1
|
Sifuna PM, Mbinji M, Lucas TO, Onyango I, Akala HM, Waitumbi JN, Ogutu BR, Hutter JN, Otieno W. The Walter Reed Project, Kisumu Field Station: Impact of Research on Malaria Policy, Management, and Prevention. Am J Trop Med Hyg 2024; 110:1069-1079. [PMID: 38653233 PMCID: PMC11154051 DOI: 10.4269/ajtmh.23-0115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 02/16/2024] [Indexed: 04/25/2024] Open
Abstract
The Walter Reed Project is a collaboration between the Walter Reed Army Institute of Research of the United States Department of Defense and the Kenya Medical Research Institute. The Kisumu field station, comprising four campuses, has until recently been devoted primarily to research on malaria countermeasures. The Kombewa Clinical Research Center is dedicated to conducting regulated clinical trials of therapeutic and vaccine candidates in development. The center's robust population-based surveillance platform, along with an active community engagement strategy, guarantees consistent recruitment and retention of participants in clinical trials. The Malaria Diagnostic Center, backed by WHO-certified microscopists and a large malaria blood film collection, champions high-quality malaria diagnosis and strict quality assurance through standardized microscopy trainings. The Malaria Drug Resistance Laboratory leverages cutting-edge technology such as real-time Polymerase Chain Reaction (qPCR) to conduct comprehensive research on resistance markers and obtain information on drug efficacy. The laboratory has been working on validating artemisinin resistance markers and improving tracking methods for current and future antimalarial compounds. Finally, the Basic Science Laboratory employs advanced genomic technology to examine endpoints such as immunogenicity and genomic fingerprinting for candidate drugs and vaccine efficacy. Herein, we examine the site's significant contributions to malaria policy, management, and prevention practices in Kenya and around the world.
Collapse
Affiliation(s)
- Peter M Sifuna
- Kenya Medical Research Institute, Kisumu, Kenya
- U.S. Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - Michal Mbinji
- Kenya Medical Research Institute, Kisumu, Kenya
- U.S. Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - Tina O Lucas
- Kenya Medical Research Institute, Kisumu, Kenya
- U.S. Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - Irene Onyango
- Kenya Medical Research Institute, Kisumu, Kenya
- U.S. Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - Hoseah M Akala
- Kenya Medical Research Institute, Kisumu, Kenya
- U.S. Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - John N Waitumbi
- Kenya Medical Research Institute, Kisumu, Kenya
- U.S. Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - Bernhards R Ogutu
- Kenya Medical Research Institute, Kisumu, Kenya
- U.S. Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - Jack N Hutter
- U.S. Army Medical Research Directorate-Africa, Kisumu, Kenya
| | - Walter Otieno
- Kenya Medical Research Institute, Kisumu, Kenya
- U.S. Army Medical Research Directorate-Africa, Kisumu, Kenya
| |
Collapse
|
2
|
Mwesigwa A, Ocan M, Musinguzi B, Nante RW, Nankabirwa JI, Kiwuwa SM, Kinengyere AA, Castelnuovo B, Karamagi C, Obuku EA, Nsobya SL, Mbulaiteye SM, Byakika-Kibwika P. Plasmodium falciparum genetic diversity and multiplicity of infection based on msp-1, msp-2, glurp and microsatellite genetic markers in sub-Saharan Africa: a systematic review and meta-analysis. Malar J 2024; 23:97. [PMID: 38589874 PMCID: PMC11000358 DOI: 10.1186/s12936-024-04925-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND In sub-Saharan Africa (SSA), Plasmodium falciparum causes most of the malaria cases. Despite its crucial roles in disease severity and drug resistance, comprehensive data on Plasmodium falciparum genetic diversity and multiplicity of infection (MOI) are sparse in SSA. This study summarizes available information on genetic diversity and MOI, focusing on key markers (msp-1, msp-2, glurp, and microsatellites). The systematic review aimed to evaluate their influence on malaria transmission dynamics and offer insights for enhancing malaria control measures in SSA. METHODS The review was conducted following the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines. Two reviewers conducted article screening, assessed the risk of bias (RoB), and performed data abstraction. Meta-analysis was performed using the random-effects model in STATA version 17. RESULTS The review included 52 articles: 39 cross-sectional studies and 13 Randomized Controlled Trial (RCT)/cohort studies, involving 11,640 genotyped parasite isolates from 23 SSA countries. The overall pooled mean expected heterozygosity was 0.65 (95% CI: 0.51-0.78). Regionally, values varied: East (0.58), Central (0.84), Southern (0.74), and West Africa (0.69). Overall pooled allele frequencies of msp-1 alleles K1, MAD20, and RO33 were 61%, 44%, and 40%, respectively, while msp-2 I/C 3D7 and FC27 alleles were 61% and 55%. Central Africa reported higher frequencies (K1: 74%, MAD20: 51%, RO33: 48%) than East Africa (K1: 46%, MAD20: 42%, RO33: 31%). For msp-2, East Africa had 60% and 55% for I/C 3D7 and FC27 alleles, while West Africa had 62% and 50%, respectively. The pooled allele frequency for glurp was 66%. The overall pooled mean MOI was 2.09 (95% CI: 1.88-2.30), with regional variations: East (2.05), Central (2.37), Southern (2.16), and West Africa (1.96). The overall prevalence of polyclonal Plasmodium falciparum infections was 63% (95% CI: 56-70), with regional prevalences as follows: East (62%), West (61%), Central (65%), and South Africa (71%). CONCLUSION The study shows substantial regional variation in Plasmodium falciparum parasite genetic diversity and MOI in SSA. These findings suggest a need for malaria control strategies and surveillance efforts considering regional-specific factors underlying Plasmodium falciparum infection.
Collapse
Affiliation(s)
- Alex Mwesigwa
- Clinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda.
- Department of Microbiology and Immunology, School of Medicine, Kabale University, P. O Box 314, Kabale, Uganda.
| | - Moses Ocan
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
- African Center for Systematic Reviews and Knowledge Translation, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Benson Musinguzi
- Departent of Medical Laboratory Science, Faculty of Health Sciences, Muni University, P.O Box 725, Arua, Uganda
| | - Rachel Wangi Nante
- African Center for Systematic Reviews and Knowledge Translation, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Joaniter I Nankabirwa
- Clinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
- Infectious Diseases Research Collaboration, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Steven M Kiwuwa
- Department of Biochemistry, School of Biomedical Sciences, College of Health Sciences, Makerere, University, P.O. Box 7072, Kampala, Uganda
| | - Alison Annet Kinengyere
- Albert Cook Library, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Barbara Castelnuovo
- Infectious Diseases Institute, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Charles Karamagi
- Clinical Epidemiology Unit, School of Medicine, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Ekwaro A Obuku
- Infectious Diseases Institute, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
- African Center for Systematic Reviews and Knowledge Translation, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Samuel L Nsobya
- Infectious Diseases Research Collaboration, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr, 6E-118, Bethesda, MD, 20892, USA
| | - Pauline Byakika-Kibwika
- Department of Medicine, School of Medicine, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
- Infectious Diseases Institute, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| |
Collapse
|
3
|
Sinha A, Kar S, Chauhan C, Yadav CP, Kori L. Meta-analysis on Plasmodium falciparum sulfadoxine-pyrimethamine resistance-conferring mutations in India identifies hot spots for genetic surveillance. Int J Antimicrob Agents 2024; 63:107071. [PMID: 38154659 DOI: 10.1016/j.ijantimicag.2023.107071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND India is on track to eliminate malaria by 2030 but emerging resistance to first-line antimalarials is a recognised threat. Two instances of rapid development, spread, and natural selection of drug-resistant mutant parasites in India (chloroquine across the country and artesunate + sulfadoxine-pyrimethamine [AS+SP] in the northeastern states) translated into drug policy changes for Plasmodium falciparum malaria in 2010 and 2013, respectively. Considering these rapid changes in the SP drug resistance-conferring mutation profile of P. falciparum, there is a need to systematically monitor the validated mutations in Pfdhfr and Pfdhps genes across India alongside AS+SP therapeutic efficacy studies. There has been no robust, systematic countrywide surveillance reported for these parameters in India, hence the current study was undertaken. METHODS Studies that reported data on WHO-validated SP resistance markers in P. falciparum across India from 2008 to January 2023 were included. Five major databases, PubMedⓇ, Web of ScienceTM, ScopusⓇ, EmbaseⓇ, and Google Scholar, were exhaustively searched. Individual and pooled prevalence estimates of mutations were obtained through random- and fixed-effect models. Data were depicted using forest plots created with a 95% confidence interval. The study is registered with PROSPERO (CRD42021236012). RESULTS A total of 37 publications, and 533 Pfdhfr and 134 Pfdhps National Centre of Biotechnology Information (NCBI) DNA sequences were included from >4000 samples. The study included information from 80 districts, 21 states and 3 union territories (UTs) from India. The two PfDHFR mutations, C59R (62%) and S108N (74%), were the most prevalent mutations (pooled estimates 61% and 71%, respectively) and appeared to be stabilised/fixed. Although rarest overall, the prevalence of I164L was observed to be as high as 32%. The PfDHFR double mutants were the most prevalent overall (51%; pooled 42%). The prevalence of triple and quadruple mutations was 6% and 5%, respectively, and is an immediate concern for some states. The most prevalent PfDHPS mutation was A437G (39%), followed by K540E (25%) and A581G (12%). There was a low overall prevalence of PfDHFR/PfDHPS quintuple and sextuple mutations but surveillance for these mutations is critical for some areas. CONCLUSION The analyses span the two critical policy changes, highlight the areas of concern, and guide policymakers in strategising and refining the anti-malaria drug policy for malaria elimination. The results of the analyses also highlight the SP-resistance hot spots, critical gaps and challenges, and indicate that focal and local malaria genetic surveillance (including drug-resistance markers) is needed until malaria is successfully eliminated.
