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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. Commun Med (Lond) 2024; 4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. METHODS We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241 P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. RESULTS We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. CONCLUSIONS Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Mulenga C Mwenda
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA.
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Ishengoma DS, Mandara CI, Madebe RA, Warsame M, Ngasala B, Kabanywanyi AM, Mahende MK, Kamugisha E, Kavishe RA, Muro F, Mandike R, Mkude S, Chacky F, Njau R, Martin T, Mohamed A, Bailey JA, Fola AA. Microsatellites reveal high polymorphism and high potential for use in anti-malarial efficacy studies in areas with different transmission intensities in mainland Tanzania. Malar J 2024; 23:79. [PMID: 38491359 PMCID: PMC10943981 DOI: 10.1186/s12936-024-04901-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Tanzania is currently implementing therapeutic efficacy studies (TES) in areas of varying malaria transmission intensities as per the World Health Organization (WHO) recommendations. In TES, distinguishing reinfection from recrudescence is critical for the determination of anti-malarial efficacy. Recently, the WHO recommended genotyping polymorphic coding genes, merozoite surface proteins 1 and 2 (msp1 and msp2), and replacing the glutamate-rich protein (glurp) gene with one of the highly polymorphic microsatellites in Plasmodium falciparum to adjust the efficacy of antimalarials in TES. This study assessed the polymorphisms of six neutral microsatellite markers and their potential use in TES, which is routinely performed in Tanzania. METHODS Plasmodium falciparum samples were obtained from four TES sentinel sites, Kibaha (Pwani), Mkuzi (Tanga), Mlimba (Morogoro) and Ujiji (Kigoma), between April and September 2016. Parasite genomic DNA was extracted from dried blood spots on filter papers using commercial kits. Genotyping was done using six microsatellites (Poly-α, PfPK2, TA1, C3M69, C2M34 and M2490) by capillary method, and the data were analysed to determine the extent of their polymorphisms and genetic diversity at the four sites. RESULTS Overall, 83 (88.3%) of the 94 samples were successfully genotyped (with positive results for ≥ 50.0% of the markers), and > 50.0% of the samples (range = 47.6-59.1%) were polyclonal, with a mean multiplicity of infection (MOI) ranging from 1.68 to 1.88 among the four sites. There was high genetic diversity but limited variability among the four sites based on mean allelic richness (RS = 7.48, range = 7.27-8.03, for an adjusted minimum sample size of 18 per site) and mean expected heterozygosity (He = 0.83, range = 0.80-0.85). Cluster analysis of haplotypes using STRUCTURE, principal component analysis, and pairwise genetic differentiation (FST) did not reveal population structure or clustering of parasites according to geographic origin. Of the six markers, Poly-α was the most polymorphic, followed by C2M34, TA1 and C3M69, while M2490 was the least polymorphic. CONCLUSION Microsatellite genotyping revealed high polyclonality and genetic diversity but no significant population structure. Poly-α, C2M34, TA1 and C3M69 were the most polymorphic markers, and Poly-α alone or with any of the other three markers could be adopted for use in TES in Tanzania.
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Affiliation(s)
- Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania.
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia.
