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Fola AA, Kobayashi T, Shields T, Hamapumbu H, Musonda M, Katowa B, Matoba J, Stevenson JC, Norris DE, Thuma PE, Wesolowski A, Moss WJ, Juliano JJ, Bailey JA. Temporal genomic analysis of Plasmodium falciparum reveals increased prevalence of mutations associated with delayed clearance following treatment with artemisinin-lumefantrine in Choma District, Southern Province, Zambia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.05.24308497. [PMID: 38883763 PMCID: PMC11178023 DOI: 10.1101/2024.06.05.24308497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
The emergence of antimalarial drug resistance is an impediment to malaria control and elimination in Africa. Analysis of temporal trends in molecular markers of resistance is critical to inform policy makers and guide malaria treatment guidelines. In a low and seasonal transmission region of southern Zambia, we successfully genotyped 85.5% (389/455) of Plasmodium falciparum samples collected between 2013-2018 from 8 spatially clustered health centres using molecular inversion probes (MIPs) targeting key drug resistance genes. Aside from one sample carrying K13 R622 I , none of the isolates carried other World Health Organization-validated or candidate artemisinin partial resistance (ART-R) mutations in K13. However, 13% (CI, 9.6-17.2) of isolates had the AP2MU S160 N mutation, which has been associated with delayed clearance following artemisinin combination therapy in Africa. This mutation increased in prevalence between 2015-2018 and bears a genomic signature of selection. During this time period, there was an increase in the MDR1 N F D haplotype that is associated with reduced susceptibility to lumefantrine. Sulfadoxine-pyrimethamine polymorphisms were near fixation. While validated ART-R mutations are rare, a mutation associated with slow parasite clearance in Africa appears to be under selection in southern Zambia.
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Rosenthal PJ, Asua V, Conrad MD. Emergence, transmission dynamics and mechanisms of artemisinin partial resistance in malaria parasites in Africa. Nat Rev Microbiol 2024; 22:373-384. [PMID: 38321292 DOI: 10.1038/s41579-024-01008-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2024] [Indexed: 02/08/2024]
Abstract
Malaria, mostly due to Plasmodium falciparum infection in Africa, remains one of the most important infectious diseases in the world. Standard treatment for uncomplicated P. falciparum malaria is artemisinin-based combination therapy (ACT), which includes a rapid-acting artemisinin derivative plus a longer-acting partner drug, and standard therapy for severe P. falciparum malaria is intravenous artesunate. The efficacy of artemisinins and ACT has been threatened by the emergence of artemisinin partial resistance in Southeast Asia, mediated principally by mutations in the P. falciparum Kelch 13 (K13) protein. High ACT treatment failure rates have occurred when resistance to partner drugs is also seen. Recently, artemisinin partial resistance has emerged in Rwanda, Uganda and the Horn of Africa, with independent emergences of different K13 mutants in each region. In this Review, we summarize our current knowledge of artemisinin partial resistance and focus on the emergence of resistance in Africa, including its epidemiology, transmission dynamics and mechanisms. At present, the clinical impact of emerging resistance in Africa is unclear and most available evidence suggests that the efficacies of leading ACTs remain excellent, but there is an urgent need to better appreciate the extent of the problem and its consequences for the treatment and control of malaria.
