bailey JA, Mazarati JB, Juliano JJ. Prevalence of Falciparum and non-Falciparum Malaria in the 2014-15 Rwanda Demographic Health Survey. medRxiv 2024:2024.01.09.24301054. [PMID: 38260604 PMCID: PMC10802648 DOI: 10.1101/2024.01.09.24301054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Malaria remains a major cause of morbidity in sub-Saharan Africa. Undetected asymptomatic falciparum malaria results in a large transmission reservoir and there is evidence of increasing non-falciparum malaria as malaria is controlled in Africa, both resulting in challenges for malaria control programs. Methods We performed quantitative real time PCR for 4 malaria species in 4,596 individuals from the 2014-2015 Rwanda Demographic Health Survey. Bivariate models were used to determine species-specific associations with risk factors. Results Asymptomatic falciparum malaria, P. ovale spp., and P. malariae infection had broad spatial distribution across Rwanda. P. vivax infection was rare. Overall infection prevalence was 23.6% (95%CI [21.7%, 26.0%]), with falciparum and non-falciparum at 17.6% [15.9%, 19.0%] and 8.3% [7.0%, 10.0%], respectively. Parasitemias tended to be low and mixed species infections were common, especially where malaria transmission was the highest. Falciparum infection was associated with socio-econiomic status, rural residence and low altitude. Few risk factors were associated with non-falciparum malaria. Conclusions Asymptomatic falciparum malaria and non-falciparum malaria are common and widely distributed across Rwanda. Continued molecular monitoring of Plasmodium spp. is needed to monitor these threats to malaria control in Africa.
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Affiliation(s)
- Claudia Gaither
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Camille Morgan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca Kirby
- Department of Pathology, Brown University, Providence, RI, USA
| | | | | | - Samuel J White
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Hillary M Topazian
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - David Geibrecht
- Department of Pathology, Brown University, Providence, RI, USA
| | - Kyaw Thwai
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Koby Boyter
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | | | | | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
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17
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Watson OJ, Tran TNA, Zupko RJ, Symons T, Thomson R, Visser T, Rumisha S, Dzianach PA, Hathaway N, Kim I, Juliano JJ, Bailey JA, Slater H, Okell L, Gething P, Ghani A, Boni MF, Parr JB, Cunningham J. Global risk of selection and spread of Plasmodium falciparum histidine-rich protein 2 and 3 gene deletions. medRxiv 2024:2023.10.21.23297352. [PMID: 37905102 PMCID: PMC10615018 DOI: 10.1101/2023.10.21.23297352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In the thirteen years since the first report of pfhrp2-deleted parasites in 2010, the World Health Organization (WHO) has found that 40 of 47 countries surveyed worldwide have reported pfhrp2/3 gene deletions. Due to a high prevalence of pfhrp2/3 deletions causing false-negative HRP2 RDTs, in the last five years, Eritrea, Djibouti and Ethiopia have switched or started switching to using alternative RDTs, that target pan-specific-pLDH or P. falciparum specific-pLDH alone of in combination with HRP2. However, manufacturing of alternative RDTs has not been brought to scale and there are no WHO prequalified combination tests that use Pf-pLDH instead of HRP2 for P. falciparum detection. For these reasons, the continued spread of pfhrp2/3 deletions represents a growing public health crisis that threatens efforts to control and eliminate P. falciparum malaria. National malaria control programmes, their implementing partners and test developers desperately seek pfhrp2/3 deletion data that can inform their immediate and future resource allocation. In response, we use a mathematical modelling approach to evaluate the global risk posed by pfhrp2/3 deletions and explore scenarios for how deletions will continue to spread in Africa. We incorporate current best estimates of the prevalence of pfhrp2/3 deletions and conduct a literature review to estimate model parameters known to impact the selection of pfhrp2/3 deletions for each malaria endemic country. We identify 20 countries worldwide to prioritise for surveillance and future deployment of alternative RDT, based on quickly selecting for pfhrp2/3 deletions once established. In scenarios designed to explore the continued spread of deletions in Africa, we identify 10 high threat countries that are most at risk of deletions both spreading to and subsequently being rapidly selected for. If HRP2-based RDTs continue to be relied on for malaria case management, we predict that the major route for pfhrp2 deletions to spread is south out from the current hotspot in the Horn of Africa, moving through East Africa over the next 20 years. We explore the variation in modelled timelines through an extensive parameter sensitivity analysis and despite wide uncertainties, we identify three countries that have not yet switched RDTs (Senegal, Zambia and Kenya) that are robustly identified as high risk for pfhrp2/3 deletions. These results provide a refined and updated prediction model for the emergence of pfhrp2/3 deletions in an effort to help guide pfhrp2/3 policy and prioritise future surveillance efforts and innovation.
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Affiliation(s)
- Oliver J Watson
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Robert J Zupko
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tasmin Symons
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | | | | | - Susan Rumisha
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Paulina A Dzianach
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Nicholas Hathaway
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Isaac Kim
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | | | - Lucy Okell
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Peter Gething
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
- Faculty of Health Sciences, Curtin University, Bentley, Australia
| | - Azra Ghani
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jonathan B Parr
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
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18
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Popkin Hall ZR, Seth MD, Madebe RA, Budodo R, Bakari C, Francis F, Pereus D, Giesbrecht DJ, Mandara CI, Mbwambo D, Aaron S, Lusasi A, Lazaro S, Bailey JA, Juliano JJ, Gutman JR, Ishengoma DS. Malaria species prevalence among asymptomatic individuals in four regions of Mainland Tanzania. medRxiv 2023:2023.12.28.23300584. [PMID: 38234751 PMCID: PMC10793544 DOI: 10.1101/2023.12.28.23300584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Recent studies point to the need to incorporate non-falciparum species detection into malaria surveillance activities in sub-Saharan Africa, where 95% of malaria cases occur. Although Plasmodium falciparum infection is typically more severe, diagnosis, treatment, and control for P. malariae, P. ovale spp., and P. vivax may be more challenging. The prevalence of these species throughout sub-Saharan Africa is poorly defined. Tanzania has geographically heterogeneous transmission levels but an overall high malaria burden. In order to estimate the prevalence of malaria species in Mainland Tanzania, 1,428 samples were randomly selected from 6,005 asymptomatic isolates collected in cross-sectional community surveys across four regions and analyzed via qPCR to detect each Plasmodium species. P. falciparum was most prevalent, with P. malariae and P. ovale spp. detected at lower prevalence (<5%) in all four regions. P. vivax was not detected. Malaria elimination efforts in Tanzania will need to account for these non-falciparum species.
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Affiliation(s)
- Zachary R Popkin Hall
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Misago D Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rule Budodo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Tanga Center, Tanga, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | | | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, RI, USA
- Center for Computational Molecular Biology, Brown University, RI, USA
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Julie R Gutman
- Malaria Branch, Global Health Center, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T. H. Chan School of Public Health, Boston, MA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
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19
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Oduor CI, Cunningham C, Rustamzade N, Zuromski J, Chin DM, Nixon CP, Kurtis JD, Juliano JJ, Bailey JA. Single cell transcriptional changes across the blood stages of artemisinin resistant K13 C580Y mutant Plasmodium falciparum upon dihydroartemisinin exposure. bioRxiv 2023:2023.12.06.570387. [PMID: 38105992 PMCID: PMC10723473 DOI: 10.1101/2023.12.06.570387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Artemisinins have been a cornerstone of malaria control, but resistance in Plasmodium falciparum, due to mutations in the Kelch 13 gene, threaten these advances. Artemisinin exposure results in a dynamic transcriptional response across multiple pathways, but most work has focused on ring stages and ex vivo transcriptional analysis, limiting evaluation of all life cycle stages. We applied single cell RNAseq to two unsynchronized isogenic parasite lines (K13C580 and K13580Y) over 6 hrs after a pulse exposure to dihydroartemisinin (DHA). Transcription was altered across all stages, with the greatest occurring at the early trophozoite and mid ring stage in both lines. This response involved the arrest of metabolic processes and the enhancement of protein trafficking and the unfolded protein response. While similar, the response was enhanced in the K13580Y mutant, which may lead to the dormancy phenomenon upon treatment. Increased surface protein expression was seen in mutant parasites at baseline and upon drug exposure, highlighted by the increased expression of PfEMP1 and GARP, a potential therapeutic target. Antibody targeting GARP maintained anti-parasitic efficacy in mutant parasites. This work provides single cell insight of gene transcription across all life cycle stages revealing transcriptional changes that could initiate dormancy state and mediate survival.
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Affiliation(s)
- Cliff I. Oduor
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Clark Cunningham
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Nazrin Rustamzade
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Jenna Zuromski
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Deborah M. Chin
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Christian P. Nixon
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Jonathan D. Kurtis
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | - Jonathan J. Juliano
- Division of Infectious Diseases, Department of Medicine, University of North Carolina, Chapel Hill, NC
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
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20
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Juliano JJ, Giesbrecht DJ, Simkin A, Fola AA, Lyimo BM, Pereus D, Bakari C, Madebe RA, Seth MD, Mandara CI, Popkin-Hall ZR, Moshi R, Mbwambo RB, Niaré K, MacInnis B, Francis F, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau RJA, Lazaro S, Mohamed A, Bailey JA, Ishengoma DS. Country wide surveillance reveals prevalent artemisinin partial resistance mutations with evidence for multiple origins and expansion of high level sulfadoxine-pyrimethamine resistance mutations in northwest Tanzania. medRxiv 2023:2023.11.07.23298207. [PMID: 37986920 PMCID: PMC10659475 DOI: 10.1101/2023.11.07.23298207] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Emergence of artemisinin partial resistance (ART-R) in Plasmodium falciparum is a growing threat to the efficacy of artemisinin combination therapies (ACT) and the efforts for malaria elimination. The emergence of Plasmodium falciparum Kelch13 (K13) R561H in Rwanda raised concern about the impact in neighboring Tanzania. In addition, regional concern over resistance affecting sulfadoxine-pyrimethamine (SP), which is used for chemoprevention strategies, is high. Methods To enhance longitudinal monitoring, the Molecular Surveillance of Malaria in Tanzania (MSMT) project was launched in 2020 with the goal of assessing and mapping antimalarial resistance. Community and clinic samples were assessed for resistance polymorphisms using a molecular inversion probe platform. Findings Genotyping of 6,278 samples collected countrywide in 2021 revealed a focus of K13 561H mutants in northwestern Tanzania (Kagera) with prevalence of 7.7% (50/649). A small number of 561H mutants (about 1%) were found as far as 800 km away in Tabora, Manyara, and Njombe. Genomic analysis suggests some of these parasites are highly related to isolates collected in Rwanda in 2015, supporting regional spread of 561H. However, a novel haplotype was also observed, likely indicating a second origin in the region. Other validated resistance polymorphisms (622I and 675V) were also identified. A focus of high sulfadoxine-pyrimethamine drug resistance was also identified in Kagera with a prevalence of dihydrofolate reductase 164L of 15% (80/526). Interpretation These findings demonstrate the K13 561H mutation is entrenched in the region and that multiple origins of ART-R, similar as to what was seen in Southeast Asia, have occurred. Mutations associated with high levels of SP resistance are increasing. These results raise concerns about the long-term efficacy of artemisinin and chemoprevention antimalarials in the region. Funding This study was funded by the Bill and Melinda Gates Foundation and the National Institutes of Health.