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Billy Ngasala
- Department of Parasitology, School of Public Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | | | | | - Erasmus Kamugisha
- Bugando Medical Centre, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Reginald A Kavishe
- Kilimanjaro Christian Medical Centre, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Florida Muro
- Kilimanjaro Christian Medical Centre, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Renata Mandike
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Sigsbert Mkude
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Ritha Njau
- Malariologist and Public Health Specialist, Dar es Salaam, Tanzania
| | - Troy Martin
- HIV Vaccine Trials Network, Fred Hutch Cancer Research Centre, Seattle, WA, USA
| | - Ally Mohamed
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Abebe A Fola
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. medRxiv 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genomic surveillance plays a critical role in monitoring malaria transmission and understanding how the parasite adapts in response to interventions. We conducted genomic surveillance of malaria by sequencing 241 Plasmodium falciparum genomes from regions with varying levels of malaria transmission across Zambia. We found genomic evidence of high levels of within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in the country. We identified country-level clustering of parasites from Zambia and neighboring countries, and distinct clustering of parasites from West Africa. Within Zambia, our identity by descent (IBD) relatedness analysis uncovered spatial clustering of closely related parasite pairs at the local level and rare cases of long-distance sharing. Genomic regions with large shared IBD segments and strong positive selection signatures identified genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Together, our findings enhance our understanding of P. falciparum transmission nationwide in Zambia and highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A. Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E. Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J. Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA
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Ishengoma DS, Mandara CI, Bakari C, Fola AA, Madebe RA, Seth MD, Francis F, Buguzi C, Moshi R, Garimo I, Lazaro S, Lusasi A, Aaron S, Chacky F, Mohamed A, Njau RJA, Kitau J, Rasmussen C, Bailey JA, Juliano JJ, Warsame M. Evidence of artemisinin partial resistance in North-western Tanzania: clinical and drug resistance markers study. medRxiv 2024:2024.01.31.24301954. [PMID: 38352311 PMCID: PMC10863006 DOI: 10.1101/2024.01.31.24301954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Background Artemisinin-based combination therapies (ACTs) are the recommended antimalarial drugs for the treatment of uncomplicated malaria. The recent emergence of artemisinin partial resistance (ART-R) in Rwanda, Uganda and Eritrea is of great concern. In Tanzania, a nationwide molecular malaria surveillance in 2021 showed a high prevalence of the Kelch13 (K13) 561H mutation in Plasmodium falciparum from the north-western region, close to the border with Rwanda and Uganda. This study was conducted in 2022 to evaluate the efficacy of artemether-lumefantrine (AL) and artesunate-amodiaquine (ASAQ) for the treatment of uncomplicated falciparum malaria and to confirm the presence of ART-R in Tanzania. Methods This single-arm study evaluated the efficacy of AL and ASAQ in eligible children aged six months to 10 years at Bukangara Dispensary in Karagwe District, Kagera Region. Clinical and parasitological responses were monitored for 28 days according to standard WHO protocol. Mutations in K13 gene and extended haplotypes with these mutations were analysed using Sanger and whole genome sequencing data, respectively. Findings 176 children (88 in each AL and ASAQ group) were enrolled and all achieved the defined outcomes. PCR-corrected adequate clinical and parasitological response (ACPR) was 98.3% (95% CI: 90.8-100) and 100.0% (95% CI: 95.8-100) for AL and ASAQ, respectively. Parasitaemia on day 3 was observed in 11/88 (12.5%) and 17/88 (19.3%) in the AL and ASAQ groups, respectively. The half-life of parasitaemia was significantly higher (>6.5 hrs) in patients with parasitaemia on day 3 and/or mutations in K13 gene at enrolment. Most patients with parasitaemia on day 3 (8/11 = 72.7% in the AL group and 10/17 = 58.8% in the ASAQ group) had 561H mutation at enrolment. The parasites with K13 mutations were not similar to those from south-east Asia and Rwanda, but had the same core haplotype of a new 561H haplotype reported in Kagera in 2021. Interpretation These findings confirm the presence of ART-R in Tanzania. A context-specific strategy to respond to artemisinin partial resistance is urgently needed. Although both AL and ASAQ showed high efficacy, increased vigilance for reduced efficacy of these ACTs and detection of ART-R in other parts of the country is critical.
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Affiliation(s)
- Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, VIC, Australia
- Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania
| | | | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Abebe A. Fola
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Creyton Buguzi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Issa Garimo
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Samwel Lazaro
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | | | - Sijenunu Aaron
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Ritha J. A. Njau
- Malariologist and Public Health Specialist, Muhimbili University of Health and Allied Sciences, School of Public Health and Social Sciences Dar es Salaam, Tanzania
| | - Jovin Kitau
- World Health Organization Country Office, Dar es Salaam, Tanzania
| | | | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | | | - Marian Warsame
- Gothenburg University, Gothenburg, Sweden
- Benadir University, Mogadishu, Somalia
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5
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Assefa A, Fola AA, Tasew G. Emergence of Plasmodium falciparum strains with artemisinin partial resistance in East Africa and the Horn of Africa: is there a need to panic? Malar J 2024; 23:34. [PMID: 38273360 PMCID: PMC10809756 DOI: 10.1186/s12936-024-04848-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
The emergence and spread of artemisinin partial resistance in East and Horn of Africa is alarming. However, artemisinin-based combination therapy (ACT) generally remains efficacious for the treatment of falciparum malaria. The emergence of partial artemisinin resistance does not currently meet the criteria to initiate change on treatment guidelines nor affect ACT routine procurement and distribution. It is high time for scientists and transitional researchers to be more critical and vigilant on further changes so that national programmes will be able to make informed decisions as well as remain alert and prepared for any change that may be required in the future.