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Affiliation(s)
| | - Victor Asua
- Infectious Diseases Research Collaboration, Kampala, Uganda
- University of Tübingen, Tübingen, Germany
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Schreidah C, Giesbrecht D, Gashema P, Young NW, Munyaneza T, Muvunyi CM, Thwai K, Mazarati JB, Bailey JA, Juliano JJ, Karema C. Expansion of artemisinin partial resistance mutations and lack of histidine rich protein-2 and -3 deletions in Plasmodium falciparum infections from Rukara, Rwanda. Malar J 2024; 23:150. [PMID: 38755607 PMCID: PMC11100144 DOI: 10.1186/s12936-024-04981-4] [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: 12/17/2023] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Emerging artemisinin partial resistance and diagnostic resistance are a threat to malaria control in Africa. Plasmodium falciparum kelch13 (k13) propeller-domain mutations that confer artemisinin partial resistance have emerged in Africa. k13-561H was initially described at a frequency of 7.4% from Masaka in 2014-2015, but not present in nearby Rukara. By 2018, 19.6% of isolates in Masaka and 22% of isolates in Rukara contained the mutation. Longitudinal monitoring is essential to inform control efforts. In Rukara, an assessment was conducted to evaluate recent k13-561H prevalence changes, as well as other key mutations. Prevalence of hrp2/3 deletions was also assessed. METHODS Samples collected in Rukara in 2021 were genotyped for key artemisinin and partner drug resistance mutations using molecular inversion probe assays and for hrp2/3 deletions using qPCR. RESULTS Clinically validated k13 artemisinin partial resistance mutations continue to increase in prevalence with the overall level of mutant infections reaching 32% in Rwanda. The increase appears to be due to the rapid emergence of k13-675V (6.4%, 6/94 infections), previously not observed, rather than continued expansion of 561H (23.5% 20/85). Mutations to partner drugs and other anti-malarials were variable, with high levels of multidrug resistance 1 (mdr1) N86 (95.5%) associated with lumefantrine decreased susceptibility and dihydrofolate reductase (dhfr) 164L (24.7%) associated with a high level of antifolate resistance, but low levels of amodiaquine resistance polymorphisms with chloroquine resistance transporter (crt) 76T: at 6.1% prevalence. No hrp2 or hrp3 gene deletions associated with diagnostic resistance were found. CONCLUSIONS Increasing prevalence of artemisinin partial resistance due to k13-561H and the rapid expansion of k13-675V is concerning for the longevity of artemisinin effectiveness in the region. False negative RDT results do not appear to be an issue with no hrp2 or hpr3 deletions detected. Continued molecular surveillance in this region and surrounding areas is needed to follow artemisinin partial resistance and provide early detection of partner drug resistance, which would likely compromise control and increase malaria morbidity and mortality in East Africa.
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Affiliation(s)
| | | | | | | | | | | | - Kyaw Thwai
- University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Jonathan J Juliano
- University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Corine Karema
- Quality Equity Health Care, Kigali, Rwanda
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
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Mesia Kahunu G, Wellmann Thomsen S, Wellmann Thomsen L, Muhindo Mavoko H, Mitashi Mulopo P, Filtenborg Hocke E, Mandoko Nkoli P, Baraka V, Minja DTR, Mousa A, Roper C, Mbongi Moke D, Mumba Ngoyi D, Mukomena Sompwe E, Muyembe Tanfum JJ, Hansson H, Alifrangis M. Identification of the PfK13 mutations R561H and P441L in the Democratic Republic of Congo. Int J Infect Dis 2024; 139:41-49. [PMID: 38016502 DOI: 10.1016/j.ijid.2023.11.026] [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: 09/19/2023] [Revised: 11/10/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023] Open
Abstract
OBJECTIVES Partial artemisinin resistance, mediated by Plasmodium falciparum K13 (PfK13) mutations, has been confirmed in certain areas of East Africa that are historically associated with high-level antimalarial resistance. The Democratic Republic of Congo (DRC) borders these areas in the East. This study aimed to determine the prevalence of resistance markers in six National Malaria Control Program surveillance sites; Boende, Kabondo, Kapolowe, Kimpese, Mikalayi, and Rutshuru. METHODS The single nucleotide polymorphisms (SNPs) in P. falciparum genes PfK13, Pfdhfr, Pfdhps, Pfmdr1, and Pfcrt were assessed using targeted next-generation sequencing of isolates collected at enrollment in therapeutic efficacy studies. RESULTS PfK13 SNPs were detected in two samples: in Kabondo (R561H) and in Rutshuru (P441L), both areas near Uganda and Rwanda. The Pfdhps ISGEGA haplotype, associated with reduced sulfadoxine-pyrimethamine chemoprevention efficacy, ranged from 0.8% in Mikalayi (central DRC) to 42.2% in Rutshuru (East DRC). CONCLUSIONS R561H and P441L observed in eastern DRC are a concern, as they are associated with delayed artemisinin-based combination therapies-clearance and candidate marker of resistance, respectively. This is consistent with previous observations of shared drug resistance profiles in parasites of that region with bordering areas of Rwanda and Uganda. The likely circulation of parasites has important implications for the ongoing surveillance of partial artemisinin-resistant P. falciparum and for future efforts to mitigate its dispersal.