Collapse
Affiliation(s)
- Abhinav Sinha
- ICMR-National Institute of Malaria Research, New Delhi, India.
| | - Sonalika Kar
- ICMR-National Institute of Malaria Research, New Delhi, India
| | - Charu Chauhan
- ICMR-National Institute of Malaria Research, New Delhi, India
| | | | - Lokesh Kori
- ICMR-National Institute of Malaria Research, New Delhi, India
| |
Collapse
|
4
|
Toure M, Shaffer JG, Sanogo D, Keita S, Keita M, Kane F, Traore B, Dabitao D, Kone A, Doumbia CO, Keating J, Yukich J, Hansson HH, Barry AE, Diakité M, Alifrangis M, Doumbia S. Seasonal Malaria Chemoprevention Therapy in Children Up To 9 Years of Age: Protocol for a Cluster-Randomized Trial Study. JMIR Res Protoc 2024; 13:e51660. [PMID: 38252481 PMCID: PMC10845024 DOI: 10.2196/51660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Seasonal malaria chemoprevention (SMC) is recommended by the World Health Organization for the sub-Sahel region in sub-Saharan Africa for preventing malaria in children 3 months old to younger than 5 years. Since 2016, the Malian National Malaria Control Program has deployed SMC countrywide during its high malaria transmission season at a rate of 4 monthly cycles annually. The standard SMC regimen includes sulfadoxine-pyrimethamine (SP) plus amodiaquine (AQ). Resistance against SP is suspected to be rising across West Africa; therefore, assessing the effectiveness of an alternative antimalarial drug for SMC is needed to provide a second-line regimen when it is ultimately needed. It is not well understood whether SMC effectively prevents malaria in children aged 5 years or older. OBJECTIVE The primary goal of the study is to compare 2 SMC regimens (SP-AQ and dihydroartemisinin-piperaquine [DHA-PQ]) in preventing uncomplicated Plasmodium falciparum malaria in children 3 months to 9 years old. Secondly, we will assess the possible use of DHA-PQ as an alternative SMC drug in areas where resistance to SP or AQ may increase following intensive use. METHODS The study design is a 3-arm cluster-randomized design comparing the SP-AQ and DHA-PQ arms in 2 age groups (younger than 5 years and 5-9 years) and a control group for children aged 5-9 years. Standard SMC (SP-AQ) for children younger than 5 years was provided to the control arm, while SMC with SP-AQ was delivered to children aged 3 months to 9 years (arm 2), and SMC with DHA-PQ will be implemented in study arm 3 for children up to 9 years of age. The study was performed in Mali's Koulikoro District, a rural area in southwest Mali with historically high malaria transmission rates. The study's primary outcome is P falciparum incidence for 2 SMC regimens in children up to 9 years of age. Should DHA-PQ provide an acceptable alternative to SP-AQ, a plausible second-line prevention option would be available in the event of SP resistance or drug supply shortages. A significant byproduct of this effort included bolstering district health information systems for rapid identification of severe malaria cases. RESULTS The study began on July 1, 2019. Through November 2022, a total of 4556 children 3 months old to younger than 5 years were enrolled. Data collection ended in spring 2023, and the findings are expected to be published later in early 2024. CONCLUSIONS Routine evaluation of antimalarial drugs is needed to establish appropriate SMC age targets. The study goals here may impact public health policy and provide alternative therapies in the event of drug shortages or resistance. TRIAL REGISTRATION ClinicalTrials.gov NCT04149106, https://clinicaltrials.gov/ct2/show/NCT04149106. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/51660.
Collapse
Affiliation(s)
- Mahamoudou Toure
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Jeffrey G Shaffer
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Daouda Sanogo
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Soumba Keita
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Moussa Keita
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Fousseyni Kane
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Bourama Traore
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Djeneba Dabitao
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Aissata Kone
- Mali National Malaria Control Program, Bamako, Mali
| | - Cheick Oumar Doumbia
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Joseph Keating
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Joshua Yukich
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Helle H Hansson
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Alyssa E Barry
- Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Melbourne, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Australia
| | - Mahamadou Diakité
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Michael Alifrangis
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Seydou Doumbia
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| |
Collapse
|
5
|
Mantena S, Pillai PP, Petros BA, Welch NL, Myhrvold C, Sabeti PC, Metsky HC. Model-directed generation of CRISPR-Cas13a guide RNAs designs artificial sequences that improve nucleic acid detection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.557569. [PMID: 37786711 PMCID: PMC10541601 DOI: 10.1101/2023.09.20.557569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Generating maximally-fit biological sequences has the potential to transform CRISPR guide RNA design as it has other areas of biomedicine. Here, we introduce model-directed exploration algorithms (MEAs) for designing maximally-fit, artificial CRISPR-Cas13a guides-with multiple mismatches to any natural sequence-that are tailored for desired properties around nucleic acid diagnostics. We find that MEA-designed guides offer more sensitive detection of diverse pathogens and discrimination of pathogen variants compared to guides derived directly from natural sequences, and illuminate interpretable design principles that broaden Cas13a targeting.
Collapse
Affiliation(s)
- Sreekar Mantena
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Brittany A. Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology, MD-PhD Program, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | |
Collapse
|
6
|
Maniga JN, Samuel M, John O, Rael M, Muchiri JN, Bwogo P, Martin O, Sankarapandian V, Wilberforce M, Albert O, Onkoba SK, Adebayo IA, Adeyemo RO, Akinola SA. Novel Plasmodium falciparum k13 gene polymorphisms from Kisii County, Kenya during an era of artemisinin-based combination therapy deployment. Malar J 2023; 22:87. [PMID: 36894982 PMCID: PMC9996564 DOI: 10.1186/s12936-023-04517-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Currently, chemotherapy stands out as the major malaria intervention strategy, however, anti-malarial resistance may hamper global elimination programs. Artemisinin-based combination therapy (ACT) stands as the drug of choice for the treatment of Plasmodium falciparum malaria. Plasmodium falciparum kelch13 gene mutations are associated with artemisinin resistance. Thus, this study was aimed at evaluating the circulation of P. falciparum k13 gene polymorphisms from Kisii County, Kenya during an era of ACT deployment. METHODS Participants suspected to have malaria were recruited. Plasmodium falciparum was confirmed using the microscopy method. Malaria-positive patients were treated with artemether-lumefantrine (AL). Blood from participants who tested positive for parasites after day 3 was kept on filter papers. DNA was extracted using chelex-suspension method. A nested polymerase chain reaction (PCR) was conducted and the second-round products were sequenced using the Sanger method. Sequenced products were analysed using DNAsp 5.10.01 software and then blasted on the NCBI for k13 propeller gene sequence identity using the Basic Local Alignment Search Tool (BLAST). To assess the selection pressure in P. falciparum parasite population, Tajima' D statistic and Fu & Li's D test in DnaSP software 5.10.01 was used. RESULTS Out of 275 enrolled participants, 231 completed the follow-up schedule. 13 (5.6%) had parasites on day 28 hence characterized for recrudescence. Out of the 13 samples suspected of recrudescence, 5 (38%) samples were positively amplified as P. falciparum, with polymorphisms in the k13-propeller gene detected. Polymorphisms detected in this study includes R539T, N458T, R561H, N431S and A671V, respectively. The sequences have been deposited in NCBI with bio-project number PRJNA885380 and accession numbers SAMN31087434, SAMN31087433, SAMN31087432, SAMN31087431 and SAMN31087430 respectively. CONCLUSIONS WHO validated polymorphisms in the k13-propeller gene previously reported to be associated with ACT resistance were not detected in the P. falciparum isolates from Kisii County, Kenya. However, some previously reported un-validated k13 resistant single nucleotide polymorphisms were reported in this study but with limited occurrences. The study has also reported new SNPs. More studies need to be carried out in the entire country to understand the association of reported mutations if any, with ACT resistance.
Collapse
Affiliation(s)
- Josephat Nyabayo Maniga
- Department of Medical Microbiology and Immunology, Kampala International University Western Campus, Bushenyi, Uganda.
| | | | - Odda John
- School of Pharmacy, Kampala International University Western Campus, Bushenyi, Uganda.,Department of Pharmacology and Therapeutics, Makerere University, Kampala, Uganda.,Department of Pharmacology and Toxicology, School of Medicine, King Caesor University, Kampala, Uganda
| | - Masai Rael
- Department of Biological Sciences, Kisii University, Kisii, Kenya
| | | | - Pacifica Bwogo
- Department of Biological Sciences, Kisii University, Kisii, Kenya
| | - Odoki Martin
- Department of Medical Microbiology and Immunology, Kampala International University Western Campus, Bushenyi, Uganda.,Department of Medical Microbiology and Immunology, School of Medicine, King Ceasor University, Kampala, Uganda.,Department of Applied Sciences, School of Sciences, Nkumba University, Entebbe, Uganda
| | - Vidya Sankarapandian
- Department of Medical Microbiology and Immunology, Kampala International University Western Campus, Bushenyi, Uganda
| | - Mfitundinda Wilberforce
- School of Pharmacy, Kampala International University Western Campus, Bushenyi, Uganda.,Department of Pharmacology and Toxicology, School of Medicine, King Caesor University, Kampala, Uganda
| | - Ochweri Albert
- School of Pharmacy, Kampala International University Western Campus, Bushenyi, Uganda
| | - Sarah Kemuma Onkoba
- Department of Medical Microbiology and Immunology, Kampala International University Western Campus, Bushenyi, Uganda
| | - Ismail Abiola Adebayo
- Department of Medical Biochemistry, Molecular Biology and Genetics, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Butare, Rwanda
| | - Rasheed Omotayo Adeyemo
- Department of Medical Microbiology and Parasitology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Butare, Rwanda
| | - Saheed Adekunle Akinola
- Department of Medical Microbiology and Parasitology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Butare, Rwanda
| |
Collapse
|
7
|
Tavares W, Morais J, Martins JF, Scalsky RJ, Stabler TC, Medeiros MM, Fortes FJ, Arez AP, Silva JC. Malaria in Angola: recent progress, challenges and future opportunities using parasite demography studies. Malar J 2022; 21:396. [PMID: 36577996 PMCID: PMC9795141 DOI: 10.1186/s12936-022-04424-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Over the past two decades, a considerable expansion of malaria interventions has occurred at the national level in Angola, together with cross-border initiatives and regional efforts in southern Africa. Currently, Angola aims to consolidate malaria control and to accelerate the transition from control to pre-elimination, along with other country members of the Elimination 8 initiative. However, the tremendous heterogeneity in malaria prevalence among Angolan provinces, as well as internal population movements and migration across borders, represent major challenges for the Angolan National Malaria Control Programme. This review aims to contribute to the understanding of factors underlying the complex malaria situation in Angola and to encourage future research studies on transmission dynamics and population structure of Plasmodium falciparum, important areas to complement host epidemiological information and to help reenergize the goal of malaria elimination in the country.