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Affiliation(s)
- Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
| | - Abebe A Fola
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Geremew Tasew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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Juliano JJ, Giesbrecht DJ, Simkin A, Fola AA, Lyimo BM, Pereus D, Bakari C, Madebe RA, Seth MD, Mandara CI, Popkin-Hall ZR, Moshi R, Mbwambo RB, Niaré K, MacInnis B, Francis F, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau RJA, Lazaro S, Mohamed A, Bailey JA, Ishengoma DS. Country wide surveillance reveals prevalent artemisinin partial resistance mutations with evidence for multiple origins and expansion of high level sulfadoxine-pyrimethamine resistance mutations in northwest Tanzania. medRxiv 2023:2023.11.07.23298207. [PMID: 37986920 PMCID: PMC10659475 DOI: 10.1101/2023.11.07.23298207] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Emergence of artemisinin partial resistance (ART-R) in Plasmodium falciparum is a growing threat to the efficacy of artemisinin combination therapies (ACT) and the efforts for malaria elimination. The emergence of Plasmodium falciparum Kelch13 (K13) R561H in Rwanda raised concern about the impact in neighboring Tanzania. In addition, regional concern over resistance affecting sulfadoxine-pyrimethamine (SP), which is used for chemoprevention strategies, is high. Methods To enhance longitudinal monitoring, the Molecular Surveillance of Malaria in Tanzania (MSMT) project was launched in 2020 with the goal of assessing and mapping antimalarial resistance. Community and clinic samples were assessed for resistance polymorphisms using a molecular inversion probe platform. Findings Genotyping of 6,278 samples collected countrywide in 2021 revealed a focus of K13 561H mutants in northwestern Tanzania (Kagera) with prevalence of 7.7% (50/649). A small number of 561H mutants (about 1%) were found as far as 800 km away in Tabora, Manyara, and Njombe. Genomic analysis suggests some of these parasites are highly related to isolates collected in Rwanda in 2015, supporting regional spread of 561H. However, a novel haplotype was also observed, likely indicating a second origin in the region. Other validated resistance polymorphisms (622I and 675V) were also identified. A focus of high sulfadoxine-pyrimethamine drug resistance was also identified in Kagera with a prevalence of dihydrofolate reductase 164L of 15% (80/526). Interpretation These findings demonstrate the K13 561H mutation is entrenched in the region and that multiple origins of ART-R, similar as to what was seen in Southeast Asia, have occurred. Mutations associated with high levels of SP resistance are increasing. These results raise concerns about the long-term efficacy of artemisinin and chemoprevention antimalarials in the region. Funding This study was funded by the Bill and Melinda Gates Foundation and the National Institutes of Health.
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Affiliation(s)
| | | | | | | | - Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ruth B. Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Bronwyn MacInnis
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Broad Institute, Boston, MA, USA
| | | | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha J. A. Njau
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | | | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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7
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Fola AA, Feleke SM, Mohammed H, Brhane BG, Hennelly CM, Assefa A, Crudal RM, Reichert E, Juliano JJ, Cunningham J, Mamo H, Solomon H, Tasew G, Petros B, Parr JB, Bailey JA. Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia. Nat Microbiol 2023; 8:1911-1919. [PMID: 37640962 PMCID: PMC10522486 DOI: 10.1038/s41564-023-01461-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/26/2023] [Indexed: 08/31/2023]
Abstract
Diagnosis and treatment of Plasmodium falciparum infections are required for effective malaria control and are pre-requisites for malaria elimination efforts; hence we need to monitor emergence, evolution and spread of drug- and diagnostics-resistant parasites. We deep sequenced key drug-resistance mutations and 1,832 SNPs in the parasite genomes of 609 malaria cases collected during a diagnostic-resistance surveillance study in Ethiopia. We found that 8.0% (95% CI 7.0-9.0) of malaria cases were caused by P. falciparum carrying the candidate artemisinin partial-resistance kelch13 (K13) 622I mutation, which was less common in diagnostic-resistant parasites mediated by histidine-rich proteins 2 and 3 (pfhrp2/3) deletions than in wild-type parasites (P = 0.03). Identity-by-descent analyses showed that K13 622I parasites were significantly more related to each other than to wild type (P < 0.001), consistent with recent expansion and spread of this mutation. Pfhrp2/3-deleted parasites were also highly related, with evidence of clonal transmissions at the district level. Of concern, 8.2% of K13 622I parasites also carried the pfhrp2/3 deletions. Close monitoring of the spread of combined drug- and diagnostic-resistant parasites is needed.