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Affiliation(s)
| | | | | | | | - Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ruth B. Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Bronwyn MacInnis
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Broad Institute, Boston, MA, USA
| | | | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha J. A. Njau
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | | | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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21
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Willard KA, Barry AP, Oduor CI, Ong'echa JM, Bailey JA, Moormann AM, Luftig MA. Viral and host factors drive a type 1 Epstein-Barr virus spontaneous lytic phenotype. mBio 2023; 14:e0220423. [PMID: 37971257 PMCID: PMC10746244 DOI: 10.1128/mbio.02204-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/21/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Epstein-Barr virus (EBV) infects over 95% of adults worldwide. Given its connection to various cancers and autoimmune disorders, it is important to understand the mechanisms by which infection with EBV can lead to these diseases. In this study, we describe an unusual spontaneous lytic phenotype in EBV strains isolated from Kenyan endemic Burkitt lymphoma patients. Because lytic replication of EBV has been linked to the pathogenesis of various diseases, these data could illuminate viral and host factors involved in this process.
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Affiliation(s)
- Katherine A. Willard
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ashley P. Barry
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Cliff I. Oduor
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Ann M. Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
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22
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Bell GJ, Gyaase S, Goel V, Adu B, Mensah B, Essone P, Dosoo D, Osei M, Niare K, Wiru K, Brandt K, Emch M, Ghansah A, Asante KP, Mvalo T, Agnandji ST, Juliano JJ, Bailey JA. Background malaria incidence and parasitemia during the three-dose RTS,S/AS01 vaccination series do not reduce magnitude of antibody response nor efficacy against the first case of malaria. BMC Infect Dis 2023; 23:716. [PMID: 37872492 PMCID: PMC10594884 DOI: 10.1186/s12879-023-08699-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND RTS,S/AS01 has been recommended by WHO for widespread implementation in medium to high malaria transmission settings. Previous analyses have noted lower vaccine efficacies in higher transmission settings, possibly due to the more rapid development of naturally acquired immunity in the control group. METHODS To investigate a reduced immune response to vaccination as a potential mechanism behind lower efficacy in high transmission areas, we examine initial vaccine antibody (anti-CSP IgG) response and vaccine efficacy against the first case of malaria (to exclude the effect of naturally acquired immunity) using data from three study areas (Kintampo, Ghana; Lilongwe, Malawi; Lambaréné, Gabon) from the 2009-2014 phase III trial (NCT00866619). Our key exposures are parasitemia during the vaccination series and background malaria incidence. We calculate vaccine efficacy (one minus hazard ratio) using a cox-proportional hazards model and allowing for the time-varying effect of RTS,S/AS01. RESULTS We find that antibody responses to the primary three-dose vaccination series were higher in Ghana than in Malawi and Gabon, but that neither antibody levels nor vaccine efficacy against the first case of malaria varied by background incidence or parasitemia during the primary vaccination series. CONCLUSIONS We find that vaccine efficacy is unrelated to infections during vaccination. Contributing to a conflicting literature, our results suggest that vaccine efficacy is also unrelated to infections before vaccination, meaning that control-group immunity is likely a major reason for lower efficacy in high transmission settings, not reduced immune responses to RTS,S/AS01. This may be reassuring for implementation in high transmission settings, though further studies are needed.
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Affiliation(s)
- Griffin J Bell
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | | | - Varun Goel
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Benedicta Mensah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Paulin Essone
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - David Dosoo
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Musah Osei
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Karamoko Niare
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
| | - Kenneth Wiru
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Katerina Brandt
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Tisungane Mvalo
- University of North Carolina Project, Lilongwe, Malawi
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Selidji Todagbe Agnandji
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
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23
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Sendor R, Banek K, Kashamuka MM, Mvuama N, Bala JA, Nkalani M, Kihuma G, Atibu J, Thwai KL, Svec WM, Goel V, Nseka T, Lin JT, Bailey JA, Emch M, Carrel M, Juliano JJ, Tshefu A, Parr JB. Epidemiology of Plasmodium malariae and Plasmodium ovale spp. in Kinshasa Province, Democratic Republic of Congo. Nat Commun 2023; 14:6618. [PMID: 37857597 PMCID: PMC10587068 DOI: 10.1038/s41467-023-42190-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
Reports suggest non-falciparum species are an underappreciated cause of malaria in sub-Saharan Africa but their epidemiology is ill-defined, particularly in highly malaria-endemic regions. We estimated incidence and prevalence of PCR-confirmed non-falciparum and Plasmodium falciparum malaria infections within a longitudinal study conducted in Kinshasa, Democratic Republic of Congo (DRC) between 2015-2017. Children and adults were sampled at biannual household surveys and routine clinic visits. Among 9,089 samples from 1,565 participants, incidences of P. malariae, P. ovale spp., and P. falciparum infections by 1-year were 7.8% (95% CI: 6.4%-9.1%), 4.8% (95% CI: 3.7%-5.9%) and 57.5% (95% CI: 54.4%-60.5%), respectively. Non-falciparum prevalences were higher in school-age children, rural and peri-urban sites, and P. falciparum co-infections. P. falciparum remains the primary driver of malaria in the DRC, though non-falciparum species also pose an infection risk. As P. falciparum interventions gain traction in high-burden settings, continued surveillance and improved understanding of non-falciparum infections are warranted.
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Affiliation(s)
- Rachel Sendor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Kristin Banek
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melchior M Kashamuka
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Nono Mvuama
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Joseph A Bala
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Marthe Nkalani
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Georges Kihuma
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Joseph Atibu
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Kyaw L Thwai
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - W Matthew Svec
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Varun Goel
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tommy Nseka
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jessica T Lin
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Margaret Carrel
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, IA, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Antoinette Tshefu
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jonathan B Parr
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Fola AA, Feleke SM, Mohammed H, Brhane BG, Hennelly CM, Assefa A, Crudal RM, Reichert E, Juliano JJ, Cunningham J, Mamo H, Solomon H, Tasew G, Petros B, Parr JB, Bailey JA. Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia. Nat Microbiol 2023; 8:1911-1919. [PMID: 37640962 PMCID: PMC10522486 DOI: 10.1038/s41564-023-01461-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/26/2023] [Indexed: 08/31/2023]
Abstract
Diagnosis and treatment of Plasmodium falciparum infections are required for effective malaria control and are pre-requisites for malaria elimination efforts; hence we need to monitor emergence, evolution and spread of drug- and diagnostics-resistant parasites. We deep sequenced key drug-resistance mutations and 1,832 SNPs in the parasite genomes of 609 malaria cases collected during a diagnostic-resistance surveillance study in Ethiopia. We found that 8.0% (95% CI 7.0-9.0) of malaria cases were caused by P. falciparum carrying the candidate artemisinin partial-resistance kelch13 (K13) 622I mutation, which was less common in diagnostic-resistant parasites mediated by histidine-rich proteins 2 and 3 (pfhrp2/3) deletions than in wild-type parasites (P = 0.03). Identity-by-descent analyses showed that K13 622I parasites were significantly more related to each other than to wild type (P < 0.001), consistent with recent expansion and spread of this mutation. Pfhrp2/3-deleted parasites were also highly related, with evidence of clonal transmissions at the district level. Of concern, 8.2% of K13 622I parasites also carried the pfhrp2/3 deletions. Close monitoring of the spread of combined drug- and diagnostic-resistant parasites is needed.
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Affiliation(s)
- Abebe A Fola
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | | | | | | | - Christopher M Hennelly
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca M Crudal
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Emily Reichert
- Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Hassen Mamo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Geremew Tasew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Beyene Petros
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jonathan B Parr
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA.
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Popkin Hall ZR, Seth MD, Madebe RA, Budodo R, Bakari C, Francis F, Pereus D, Giesbrecht DJ, Mandara CI, Mbwambo D, Aaron S, Lazaro S, Bailey JA, Juliano JJ, Ishengoma DS. Malaria species positivity rates among symptomatic individuals across regions of differing transmission intensities in Mainland Tanzania. medRxiv 2023:2023.09.19.23295562. [PMID: 37790396 PMCID: PMC10543240 DOI: 10.1101/2023.09.19.23295562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Recent data indicate that non- Plasmodium falciparum species may be more prevalent than previously realized in sub-Saharan Africa, the region where 95% of the world's malaria cases occur. Although Plasmodium malariae, Plasmodium ovale spp., and Plasmodium vivax are generally less severe than P. falciparum , treatment and control are more challenging, and their geographic distributions are not well characterized. In order to characterize the distribution of malaria species in Mainland Tanzania (which has a high burden and geographically heterogeneous transmission levels), we randomly selected 3,284 samples from 12,845 samples to determine presence and parasitemia of different malaria species. The samples were collected from cross-sectional surveys in 100 health facilities across ten regions and analyzed via quantitative real-time PCR to characterize regional positivity rates for each species. P. falciparum was most prevalent, but P. malariae and P. ovale were found in all regions except Dar es Salaam, with high levels (>5%) of P. ovale in seven regions (70%). The highest positivity rate of P. malariae was 4.5% in Mara region and eight regions (80%) had positivity rates ≥1%. We also detected three P. vivax infections in the very low-transmission Kilimanjaro region. While most samples that tested positive for non-falciparum malaria were co-infected with P. falciparum , 23.6% (n = 13/55) of P. malariae and 14.7% (n = 24/163) of P. ovale spp. samples were mono-infections. P. falciparum remains by far the largest threat, but our data indicate that malaria elimination efforts in Tanzania will require increased surveillance and improved understanding of the biology of non-falciparum species.