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Affiliation(s)
- Gauthier Mesia Kahunu
- Department of Pharmacology and Therapeutics, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Sarah Wellmann Thomsen
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Louise Wellmann Thomsen
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Emma Filtenborg Hocke
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Papy Mandoko Nkoli
- National Institute of Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Vito Baraka
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Daniel T R Minja
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Andria Mousa
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Cally Roper
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Dieudonné Mumba Ngoyi
- Department of Tropical Medicine, University of Kinshasa, Democratic Republic of Congo; National Institute of Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Eric Mukomena Sompwe
- Faculty of Medicine, University of Lubumbashi, Democratic Republic of the Congo, National Malaria Control Program, Ministry of Health, Kinshasa, Democratic Republic of the Congo
| | - Jean Jacques Muyembe Tanfum
- Department of Tropical Medicine, University of Kinshasa, Democratic Republic of Congo; National Institute of Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Helle Hansson
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michael Alifrangis
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark.
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Gaither C, Morgan C, Kirby R, Karema C, Gashema P, White SJ, Topazian HM, Geibrecht D, Thwai K, Boyter K, Munyaneza T, Muvunyi CM, De Dieu Butera J, Bailey JA, Mazarati JB, Juliano JJ. Prevalence of Falciparum and non-Falciparum Malaria in the 2014-15 Rwanda Demographic Health Survey. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.09.24301054. [PMID: 38260604 PMCID: PMC10802648 DOI: 10.1101/2024.01.09.24301054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Malaria remains a major cause of morbidity in sub-Saharan Africa. Undetected asymptomatic falciparum malaria results in a large transmission reservoir and there is evidence of increasing non-falciparum malaria as malaria is controlled in Africa, both resulting in challenges for malaria control programs. Methods We performed quantitative real time PCR for 4 malaria species in 4,596 individuals from the 2014-2015 Rwanda Demographic Health Survey. Bivariate models were used to determine species-specific associations with risk factors. Results Asymptomatic falciparum malaria, P. ovale spp., and P. malariae infection had broad spatial distribution across Rwanda. P. vivax infection was rare. Overall infection prevalence was 23.6% (95%CI [21.7%, 26.0%]), with falciparum and non-falciparum at 17.6% [15.9%, 19.0%] and 8.3% [7.0%, 10.0%], respectively. Parasitemias tended to be low and mixed species infections were common, especially where malaria transmission was the highest. Falciparum infection was associated with socio-econiomic status, rural residence and low altitude. Few risk factors were associated with non-falciparum malaria. Conclusions Asymptomatic falciparum malaria and non-falciparum malaria are common and widely distributed across Rwanda. Continued molecular monitoring of Plasmodium spp. is needed to monitor these threats to malaria control in Africa.
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Affiliation(s)
- Claudia Gaither
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Camille Morgan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca Kirby
- Department of Pathology, Brown University, Providence, RI, USA
| | | | | | - Samuel J White
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Hillary M Topazian
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - David Geibrecht
- Department of Pathology, Brown University, Providence, RI, USA
| | - Kyaw Thwai
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Koby Boyter
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | | | | | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
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Watson OJ, Tran TNA, Zupko RJ, Symons T, Thomson R, Visser T, Rumisha S, Dzianach PA, Hathaway N, Kim I, Juliano JJ, Bailey JA, Slater H, Okell L, Gething P, Ghani A, Boni MF, Parr JB, Cunningham J. Global risk of selection and spread of Plasmodium falciparum histidine-rich protein 2 and 3 gene deletions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.21.23297352. [PMID: 37905102 PMCID: PMC10615018 DOI: 10.1101/2023.10.21.23297352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In the thirteen years since the first report of pfhrp2-deleted parasites in 2010, the World Health Organization (WHO) has found that 40 of 47 countries surveyed worldwide have reported pfhrp2/3 gene deletions. Due to a high prevalence of pfhrp2/3 deletions causing false-negative HRP2 RDTs, in the last five years, Eritrea, Djibouti and Ethiopia have switched or started switching to using alternative RDTs, that target pan-specific-pLDH or P. falciparum specific-pLDH alone of in combination with HRP2. However, manufacturing of alternative RDTs has not been brought to scale and there are no WHO prequalified combination tests that use Pf-pLDH instead of HRP2 for P. falciparum detection. For these reasons, the continued