Collapse
Affiliation(s)
- Wilson Tavares
- grid.10772.330000000121511713Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Joana Morais
- Instituto Nacional de Investigação Em Saúde, INIS, Luanda, Angola
| | - José F. Martins
- Programa Nacional de Controlo da Malária, PNCM, Luanda, Angola
| | - Ryan J. Scalsky
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - Thomas C. Stabler
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, Basel, Switzerland
| | - Márcia M. Medeiros
- grid.10772.330000000121511713Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Filomeno J. Fortes
- grid.10772.330000000121511713Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Ana Paula Arez
- grid.10772.330000000121511713Global Health and Tropical Medicine, GHTM, Instituto de Higiene E Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Joana C. Silva
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA ,grid.411024.20000 0001 2175 4264Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| |
Collapse
|
8
|
Genetic Diversity of Merozoite Surface Protein-1 and -2 Genes in Plasmodium falciparum Isolates among Asymptomatic Population in Boset and Badewacho Districts, Southern Ethiopia. J Parasitol Res 2022; 2022:7728975. [PMID: 36569519 PMCID: PMC9771644 DOI: 10.1155/2022/7728975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/13/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022] Open
Abstract
Background The genetic variation of Plasmodium falciparum has been studied to assess local malaria transmission genetic profile using evidence-based intervention measures. However, there are no known previous reports of P. falciparum polymorphism in Badewacho and Boset districts, Southern Ethiopia. The purpose of this study was to determine the genetic diversity of the merozoite surface protein-1 and -2 (msp-1 and msp-2) allelic families in P. falciparum isolates from an asymptomatic populations. Methods This study was conducted from finger-prick blood samples spotted on 3 mm Whatman filter paper collected during a community-based cross-sectional study. Nested polymerase chain reaction amplification was used to type the allelic variants of msp-1 and msp-2. Results From 669 asymptomatic study participants, a total of 50 samples positive for P. falciparum were included for molecular analysis. Of 50 positive samples, 43 P. falciparum isolates were successfully amplified for the msp-1 and msp-2 allelic families. A total of twelve different allele sizes (75-250 bp) were identified within the three allelic families of msp-1, whereas ten different allele sizes (250-500 bp) were detected within the two allelic families of msp-2. MAD20 had a higher allelic proportion, 65% among allelic families of msp-1, whereas the 3D7 allelic family 90.7% was higher in msp-2. A slightly higher frequency of polyclonal infection 53.5% was found in msp-2 allelic family, whereas a low proportion polyclonal infection 46.5% was found in msp-1 allelic family. The overall mean multiplicity of infection (MOI) for msp-1 and msp-2 was identical (MOI = 1.56). Correspondingly, the expected heterozygosity (He) value for msp-1 (He = 0.23) and msp-2 (He = 0.22) was almost similar. Conclusions The findings of this study revealed low genetic diversity of the msp-1 and msp-2 allelic families in P. falciparum isolates. However, continued monitoring status of the local genetic diversity profile in the P. falciparum population is required to support current malaria control and elimination strategies.
Collapse
|
9
|
Prevention of Malaria in Pregnancy: What Do the Pregnant Women of Nigeria Know and Do about It? Infect Dis Obstet Gynecol 2022; 2022:7061548. [PMID: 36438171 PMCID: PMC9699741 DOI: 10.1155/2022/7061548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
Objective We assessed knowledge, attitude, and practice regarding two malaria prevention measures (long-lasting impregnated mosquito nets, LLINs, and intermittent preventative therapy with sulphadoxine-pyrimethamine (IPTp-SP)) among pregnant women in Nigeria. Methods Pregnant women selected from among the four communities of Nnewi were interviewed by using a semistructured, interviewer-administered questionnaire on the respondents' demography, knowledge of the cause, consequences, and malaria prevention methods. Also, a total of 48 focused group discussions, 24 key informant interviews, and 24 in-depth interviews were held among women leaders, village heads, pregnant women, community health workers, husbands of pregnant wives, and drug and insecticide-treated net sellers. Results A total of 384 women (88.0% third trimester, 90.0% literate, and 41.1% primigravidae) participated. About 80.0% suffered from malaria during their current pregnancy. The majority was aware of the cause of malaria, local name of malaria, mode of transmission, risk of malaria among pregnant women, etc. However, their knowledge and attitude were inadequate regarding the symptomatology and complications of malaria in pregnancy, benefits of sleeping under the net or taking chemoprophylactic doses, or the concurrent use of both. About 80.0% had LLINs, yet only 41.5% slept under it the previous night. Only 31.0% had IPTp-SP doses under direct observation. Only 35.9% had a good understanding of IPTp-SP during pregnancy. Conclusion Our work presents important practice gaps associated with the prevention of malaria during pregnancy. The pregnant women seemed to be aware of the basic concepts related to malaria but that does not translate into adequate attitude and practice necessary for malaria reduction.
Collapse
|
10
|
Mensah BA, Akyea-Bobi NE, Ghansah A. Genomic approaches for monitoring transmission dynamics of malaria: A case for malaria molecular surveillance in Sub-Saharan Africa. FRONTIERS IN EPIDEMIOLOGY 2022; 2:939291. [PMID: 38455324 PMCID: PMC10911004 DOI: 10.3389/fepid.2022.939291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/10/2022] [Indexed: 03/09/2024]
Abstract
Transmission dynamics is an important indicator for malaria control and elimination. As we move closer to eliminating malaria in Sub-Saharan Africa (sSA), transmission indices with higher resolution (genomic approaches) will complement our current measurements of transmission. Most of the present programmatic knowledge of malaria transmission patterns are derived from assessments of epidemiologic and clinical data, such as case counts, parasitological estimates of parasite prevalence, and Entomological Inoculation Rates (EIR). However, to eliminate malaria from endemic areas, we need to track changes in the parasite population and how they will impact transmission. This is made possible through the evolving field of genomics and genetics, as well as the development of tools for more in-depth studies on the diversity of parasites and the complexity of infections, among other topics. If malaria elimination is to be achieved globally, country-specific elimination activities should be supported by parasite genomic data from regularly collected blood samples for diagnosis, surveillance and possibly from other programmatic interventions. This presents a unique opportunity to track the spread of malaria parasites and shed additional light on intervention efficacy. In this review, various genetic techniques are highlighted along with their significance for an enhanced understanding of transmission patterns in distinct topological settings throughout Sub-Saharan Africa. The importance of these methods and their limitations in malaria surveillance to guide control and elimination strategies, are explored.
Collapse
Affiliation(s)
- Benedicta A. Mensah
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Nukunu E. Akyea-Bobi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| |
Collapse
|
11
|
Duah-Quashie NO, Opoku-Agyeman P, Bruku S, Adams T, Tandoh KZ, Ennuson NA, Matrevi SA, Abuaku B, Quashie NB, Watters C, Wolfe D, Quijada HM, Sanders T. Genetic deletions and high diversity of Plasmodium falciparum histidine-rich proteins 2 and 3 genes in parasite populations in Ghana. FRONTIERS IN EPIDEMIOLOGY 2022; 2:1011938. [PMID: 38455301 PMCID: PMC10911008 DOI: 10.3389/fepid.2022.1011938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/22/2022] [Indexed: 03/09/2024]
Abstract
Rapid diagnostic tests (RDTs) are used to diagnose malaria in Ghana and other malaria endemic countries. Plasmodium falciparum histidine-rich protein 2 (PFHRP2) based RDTs are widely used, however the occurrence of deletions of the pfhrp2 gene in some parasites have resulted in false negative test results. Monoclonal antibodies of PFHRP2 cross reacts with PFHRP3 because they share structural similarities and this complements the detection of the parasites by RDT. These two genes were investigated in Ghanaian P. falciparum parasite population to detect deletions and the polymorphisms in exon 2 of the pfhrp2 and pfhrp3 genes. Parasite isolates (2,540) from children ≤ 12 years with uncomplicated malaria from 2015 to 2020 transmission seasons were used. Both genes were amplified using nested PCR and negative results indicated the presence of the deletion of genes. Amplified genes were sequenced for the detection of the amino acid repeats. Deletions were observed in 30.7% (780/2,540) and 17.2% (438/2,540) of the samples for pfhrp2 and pfhrp3 respectively with increasing trends over the three time periods (χ2 -10.305, p = 0.001). A total of 1,632 amplicons were sequenced for each gene, analysis was done on 1,124 and 1,307 good quality sequences for pfhrp2 and pfhrp3 respectively. Pfhrp2 repeat polymorphisms were dominantly of types 2 (AHHAHHAAD) and 7 (AHHAAD) with large numbers of variants. A novel variant of type 14 (AHHANHATD) was seen for pfhrp2. For the pfhrp3 repeat types, 16 (AHHAAN), 17 (AHHDG) and 18 (AHHDD) were the dominant types observed. Variants of type 16 (AHHAAH) and (AHHASH) were also dominant. Repeat types 1, 2, 3, 4, 5, 6, 7, 8, 11, 13, 15, 16, and 19 were observed be shared by both genes. The haplotype diversity of both genes ranged between 0.872 and 1 indicating high diversity of the polymorphisms in the isolates. The implication of the findings of the frequencies of the pfhrp2 and pfhrp3 deletions as well as the variants of the main epitopes of the monoclonal antibodies for the RDT (types 2 and 7) in our isolates is an indication of decreased sensitivity of the RDTs in diagnosing malaria infections in Ghana.