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Affiliation(s)
- Abebe A Fola
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | | | | | | | - Christopher M Hennelly
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca M Crudal
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Emily Reichert
- Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Hassen Mamo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Geremew Tasew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Beyene Petros
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jonathan B Parr
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA.
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8
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Fola AA, Moser KA, Aydemir O, Hennelly C, Kobayashi T, Shields T, Hamapumbu H, Musonda M, Katowa B, Matoba J, Stevenson JC, Norris DE, Thuma PE, Wesolowski A, Moss WJ, Bailey JA, Juliano JJ. Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of parasite connectivity in a low-transmission district in Southern Province, Zambia. Malar J 2023; 22:208. [PMID: 37420265 PMCID: PMC10327325 DOI: 10.1186/s12936-023-04637-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Understanding temporal and spatial dynamics of malaria transmission will help to inform effective interventions and strategies in regions approaching elimination. Parasite genomics are increasingly used to monitor epidemiologic trends, including assessing residual transmission across seasons and importation of malaria into these regions. METHODS In a low and seasonal transmission setting of southern Zambia, a total of 441 Plasmodium falciparum samples collected from 8 neighbouring health centres between 2012 and 2018 were genotyped using molecular inversion probes (MIPs n = 1793) targeting a total of 1832 neutral and geographically informative SNPs distributed across the parasite genome. After filtering for quality and missingness, 302 samples and 1410 SNPs were retained and used for downstream population genomic analyses. RESULTS The analyses revealed most (67%, n = 202) infections harboured one clone (monogenomic) with some variation at local level suggesting low, but heterogenous malaria transmission. Relatedness identity-by-descent (IBD) analysis revealed variable distribution of IBD segments across the genome and 6% of pairs were highly-related (IBD ≥ 0.25). Some of the highly-related parasite populations persisted across multiple seasons, suggesting that persistence of malaria in this low-transmission region is fueled by parasites "seeding" across the dry season. For recent years, clusters of clonal parasites were identified that were dissimilar to the general parasite population, suggesting parasite populations were increasingly fragmented at small spatial scales due to intensified control efforts. Clustering analysis using PCA and t-SNE showed a lack of substantial parasite population structure. CONCLUSION Leveraging both genomic and epidemiological data provided comprehensive picture of fluctuations in parasite populations in this pre-elimination setting of southern Zambia over 7 years.
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Affiliation(s)
- Abebe A. Fola
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Kara A. Moser
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Chris Hennelly
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Tamaki Kobayashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Timothy Shields
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | | | | | - Ben Katowa
- Macha Research Trust, Choma District, Choma, Zambia
| | | | | | - Douglas E. Norris
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | | | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - William J. Moss
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Jonathan J. Juliano
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - the Southern, Central Africa International Center of Excellence for Malaria Research (ICEMR)
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Macha Research Trust, Choma District, Choma, Zambia
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
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9
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Ciubotariu II, Dorman J, Perry NM, Gorenstein L, Kattoor JJ, Fola AA, Zine A, Hendrix GK, Wilkes RP, Kitchen A, Carpi G. Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant. Open Forum Infect Dis 2022; 9:ofac268. [PMID: 35818365 PMCID: PMC9213861 DOI: 10.1093/ofid/ofac268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Using a combination of data from routine surveillance, genomic sequencing, and phylogeographic analysis we tracked the spread and introduction events of SARS-CoV-2 variants focusing on a large university community.
Methods
Here, we sequenced and analyzed 677 high-quality SARS-CoV-2 genomes from positive RNA samples collected from Purdue University students, faculty, and staff who tested positive for the virus between January 2021 and May 2021, comprising an average of 32% of weekly cases across the time frame.
Results
Our analysis of circulating SARS-CoV-2 variants over time revealed periods when Variant of Concern (VOC) Alpha (B.1.1.7) and Iota (B.1.526) reached rapid dominance and documented that VOC Gamma (P.1) was increasing in frequency as campus surveillance was ending. Phylodynamic analysis of Gamma genomes from campus alongside a subsampling of >20,000 previously published P.1 genomes revealed ten independent introductions of this variant into the Purdue community, predominantly from elsewhere in the United States, with introductions from within the state of Indiana and from Illinois, and possibly Washington and New York, suggesting a degree of domestic spread.