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Muriuki BM, Forconi CS, Kirwa EK, Maina TK, Ariera BO, Bailey JA, Ghansah A, Moormann AM, Ong’echa JM. Evaluation of KIR3DL1/KIR3DS1 allelic polymorphisms in Kenyan children with endemic Burkitt lymphoma. PLoS One 2023; 18:e0275046. [PMID: 37647275 PMCID: PMC10468049 DOI: 10.1371/journal.pone.0275046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/15/2023] [Indexed: 09/01/2023] Open
Abstract
Endemic Burkitt lymphoma (eBL) is a fast-growing germinal center B cell lymphoma, affecting 5-10 per 100,000 children annually, in the equatorial belt of Africa. We hypothesize that co-infections with Plasmodium falciparum (Pf) malaria and Epstein-Barr virus (EBV) impair host natural killer (NK) and T cell responses to tumor cells, and thus increase the risk of eBL pathogenesis. NK cell education is partially controlled by killer immunoglobulin-like receptors and variable expression of KIR3DL1 has been associated with other malignancies. Here, we investigated whether KIR3D-mediated mechanisms contribute to eBL, by testing for an association of KIR3DL1/KIR3DS1 genotypes with the disease in 108 eBL patients and 99 healthy Kenyan children. KIR3DL1 allelic typing and EBV loads were assessed by PCR. We inferred previously observed phenotypes from the genotypes. The frequencies of KIR3DL1/KIR3DL1 and KIR3DL1/KIR3DS1 did not differ significantly between cases and controls. Additionally, none of the study participants was homozygous for KIR3DS1 alleles. EBV loads did not differ by the KIR3DL1 genotypes nor were they different between eBL survivors and non-survivors. Our results suggest that eBL pathogenesis may not simply involve variations in KIR3DL1 and KIR3DS1 genotypes. However, considering the complexity of the KIR3DL1 locus, this study could not exclude a role for copy number variation in eBL pathogenesis.
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Affiliation(s)
- Beatrice M. Muriuki
- West African Center for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Catherine S. Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States of America
| | - Erastus K. Kirwa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Titus K. Maina
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Bonface O. Ariera
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, United States of America
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Ann M. Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States of America
| | - John M. Ong’echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
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27
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Conrad MD, Asua V, Garg S, Giesbrecht D, Niaré K, Smith S, Namuganga JF, Katairo T, Legac J, Crudale RM, Tumwebaze PK, Nsobya SL, Cooper RA, Kamya MR, Dorsey G, Bailey JA, Rosenthal PJ. Evolution of Partial Resistance to Artemisinins in Malaria Parasites in Uganda. N Engl J Med 2023; 389:722-732. [PMID: 37611122 PMCID: PMC10513755 DOI: 10.1056/nejmoa2211803] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
BACKGROUND Partial resistance of Plasmodium falciparum to the artemisinin component of artemisinin-based combination therapies, the most important malaria drugs, emerged in Southeast Asia and now threatens East Africa. Partial resistance, which manifests as delayed clearance after therapy, is mediated principally by mutations in the kelch protein K13 (PfK13). Limited longitudinal data are available on the emergence and spread of artemisinin resistance in Africa. METHODS We performed annual surveillance among patients who presented with uncomplicated malaria at 10 to 16 sites across Uganda from 2016 through 2022. We sequenced the gene encoding kelch 13 (pfk13) and analyzed relatedness using molecular methods. We assessed malaria metrics longitudinally in eight Ugandan districts from 2014 through 2021. RESULTS By 2021-2022, the prevalence of parasites with validated or candidate resistance markers reached more than 20% in 11 of the 16 districts where surveillance was conducted. The PfK13 469Y and 675V mutations were seen in far northern Uganda in 2016-2017 and increased and spread thereafter, reaching a combined prevalence of 10 to 54% across much of northern Uganda, with spread to other regions. The 469F mutation reached a prevalence of 38 to 40% in one district in southwestern Uganda in 2021-2022. The 561H mutation, previously described in Rwanda, was first seen in southwestern Uganda in 2021, reaching a prevalence of 23% by 2022. The 441L mutation reached a prevalence of 12 to 23% in three districts in western Uganda in 2022. Genetic analysis indicated local emergence of mutant parasites independent of those in Southeast Asia. The emergence of resistance was observed predominantly in areas where effective malaria control had been discontinued or transmission was unstable. CONCLUSIONS Data from Uganda showed the emergence of partial resistance to artemisinins in multiple geographic locations, with increasing prevalence and regional spread over time. (Funded by the National Institutes of Health.).
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Affiliation(s)
- Melissa D Conrad
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Victor Asua
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Shreeya Garg
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - David Giesbrecht
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Karamoko Niaré
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Sawyer Smith
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Jane F Namuganga
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Thomas Katairo
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Jennifer Legac
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Rebecca M Crudale
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Patrick K Tumwebaze
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Samuel L Nsobya
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Roland A Cooper
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Moses R Kamya
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Grant Dorsey
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Jeffrey A Bailey
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
| | - Philip J Rosenthal
- From the University of California, San Francisco, San Francisco (M.D.C., S.G., J.L., G.D., P.J.R.); the Infectious Diseases Research Collaboration (V.A., J.F.N., T.K., P.K.T., S.L.N., M.R.K.) and Makerere University (M.R.K.) - both in Kampala, Uganda; the University of Tübingen, Tübingen, Germany (V.A.); Brown University, Providence, RI (D.G., K.N., S.S., R.M.C., J.A.B.); and Dominican University of California, San Rafael (R.A.C.)
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28
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François R, Kashamuka MM, Banek K, Bala JA, Nkalani M, Kihuma G, Atibu J, Mahilu GE, Thwai KL, Assefa A, Bailey JA, Dinglasan RR, Juliano JJ, Tshefu AK, Parr JB. Plasmodium falciparum with pfhrp2/3 Deletion Not Detected in a 2018-2021 Malaria Longitudinal Cohort Study in Kinshasa Province, Democratic Republic of the Congo. Am J Trop Med Hyg 2023; 109:273-276. [PMID: 37339759 PMCID: PMC10397445 DOI: 10.4269/ajtmh.22-0715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/13/2023] [Indexed: 06/22/2023] Open
Abstract
Histidine-rich protein 2- (HRP2-) based rapid diagnostic tests (RDTs) are widely used to detect Plasmodium falciparum in sub-Saharan Africa. Reports of parasites with pfhrp2 and/or pfhrp3 (pfhrp2/3) gene deletions in Africa raise concerns about the long-term viability of HRP2-based RDTs. We evaluated changes in pfhrp2/3 deletion prevalence over time using a 2018-2021 longitudinal study of 1,635 enrolled individuals in Kinshasa Province, Democratic Republic of the Congo (DRC). Samples collected during biannual household visits with ≥ 100 parasites/µL by quantitative real-time polymerase chain reaction were genotyped using a multiplex real-time PCR assay. Among 2,726 P. falciparum PCR-positive samples collected from 993 participants during the study period, 1,267 (46.5%) were genotyped. No pfhrp2/3 deletions or mixed pfhrp2/3-intact and -deleted infections were identified in our study. Pfhrp2/3-deleted parasites were not detected in Kinshasa Province; ongoing use of HRP2-based RDTs is appropriate.
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Affiliation(s)
- Ruthly François
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Kristin Banek
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joseph A. Bala
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Marthe Nkalani
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Georges Kihuma
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Joseph Atibu
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Georges E. Mahilu
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Kyaw L. Thwai
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ashenafi Assefa
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Rhoel R. Dinglasan
- Department of Infectious Diseases & Immunology, University of Florida, Gainesville, Florida
| | - Jonathan J. Juliano
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Jonathan B. Parr
- Institute for Global Health and Infectious Diseases and Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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29
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Niaré K, Greenhouse B, Bailey JA. An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis. Malar J 2023; 22:207. [PMID: 37420214 DOI: 10.1186/s12936-023-04632-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Accurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics. Here a falciparum variant calling pipeline based on GATK version 4 (GATK4) was optimized and applied to 6626 public Illumina WGS samples. METHODS Control WGS and accurate PacBio assemblies of 10 laboratory strains were leveraged to optimize parameters that control the heterozygosity, local assembly region size, ploidy, mapping and base quality in both GATK HaplotypeCaller and GenotypeGVCFs. From these controls, a high-quality training dataset was generated to recalibrate the raw variant data. RESULTS On current high-quality samples (read length = 250 bp, insert size = 405-524 bp), the optimized pipeline shows improved sensitivity (86.6 ± 1.7% for SNPs and 82.2 ± 5.9% for indels) compared to the default GATK4 pipeline (77.7 ± 1.3% for SNPs; and 73.1 ± 5.1% for indels, adjusted P < 0.001) and previous variant calling with GATK version 3 (GATK3, 70.3 ± 3.0% for SNPs and 59.7 ± 5.8% for indels, adjusted P < 0.001). Its sensitivity on simulated mixed infection samples (80.8 ± 6.1% for SNPs and 78.3 ± 5.1% for indels) was again improved relative to default GATK4 (68.8 ± 6.0% for SNPs and 38.9 ± 0.7% for indels, adjusted, adjusted P < 0.001). Precision was high and comparable across all pipelines on each type of data tested. The resulting combination of high-quality SNPs and indels increases the resolution of local population population structure detection in sub-Saharan Africa. Finally, increasing ploidy improves the detection of drug resistance mutations and estimation of complexity of infection. CONCLUSIONS Overall, this study provides an optimized falciparum GATK4 pipeline resource for variant calling which should help improve genomic studies of malaria.
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Affiliation(s)
- Karamoko Niaré
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA.
| | - Bryan Greenhouse
- EPPIcenter Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA.
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Fola AA, Moser KA, Aydemir O, Hennelly C, Kobayashi T, Shields T, Hamapumbu H, Musonda M, Katowa B, Matoba J, Stevenson JC, Norris DE, Thuma PE, Wesolowski A, Moss WJ, Bailey JA, Juliano JJ. Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of parasite connectivity in a low-transmission district in Southern Province, Zambia. Malar J 2023; 22:208. [PMID: 37420265 PMCID: PMC10327325 DOI: 10.1186/s12936-023-04637-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Understanding temporal and spatial dynamics of malaria transmission will help to inform effective interventions and strategies in regions approaching elimination. Parasite genomics are increasingly used to monitor epidemiologic trends, including assessing residual transmission across seasons and importation of malaria into these regions. METHODS In a low and seasonal transmission setting of southern Zambia, a total of 441 Plasmodium falciparum samples collected from 8 neighbouring health centres between 2012 and 2018 were genotyped using molecular inversion probes (MIPs n = 1793) targeting a total of 1832 neutral and geographically informative SNPs distributed across the parasite genome. After filtering for quality and missingness, 302 samples and 1410 SNPs were retained and used for downstream population genomic analyses. RESULTS The analyses revealed most (67%, n = 202) infections harboured one clone (monogenomic) with some variation at local level suggesting low, but heterogenous malaria transmission. Relatedness identity-by-descent (IBD) analysis revealed variable distribution of IBD segments across the genome and 6% of pairs were highly-related (IBD ≥ 0.25). Some of the highly-related parasite populations persisted across multiple seasons, suggesting that persistence of malaria in this low-transmission region is fueled by parasites "seeding" across the dry season. For recent years, clusters of clonal parasites were identified that were dissimilar to the general parasite population, suggesting parasite populations were increasingly fragmented at small spatial scales due to intensified control efforts. Clustering analysis using PCA and t-SNE showed a lack of substantial parasite population structure. CONCLUSION Leveraging both genomic and epidemiological data provided comprehensive picture of fluctuations in parasite populations in this pre-elimination setting of southern Zambia over 7 years.