Collapse
Affiliation(s)
- Nancy Odurowah Duah-Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Philip Opoku-Agyeman
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Selassie Bruku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Tryphena Adams
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Kwesi Zandoh Tandoh
- West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Nana Aba Ennuson
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Sena Adzoa Matrevi
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Benjamin Abuaku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Neils Ben Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Chaselynn Watters
- US Naval Medical Research Unit No. 3, Ghana Detachment, Accra, Ghana
| | - David Wolfe
- US Naval Medical Research Unit No. 3, Ghana Detachment, Accra, Ghana
| | | | - Terrel Sanders
- US Naval Medical Research Unit No. 3, Ghana Detachment, Accra, Ghana
| |
Collapse
|
12
|
Han KT, Han ZY, Zainabadi K. Developing Molecular Surveillance Capacity for Asymptomatic and Drug-Resistant Malaria in a Resource-Limited Setting-Experiences and Lessons Learned. Am J Trop Med Hyg 2022; 107:222-230. [PMID: 35895423 PMCID: PMC9393433 DOI: 10.4269/ajtmh.21-0543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/15/2021] [Indexed: 08/03/2023] Open
Abstract
The COVID-19 pandemic has highlighted the important role molecular surveillance plays in public health. Such capacity however is either weak or nonexistent in many low-income countries. This article outlines a 2-year effort to establish two high-throughput molecular surveillance laboratories in Myanmar for tracking asymptomatic and drug resistant Plasmodium falciparum malaria. The lessons learned from this endeavor may prove useful for others seeking to establish similar molecular surveillance capacity in other resource-limited settings.
Collapse
Affiliation(s)
- Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Zay Yar Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, New York
| |
Collapse
|
13
|
Lyimo BM, Popkin-Hall ZR, Giesbrecht DJ, Mandara CI, Madebe RA, Bakari C, Pereus D, Seth MD, Ngamba RM, Mbwambo RB, MacInnis B, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey J, Ishengoma DS. Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa. Front Cell Infect Microbiol 2022; 12:757844. [PMID: 35909968 PMCID: PMC9326448 DOI: 10.3389/fcimb.2022.757844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent.
Collapse
Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | - David J. Giesbrecht
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | | | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Ruth B. Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Bronwyn MacInnis
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute, Boston, MA, United States
| | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha Njau
- World Health Organization, Country Office, Dar es Salaam, Tanzania
| | - Jane A. Cunningham
- Global Malaria Programme, World Health Organization, Headquarters, Geneva, Switzerland
| | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jonathan J. Juliano
- School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey A. Bailey
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| |
Collapse
|
14
|
Kimenyi KM, Wamae K, Ngoi JM, de Laurent ZR, Ndwiga L, Osoti V, Obiero G, Abdi AI, Bejon P, Ochola-Oyier LI. Maintenance of high temporal Plasmodium falciparum genetic diversity and complexity of infection in asymptomatic and symptomatic infections in Kilifi, Kenya from 2007 to 2018. Malar J 2022; 21:192. [PMID: 35725456 PMCID: PMC9207840 DOI: 10.1186/s12936-022-04213-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/03/2022] [Indexed: 11/30/2022] Open
Abstract
Background High levels of genetic diversity are common characteristics of Plasmodium falciparum parasite populations in high malaria transmission regions. There has been a decline in malaria transmission intensity over 12 years of surveillance in the community in Kilifi, Kenya. This study sought to investigate whether there was a corresponding reduction in P. falciparum genetic diversity, using msp2 as a genetic marker. Methods Blood samples were obtained from children (< 15 years) enrolled into a cohort with active weekly surveillance between 2007 and 2018 in Kilifi, Kenya. Asymptomatic infections were defined during the annual cross-sectional blood survey and the first-febrile malaria episode was detected during the weekly follow-up. Parasite DNA was extracted and successfully genotyped using allele-specific nested polymerase chain reactions for msp2 and capillary electrophoresis fragment analysis. Results Based on cross-sectional surveys conducted in 2007–2018, there was a significant reduction in malaria prevalence (16.2–5.5%: P-value < 0.001), however msp2 genetic diversity remained high. A high heterozygosity index (He) (> 0.95) was observed in both asymptomatic infections and febrile malaria over time. About 281 (68.5%) asymptomatic infections were polyclonal (> 2 variants per infection) compared to 46 (56%) polyclonal first-febrile infections. There was significant difference in complexity of infection (COI) between asymptomatic 2.3 [95% confidence interval (CI) 2.2–2.5] and febrile infections 2.0 (95% CI 1.7–2.3) (P = 0.016). Majority of asymptomatic infections (44.2%) carried mixed alleles (i.e., both FC27 and IC/3D7), while FC27 alleles were more frequent (53.3%) among the first-febrile infections. Conclusions Plasmodium falciparum infections in Kilifi are still highly diverse and polyclonal, despite the reduction in malaria transmission in the community. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04213-7.
Collapse
Affiliation(s)
- Kelvin M Kimenyi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya. .,Department of Biochemistry, University of Nairobi, Nairobi, Kenya.
| | - Kevin Wamae
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce M Ngoi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,West Africa Centre for Cell Biology and Infectious Pathogen, Accra, Ghana
| | | | | | - Victor Osoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - George Obiero
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | | | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | |
Collapse
|
15
|
Dara A, Dogga SK, Rop J, Ouologuem D, Tandina F, Talman AM, Djimdé A, Lawniczak MKN. Tackling malaria transmission at a single cell level in an endemic setting in sub-Saharan Africa. Nat Commun 2022; 13:2679. [PMID: 35562353 PMCID: PMC9106669 DOI: 10.1038/s41467-022-30268-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Antoine Dara
- Malaria Research and Training Centre (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805, Bamako, Mali.
| | | | - Jesse Rop
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Dinkorma Ouologuem
- Malaria Research and Training Centre (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805, Bamako, Mali
| | - Fatalmoudou Tandina
- Malaria Research and Training Centre (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805, Bamako, Mali
| | - Arthur M Talman
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Abdoulaye Djimdé
- Malaria Research and Training Centre (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805, Bamako, Mali
| | | |
Collapse
|
16
|
Matrevi SA, Tandoh KZ, Bruku S, Opoku-Agyeman P, Adams T, Ennuson NA, Asare B, Hagan OCK, Abuaku B, Koram KA, Fox A, Quashie NB, Letizia AG, Duah-Quashie NO. Novel pfk13 polymorphisms in Plasmodium falciparum population in Ghana. Sci Rep 2022; 12:7797. [PMID: 35551239 PMCID: PMC9098865 DOI: 10.1038/s41598-022-11790-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/29/2022] [Indexed: 01/22/2023] Open
Abstract
The molecular determinants of Plasmodium falciparum artemisinin resistance are the single nucleotide polymorphisms in the parasite’s kelch propeller domain, pfk13. Validated and candidate markers are under surveillance in malaria endemic countries using artemisinin-based combination therapy. However, pfk13 mutations which may confer parasite artemisinin resistance in Africa remains elusive. It has therefore become imperative to report all observed pfk13 gene polymorphisms in malaria therapeutic efficacy studies for functional characterization. We herein report all novel pfk13 mutations observed only in the Ghanaian parasite population. In all, 977 archived samples from children aged 12 years and below with uncomplicated malaria from 2007 to 2017 were used. PCR/Sanger sequencing analysis revealed 78% (763/977) of the samples analyzed were wild type (WT) for pfk13 gene. Of the 214 (22%) mutants, 78 were novel mutations observed only in Ghana. The novel SNPs include R404G, P413H, N458D/H/I, C473W/S, R529I, M579T/Y, C580R/V, D584L, N585H/I, Q661G/L. Some of the mutations were sites and ecological zones specific. There was low nucleotide diversity and purifying selection at the pfk13 locus in Ghanaian parasite population. With increasing drug pressure and its consequent parasite resistance, documenting these mutations as baseline data is crucial for future molecular surveillance of P. falciparum resistance to artemisinin in Ghana.
Collapse
Affiliation(s)
- Sena Adzoa Matrevi
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Kwesi Zandoh Tandoh
- West Africa Centre for Cell Biology and Infectious Pathogens, Department of Biochemistry Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Selassie Bruku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Philip Opoku-Agyeman
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Tryphena Adams
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Nana Aba Ennuson
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Bright Asare
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Oheneba Charles Kofi Hagan
- West Africa Centre for Cell Biology and Infectious Pathogens, Department of Biochemistry Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Benjamin Abuaku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Kwadwo Ansah Koram
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Ann Fox
- United States Naval Medical Research Unit 3, Ghana Laboratory, Accra, Ghana
| | - Neils Ben Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.,Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Andrew G Letizia
- United States Naval Medical Research Unit 3, Ghana Laboratory, Accra, Ghana
| | - Nancy Odurowah Duah-Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.
| |
Collapse
|
17
|
Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
Collapse
Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| |
Collapse
|
18
|
Makunin A, Korlević P, Park N, Goodwin S, Waterhouse RM, von Wyschetzki K, Jacob CG, Davies R, Kwiatkowski D, St Laurent B, Ayala D, Lawniczak MKN. A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus. Mol Ecol Resour 2022; 22:28-44. [PMID: 34053186 PMCID: PMC7612955 DOI: 10.1111/1755-0998.13436] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 05/19/2021] [Indexed: 01/04/2023]
Abstract
Anopheles is a diverse genus of mosquitoes comprising over 500 described species, including all known human malaria vectors. While a limited number of key vector species have been studied in detail, the goal of malaria elimination calls for surveillance of all potential vector species. Here, we develop a multilocus amplicon sequencing approach that targets 62 highly variable loci in the Anopheles genome and two conserved loci in the Plasmodium mitochondrion, simultaneously revealing both the mosquito species and whether that mosquito carries malaria parasites. We also develop a cheap, nondestructive, and high-throughput DNA extraction workflow that provides template DNA from single mosquitoes for the multiplex PCR, which means specimens producing unexpected results can be returned to for morphological examination. Over 1000 individual mosquitoes can be sequenced in a single MiSeq run, and we demonstrate the panel's power to assign species identity using sequencing data for 40 species from Africa, Southeast Asia, and South America. We also show that the approach can be used to resolve geographic population structure within An. gambiae and An. coluzzii populations, as the population structure determined based on these 62 loci from over 1000 mosquitoes closely mirrors that revealed through whole genome sequencing. The end-to-end approach is quick, inexpensive, robust, and accurate, which makes it a promising technique for very large-scale mosquito genetic surveillance and vector control.