Conclusions
We conclude that a robust and sustained active and passive surveillance program coupled with genomic sequencing during a pandemic offers important insights into the dynamics of pathogen arrival and spread in a campus community and can help guide mitigation measures.
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Affiliation(s)
- Ilinca I. Ciubotariu
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Jack Dorman
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Nicole M. Perry
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Lev Gorenstein
- Purdue University Information Technology Research Computing, , West Lafayette, Indiana 47907, USA
| | - Jobin J. Kattoor
- Purdue University College of Veterinary Medicine Department of Comparative Biology, Animal Disease Diagnostic Laboratory, , West Lafayette, Indiana 47907, USA
| | - Abebe A. Fola
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Amy Zine
- University of Iowa Department of Anthropology, , Iowa City, Iowa, USA
| | - G. Kenitra Hendrix
- Purdue University College of Veterinary Medicine Department of Comparative Biology, Animal Disease Diagnostic Laboratory, , West Lafayette, Indiana 47907, USA
| | - Rebecca P. Wilkes
- Purdue University College of Veterinary Medicine Department of Comparative Biology, Animal Disease Diagnostic Laboratory, , West Lafayette, Indiana 47907, USA
| | - Andrew Kitchen
- University of Iowa Department of Anthropology, , Iowa City, Iowa, USA
| | - Giovanna Carpi
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation , Immunology and Infectious Disease, West Lafayette, Indiana 47907, USA
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10
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Mwenda MC, Fola AA, Ciubotariu II, Mulube C, Mambwe B, Kasaro R, Hawela MB, Hamainza B, Miller JM, Carpi G, Bridges DJ. Performance evaluation of RDT, light microscopy, and PET-PCR for detecting Plasmodium falciparum malaria infections in the 2018 Zambia National Malaria Indicator Survey. Malar J 2021; 20:386. [PMID: 34583692 PMCID: PMC8477358 DOI: 10.1186/s12936-021-03917-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/14/2021] [Indexed: 11/29/2022] Open
Abstract
Background Zambia continues to advance on the path to elimination with significant reductions in malaria morbidity and mortality. Crucial components that have contributed to progress thus far and are necessary for achieving the national malaria elimination goals include properly identifying and treating all malaria cases through accurate diagnosis. This study sought to compare and assess the diagnostic performance of Rapid Diagnostic Tests (RDT) and Light Microscopy (LM) with photo-induced electron transfer polymerase chain reaction (PET-PCR) as the gold standard using 2018 Malaria Indicator Survey (MIS) data across Zambia to better understand diagnostic accuracy metrics and how these vary across a transmission gradient. Methods Cross-sectional samples collected in a nationally representative survey from 7 provinces in Zambia were tested for the presence of malaria parasites by light microscopy (LM), rapid diagnostic test (RDT) and the gold standard PET-PCR. Diagnostic performance was assessed including sensitivity, specificity, negative- and positive-predictive values across a wide malaria transmission spectrum. Diagnostic accuracy metrics were measured, and statistically significant differences were calculated between test methods for different outcome variables. Results From the individuals included in the MIS, the overall prevalence of Plasmodium falciparum malaria was 32.9% by RDT, 19.4% by LM, and 23.2% by PET-PCR. Herein, RDT and LM diagnostic performance was compared against gold standard PET-PCR with LM displaying a higher diagnostic accuracy than RDTs (91.3% vs. 84.6% respectively) across the transmission spectrum in Zambia. However, the performance of both diagnostics was significantly reduced in low parasitaemia samples. Consistent with previous studies, RDT diagnostic accuracy was predominantly affected by a high rate of false positives. Conclusions RDTs and LM both perform well across a range of transmission intensities within their respective target applications, i.e., in the community, for the former, where ease of use and speed of result is critical, and at the health facility, for the latter, where accuracy is prioritized. However, the performance of both diagnostic methods is adversely affected by low parasitaemia infections. As Zambia moves towards elimination more sensitive tools may be required to identify the last cases. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03917-6.
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Affiliation(s)
- Mulenga C Mwenda
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Conceptor Mulube
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Brenda Mambwe
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Rachael Kasaro
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Moonga B Hawela
- National Malaria Elimination Centre, Ministry of Health, Chainama Hospital and College Grounds, Lusaka, Zambia
| | - Busiku Hamainza
- National Malaria Elimination Centre, Ministry of Health, Chainama Hospital and College Grounds, Lusaka, Zambia
| | - John M Miller
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, Indiana, USA
| | - Daniel J Bridges
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia.