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Affiliation(s)
- Abebe A. Fola
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Kara A. Moser
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Chris Hennelly
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Tamaki Kobayashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Timothy Shields
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | | | | | - Ben Katowa
- Macha Research Trust, Choma District, Choma, Zambia
| | | | | | - Douglas E. Norris
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | | | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - William J. Moss
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Jonathan J. Juliano
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - the Southern, Central Africa International Center of Excellence for Malaria Research (ICEMR)
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Macha Research Trust, Choma District, Choma, Zambia
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
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Jenike AE, Bunkelman B, Perzel Mandell KA, Oduor CI, Chin D, Mair D, Jenike KM, Kim DH, Bailey JA, Rafailovich MH, Rosenberg AZ, Halushka MK. Expression Microdissection for the Analysis of miRNA in a Single-Cell Type. J Transl Med 2023; 103:100133. [PMID: 36990152 PMCID: PMC10524025 DOI: 10.1016/j.labinv.2023.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/19/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Cell-specific microRNA (miRNA) expression estimates are important in characterizing the localization of miRNA signaling within tissues. Much of these data are obtained from cultured cells, a process known to significantly alter miRNA expression levels. Thus, our knowledge of in vivo cell miRNA expression estimates is poor. We previously demonstrated expression microdissection-miRNA-sequencing (xMD-miRNA-seq) to acquire in vivo estimates, directly from formalin-fixed tissues, albeit with a limited yield. In this study, we optimized each step of the xMD process, including tissue retrieval, tissue transfer, film preparation, and RNA isolation, to increase RNA yields and ultimately show strong enrichment for in vivo miRNA expression by qPCR array. These method improvements, such as the development of a noncrosslinked ethylene vinyl acetate membrane, resulted in a 23- to 45-fold increase in miRNA yield, depending on the cell type. By qPCR, miR-200a increased by 14-fold in xMD-derived small intestine epithelial cells, with a concurrent 336-fold reduction in miR-143 relative to the matched nondissected duodenal tissue. xMD is now an optimized method to obtain robust in vivo miRNA expression estimates from cells. xMD will allow formalin-fixed tissues from surgical pathology archives to make theragnostic biomarker discoveries.
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Affiliation(s)
- Ana E Jenike
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brady Bunkelman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kira A Perzel Mandell
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cliff I Oduor
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Deborah Chin
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Devin Mair
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Katharine M Jenike
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Deok-Ho Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Miriam H Rafailovich
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Kreutzfeld O, Tumwebaze PK, Okitwi M, Orena S, Byaruhanga O, Katairo T, Conrad MD, Rasmussen SA, Legac J, Aydemir O, Giesbrecht D, Forte B, Campbell P, Smith A, Kano H, Nsobya SL, Blasco B, Duffey M, Bailey JA, Cooper RA, Rosenthal PJ. Susceptibility of Ugandan Plasmodium falciparum Isolates to the Antimalarial Drug Pipeline. Microbiol Spectr 2023; 11:e0523622. [PMID: 37158739 PMCID: PMC10269555 DOI: 10.1128/spectrum.05236-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/10/2023] [Indexed: 05/10/2023] Open
Abstract
Malaria, especially Plasmodium falciparum infection, remains an enormous problem, and its treatment and control are seriously challenged by drug resistance. New antimalarial drugs are needed. To characterize the Medicines for Malaria Venture pipeline of antimalarials under development, we assessed the ex vivo drug susceptibilities to 19 compounds targeting or potentially impacted by mutations in P. falciparum ABC transporter I family member 1, acetyl-CoA synthetase, cytochrome b, dihydroorotate dehydrogenase, elongation factor 2, lysyl-tRNA synthetase, phenylalanyl-tRNA synthetase, plasmepsin X, prodrug activation and resistance esterase, and V-type H+ ATPase of 998 fresh P. falciparum clinical isolates collected in eastern Uganda from 2015 to 2022. Drug susceptibilities were assessed by 72-h growth inhibition (half-maximum inhibitory concentration [IC50]) assays using SYBR green. Field isolates were highly susceptible to lead antimalarials, with low- to midnanomolar median IC50s, near values previously reported for laboratory strains, for all tested compounds. However, outliers with decreased susceptibilities were identified. Positive correlations between IC50 results were seen for compounds with shared targets. We sequenced genes encoding presumed targets to characterize sequence diversity, search for polymorphisms previously selected with in vitro drug pressure, and determine genotype-phenotype associations. We identified many polymorphisms in target genes, generally in <10% of isolates, but none were those previously selected in vitro with drug pressure, and none were associated with significantly decreased ex vivo drug susceptibility. Overall, Ugandan P. falciparum isolates were highly susceptible to 19 compounds under development as next-generation antimalarials, consistent with a lack of preexisting or novel resistance-conferring mutations in circulating Ugandan parasites. IMPORTANCE Drug resistance necessitates the development of new antimalarial drugs. It is important to assess the activities of compounds under development against parasites now causing disease in Africa, where most malaria cases occur, and to determine if mutations in these parasites may limit the efficacies of new agents. We found that African isolates were generally highly susceptible to the 19 studied lead antimalarials. Sequencing of the presumed drug targets identified multiple mutations in these genes, but these mutations were generally not associated with decreased antimalarial activity. These results offer confidence that the activities of the tested antimalarial compounds now under development will not be limited by preexisting resistance-mediating mutations in African malaria parasites.
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Affiliation(s)
- Oriana Kreutzfeld
- University of California, San Francisco, San Francisco, California, USA
| | | | - Martin Okitwi
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Stephen Orena
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Thomas Katairo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Melissa D. Conrad
- University of California, San Francisco, San Francisco, California, USA
| | | | - Jennifer Legac
- University of California, San Francisco, San Francisco, California, USA
| | - Ozkan Aydemir
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Barbara Forte
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Peter Campbell
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Alasdair Smith
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Hiroki Kano
- Mitsubishi Tanabe Pharma Corporation, Yokohama, Japan
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Paschalidis A, Watson OJ, Aydemir O, Verity R, Bailey JA. coiaf: Directly estimating complexity of infection with allele frequencies. PLoS Comput Biol 2023; 19:e1010247. [PMID: 37294835 DOI: 10.1371/journal.pcbi.1010247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 05/01/2023] [Indexed: 06/11/2023] Open
Abstract
In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current approaches in the literature. Through a sensitivity analysis, we characterize how the distribution of parasite densities, the assumed sequencing depth, and the number of sampled loci impact the bias and accuracy of our two methods. Using our developed methods, we further estimate the COI globally from Plasmodium falciparum sequencing data and compare the results against the literature. We show significant differences in the estimated COI globally between continents and a weak relationship between malaria prevalence and COI.
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Affiliation(s)
- Aris Paschalidis
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
| | - Oliver J Watson
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Robert Verity
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
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34
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Bell GJ, Gyaase S, Goel V, Adu B, Mensah B, Essone P, Dosoo D, Osei M, Niare K, Wiru K, Brandt K, Emch M, Ghansah A, Asante KP, Mvalo T, Agnandji ST, Juliano JJ, Bailey JA. Malaria Transmission Intensity and Parasitemia during the Three-Dose RTS,S/AS01 Vaccination Series do not Reduce Magnitude of Antibody Response nor Efficacy Against the First Case of Malaria. Res Sq 2023:rs.3.rs-2960373. [PMID: 37292711 PMCID: PMC10246269 DOI: 10.21203/rs.3.rs-2960373/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background RTS,S/AS01 has been recommended by WHO for widespread implementation in medium to high malaria transmission settings. Previous analyses have noted lower vaccine efficacies in higher transmission settings, possibly due to the more rapid development of naturally acquired immunity in the control group. Methods To investigate a reduced immune response to vaccination as a potential mechanism behind lower efficacy in high transmission areas, we examine initial vaccine antibody (anti-CSP IgG) response and vaccine efficacy against the first case of malaria to exclude the delayed malaria effect using data from three study areas (Kintampo, Ghana; Lilongwe, Malawi; Lambaréné, Gabon) from the 2009-2014 phase III trial (NCT00866619). Our key exposures are parasitemia during the vaccination series and malaria transmission intensity. We calculate vaccine efficacy (one minus hazard ratio) using a cox-proportional hazards model and allowing for the time-varying effect of RTS,S/AS01. Results We find that antibody responses to the primary three-dose vaccination series were higher in Ghana than in Malawi and Gabon, but that neither antibody levels nor vaccine efficacy against the first case of malaria varied by transmission intensity or parasitemia during the primary vaccination series. Conclusions We find that vaccine efficacy is unrelated to infections during vaccination. Contributing to a conflicting literature, our results suggest that vaccine efficacy is also unrelated to infections before vaccination, meaning that delayed malaria is likely the main reason for lower efficacy in high transmission settings, not reduced immune responses. This may be reassuring for implementation in high transmission settings, though further studies are needed.
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Saikumar Lakshmi P, Oduor CI, Forconi CS, M'Bana V, Bly C, Gerstein RM, Otieno JA, Ong'echa JM, Münz C, Luftig MA, Brehm MA, Bailey JA, Moormann AM. Endemic Burkitt lymphoma avatar mouse models for exploring inter-patient tumor variation and testing targeted therapies. Life Sci Alliance 2023; 6:e202101355. [PMID: 36878637 PMCID: PMC9990458 DOI: 10.26508/lsa.202101355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/08/2023] Open
Abstract
Endemic Burkitt lymphoma (BL) is a childhood cancer in sub-Saharan Africa characterized by Epstein-Barr virus and malaria-associated aberrant B-cell activation and MYC chromosomal translocation. Survival rates hover at 50% after conventional chemotherapies; therefore, clinically relevant models are necessary to test additional therapies. Hence, we established five patient-derived BL tumor cell lines and corresponding NSG-BL avatar mouse models. Transcriptomics confirmed that our BL lines maintained fidelity from patient tumors to NSG-BL tumors. However, we found significant variation in tumor growth and survival among NSG-BL avatars and in Epstein-Barr virus protein expression patterns. We tested rituximab responsiveness and found one NSG-BL model exhibiting direct sensitivity, characterized by apoptotic gene expression counterbalanced by unfolded protein response and mTOR pro-survival pathways. In rituximab-unresponsive tumors, we observed an IFN-α signature confirmed by the expression of IRF7 and ISG15. Our results demonstrate significant inter-patient tumor variation and heterogeneity, and that contemporary patient-derived BL cell lines and NSG-BL avatars are feasible tools to guide new therapeutic strategies and improve outcomes for these children.