Collapse
Affiliation(s)
- Alex Makunin
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Petra Korlević
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Naomi Park
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | | | | | | | - Diego Ayala
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
- CIRMF, Franceville, Gabon
| | | |
Collapse
|
19
|
Le Clec'h W, Chevalier FD, Mattos ACA, Strickland A, Diaz R, McDew-White M, Rohr CM, Kinung'hi S, Allan F, Webster BL, Webster JP, Emery AM, Rollinson D, Djirmay AG, Al Mashikhi KM, Al Yafae S, Idris MA, Moné H, Mouahid G, LoVerde P, Marchant JS, Anderson TJC. Genetic analysis of praziquantel response in schistosome parasites implicates a transient receptor potential channel. Sci Transl Med 2021; 13:eabj9114. [PMID: 34936381 DOI: 10.1126/scitranslmed.abj9114] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Winka Le Clec'h
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | | | - Ana Carolina A Mattos
- University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | | | - Robbie Diaz
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | | | - Claudia M Rohr
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Safari Kinung'hi
- National Institute for Medical Research, Mwanza, United Republic of Tanzania
| | - Fiona Allan
- London Centre for Neglected Tropical Disease Research (LCNDTR), Imperial College, London, UK.,Wolfson Wellcome Biomedical Laboratories, Natural History Museum, London, UK
| | - Bonnie L Webster
- London Centre for Neglected Tropical Disease Research (LCNDTR), Imperial College, London, UK.,Wolfson Wellcome Biomedical Laboratories, Natural History Museum, London, UK
| | - Joanne P Webster
- London Centre for Neglected Tropical Disease Research (LCNDTR), Imperial College, London, UK.,Centre for Emerging, Endemic and Exotic Diseases (CEEED), Royal Veterinary College, University of London, London, UK
| | - Aidan M Emery
- London Centre for Neglected Tropical Disease Research (LCNDTR), Imperial College, London, UK.,Wolfson Wellcome Biomedical Laboratories, Natural History Museum, London, UK
| | - David Rollinson
- London Centre for Neglected Tropical Disease Research (LCNDTR), Imperial College, London, UK.,Wolfson Wellcome Biomedical Laboratories, Natural History Museum, London, UK
| | - Amadou Garba Djirmay
- Réseau International Schistosomiases Environnemental Aménagement et Lutte (RISEAL), Niamey, Niger.,World Health Organization, Geneva, Switzerland
| | - Khalid M Al Mashikhi
- Directorate General of Health Services, Dhofar Governorate, Salalah, Sultanate of Oman
| | - Salem Al Yafae
- Directorate General of Health Services, Dhofar Governorate, Salalah, Sultanate of Oman
| | | | - Hélène Moné
- Host-Pathogen-Environment Interactions Laboratory, University of Perpignan, Perpignan, France
| | - Gabriel Mouahid
- Host-Pathogen-Environment Interactions Laboratory, University of Perpignan, Perpignan, France
| | - Philip LoVerde
- University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jonathan S Marchant
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | |
Collapse
|
20
|
Aydemir O, Mensah B, Marsh PW, Abuaku B, Myers-Hansen JL, Bailey JA, Ghansah A. Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations. PeerJ 2021; 9:e11794. [PMID: 34820155 PMCID: PMC8588852 DOI: 10.7717/peerj.11794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/25/2021] [Indexed: 12/03/2022] Open
Abstract
Antimalarial resistance surveillance in sub-Saharan Africa is often constrained by logistical and financial challenges limiting its breadth and frequency. At two sites in Ghana, we have piloted a streamlined sample pooling process created immediately by sequential addition of positive malaria cases at the time of diagnostic testing. This streamlined process involving a single tube minimized clinical and laboratory work and provided accurate frequencies of all known drug resistance mutations after high-throughput targeted sequencing using molecular inversion probes. Our study validates this method as a cost-efficient, accurate and highly-scalable approach for drug resistance mutation monitoring that can potentially be applied to other infectious diseases such as tuberculosis.
Collapse
Affiliation(s)
- Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Brown University, Providence, RI, United States of America
| | - Benedicta Mensah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Patrick W Marsh
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Brown University, Providence, RI, United States of America
| | - Benjamin Abuaku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - James Leslie Myers-Hansen
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Brown University, Providence, RI, United States of America
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| |
Collapse
|
21
|
Xu C, Huang B, Wei Q, Li J, Kong X, Xiao T, Sun H, Zhao G, Yan G, Gong M, Yin K. High genetic diversity in Plasmodium falciparum isolates among Chinese migrant workers returnee from Africa. Parasitol Res 2021; 121:461-464. [PMID: 34750654 DOI: 10.1007/s00436-021-07368-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
Malaria is one of the most important parasitic diseases that causes a serious public health problem. The genetic diversity of malaria parasites may affect malaria transmission and malaria control strategies. In China, imported malaria was significantly increased in recent years, among which numerous migrant workers were infected with Plasmodium falciparum from Africa. However, little was known about genetic diversity of these populations in China. In this study, we evaluated genetic polymorphism and allele frequencies of msp1, msp2, and glurp genes in P. falciparum among Chinese migrant workers returnee from Africa between 2013 and 2017. Of the 381 P. falciparum isolates, 89.0% for msp1 gene, 71.7% for msp2 gene, and 78.0% for glurp gene were successfully genotyped. In msp1, 29 different alleles were observed, among which the K1 allelic family (71.7%) was predominant. In msp2, 21 different alleles were detected, of which the 3D7 allelic family (91.2%) was more frequent than FC27 allelic family (72.5%). For glurp, 12 individual alleles were detected in the samples. Taken together, the findings showed a high genetic diversity of these isolates, which provided the baseline data for African P. falciparum population imported to China.
Collapse
Affiliation(s)
- Chao Xu
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Bingcheng Huang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Qingkuan Wei
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Jin Li
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Xiangli Kong
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Ting Xiao
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Hui Sun
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Guihua Zhao
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Ge Yan
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China
| | - Maoqing Gong
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China.
| | - Kun Yin
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, China.
| |
Collapse
|
22
|
Comparative Analysis of Plasmodium falciparum Genotyping via SNP Detection, Microsatellite Profiling, and Whole-Genome Sequencing. Antimicrob Agents Chemother 2021; 66:e0116321. [PMID: 34694871 PMCID: PMC8765236 DOI: 10.1128/aac.01163-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Research efforts to combat antimalarial drug resistance rely on quick, robust, and sensitive methods to genetically characterize Plasmodium falciparum parasites. We developed a single-nucleotide polymorphism (SNP)-based genotyping method that can assess 33 drug resistance-conferring SNPs in dhfr, dhps, pfmdr1, pfcrt, and k13 in nine PCRs, performed directly from P. falciparum cultures or infected blood. We also optimized multiplexed fragment analysis and gel electrophoresis-based microsatellite typing methods using a set of five markers that can distinguish 12 laboratory strains of diverse geographical and temporal origin. We demonstrate how these methods can be applied to screen for the multidrug-resistant KEL1/PLA1/PfPailin (KelPP) lineage that has been sweeping across the Greater Mekong Subregion, verify parasite in vitro SNP-editing, identify novel recombinant genetic cross progeny, or cluster strains to infer their geographical origins. Results were compared with Illumina-based whole-genome sequence analysis that provides the most detailed sequence information but is cost-prohibitive. These adaptable, simple, and inexpensive methods can be easily implemented into routine genotyping of P. falciparum parasites in both laboratory and field settings.
Collapse
|
23
|
Alemayehu GS, Messele A, Blackburn K, Lopez K, Lo E, Janies D, Golassa L. Genetic variation of Plasmodium falciparum histidine-rich protein 2 and 3 in Assosa zone, Ethiopia: its impact on the performance of malaria rapid diagnostic tests. Malar J 2021; 20:394. [PMID: 34627242 PMCID: PMC8502267 DOI: 10.1186/s12936-021-03928-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/26/2021] [Indexed: 11/21/2022] Open
Abstract
Background Rapid diagnostic tests (RDT) are commonly used for the diagnosis of malaria caused by Plasmodium falciparum. However, false negative results of RDT caused by genetic variation of P. falciparum histidine-rich protein 2 and 3 genes (pfhrp2/3) threaten existing malaria case management and control efforts. The main objective of this study was to investigate the genetic variations of the pfhrp2/3 genes. Methods A cross-sectional study was conducted from malaria symptomatic individuals in 2018 in Assosa zone, Ethiopia. Finger-prick blood samples were collected for RDT and microscopic examination of thick and thin blood films. Dried blood spots (DBS) were used for genomic parasite DNA extraction and molecular detection. Amplification of parasite DNA was made by quantitative PCR. DNA amplicons of pfhrp2/3 were purified and sequenced. Results The PfHRP2 amino acid repeat type isolates were less conserved compared to the PfHRP3 repeat type. Eleven and eight previously characterized PfHRP2 and PfHRP3 amino acid repeat types were identified, respectively. Type 1, 4 and 7 repeats were shared by PfHRP2 and PfHRP3 proteins. Type 2 repeats were found only in PfHRP2, while types 16 and 17 were found only in PfHRP3 with a high frequency in all isolates. 18 novel repeat types were found in PfHRP2 and 13 novel repeat types were found in PfHRP3 in single or multiple copies per isolate. The positivity rate for PfHRP2 RDT was high, 82.9% in PfHRP2 and 84.3% in PfHRP3 sequence isolates at parasitaemia levels > 250 parasites/µl. Using the Baker model, 100% of the isolates in group A (If product of types 2 × type 7 repeats ≥ 100) and 73.7% of the isolates in group B (If product of types 2 × type 7 repeats 50–99) were predicted to be detected by PfHRP2 RDT at parasitaemia level > 250 parasite/μl. Conclusion The findings of this study indicate the presence of different PfHRP2 and PfHRP3 amino acid repeat including novel repeats in P. falciparum from Ethiopia. These results indicate that there is a need to closely monitor the performance of PfHRP2 RDT associated with the genetic variation of the pfhrp2 and pfhrp3 gene in P. falciparum isolates at the country-wide level. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03928-3.