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11
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Kattenberg JH, Razook Z, Keo R, Koepfli C, Jennison C, Lautu-Gumal D, Fola AA, Ome-Kaius M, Barnadas C, Siba P, Felger I, Kazura J, Mueller I, Robinson LJ, Barry AE. Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea. Mol Ecol 2020; 29:4525-4541. [PMID: 32985031 PMCID: PMC10008436 DOI: 10.1111/mec.15654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/27/2020] [Indexed: 02/01/2023]
Abstract
Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of two major human malaria parasites, Plasmodium falciparum (Pf) and Plasmodium vivax (Pv), following nationwide distribution of long-lasting insecticide-treated nets (LLINs) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-2006) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik Province: Pf = 54.9%-8.5%, Pv = 35.7%-5.6%, Madang Province: Pf = 38.0%-9.0%, Pv: 31.8%-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, HE = 0.77-0.71; Madang: Rs = 8.2-6.1, HE = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs = 11.4-9.3, HE = 0.83-0.80; Madang: Rs = 12.2-14.5, HE = 0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium post-LLIN were positive indicators of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.
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Affiliation(s)
- Johanna Helena Kattenberg
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea
| | - Zahra Razook
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Raksmei Keo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Cristian Koepfli
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Charlie Jennison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Abebe A Fola
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Maria Ome-Kaius
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Céline Barnadas
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - James Kazura
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Leanne J Robinson
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Disease Elimination, Burnet Institute, Melbourne, VIC, Australia
| | - Alyssa E Barry
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
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12
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Fola AA, Kattenberg E, Razook Z, Lautu-Gumal D, Lee S, Mehra S, Bahlo M, Kazura J, Robinson LJ, Laman M, Mueller I, Barry AE. SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics. Malar J 2020; 19:375. [PMID: 33081815 PMCID: PMC7576724 DOI: 10.1186/s12936-020-03440-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/03/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since 'universal' barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. METHODS Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. RESULTS From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56-7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level. CONCLUSIONS High-throughput SNP barcoding can be used to map variation of malaria transmission dynamics at sub-national resolution. The low cost per sample and genotyping strategy makes the transfer of this technology to field settings highly feasible.
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Affiliation(s)
- Abebe A Fola
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Eline Kattenberg
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Zahra Razook
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Stuart Lee
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Somya Mehra
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James Kazura
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Leanne J Robinson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
| | - Moses Laman
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Ivo Mueller
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Alyssa E Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia.
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia.
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13
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Fola AA, Harrison GLA, Hazairin MH, Barnadas C, Hetzel MW, Iga J, Siba PM, Mueller I, Barry AE. Higher Complexity of Infection and Genetic Diversity of Plasmodium vivax Than Plasmodium falciparum Across All Malaria Transmission Zones of Papua New Guinea. Am J Trop Med Hyg 2017; 96:630-641. [PMID: 28070005 DOI: 10.4269/ajtmh.16-0716] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Plasmodium falciparum and Plasmodium vivax have varying transmission dynamics that are informed by molecular epidemiology. This study aimed to determine the complexity of infection and genetic diversity of P. vivax and P. falciparum throughout Papua New Guinea (PNG) to evaluate transmission dynamics across the country. In 2008-2009, a nationwide malaria indicator survey collected 8,936 samples from all 16 endemic provinces of PNG. Of these, 892 positive P. vivax samples were genotyped at PvMS16 and PvmspF3, and 758 positive P. falciparum samples were genotyped at Pfmsp2. The data were analyzed for multiplicity of infection (MOI) and genetic diversity. Overall, P. vivax had higher polyclonality (71%) and mean MOI (2.32) than P. falciparum (20%, 1.39). These measures were significantly associated with prevalence for P. falciparum but not for P. vivax. The genetic diversity of P. vivax (PvMS16: expected heterozygosity = 0.95, 0.85-0.98; PvMsp1F3: 0.78, 0.66-0.89) was higher and less variable than that of P. falciparum (Pfmsp2: 0.89, 0.65-0.97). Significant associations of MOI with allelic richness (rho = 0.69, P = 0.009) and expected heterozygosity (rho = 0.87, P < 0.001) were observed for P. falciparum. Conversely, genetic diversity was not correlated with polyclonality nor mean MOI for P. vivax. The results demonstrate higher complexity of infection and genetic diversity of P. vivax across the country. Although P. falciparum shows a strong association of these parameters with prevalence, a lack of association was observed for P. vivax and is consistent with higher potential for outcrossing of this species.