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Affiliation(s)
- Priya Saikumar Lakshmi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Cliff I Oduor
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Catherine S Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Viriato M'Bana
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Courtney Bly
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rachel M Gerstein
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Juliana A Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Medical Services, Kisumu, Kenya
| | - John M Ong'echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Christian Münz
- Department of Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Michael A Brehm
- Program in Molecular Medicine and the Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Ann M Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Sendor R, Banek K, Kashamuka MM, Mvuama N, Bala JA, Nkalani M, Kihuma G, Atibu J, Thwai KL, Svec WM, Goel V, Nseka T, Lin JT, Bailey JA, Emch M, Carrel M, Juliano JJ, Tshefu A, Parr JB. Epidemiology of Plasmodium malariae and Plasmodium ovale spp. in a highly malaria-endemic country: a longitudinal cohort study in Kinshasa Province, Democratic Republic of Congo. medRxiv 2023:2023.04.20.23288826. [PMID: 37790376 PMCID: PMC10543032 DOI: 10.1101/2023.04.20.23288826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background Increasing reports suggest that non-falciparum species are an underappreciated cause of malaria in sub-Saharan Africa, but their epidemiology is not well-defined. This is particularly true in regions of high P. falciparum endemicity such as the Democratic Republic of Congo (DRC), where 12% of the world's malaria cases and 13% of deaths occur. Methods and Findings The cumulative incidence and prevalence of P. malariae and P. ovale spp. infection detected by real-time PCR were estimated among children and adults within a longitudinal study conducted in seven rural, peri-urban, and urban sites from 2015-2017 in Kinshasa Province, DRC. Participants were sampled at biannual household survey visits (asymptomatic) and during routine health facility visits (symptomatic). Participant-level characteristics associated with non-falciparum infections were estimated for single- and mixed-species infections. Among 9,089 samples collected from 1,565 participants over a 3-year period, the incidence of P. malariae and P. ovale spp. infection was 11% (95% CI: 9%-12%) and 7% (95% CI: 5%-8%) by one year, respectively, compared to a 67% (95% CI: 64%-70%) one-year cumulative incidence of P. falciparum infection. Incidence continued to rise in the second year of follow-up, reaching 26% and 15% in school-age children (5-14yo) for P. malariae and P. ovale spp., respectively. Prevalence of P. malariae, P. ovale spp., and P. falciparum infections during household visits were 3% (95% CI: 3%-4%), 1% (95% CI: 1%-2%), and 35% (95% CI: 33%-36%), respectively. Non-falciparum malaria was more prevalent in rural and peri-urban vs. urban sites, in school-age children, and among those with P. falciparum co-infection. A crude association was detected between P. malariae and any anemia in the symptomatic clinic population, although this association did not hold when stratified by anemia severity. No crude associations were detected between non-falciparum infection and fever prevalence. Conclusions P. falciparum remains the primary driver of malaria morbidity and mortality in the DRC. However, non-falciparum species also pose an infection risk across sites of varying urbanicity and malaria endemicity within Kinshasa, DRC, particularly among children under 15 years of age. As P. falciparum interventions gain traction in high-burden settings like the DRC, continued surveillance and improved understanding of non-falciparum infections are warranted.
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Affiliation(s)
- Rachel Sendor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kristin Banek
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Nono Mvuama
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Joseph A. Bala
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Marthe Nkalani
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Georges Kihuma
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Joseph Atibu
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Kyaw L. Thwai
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - W. Matthew Svec
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Varun Goel
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tommy Nseka
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jessica T. Lin
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Margaret Carrel
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, Iowa, United States of America
| | - Jonathan J. Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Antoinette Tshefu
- Ecole de Santé Publique, Faculté de Médecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jonathan B. Parr
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Oluoch PO, Forconi CS, Oduor CI, Ritacco DA, Akala HM, Bailey JA, Juliano JJ, Ong'echa JM, Münz C, Moormann AM. Distinctive Kaposi Sarcoma-Associated Herpesvirus Serological Profile during Acute Plasmodium falciparum Malaria Episodes. Int J Mol Sci 2023; 24:ijms24076711. [PMID: 37047683 PMCID: PMC10095526 DOI: 10.3390/ijms24076711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
The seroprevalence of Kaposi sarcoma-associated herpesvirus (KSHV) and the incidence of endemic Kaposi sarcoma (KS) overlap with regions of malaria endemicity in sub-Saharan Africa. Multiple studies have shown an increased risk of KSHV seroconversion in children from high malaria compared to low malaria regions; however, the impact of acute episodes of Plasmodium falciparum (P. falciparum) malaria on KSHV's biphasic life cycle and lytic reactivation has not been determined. Here, we examined KSHV serological profiles and viral loads in 134 children with acute malaria and 221 healthy children from high malaria regions in Kisumu, as well as 77 healthy children from low malaria regions in Nandi. We assayed KSHV, Epstein-Barr virus (EBV), and P. falciparum malaria antibody responses in these three by multiplexed Luminex assay. We confirmed that KSHV seroprevalence was significantly associated with malaria endemicity (OR = 1.95, 1.18-3.24 95% CI, p = 0.01) with 71-77% seropositivity in high-malaria (Kisumu) compared to 28% in low-malaria (Nandi) regions. Furthermore, KSHV serological profiles during acute malaria episodes were distinct from age-matched non-malaria-infected children from the same region. Paired IgG levels also varied after malaria treatment, with significantly higher anti-ORF59 at day 0 but elevated ORF38, ORF73, and K8.1 at day 3. Acute malaria episodes is characterized by perturbation of KSHV latency in seropositive children, providing further evidence that malaria endemicity contributes to the observed increase in endemic KS incidence in sub-Saharan Africa.
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Affiliation(s)
- Peter O Oluoch
- Division of Infectious Diseases and Immunology, Department of Medicine, Chan Medical School, University of Massachusetts, Worcester, MA 01605, USA
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya
| | - Catherine S Forconi
- Division of Infectious Diseases and Immunology, Department of Medicine, Chan Medical School, University of Massachusetts, Worcester, MA 01605, USA
| | - Cliff I Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Dominic A Ritacco
- Division of Infectious Diseases and Immunology, Department of Medicine, Chan Medical School, University of Massachusetts, Worcester, MA 01605, USA
| | - Hoseah M Akala
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - John M Ong'echa
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu 40100, Kenya
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Ann M Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, Chan Medical School, University of Massachusetts, Worcester, MA 01605, USA
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Kirby R, Giesbrecht D, Karema C, Watson O, Lewis S, Munyaneza T, Butera JDD, Juliano JJ, Bailey JA, Mazarati JB. Examining the Early Distribution of the Artemisinin-Resistant Plasmodium falciparum kelch13 R561H Mutation in Areas of Higher Transmission in Rwanda. Open Forum Infect Dis 2023; 10:ofad149. [PMID: 37096145 PMCID: PMC10122489 DOI: 10.1093/ofid/ofad149] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/15/2023] [Indexed: 04/26/2023] Open
Abstract
Background Artemisinin resistance mutations in Plasmodium falciparum kelch13 (Pfk13) have begun to emerge in Africa, with Pfk13-R561H being the first reported in Rwanda in 2014, but limited sampling left questions about its early distribution and origin. Methods We genotyped P. falciparum positive dried blood spot (DBS) samples from a nationally representative 2014-2015 Rwanda Demographic Health Surveys (DHS) HIV study. DBS were subsampled from DHS sampling clusters with >15% P. falciparum prevalence, as determined by rapid testing or microscopy done during the DHS study (n clusters = 67, n samples = 1873). Results We detected 476 parasitemias among 1873 residual blood spots from a 2014-2015 Rwanda Demographic Health Survey. We sequenced 351 samples: 341/351 were wild-type (97.03% weighted), and 4 samples (1.34% weighted) harbored R561H that were significantly spatially clustered. Other nonsynonymous mutations found were V555A (3), C532W (1), and G533A (1). Conclusions Our study better defines the early distribution of R561H in Rwanda. Previous studies only observed the mutation in Masaka as of 2014, but our study indicates its presence in higher-transmission regions in the southeast of the country at that time.
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Affiliation(s)
| | | | - Corine Karema
- Quality Equity Health Care, Kigali, Rwanda
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Oliver Watson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Haut ER, Kirby JP, Bailey JA, Phuong J, Gavitt B, Remick KN, Staudenmayer K, Cannon JW, Price MA, Bulger EM. Developing a National Trauma Research Action Plan: Results from the trauma systems and informatics panel Delphi survey. J Trauma Acute Care Surg 2023; 94:584-591. [PMID: 36623269 DOI: 10.1097/ta.0000000000003867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND The National Academies of Sciences, Engineering, and Medicine 2016 report on the trauma care system recommended establishing a National Trauma Research Action Plan to strengthen and guide future trauma research. To address this recommendation, the Department of Defense funded a study to generate a comprehensive research agenda spanning the trauma and burn care continuum. Panels were created to conduct a gap analysis and identify high-priority research questions. The National Trauma Research Action Plan panel reported here addressed trauma systems and informatics. METHODS Experts were recruited to identify current gaps in trauma systems research, generate research questions, and establish the priorities using an iterative Delphi survey approach from November 2019 through August 2020. Panelists were identified to ensure heterogeneity and generalizability, including military and civilian representation. Panelists were encouraged to use a PICO format to generate research questions: patient/population, intervention, compare/control, and outcome. In subsequent surveys, panelists prioritized each research question on a 9-point Likert scale, categorized as low-, medium-, and high-priority items. Consensus was defined as ≥60% agreement. RESULTS Twenty-seven subject matter experts generated 570 research questions, of which 427 (75%) achieved the consensus threshold. Of the consensus reaching questions, 209 (49%) were rated high priority, 213 (50%) medium priority, and 5 (1%) low priority. Gaps in understanding the broad array of interventions were identified, including those related to health care infrastructure, technology products, education/training, resuscitation, and operative intervention. The prehospital phase of care was highlighted as an area needing focused research. CONCLUSION This Delphi gap analysis of trauma systems and informatics research identified high-priority research questions that will help guide investigators and funding agencies in setting research priorities to continue to work toward Zero Preventable Deaths after trauma. LEVEL OF EVIDENCE Therapeutic/Care Management; Level IV.