Collapse
Affiliation(s)
| | - Alebachew Messele
- Addis Ababa University, Aklilu Lemma Institute of Pathobiology, Addis Ababa, Ethiopia
| | - Kayla Blackburn
- Departments of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Karen Lopez
- Departments of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.,School of Data Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Daniel Janies
- Departments of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Lemu Golassa
- Addis Ababa University, Aklilu Lemma Institute of Pathobiology, Addis Ababa, Ethiopia
| |
Collapse
|
24
|
Identification of first-in-class plasmodium OTU inhibitors with potent anti-malarial activity. Biochem J 2021; 478:3445-3466. [PMID: 34486667 DOI: 10.1042/bcj20210481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 11/17/2022]
Abstract
OTU proteases antagonize the cellular defense in the host cells and involve in pathogenesis. Intriguingly, P. falciparum, P. vivax, and P. yoelii have an uncharacterized and highly conserved viral OTU-like proteins. However, their structure, function or inhibitors have not been previously reported. To this end, we have performed structural modeling, small molecule screening, deconjugation assays to characterize and develop first-in-class inhibitors of P. falciparum, P. vivax, and P. yoelii OTU-like proteins. These Plasmodium OTU-like proteins have highly conserved residues in the catalytic and inhibition pockets similar to viral OTU proteins. Plasmodium OTU proteins demonstrated Ubiquitin and ISG15 deconjugation activities as evident by intracellular ubiquitinated protein content analyzed by western blot and flow cytometry. We screened a library of small molecules to determine plasmodium OTU inhibitors with potent anti-malarial activity. Enrichment and correlation studies identified structurally similar molecules. We have identified two small molecules that inhibit P. falciparum, P. vivax, and P. yoelii OTU proteins (IC50 values as low as 30 nM) with potent anti-malarial activity (IC50 of 4.1-6.5 µM). We also established enzyme kinetics, druglikeness, ADME, and QSAR model. MD simulations allowed us to resolve how inhibitors interacted with plasmodium OTU proteins. These findings suggest that targeting malarial OTU-like proteases is a plausible strategy to develop new anti-malarial therapies.
Collapse
|
25
|
He X, Zhong D, Zou C, Pi L, Zhao L, Qin Y, Pan M, Wang S, Zeng W, Xiang Z, Chen X, Wu Y, Si Y, Cui L, Huang Y, Yan G, Yang Z. Unraveling the Complexity of Imported Malaria Infections by Amplicon Deep Sequencing. Front Cell Infect Microbiol 2021; 11:725859. [PMID: 34595134 PMCID: PMC8477663 DOI: 10.3389/fcimb.2021.725859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/16/2021] [Indexed: 11/22/2022] Open
Abstract
Imported malaria and recurrent infections are becoming an emerging issue in many malaria non-endemic countries. This study aimed to determine the molecular patterns of the imported malaria infections and recurrence. Blood samples were collected from patients with imported malaria infections during 2016-2018 in Guangxi Zhuang Autonomous Region, China. Next-generation amplicon deep-sequencing approaches were used to assess parasite genetic diversity, multiplexity of infection, relapse, recrudescence, and antimalarial drug resistance. A total of 44 imported malaria cases were examined during the study, of which 35 (79.5%) had recurrent malaria infections within 1 year. The majority (91.4%) had one recurrent malaria episode, whereas two patients had two recurrences and one patient had three recurrences. A total of 19 recurrence patterns (the species responsible for primary and successive clinical episodes) were found in patients returning from malaria epidemic countries. Four parasite species were detected with a higher than usual proportion (46.2%) of non-falciparum infections or mixed-species infections. An increasing trend of recurrence infections and reduced drug treatment efficacy were observed among the cases of imported malaria. The high recurrence rate and complex patterns of imported malaria from Africa to non-endemic countries have the potential to initiate local transmission, thereby undermining efforts to eliminate locally acquired malaria. Our findings highlight the power of amplicon deep-sequencing applications in molecular epidemiological studies of the imported malaria recurrences.
Collapse
Affiliation(s)
- Xi He
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, United States
| | - Chunyan Zou
- Department of Electrocardiogram, Guangxi Zhuang Autonomous Region People’s Hospital, Nanning, China
| | - Liang Pi
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Luyi Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yucheng Qin
- Department of Infectious Diseases, Shanglin County People’s Hospital, Shanglin, China
| | - Maohua Pan
- Department of Infectious Diseases, Shanglin County People’s Hospital, Shanglin, China
| | - Siqi Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Weiling Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Zheng Xiang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yanrui Wu
- Department of Cell Biology & Genetics, Kunming Medical University, Kunming, China
| | - Yu Si
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Yaming Huang
- Department of Protozoa, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, United States
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| |
Collapse
|
26
|
Diagnosing the drug resistance signature in Plasmodium falciparum: a review from contemporary methods to novel approaches. J Parasit Dis 2021; 45:869-876. [PMID: 34475670 DOI: 10.1007/s12639-020-01333-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022] Open
Abstract
The genome sequence project of the human malaria parasite Plasmodium falciparum reveal variations in the parasite DNA sequence. Most of these variations are single nucleotide polymorphism (SNP). A high frequency of single nucleotide polymorphism (SNP) in the Plasmodium falciparum population is usually a benchmark for anti-malarial resistance which allows parasites to be elusive to the chemotherapeutic agents, vaccine and vector control strategies, resulting in the leading cause of morbidity and mortality globally. The high density of drug resistance signature markers such as pfcrt,pfmdr1, pfdhps, pfdhfr, pfkelch13, pfatpase6 and pfmrp1 in the genome opens up a scope for the study of the genetic basis of this elusive parasite. The precise and prompt diagnosis of resistance strains of parasite plays vital role in malaria elimination program.This review probably shed light on contemporary SNP diagnostic tools used in molecular surveillance of Plasmodium falciparum drug resistance in terms of mechanism, reaction modalities, and development with their virtues and shortcomings.
Collapse
|
27
|
Rasmussen C, Alonso P, Ringwald P. Current and emerging strategies to combat antimalarial resistance. Expert Rev Anti Infect Ther 2021; 20:353-372. [PMID: 34348573 DOI: 10.1080/14787210.2021.1962291] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Since the spread of chloroquine resistance in Plasmodium falciparum in the 1960s, recommendations have been made on how to respond to antimalarial resistance. Only with the advent of artemisinin partial resistance were large scale efforts made in the Greater Mekong Subregion to carry out recommendations in a coordinated and well-funded manner. Independent emergence of parasites partially resistant to artemisinins has now been reported in Rwanda. AREAS COVERED We reviewed past recommendations and activities to respond to resistance as well as the research ongoing into new ways to stop or delay the spread of resistant parasites. EXPERT OPINION Inadequate information limits the options and support for a strong, coordinated response to artemisinin partial resistance in Africa, making better phenotypic and genotypic surveillance a priority. A response to resistance needs to address factors that may have hastened the emergence and could speed the spread, including overuse of drugs and lack of access to quality treatment. New ways to use the existing treatments in the response to resistance such as multiple first-lines are currently impeded by the limited number of drugs available.
Collapse
Affiliation(s)
| | - Pedro Alonso
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Pascal Ringwald
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| |
Collapse
|
28
|
Abstract
Almost 20 years have passed since the first reference genome assemblies were published for Plasmodium falciparum, the deadliest malaria parasite, and Anopheles gambiae, the most important mosquito vector of malaria in sub-Saharan Africa. Reference genomes now exist for all human malaria parasites and nearly half of the ~40 important vectors around the world. As a foundation for genetic diversity studies, these reference genomes have helped advance our understanding of basic disease biology and drug and insecticide resistance, and have informed vaccine development efforts. Population genomic data are increasingly being used to guide our understanding of malaria epidemiology, for example by assessing connectivity between populations and the efficacy of parasite and vector interventions. The potential value of these applications to malaria control strategies, together with the increasing diversity of genomic data types and contexts in which data are being generated, raise both opportunities and challenges in the field. This Review discusses advances in malaria genomics and explores how population genomic data could be harnessed to further support global disease control efforts.