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Affiliation(s)
- Abebe A Fola
- Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - G L Abby Harrison
- Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Mita Hapsari Hazairin
- Department of Epidemiology and Preventative Medicine, Monash University, Clayton, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Céline Barnadas
- Statens Serum Institut, Copenhagen, Denmark.,European Public Health Microbiology (EUPHEM) Training Programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Manuel W Hetzel
- University of Basel, Basel, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Jonah Iga
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Peter M Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ivo Mueller
- Institut Pasteur, Paris, France.,Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Alyssa E Barry
- Department of Medical Biology, University of Melbourne, Parkville, Australia.,Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
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Ménard D, Khim N, Beghain J, Adegnika AA, Shafiul-Alam M, Amodu O, Rahim-Awab G, Barnadas C, Berry A, Boum Y, Bustos MD, Cao J, Chen JH, Collet L, Cui L, Thakur GD, Dieye A, Djallé D, Dorkenoo MA, Eboumbou-Moukoko CE, Espino FECJ, Fandeur T, Ferreira-da-Cruz MF, Fola AA, Fuehrer HP, Hassan AM, Herrera S, Hongvanthong B, Houzé S, Ibrahim ML, Jahirul-Karim M, Jiang L, Kano S, Ali-Khan W, Khanthavong M, Kremsner PG, Lacerda M, Leang R, Leelawong M, Li M, Lin K, Mazarati JB, Ménard S, Morlais I, Muhindo-Mavoko H, Musset L, Na-Bangchang K, Nambozi M, Niaré K, Noedl H, Ouédraogo JB, Pillai DR, Pradines B, Quang-Phuc B, Ramharter M, Randrianarivelojosia M, Sattabongkot J, Sheikh-Omar A, Silué KD, Sirima SB, Sutherland C, Syafruddin D, Tahar R, Tang LH, Touré OA, Tshibangu-wa-Tshibangu P, Vigan-Womas I, Warsame M, Wini L, Zakeri S, Kim S, Eam R, Berne L, Khean C, Chy S, Ken M, Loch K, Canier L, Duru V, Legrand E, Barale JC, Stokes B, Straimer J, Witkowski B, Fidock DA, Rogier C, Ringwald P, Ariey F, Mercereau-Puijalon O. A Worldwide Map of Plasmodium falciparum K13-Propeller Polymorphisms. N Engl J Med 2016; 374:2453-64. [PMID: 27332904 PMCID: PMC4955562 DOI: 10.1056/nejmoa1513137] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Recent gains in reducing the global burden of malaria are threatened by the emergence of Plasmodium falciparum resistance to artemisinins. The discovery that mutations in portions of a P. falciparum gene encoding kelch (K13)-propeller domains are the major determinant of resistance has provided opportunities for monitoring such resistance on a global scale. METHODS We analyzed the K13-propeller sequence polymorphism in 14,037 samples collected in 59 countries in which malaria is endemic. Most of the samples (84.5%) were obtained from patients who were treated at sentinel sites used for nationwide surveillance of antimalarial resistance. We evaluated the emergence and dissemination of mutations by haplotyping neighboring loci. RESULTS We identified 108 nonsynonymous K13 mutations, which showed marked geographic disparity in their frequency and distribution. In Asia, 36.5% of the K13 mutations were distributed within two areas--one in Cambodia, Vietnam, and Laos and the other in western Thailand, Myanmar, and China--with no overlap. In Africa, we observed a broad array of rare nonsynonymous mutations that were not associated with delayed parasite clearance. The gene-edited Dd2 transgenic line with the A578S mutation, which expresses the most frequently observed African allele, was found to be susceptible to artemisinin in vitro on a ring-stage survival assay. CONCLUSIONS No evidence of artemisinin resistance was found outside Southeast Asia and China, where resistance-associated K13 mutations were confined. The common African A578S allele was not associated with clinical or in vitro resistance to artemisinin, and many African mutations appear to be neutral. (Funded by Institut Pasteur Paris and others.).