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Affiliation(s)
- Elliott R Haut
- From the Division of Acute Care Surgery, Department of Surgery (E.R.H.), Department of Anesthesiology and Critical Care Medicine (E.R.H.), and Department of Emergency Medicine (E.R.H.), The Johns Hopkins University School of Medicine; The Armstrong Institute for Patient Safety and Quality (E.R.H.), Johns Hopkins Medicine; Department of Health Policy and Management (E.R.H.), The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland Acute and Critical Care Surgery (J.P.K.) and Department of Surgery (J.A.B.), Washington University in St. Louis, St. Louis, Missouri Harborview Injury Prevention and Research Center (J.P.), University of Washington, Seattle, Washington Trauma Surgery and Surgical Critical Care (B.G.), University of Cincinnati Medical Center, Cincinnati, Ohio Department of Surgery (K.N.R.), Uniformed Services University School of Medicine, Bethesda, Maryland Department of General Surgery (K.S.), Stanford University, Stanford, California Division of Traumatology, Surgical Critical Care and Emergency Surgery (J.W.C.), University of Pennsylvania, Philadelphia, Pennsylvania The Coalition for National Trauma Research (M.A.P.), San Antonio, Texas Department of Surgery (E.M.B.), University of Washington, Seattle, Washington Coalition for National Trauma Research (NRAP Trauma Systems and Informatics Panel), San Antonio, Texas
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Niaré K, Greenhouse B, Bailey JA. An Optimized GATK4 Pipeline for Plasmodium falciparum Whole Genome Sequencing Variant Calling and Analysis. Res Sq 2023:rs.3.rs-2561857. [PMID: 36824880 PMCID: PMC9949269 DOI: 10.21203/rs.3.rs-2561857/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background Accurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics. Here we optimized a falciparum variant calling pipeline based on GATK version 4 (GATK4) and applied it to 6,626 public Illumina WGS samples. Methods We optimized parameters that control the heterozygosity, local assembly region size, ploidy, mapping and base quality in both GATK HaplotypeCaller and GenotypeGVCFs leveraging control WGS and accurate PacBio assemblies of 10 laboratory strains. From these controls we generated a high-quality training dataset to recalibrate the raw variant data. Results On current high-quality samples (read length = 250bp, insert size = 405 - 524 bp ), we show improved sensitivity (86.6 ± 1.7% for SNPs and 82.2 ± 5.9% for indels) compared to the default GATK4 pipeline (77.7 ± 1.3% for SNPs; and 73.1 ± 5.1% for indels, adjusted P < 0.001) and previous variant calling with GATK version 3 (GATK3, 70.3 ± 3.0% for SNPs and 59.7 ± 5.8% for indels, adjusted P < 0.001). The sensitivity of our pipeline on simulated mixed infection samples (80.8 ± 6.1% for SNPs and 78.3 ± 5.1% for indels) was again improved relative to default GATK4 (68.8 ± 6.0% for SNPs and 38.9 ± 0.7% for indels, adjusted P < 0.001). Precision was high and comparable across all pipelines on each type of data tested. We further show that using the combination of high-quality SNPs and indels increases the resolution of local population population structure detection in sub-Saharan Africa. We finally demonstrate that increasing ploidy improves the detection of drug resistance mutations and estimation of complexity of infection. Conclusions Overall, we provide an optimized GATK4 pipeline and resource for falciparum variant calling which should help improve genomic studies of malaria.
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Agwati EO, Oduor CI, Ayieko C, Ong’echa JM, Moormann AM, Bailey JA. Profiling genome-wide recombination in Epstein Barr virus reveals type-specific patterns and associations with endemic-Burkitt lymphoma. Virol J 2022; 19:208. [PMID: 36482473 PMCID: PMC9733152 DOI: 10.1186/s12985-022-01942-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Endemic Burkitt lymphoma (eBL) is potentiated through the interplay of Epstein Barr virus (EBV) and holoendemic Plasmodium falciparum malaria. To better understand EBV's biology and role in eBL, we characterized genome-wide recombination sites and patterns as a source of genetic diversity in EBV genomes in our well-defined population of eBL cases and controls from Western Kenya. METHODS EBV genomes representing 54 eBL cases and 32 healthy children from the same geographic region in Western Kenya that we previously sequenced were analyzed. Whole-genome multiple sequence alignment, recombination analyses, and phylogenetic inference were made using multiple alignment with fast Fourier transform, recombination detection program 4, and molecular evolutionary genetics analysis. RESULTS We identified 28 different recombination events and 71 (82.6%) of the 86 EBV genomes analyzed contained evidence of one or more recombinant segments. Associated recombination breakpoints were found to occur in a total of 42 different genes, with only 7 (16.67%) being latent genes. Recombination events were major drivers of clustering within genome-wide phylogenetic trees. The occurrence of recombination segments was comparable between genomes from male and female participants and across age groups. More recombinant segments were found in EBV type 1 genomes (p = 6.4e - 06) and the genomes from the eBLs (p = 0.037). Two recombination events were enriched in the eBLs; event 47 (OR = 4.07, p = 0.038) and event 50 (OR = 14.24, p = 0.012). CONCLUSIONS EBV genomes have extensive evidence of recombination likely acquired progressively and cumulatively over time. Recombination patterns display a heterogeneous occurrence rate across the genome with enrichment in lytic genes. Overall, recombination appears to be a major evolutionary force impacting EBV diversity and genome structure with evidence of the association of specific recombinants with eBL.
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Affiliation(s)
- Eddy O. Agwati
- grid.442486.80000 0001 0744 8172Department of Zoology, Maseno University, Maseno, Kenya ,grid.33058.3d0000 0001 0155 5938Center for Global Health Research (CGHR), Kenya Medical Research Institute, Kisumu, Kenya
| | - Cliff I. Oduor
- grid.40263.330000 0004 1936 9094Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903 USA
| | - Cyrus Ayieko
- grid.442486.80000 0001 0744 8172Department of Zoology, Maseno University, Maseno, Kenya
| | - John Michael Ong’echa
- grid.33058.3d0000 0001 0155 5938Center for Global Health Research (CGHR), Kenya Medical Research Institute, Kisumu, Kenya
| | - Ann M. Moormann
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine and the Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Jeffrey A. Bailey
- grid.40263.330000 0004 1936 9094Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903 USA
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Ippolito MM, Kabuya JBB, Hauser M, Kamavu LK, Banda PM, Yanek LR, Malik R, Mulenga M, Bailey JA, Chongwe G, Louis TA, Shapiro TA, Moss WJ. Whole Blood Transfusion for Severe Malarial Anemia in a High Plasmodium falciparum Transmission Setting. Clin Infect Dis 2022; 75:1893-1902. [PMID: 35439307 PMCID: PMC10200327 DOI: 10.1093/cid/ciac304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Severe malaria resulting from Plasmodium falciparum infection is the leading parasitic cause of death in children worldwide, and severe malarial anemia (SMA) is the most common clinical presentation. The evidence in support of current blood transfusion guidelines for patients with SMA is limited. METHODS We conducted a retrospective cohort study of 911 hospitalized children with SMA in a holoendemic region of Zambia to examine the association of whole blood transfusion with in-hospital survival. Data were analyzed in adjusted logistic regression models using multiple imputation for missing data. RESULTS The median age of patients was 24 months (interquartile range, 16-30) and overall case fatality was 16%. Blood transfusion was associated with 35% reduced odds of death in children with SMA (odds ratio, 0.65; 95% confidence interval, .52-.81; P = .0002) corresponding to a number-needed-to-treat (NNT) of 14 patients. Children with SMA complicated by thrombocytopenia were more likely to benefit from transfusion than those without thrombocytopenia (NNT = 5). Longer storage time of whole blood was negatively associated with survival and with the posttransfusion rise in the platelet count but was not associated with the posttransfusion change in hemoglobin concentration. CONCLUSIONS Whole blood given to pediatric patients with SMA was associated with improved survival, mainly among those with thrombocytopenia who received whole blood stored for <4 weeks. These findings point to a potential use for incorporating thrombocytopenia into clinical decision making and management of severe malaria, which can be further assessed in prospective studies, and underline the importance of maintaining reliable blood donation networks in areas of high malaria transmission.
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Affiliation(s)
- Matthew M Ippolito
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jean-Bertin B Kabuya
- Department of Clinical Sciences, Tropical Diseases Research Centre, Ndola, Zambia
| | - Manuela Hauser
- Faculty of Medicine, University of Basel, Basel, Switzerland
- Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Luc K Kamavu
- Saint Paul’s General Hospital, Nchelenge, Luapula Province, Zambia
| | | | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rubab Malik
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Modest Mulenga
- Directorate of Research and Postgraduate Studies, Lusaka Apex Medical University, Lusaka, Zambia
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University Warren Alpert Medical School, Providence, Rhode Island, USA
| | - Gershom Chongwe
- Department of Clinical Sciences, Tropical Diseases Research Centre, Ndola, Zambia
| | - Thomas A Louis
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Theresa A Shapiro
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - William J Moss
- The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Bell GJ, Goel V, Essone P, Dosoo D, Adu B, Mensah BA, Gyaase S, Wiru K, Mougeni F, Osei M, Minsoko P, Sinai C, Niaré K, Juliano JJ, Hudgens M, Ghansah A, Kamthunzi P, Mvalo T, Agnandji ST, Bailey JA, Asante KP, Emch M. Malaria Transmission Intensity Likely Modifies RTS, S/AS01 Efficacy Due to a Rebound Effect in Ghana, Malawi, and Gabon. J Infect Dis 2022; 226:1646-1656. [PMID: 35899811 PMCID: PMC10205900 DOI: 10.1093/infdis/jiac322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/26/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND RTS,S/AS01 is the first malaria vaccine to be approved and recommended for widespread implementation by the World Health Organization (WHO). Trials reported lower vaccine efficacies in higher-incidence sites, potentially due to a "rebound" in malaria cases in vaccinated children. When naturally acquired protection in the control group rises and vaccine protection in the vaccinated wanes concurrently, malaria incidence can become greater in the vaccinated than in the control group, resulting in negative vaccine efficacies. METHODS Using data from the 2009-2014 phase III trial (NCT00866619) in Lilongwe, Malawi; Kintampo, Ghana; and Lambaréné, Gabon, we evaluate this hypothesis by estimating malaria incidence in each vaccine group over time and in varying transmission settings. After estimating transmission intensities using ecological variables, we fit models with 3-way interactions between vaccination, time, and transmission intensity. RESULTS Over time, incidence decreased in the control group and increased in the vaccine group. Three-dose efficacy in the lowest-transmission-intensity group (0.25 cases per person-year [CPPY]) decreased from 88.2% to 15.0% over 4.5 years, compared with 81.6% to -27.7% in the highest-transmission-intensity group (3 CPPY). CONCLUSIONS These findings suggest that interventions, including the fourth RTS,S dose, that protect vaccinated individuals during the potential rebound period should be implemented for high-transmission settings.