Collapse
Affiliation(s)
- Daniel E Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
| | - Aimee R Taylor
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
| |
Collapse
|
29
|
Ehrlich HY, Bei AK, Weinberger DM, Warren JL, Parikh S. Mapping partner drug resistance to guide antimalarial combination therapy policies in sub-Saharan Africa. Proc Natl Acad Sci U S A 2021; 118:e2100685118. [PMID: 34261791 PMCID: PMC8307356 DOI: 10.1073/pnas.2100685118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Resistance to artemisinin-based combination therapies (ACTs) threatens the global control of Plasmodium falciparum malaria. ACTs combine artemisinin-derived compounds with partner drugs to enable multiple mechanisms of clearance. Although ACTs remain widely effective in sub-Saharan Africa, long-standing circulation of parasite alleles associated with reduced partner drug susceptibility may contribute to the development of clinical resistance. We fitted a hierarchical Bayesian spatial model to data from over 500 molecular surveys to predict the prevalence and frequency of four key markers in transporter genes (pfcrt 76T and pfmdr1 86Y, 184F, and 1246Y) in first-level administrative divisions in sub-Saharan Africa from the uptake of ACTs (2004 to 2009) to their widespread usage (2010 to 2018). Our models estimated that the pfcrt 76T mutation decreased in prevalence in 90% of regions; the pfmdr1 N86 and D1246 wild-type genotypes increased in prevalence in 96% and 82% of regions, respectively; and there was no significant directional selection at the pfmdr1 Y184F locus. Rainfall seasonality was the strongest predictor of the prevalence of wild-type genotypes, with other covariates, including first-line drug policy and transmission intensity more weakly associated. We lastly identified regions of high priority for enhanced surveillance that could signify decreased susceptibility to the local first-line ACT. Our results can be used to infer the degree of molecular resistance and magnitude of wild-type reversion in regions without survey data to inform therapeutic policy decisions.
Collapse
Affiliation(s)
- Hanna Y Ehrlich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT 06510;
| | - Amy K Bei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT 06510
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT 06510
- Public Health Modeling Unit, Yale School of Public Health, Yale University, New Haven, CT 06510
| | - Joshua L Warren
- Public Health Modeling Unit, Yale School of Public Health, Yale University, New Haven, CT 06510
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT 06510
| | - Sunil Parikh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT 06510
| |
Collapse
|
30
|
Evaluation of the Antimalarial Activity of the Leaf Latex of Aloe weloensis (Aloaceae) against Plasmodium Parasites. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:6664711. [PMID: 34221087 PMCID: PMC8221875 DOI: 10.1155/2021/6664711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 04/18/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022]
Abstract
Background The lack of available vaccines and the emerging resistance to antimalarial drugs have provided the necessity to find noble antimalarial plant-based medicines. The leaf latex Aloe weloensis has been used in folk medicine against malarial and other human ailments in Ethiopia. Hence, the present study aimed to investigate the antimalarial activity of the leaf latex of A. weloensis against Plasmodium parasites. Materials and Methods The prophylactic and curative models were employed to determine the in vivo antimalarial activity of the leaf latex A. weloensis against P. berghei infected mice, and the antioxidant activity of the latex was assessed using diphenyl-1-picrylhydrazine (DPPH) assay. Female mice were recruited for toxicity study, and the leaf latex was administered to fasted mice at a dose of 5000 mg/kg. The mice were kept under continuous observation for fourteen days for any signs of overt toxicity. Results The leaf latex of A. weloensis was safe up to 5000 mg/kg, and the latex endowed free radical inhibition activity (IC50 = 10.25 μg/ml). The latex of A. weloensis leaf demonstrated the inhibitory activity against the 3D7 strain of P. falciparum (IC50 = 9.14 μg/ml). The prophylactic and curative effect of the latex was found to be dose-dependent. The mice's parasitemia level was significantly (p < 0.001) reduced at all tested doses of the leaf latex compared to negative control in the curative test. Parasitemia reduction was significant (200 mg/kg, p < 0.01, and 400 and 600 mg/kg, p < 0.001) in the prophylactic test compared to the control. In addition, the leaf latex significantly (p < 0.01) improved mean survival time, packed cell volume, rectal temperature, and bodyweight of P. berghei infected mice. Conclusion The leaf latex of Aloe weloensis was endowed with the antimalarial activity at various doses, corroborating the plant's claimed traditional use.
Collapse
|
31
|
Grinev A, Fokina N, Bogomolov D, Berechikidze I, Lazareva Y. Prediction of gene expression regulation by human microRNAs in Plasmodium falciparum. Genes Environ 2021; 43:22. [PMID: 34130734 PMCID: PMC8204574 DOI: 10.1186/s41021-021-00198-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/03/2021] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Malaria is a disease annually causing over 400,000 deaths. Deep understanding of molecular and genetic processes underlying its life cycle and pathogenicity is required to efficiently resist it. RNA interference is a mechanism of the gene expression regulation typical for a wide variety of species. Even though the existence of this phenomenon in Plasmodium falciparum has long been rejected, several recent works pose hypotheses and provide direct and indirect evidence of the existence of mechanisms similar to RNA interference in this organism. In particular, the possibility of regulation of P. falciparum gene expression through human microRNAs is of great importance both for fundamental biology and for medicine. In the present work we address the problem of possibility of the existence in the P. falciparum genome of the nucleotide sequences such that mRNAs transcribed from genes containing these sequences could form duplexes with human microRNAs. Using bioinformatics methods we have analysed genomes of 15 P. falciparum isolates for sequences homological to these microRNAs. RESULTS The analysis has demonstrated the existence of a vast number of genes that could potentially be regulated by the human microRNAs in the plasmodial genome. CONCLUSIONS Despite the fact that the numbers of homological intervals vary significantly between isolates, the hsa-miR-451a and hsa-miR-223-3p microRNAs are expected to make the most notable contribution to the pathogenesis of P. falciparum malaria. The majority of homological intervals occur in genes encoding cell adhesion proteins.
Collapse
Affiliation(s)
- Alexandr Grinev
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.
| | - Natalya Fokina
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Denis Bogomolov
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Iza Berechikidze
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Yuliya Lazareva
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| |
Collapse
|
32
|
Alemayehu GS, Blackburn K, Lopez K, Cambel Dieng C, Lo E, Janies D, Golassa L. Detection of high prevalence of Plasmodium falciparum histidine-rich protein 2/3 gene deletions in Assosa zone, Ethiopia: implication for malaria diagnosis. Malar J 2021; 20:109. [PMID: 33622309 PMCID: PMC8095343 DOI: 10.1186/s12936-021-03629-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 02/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Rapid diagnostic tests (RDTs) targeting histidine rich protein 2(HRP2) are widely used for diagnosis of Plasmodium falciparum infections. Besides PfHRP2, the PfHRP3 antigen contributes to the detection of P. falciparum infections in PfHRP2 RDTs. However, the performance HRP2-based RDT is affected by pfhrp2/3 gene deletions resulting in false-negative test results. The objective of this study was to determine the presence and prevalence of pfhrp2/3 gene deletions including the respective flanking regions among symptomatic patients in Assosa zone, Northwest Ethiopia. Methods A health-facility based cross-sectional study was conducted in febrile patients seeking a malaria diagnosis in 2018. Blood samples were collected by finger-prick for microscopic examination of blood smears, malaria RDT, and molecular analysis using dried blood spots (DBS) prepared on Whatman filter paper. A total of 218 P. falciparum positive samples confirmed by quantitative PCR were included for molecular assay of pfhrp2/3 target gene. Results Of 218 P. falciparum positive samples, exon 2 deletions were observed in 17.9% of pfhrp2 gene and in 9.2% of pfhrp3 gene. A high proportion of deletions in short segments of pfhrp2 exon1-2 (50%) was also detected while the deletions of the pfhrp3 exon1-2 gene were 4.1%. The deletions were extended to the downstream and upstream of the flanking regions in pfhrp2/3 gene (above 30%). Of eighty-six PfHRP2 RDT negative samples, thirty-six lacked pfhrp2 exon 2. Five PfHRP2 RDT negative samples had double deletions in pfhrp2 exon 2 and pfhrp3 exon2. Of these double deletions, only two of the samples with a parasite density above 2000 parasite/µl were positive by the microscopy. Three samples with intact pfhrp3 exon2 in the pfhrp2 exon2 deleted parasite isolates were found to be positive by PfHRP2 RDT and microscopy with a parasite density above 10,000/µl. Conclusion This study confirms the presence of deletions of pfhrp2/3 gene including the flanking regions. Pfhrp2/3 gene deletions results in false-negative results undoubtedly affect the current malaria control and elimination effort in the country. However, further countrywide investigations are required to determine the magnitude of pfhrp2/3 gene deletions and its consequences on routine malaria diagnosis.
Collapse
Affiliation(s)
| | - Kayla Blackburn
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Karen Lopez
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Cheikh Cambel Dieng
- Department of Biological Sciences, Charlotte, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Eugenia Lo
- Department of Biological Sciences, Charlotte, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Lemu Golassa
- Addis Ababa University, Aklilu Lemma Institute of Pathobiology, Addis Ababa, Ethiopia
| |
Collapse
|
33
|
Varo R, Balanza N, Mayor A, Bassat Q. Diagnosis of clinical malaria in endemic settings. Expert Rev Anti Infect Ther 2020; 19:79-92. [PMID: 32772759 DOI: 10.1080/14787210.2020.1807940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Malaria continues to be a major global health problem, with over 228 million cases and 405,000 deaths estimated to occur annually. Rapid and accurate diagnosis of malaria is essential to decrease the burden and impact of this disease, particularly in children. We aimed to review the main available techniques for the diagnosis of clinical malaria in endemic settings and explore possible future options to improve its rapid recognition. AREAS COVERED literature relevant to malaria diagnosis was identified through electronic searches in Pubmed, with no language or date restrictions and limited to humans. EXPERT OPINION Light microscopy is still considered the gold standard method for malaria diagnosis and continues to be at the frontline of malaria diagnosis. However, technologies as rapid diagnostic tests, mainly those who detect histidine-rich protein-2, offer an accurate, rapid and affordable alternative for malaria diagnosis in endemic areas. They are now the technique most extended in endemic areas for parasitological confirmation. In these settings, PCR-based assays are usually restricted to research and they are not currently helpful in the management of clinical malaria. Other technologies, such as isothermal methods could be an interesting and alternative approach to PCR in the future.