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Affiliation(s)
- Didier Ménard
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Nimol Khim
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Johann Beghain
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Ayola A Adegnika
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Mohammad Shafiul-Alam
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Olukemi Amodu
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Ghulam Rahim-Awab
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Céline Barnadas
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Antoine Berry
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Yap Boum
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Maria D Bustos
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jun Cao
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jun-Hu Chen
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Louis Collet
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Liwang Cui
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Garib-Das Thakur
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Alioune Dieye
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Djibrine Djallé
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Monique A Dorkenoo
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | | | - Thierry Fandeur
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | - Abebe A Fola
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Hans-Peter Fuehrer
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Abdillahi M Hassan
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Socrates Herrera
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Bouasy Hongvanthong
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sandrine Houzé
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Maman L Ibrahim
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Mohammad Jahirul-Karim
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Lubin Jiang
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Shigeyuki Kano
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Wasif Ali-Khan
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Maniphone Khanthavong
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Peter G Kremsner
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Marcus Lacerda
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Rithea Leang
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Mindy Leelawong
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Mei Li
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Khin Lin
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jean-Baptiste Mazarati
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sandie Ménard
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Isabelle Morlais
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | - Lise Musset
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Kesara Na-Bangchang
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Michael Nambozi
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Karamoko Niaré
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Harald Noedl
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jean-Bosco Ouédraogo
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Dylan R Pillai
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Bruno Pradines
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Bui Quang-Phuc
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Michael Ramharter
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | - Jetsumon Sattabongkot
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Abdiqani Sheikh-Omar
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Kigbafori D Silué
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sodiomon B Sirima
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Colin Sutherland
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Din Syafruddin
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Rachida Tahar
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Lin-Hua Tang
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Offianan A Touré
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | - Inès Vigan-Womas
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Marian Warsame
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Lyndes Wini
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sedigheh Zakeri
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Saorin Kim
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Rotha Eam
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Laura Berne
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Chanra Khean
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sophy Chy
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Malen Ken
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Kaknika Loch
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Lydie Canier
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Valentine Duru
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Eric Legrand
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jean-Christophe Barale
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Barbara Stokes
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Judith Straimer
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Benoit Witkowski
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - David A Fidock
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Christophe Rogier
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Pascal Ringwald
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Frederic Ariey
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
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Getnet G, Getie S, Srivastava M, Birhan W, Fola AA, Noedl H. Diagnostic performance of rapid diagnostic tests for the diagnosis of malaria at public health facilities in north-west Ethiopia. Trop Med Int Health 2015. [PMID: 26211505 DOI: 10.1111/tmi.12570] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To assess the performance of RDTs against nested polymerase chain reaction (nPCR) for the diagnosis of malaria in public health facilities in north-western Ethiopia. METHODS Cross-sectional study at public health facilities in North Gondar, Ethiopia, of 359 febrile patients with signs and symptoms consistent with malaria. Finger prick blood samples were collected for testing in a P. falciparum/pan-malaria RDTs and for molecular analysis. Sensitivity, specificity and predictive values were determined for the RDTs using nPCR as reference diagnostic method. Kappa value was determined to demonstrate the consistency of the results between the diagnostic tools. RESULTS By RDTs, 22.28% (80/359) of patients tested positive for malaria, and by nPCR, 27.02% (97/359) did. In nPCR, 1.67% (6/359) and 0.28% (1/359) samples were positive for P. ovale and P. malariae, which had almost all tested negative in the RDTs. The sensitivity, specificity, positive and negative predictive values of RDTs for the diagnosis of malaria were 62.9%, 92.7%, 76.3% and 87.1%, respectively, with 0.589 measurement agreement between RDTs and nPCR. The sensitivity and specificity of RDTs for P. falciparum identification only were 70.8% and 95.2%, and 65.2% and 93.1% for P. vivax. CONCLUSION Although RDTs are commonly used at health posts in resource-limited environments, their sensitivity and specificity for the detection and species identification of Plasmodium parasites were poor compared to nPCR, suggesting caution in interpreting RDTs results. Particularly, in the light of expanded efforts to eliminate malaria in the country, more sensitive diagnostic procedures will be needed.
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Affiliation(s)
- Gebeyaw Getnet
- Department of Medical Parasitology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Sisay Getie
- Department of Medical Parasitology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mitaly Srivastava
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Wubet Birhan
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Abebe A Fola
- School of Medicine, College of Medicine and Health Sciences, Wolaita Sodo University, Wolaita, Ethiopia.,Walter and Eliza Hall Institute for Medical Research, Melbourne, Vic., Australia
| | - Harald Noedl
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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