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Affiliation(s)
- Griffin J Bell
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Varun Goel
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Paulin Essone
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - David Dosoo
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | | | - Kenneth Wiru
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Fabrice Mougeni
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Musah Osei
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Pamela Minsoko
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Cyrus Sinai
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Karamoko Niaré
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michael Hudgens
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | | | - Selidji Todagbe Agnandji
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | | | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
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Binder RA, Fujimori GF, Forconi CS, Reed GW, Silva LS, Lakshmi PS, Higgins A, Cincotta L, Dutta P, Salive MC, Mangolds V, Anya O, Calvo Calle JM, Nixon T, Tang Q, Wessolossky M, Wang Y, Ritacco DA, Bly CS, Fischinger S, Atyeo C, Oluoch PO, Odwar B, Bailey JA, Maldonado-Contreras A, Haran JP, Schmidt AG, Cavacini L, Alter G, Moormann AM. SARS-CoV-2 Serosurveys: How Antigen, Isotype and Threshold Choices Affect the Outcome. J Infect Dis 2022; 227:371-380. [PMID: 36314635 PMCID: PMC9891417 DOI: 10.1093/infdis/jiac431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Evaluating the performance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays and clearly articulating the utility of selected antigens, isotypes, and thresholds is crucial to understanding the prevalence of infection within selected communities. METHODS This cross-sectional study, implemented in 2020, screened PCRconfirmed coronavirus disease 2019 patients (n 86), banked prepandemic and negative samples (n 96), healthcare workers and family members (n 552), and university employees (n 327) for antiSARS-CoV-2 receptor-binding domain, trimeric spike protein, and nucleocapsid protein immunoglobulin (Ig)G and IgA antibodies with a laboratory-developed enzyme-linked immunosorbent assay and tested how antigen, isotype and threshold choices affected the seroprevalence outcomes. The following threshold methods were evaluated: (i) mean 3 standard deviations of the negative controls; (ii) 100 specificity for each antigen-isotype combination; and (iii) the maximal Youden index. RESULTS We found vastly different seroprevalence estimates depending on selected antigens and isotypes and the applied threshold method, ranging from 0.0 to 85.4. Subsequently, we maximized specificity and reported a seroprevalence, based on more than one antigen, ranging from 9.3 to 25.9. CONCLUSIONS This study revealed the importance of evaluating serosurvey tools for antigen-, isotype-, and threshold-specific sensitivity and specificity, to interpret qualitative serosurvey outcomes reliably and consistently across studies.
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Affiliation(s)
- Raquel A Binder
- Correspondence: Raquel A. Binder, University of Massachusetts Chan Medical School, Worcester, MA 01605 ()
| | | | | | - George W Reed
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Leandro S Silva
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Priya Saikumar Lakshmi
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Amanda Higgins
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Lindsey Cincotta
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Protiva Dutta
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Marie-Claire Salive
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Virginia Mangolds
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Otuwe Anya
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - J Mauricio Calvo Calle
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Thomas Nixon
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Qiushi Tang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Mireya Wessolossky
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Yang Wang
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, USA
| | - Dominic A Ritacco
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Courtney S Bly
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Peter O Oluoch
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Boaz Odwar
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Ana Maldonado-Contreras
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - John P Haran
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA,Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lisa Cavacini
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
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Wesolowski A, Ippolito MM, Gebhardt ME, Ferriss E, Schue JL, Kobayashi T, Chaponda M, Kabuya JB, Muleba M, Mburu M, Matoba J, Musonda M, Katowa B, Lubinda M, Hamapumbu H, Simubali L, Mudenda T, Shields TM, Hackman A, Shiff C, Coetzee M, Koekemoer LL, Munyati S, Gwanzura L, Mutambu S, Stevenson JC, Thuma PE, Norris DE, Bailey JA, Juliano JJ, Chongwe G, Mulenga M, Simulundu E, Mharakurwa S, Agre P, Moss WJ. Policy Implications of the Southern and Central Africa International Center of Excellence for Malaria Research: Ten Years of Malaria Control Impact Assessments in Hypo-, Meso-, and Holoendemic Transmission Zones in Zambia and Zimbabwe. Am J Trop Med Hyg 2022; 107:68-74. [PMID: 36228913 PMCID: PMC9662215 DOI: 10.4269/ajtmh.21-1288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/28/2022] [Indexed: 11/07/2022] Open
Abstract
The International Centers of Excellence for Malaria Research (ICEMR) were established by the National Institute of Allergy and Infectious Diseases more than a decade ago to provide multidisciplinary research support to malaria control programs worldwide, operating in endemic areas and contributing technology, expertise, and ultimately policy guidance for malaria control and elimination. The Southern and Central Africa ICEMR has conducted research across three main sites in Zambia and Zimbabwe that differ in ecology, entomology, transmission intensity, and control strategies. Scientific findings led to new policies and action by the national malaria control programs and their partners in the selection of methods, materials, timing, and locations of case management and vector control. Malaria risk maps and predictive models of case detection furnished by the ICEMR informed malaria elimination programming in southern Zambia, and time series analyses of entomological and parasitological data motivated several major changes to indoor residual spray campaigns in northern Zambia. Along the Zimbabwe-Mozambique border, temporal and geospatial data are currently informing investigations into a recent resurgence of malaria. Other ICEMR findings pertaining to parasite and mosquito genetics, human behavior, and clinical epidemiology have similarly yielded immediate and long-term policy implications at each of the sites, often with generalizable conclusions. The ICEMR programs thereby provide rigorous scientific investigations and analyses to national control and elimination programs, without which the impediments to malaria control and their potential solutions would remain understudied.
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Affiliation(s)
- Amy Wesolowski
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Matthew M. Ippolito
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mary E. Gebhardt
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ellen Ferriss
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Jessica L. Schue
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Tamaki Kobayashi
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | | | | | | | | | | | | | | | | | | | | | - Andre Hackman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Clive Shiff
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Maureen Coetzee
- Wits Research Institute for Malaria, Faculty of Health Sciences, University of the Witwatersrand and National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lizette L. Koekemoer
- Wits Research Institute for Malaria, Faculty of Health Sciences, University of the Witwatersrand and National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Shungu Munyati
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Lovemore Gwanzura
- Biomedical Research and Training Institute, Harare, Zimbabwe
- University of Zimbabwe Faculty of Medicine and Health Sciences, Harare, Zimbabwe
| | | | - Jennifer C. Stevenson
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Macha Research Trust, Choma, Zambia
| | - Philip E. Thuma
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Macha Research Trust, Choma, Zambia
| | - Douglas E. Norris
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Jonathan J. Juliano
- University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | | | - Modest Mulenga
- Directorate of Research and Postgraduate Studies, Lusaka Apex Medical University, Lusaka, Zambia
| | | | - Sungano Mharakurwa
- Biomedical Research and Training Institute, Harare, Zimbabwe
- Africa University, Mutare, Zimbabwe
| | - Peter Agre
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - William J. Moss
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Ippolito MM, Gebhardt ME, Ferriss E, Schue JL, Kobayashi T, Chaponda M, Kabuya JB, Muleba M, Mburu M, Matoba J, Musonda M, Katowa B, Lubinda M, Hamapumbu H, Simubali L, Mudenda T, Wesolowski A, Shields TM, Hackman A, Shiff C, Coetzee M, Koekemoer LL, Munyati S, Gwanzura L, Mutambu S, Stevenson JC, Thuma PE, Norris DE, Bailey JA, Juliano JJ, Chongwe G, Mulenga M, Simulundu E, Mharakurwa S, Agre PC, Moss WJ. Scientific Findings of the Southern and Central Africa International Center of Excellence for Malaria Research: Ten Years of Malaria Control Impact Assessments in Hypo-, Meso-, and Holoendemic Transmission Zones in Zambia and Zimbabwe. Am J Trop Med Hyg 2022; 107:55-67. [PMID: 36228903 PMCID: PMC9662223 DOI: 10.4269/ajtmh.21-1287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/08/2022] [Indexed: 11/07/2022] Open
Abstract
For a decade, the Southern and Central Africa International Center of Excellence for Malaria Research has operated with local partners across study sites in Zambia and Zimbabwe that range from hypo- to holoendemic and vary ecologically and entomologically. The burden of malaria and the impact of control measures were assessed in longitudinal cohorts, cross-sectional surveys, passive and reactive case detection, and other observational designs that incorporated multidisciplinary scientific approaches: classical epidemiology, geospatial science, serosurveillance, parasite and mosquito genetics, and vector bionomics. Findings to date have helped elaborate the patterns and possible causes of sustained low-to-moderate transmission in southern Zambia and eastern Zimbabwe and recalcitrant high transmission and fatality in northern Zambia. Cryptic and novel mosquito vectors, asymptomatic parasite reservoirs in older children, residual parasitemia and gametocytemia after treatment, indoor residual spraying timed dyssynchronously to vector abundance, and stockouts of essential malaria commodities, all in the context of intractable rural poverty, appear to explain the persistent malaria burden despite current interventions. Ongoing studies of high-resolution transmission chains, parasite population structures, long-term malaria periodicity, and molecular entomology are further helping to lay new avenues for malaria control in southern and central Africa and similar settings.