Collapse
Affiliation(s)
- Rosauro Varo
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain.,Centro De Investigação Em Saúde De Manhiça (CISM) , Maputo, Mozambique
| | - Núria Balanza
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain
| | - Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain.,Centro De Investigação Em Saúde De Manhiça (CISM) , Maputo, Mozambique
| | - Quique Bassat
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain.,Centro De Investigação Em Saúde De Manhiça (CISM) , Maputo, Mozambique.,ICREA, Pg. Lluís Companys 23 , Barcelona, Spain.,Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan De Deu (University of Barcelona) , Barcelona, Spain.,Consorcio De Investigación Biomédica En Red De Epidemiología Y Salud Publica (CIBERESP) , Madrid, Spain
| |
Collapse
|
34
|
Tessema SK, Hathaway NJ, Teyssier NB, Murphy M, Chen A, Aydemir O, Duarte EM, Simone W, Colborn J, Saute F, Crawford E, Aide P, Bailey JA, Greenhouse B. Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome. J Infect Dis 2020; 225:1227-1237. [PMID: 32840625 PMCID: PMC8974853 DOI: 10.1093/infdis/jiaa527] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/24/2020] [Indexed: 01/28/2023] Open
Abstract
Background Targeted next-generation sequencing offers the potential for consistent, deep coverage of information-rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited. Methods A bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, whole-genome sequencing data were generated for the same controls. Results Using publicly available genomes, 4465 high-diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median expected heterozygosity = 0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%), and sensitivity (90% for haplotypes with 5% within sample frequency in dried blood spots with 100 parasites/µL). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic single-nucleotide polymorphism barcodes. Conclusions The bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high-throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.
Collapse
Affiliation(s)
- Sofonias K Tessema
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Nicholas J Hathaway
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Noam B Teyssier
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Maxwell Murphy
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Anna Chen
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Elias M Duarte
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Wilson Simone
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - James Colborn
- Clinton Health Access Initiative, Maputo, Mozambique
| | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Bryan Greenhouse
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, California, United States
| |
Collapse
|
35
|
Guirou EA, Schindler T, Hosch S, Donfack OT, Yoboue CA, Krähenbühl S, Deal A, Cosi G, Gondwe L, Mwangoka G, Masuki H, Salim N, Mpina M, Said J, Abdulla S, Hoffman SL, Nlavo BM, Maas C, Falla CC, Phiri WP, Garcia GA, Tanner M, Daubenberger C. Molecular malaria surveillance using a novel protocol for extraction and analysis of nucleic acids retained on used rapid diagnostic tests. Sci Rep 2020; 10:12305. [PMID: 32703999 PMCID: PMC7378824 DOI: 10.1038/s41598-020-69268-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
The use of malaria rapid diagnostic tests (RDTs) as a source for nucleic acids that can be analyzed via nucleic acid amplification techniques has several advantages, including minimal amounts of blood, sample collection, simplified storage and shipping conditions at room temperature. We have systematically developed and extensively evaluated a procedure to extract total nucleic acids from used malaria RDTs. The co-extraction of DNA and RNA molecules from small volumes of dried blood retained on the RDTs allows detection and quantification of P. falciparum parasites from asymptomatic patients with parasite densities as low as 1 Pf/µL blood using reverse transcription quantitative PCR. Based on the extraction protocol we have developed the ENAR (Extraction of Nucleic Acids from RDTs) approach; a complete workflow for large-scale molecular malaria surveillance. Using RDTs collected during a malaria indicator survey we demonstrated that ENAR provides a powerful tool to analyze nucleic acids from thousands of RDTs in a standardized and high-throughput manner. We found several, known and new, non-synonymous single nucleotide polymorphisms in the propeller region of the kelch 13 gene among isolates circulating on Bioko Island, Equatorial Guinea.
Collapse
Affiliation(s)
- Etienne A Guirou
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Tobias Schindler
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Salome Hosch
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Charlene Aya Yoboue
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Silvan Krähenbühl
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Anna Deal
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Glenda Cosi
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Linda Gondwe
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | - Grace Mwangoka
- Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | - Heavenlight Masuki
- Department of Paediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Nahya Salim
- Department of Paediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Maxmillian Mpina
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | - Jongo Said
- Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | - Salim Abdulla
- Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | | | | | - Carl Maas
- Marathon EG Production Ltd, Malabo, Equatorial Guinea
| | | | - Wonder P Phiri
- Medical Care Development International, Malabo, Equatorial Guinea
| | | | - Marcel Tanner
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| |
Collapse
|
36
|
Siddiqui AJ, Adnan M, Jahan S, Redman W, Saeed M, Patel M. Neurological disorder and psychosocial aspects of cerebral malaria: what is new on its pathogenesis and complications? A minireview. Folia Parasitol (Praha) 2020; 67. [PMID: 32636351 DOI: 10.14411/fp.2020.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/06/2020] [Indexed: 01/21/2023]
Abstract
Recently, malaria is remain considered as the most prevalent infectious disease, affecting the human health globally. High morbidity and mortality worldwide is often allied with cerebral malaria (CM) based disorders of the central nervous system, especially across many tropical and sub-tropical regions. These disorders are characterised by the infection of Plasmodium species, which leads to acute or chronic neurological disorders, even after having active/effective antimalarial drugs. Furthermore, even during the treatment, individual remain sensitive for neurological impairments in the form of decrease blood flow and vascular obstruction in brain including many more other changes. This review briefly explains and update on the epidemiology, burden of disease, pathogenesis and role of CM in neurological disorders with behaviour and function in mouse and human models. Moreover, the social stigma, which plays an important role in neurological disorders and a factor for assessing CM, is also discussed in this review.
Collapse
Affiliation(s)
| | | | - Sadaf Jahan
- Department of Medical Laboratory, College of Applied Medical Sciences, Majmaah University, Majmaah city, Saudi Arabia
| | - Whitni Redman
- Surgery Department, Division of Biomedical Research, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Mοhd Saeed
- Department of Biology, College of Science, University of Hail, Hail, PO Box 2440, Saudi Arabia
| | - Mitesh Patel
- Bapalal Vaidya Botanical Research Centre, Department of Biosciences, Veer Narmad South Gujarat University, Surat, Gujarat, India
| |
Collapse
|
37
|
Touray AO, Mobegi VA, Wamunyokoli F, Herren JK. Diversity and Multiplicity of P. falciparum infections among asymptomatic school children in Mbita, Western Kenya. Sci Rep 2020; 10:5924. [PMID: 32246127 PMCID: PMC7125209 DOI: 10.1038/s41598-020-62819-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/18/2020] [Indexed: 11/25/2022] Open
Abstract
Multiplicity of infection (MOI) and genetic diversity of P. falciparum infections are important surrogate indicators for assessing malaria transmission intensity in different regions of endemicity. Determination of MOI and diversity of P. falciparum among asymptomatic carriers will enhance our understanding of parasite biology and transmission to mosquito vectors. This study examined the MOI and genetic diversity of P. falciparum parasite populations circulating in Mbita, a region characterized as one of the malaria hotspots in Kenya. The genetic diversity and multiplicity of P. falciparum infections in 95 asymptomatic school children (age 5–15 yrs.) residing in Mbita, western Kenya were assessed using 10 polymorphic microsatellite markers. An average of 79.69% (Range: 54.84–95.74%) of the isolates analysed in this study were polyclonal infections as detected in at least one locus. A high mean MOI of 3.39 (Range: 2.24–4.72) and expected heterozygosity (He) of 0.81 (Range: 0.57–0.95) was reported in the study population. The analysed samples were extensively polyclonal infections leading to circulation of highly genetically diverse parasite populations in the study area. These findings correlated with the expectations of high malaria transmission intensity despite scaling up malaria interventions in the area thereby indicating the need for a robust malaria interventions particularly against asymptomatic carriers in order to attain elimination in the region.
Collapse
Affiliation(s)
- Abdoulie O Touray
- Department of Molecular Biology and Biotechnology, Institute of Basic Sciences, Technology and Innovation, Pan African University (PAUSTI), Nairobi, Kenya. .,International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya.
| | - Victor A Mobegi
- Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya.
| | - Fred Wamunyokoli
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Jeremy K Herren
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| |
Collapse
|
38
|
Nsanzabana C. Strengthening Surveillance Systems for Malaria Elimination by Integrating Molecular and Genomic Data. Trop Med Infect Dis 2019; 4:E139. [PMID: 31816974 PMCID: PMC6958499 DOI: 10.3390/tropicalmed4040139] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/05/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022] Open
Abstract
Unprecedented efforts in malaria control over the last 15 years have led to a substantial decrease in both morbidity and mortality in most endemic settings. However, these progresses have stalled over recent years, and resurgence may cause dramatic impact on both morbidity and mortality. Nevertheless, elimination efforts are currently going on with the objective of reducing malaria morbidity and mortality by 90% and malaria elimination in at least 35 countries by 2030. Strengthening surveillance systems is of paramount importance to reach those targets, and the integration of molecular and genomic techniques into routine surveillance could substantially improve the quality and robustness of data. Techniques such as polymerase chain reaction (PCR) and quantitative PCR (qPCR) are increasingly available in malaria endemic countries, whereas others such as sequencing are already available in a few laboratories. However, sequencing, especially next-generation sequencing (NGS), requires sophisticated infrastructure with adequate computing power and highly trained personnel for data analysis that require substantial investment. Different techniques will be required for different applications, and cost-effective planning must ensure the appropriate use of available resources. The development of national and sub-regional reference laboratories could help in minimizing the resources required in terms of equipment and trained staff. Concerted efforts from different stakeholders at national, sub-regional, and global level are needed to develop the required framework to establish and maintain these reference laboratories.
Collapse
Affiliation(s)
- Christian Nsanzabana
- Department of Medicine, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; ; Tel.: +41-61-284-82-52
- University of Basel, P.O. Box, CH-4003 Basel, Switzerland
| |
Collapse
|