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Affiliation(s)
- Matthew M. Ippolito
- Johns Hopkins University School of Medicine, Baltimore, Maryland
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Mary E. Gebhardt
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ellen Ferriss
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Jessica L. Schue
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Tamaki Kobayashi
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | | | | | | | | | | | | | | | | | | | - Amy Wesolowski
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Andre Hackman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Clive Shiff
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Maureen Coetzee
- Wits Research Institute for Malaria, Faculty of Health Sciences, University of the Witwatersrand and National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lizette L. Koekemoer
- Wits Research Institute for Malaria, Faculty of Health Sciences, University of the Witwatersrand and National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Shungu Munyati
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Lovemore Gwanzura
- Biomedical Research and Training Institute, Harare, Zimbabwe
- University of Zimbabwe Faculty of Medicine and Health Sciences, Harare, Zimbabwe
| | | | - Jennifer C. Stevenson
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Macha Research Trust, Choma, Zambia
| | | | - Douglas E. Norris
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Jonathan J. Juliano
- University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | | | - Modest Mulenga
- Directorate of Research and Postgraduate Studies, Lusaka Apex Medical University, Lusaka, Zambia
| | | | - Sungano Mharakurwa
- Biomedical Research and Training Institute, Harare, Zimbabwe
- Africa University, Mutare, Zimbabwe
| | - Peter C. Agre
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - William J. Moss
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Movassagh M, Morton SU, Hehnly C, Smith J, Doan TT, Irizarry R, Broach JR, Schiff SJ, Bailey JA, Paulson JN. mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. BMC Genomics 2022; 23:439. [PMID: 35698050 PMCID: PMC9191533 DOI: 10.1186/s12864-022-08558-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/17/2022] [Indexed: 11/10/2022] Open
Abstract
We introduce mirTarRnaSeq, an R/Bioconductor package for quantitative assessment of miRNA-mRNA relationships within sample cohorts. mirTarRnaSeq is a statistical package to explore predicted or pre-hypothesized miRNA-mRNA relationships following target prediction.We present two use cases applying mirTarRnaSeq. First, to identify miRNA targets, we examined EBV miRNAs for interaction with human and virus transcriptomes of stomach adenocarcinoma. This revealed enrichment of mRNA targets highly expressed in CD105+ endothelial cells, monocytes, CD4+ T cells, NK cells, CD19+ B cells, and CD34 cells. Next, to investigate miRNA-mRNA relationships in SARS-CoV-2 (COVID-19) infection across time, we used paired miRNA and RNA sequenced datasets of SARS-CoV-2 infected lung epithelial cells across three time points (4, 12, and 24 hours post-infection). mirTarRnaSeq identified evidence for human miRNAs targeting cytokine signaling and neutrophil regulation immune pathways from 4 to 24 hours after SARS-CoV-2 infection. Confirming the clinical relevance of these predictions, three of the immune specific mRNA-miRNA relationships identified in human lung epithelial cells after SARS-CoV-2 infection were also observed to be differentially expressed in blood from patients with COVID-19. Overall, mirTarRnaSeq is a robust tool that can address a wide-range of biological questions providing improved prediction of miRNA-mRNA interactions.
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Affiliation(s)
- Mercedeh Movassagh
- Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Sarah U Morton
- Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Christine Hehnly
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Jasmine Smith
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Trang T Doan
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, United States.,Center for Neural Engineering and Center for Infectious Disease Dynamics, Departments of Engineering Science and Mechanics, Neurosurgery and Physics, The Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Rafael Irizarry
- Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - James R Broach
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Steven J Schiff
- Center for Neural Engineering and Center for Infectious Disease Dynamics, Departments of Engineering Science and Mechanics, Neurosurgery and Physics, The Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Jeffrey A Bailey
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Joseph N Paulson
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, United States.
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Topazian HM, Moser KA, Ngasala B, Oluoch PO, Forconi CS, Mhamilawa LE, Aydemir O, Kharabora O, Deutsch-Feldman M, Read AF, Denton M, Lorenzo A, Mideo N, Ogutu B, Moormann AM, Mårtensson A, Odwar B, Bailey JA, Akala H, Ong'echa JM, Juliano JJ. Low Complexity of Infection Is Associated With Molecular Persistence of Plasmodium falciparum in Kenya and Tanzania. Front Epidemiol 2022; 2:852237. [PMID: 38455314 PMCID: PMC10910917 DOI: 10.3389/fepid.2022.852237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/06/2022] [Indexed: 03/09/2024]
Abstract
Background Plasmodium falciparum resistance to artemisinin-based combination therapies (ACTs) is a threat to malaria elimination. ACT-resistance in Asia raises concerns for emergence of resistance in Africa. While most data show high efficacy of ACT regimens in Africa, there have been reports describing declining efficacy, as measured by both clinical failure and prolonged parasite clearance times. Methods Three hundred children aged 2-10 years with uncomplicated P. falciparum infection were enrolled in Kenya and Tanzania after receiving treatment with artemether-lumefantrine. Blood samples were taken at 0, 24, 48, and 72 h, and weekly thereafter until 28 days post-treatment. Parasite and host genetics were assessed, as well as clinical, behavioral, and environmental characteristics, and host anti-malarial serologic response. Results While there was a broad range of clearance rates at both sites, 85% and 96% of Kenyan and Tanzanian samples, respectively, were qPCR-positive but microscopy-negative at 72 h post-treatment. A greater complexity of infection (COI) was negatively associated with qPCR-detectable parasitemia at 72 h (OR: 0.70, 95% CI: 0.53-0.94), and a greater baseline parasitemia was marginally associated with qPCR-detectable parasitemia (1,000 parasites/uL change, OR: 1.02, 95% CI: 1.01-1.03). Demographic, serological, and host genotyping characteristics showed no association with qPCR-detectable parasitemia at 72 h. Parasite haplotype-specific clearance slopes were grouped around the mean with no association detected between specific haplotypes and slower clearance rates. Conclusions Identifying risk factors for slow clearing P. falciparum infections, such as COI, are essential for ongoing surveillance of ACT treatment failure in Kenya, Tanzania, and more broadly in sub-Saharan Africa.
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Affiliation(s)
- Hillary M. Topazian
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Kara A. Moser
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Peter O. Oluoch
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Catherine S. Forconi
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Lwidiko E. Mhamilawa
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women's and Children's Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Oksana Kharabora
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Molly Deutsch-Feldman
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Andrew F. Read
- Department of Entomology, Penn State University, University Park, PA, United States
| | - Madeline Denton
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Antonio Lorenzo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Bernhards Ogutu
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Ann M. Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
| | - Boaz Odwar
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Hoseah Akala
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | | | - Jonathan J. Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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Gurney JM, John SK, Whitt EH, Slinger BJ, Luan WP, Lindly J, Graybill JC, Bailey JA. Data Driven Readiness: A Preliminary Report on Cataloguing Best Practices in Military Civilian Partnerships. J Trauma Acute Care Surg 2022; 93:S155-S159. [PMID: 35562843 DOI: 10.1097/ta.0000000000003694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Between conflicts, many of the combat casualty care lessons learned are lost as the nation shifts priorities and providers leave the military. Solutions are needed to bridge the knowledge gap created by interwar periods. One of the foremost solutions are partnerships between civilian trauma centers and the military health system. Over the past two decades, a myriad of Military Civilian Partnerships (MCPs) were created which vary in their composition, duration, and focus. The objective of this report is to describe the initial attempt of the DoD to catalogue existing MCPs to inform both civilian and military stakeholders. This initial catalogue is intended as a reference to aid in future MCP development and facilitate the synchronization of efforts to improve trauma care delivery and readiness. METHODS Using methodology from the Institute of Defense Analysis (IDA) the total number of eligible trauma centers in the US were determined. The IDA determined eligibility based American College of Surgeons Trauma Center verification or state trauma center designation. Each military Service provided their list of MCPs which were categorized. MCPs were catalogued by various characteristics and program components. Key variables include number and type of personnel trained, duration of training, and focus, e.g. team vs individual focused and training vs maintaining proficiency focused. RESULTS 1139 hospitals in the United States are potentially eligible for MCPs. There are at least 87 unique partnerships, the majority are part-time sustainment MCPs. The Air Force has the largest number of providers in MCPs. There are many challenges to maintain accurate and up to date data on MCPs. CONCLUSIONS With the collated information, the DHA, military services, special operations community, and civilian partners will be better empowered to optimize the readiness value of their programs and better prepare our military medical providers for the nation's and military's future needs. LEVEL OF EVIDENCE Care Management, Level IV.
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Affiliation(s)
| | - Sarah K John
- Institute for Defense Analyses, 730 East Glebe Road, Alexandria, VA 22305
| | - Edward H Whitt
- Joint Trauma System, DoD Center of Excellence for Trauma, 3698 Chambers Pass, Joint Base San Antonio-Fort Sam Houston, TX 78234
| | - Bryce J Slinger
- Office of the Assistant Secretary of Defense for Health Affairs, Falls Church, VA 22042-5101
| | - William P Luan
- Institute for Defense Analyses, 730 East Glebe Road, Alexandria, VA 22305
| | - Jamie Lindly
- Institute for Defense Analyses, 730 East Glebe Road, Alexandria, VA 22305
| | - J Christopher Graybill
- Joint Trauma System, DoD Center of Excellence for Trauma, 3698 Chambers Pass, Joint Base San Antonio-Fort Sam Houston, TX 78234
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50
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Wamae K, Kimenyi KM, Osoti V, de Laurent ZR, Ndwiga L, Kharabora O, Hathaway NJ, Bailey JA, Juliano JJ, Bejon P, Ochola-Oyier LI. Amplicon sequencing as a potential surveillance tool for complexity of infection and drug resistance markers in Plasmodium falciparum asymptomatic infections. J Infect Dis 2022; 226:920-927. [PMID: 35429395 PMCID: PMC7613600 DOI: 10.1093/infdis/jiac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
Background Genotyping Plasmodium falciparum subpopulations in malaria infections is an important aspect of malaria molecular epidemiology to understand within-host diversity and the frequency of drug resistance markers. Methods We characterized P. falciparum genetic diversity in asymptomatic infections and subsequent first febrile infections using amplicon sequencing (AmpSeq) of ama1 in Coastal Kenya. We also examined temporal changes in haplotype frequencies of mdr1, a drug-resistant marker. Results We found >60% of the infections were polyclonal (complexity of infection [COI] >1) and there was a reduction in COI over time. Asymptomatic infections had a significantly higher mean COI than febrile infections based on ama1 sequences (2.7 [95% confidence interval {CI}, 2.65–2.77] vs 2.22 [95% CI, 2.17–2.29], respectively). Moreover, an analysis of 30 paired asymptomatic and first febrile infections revealed that many first febrile infections (91%) were due to the presence of new ama1 haplotypes. The mdr1-YY haplotype, associated with chloroquine and amodiaquine resistance, decreased over time, while the NY (wild type) and the NF (modulates response to lumefantrine) haplotypes increased. Conclusions This study emphasizes the utility of AmpSeq in characterizing parasite diversity as it can determine relative proportions of clones and detect minority clones. The usefulness of AmpSeq in antimalarial drug resistance surveillance is also highlighted.
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Affiliation(s)
- Kevin Wamae
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kelvin M. Kimenyi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Victor Osoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | - Oksana Kharabora
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nicholas J. Hathaway
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Jonathan J. Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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