spread of pfhrp2/3 deletions represents a growing public health crisis that threatens efforts to control and eliminate P. falciparum malaria. National malaria control programmes, their implementing partners and test developers desperately seek pfhrp2/3 deletion data that can inform their immediate and future resource allocation. In response, we use a mathematical modelling approach to evaluate the global risk posed by pfhrp2/3 deletions and explore scenarios for how deletions will continue to spread in Africa. We incorporate current best estimates of the prevalence of pfhrp2/3 deletions and conduct a literature review to estimate model parameters known to impact the selection of pfhrp2/3 deletions for each malaria endemic country. We identify 20 countries worldwide to prioritise for surveillance and future deployment of alternative RDT, based on quickly selecting for pfhrp2/3 deletions once established. In scenarios designed to explore the continued spread of deletions in Africa, we identify 10 high threat countries that are most at risk of deletions both spreading to and subsequently being rapidly selected for. If HRP2-based RDTs continue to be relied on for malaria case management, we predict that the major route for pfhrp2 deletions to spread is south out from the current hotspot in the Horn of Africa, moving through East Africa over the next 20 years. We explore the variation in modelled timelines through an extensive parameter sensitivity analysis and despite wide uncertainties, we identify three countries that have not yet switched RDTs (Senegal, Zambia and Kenya) that are robustly identified as high risk for pfhrp2/3 deletions. These results provide a refined and updated prediction model for the emergence of pfhrp2/3 deletions in an effort to help guide pfhrp2/3 policy and prioritise future surveillance efforts and innovation.
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Affiliation(s)
- Oliver J Watson
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Robert J Zupko
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tasmin Symons
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | | | | | - Susan Rumisha
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Paulina A Dzianach
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Nicholas Hathaway
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Isaac Kim
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI
| | | | - Lucy Okell
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Peter Gething
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
- Faculty of Health Sciences, Curtin University, Bentley, Australia
| | - Azra Ghani
- Medical Research Council Centre for Global Infectious Disease Analysis, Faculty of Medicine, Imperial College London, London, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jonathan B Parr
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
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Schreidah C, Giesbrecht D, Gashema P, Young N, Munyaneza T, Muvunyi CM, Thwai K, Mazarati JB, Bailey J, Juliano JJ, Karema C. Expansion of Artemisinin Partial Resistance Mutations and Lack of Histidine Rich Protein-2 and -3 Deletions in Plasmodium falciparum infections from Rukara, Rwanda. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.17.23300081. [PMID: 38196592 PMCID: PMC10775326 DOI: 10.1101/2023.12.17.23300081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Background Emerging artemisinin resistance and diagnostic resistance are a threat to malaria control in Africa. Plasmodium falciparum kelch13 (K13) propeller-domain mutations that confer artemisinin partial resistance have emerged in Africa. K13-561H was initially described at a frequency of 7.4% from Masaka in 2014-2015 but not present in nearby Rukara. By 2018, 19.6% of isolates in Masaka and 22% of isolates in Rukara contained the mutation. Longitudinal monitoring is essential to inform control efforts. In Rukara, we sought to assess recent K13-561H prevalence changes, as well as for other key mutations. Prevalence of hrp2/3 deletions was also assessed. Methods We genotyped samples collected in Rukara in 2021 for key artemisinin and partner drug resistance mutations using molecular inversion probe assays and for hrp2/3 deletions using qPCR. Results Clinically validated K13 artemisinin partial resistance mutations continue to increase in prevalence with the overall level of artemisinin resistance mutant infections reaching 32% in Rwanda. The increase appears to be due to the rapid emergence of K13-675V (6.4%, 6/94 infections), previously not observed, rather than continued expansion of 561H (23.5% 20/85). Mutations to partner drugs and other antimalarials were variable, with high levels of multidrug resistance 1 (MDR1) N86 (95.5%) associated with lumefantrine resistance and dihydrofolate reductase (DHFR) 164L (24.7%) associated with antifolate resistance, but low levels of amodiaquine resistance polymorphisms with chloroquine resistance transporter (CRT ) 76T: at 6.1% prevalence. No hrp2 or hrp3 gene deletions associated with diagnostic resistance were found. Conclusions Increasing prevalence of artemisinin partial resistance due to K13-561H and the rapid expansion of K13-675V is concerning for the longevity of artemisinin effectiveness in the region. False negative mRDT results do not appear to be an issue with no hrp2 or hpr3 deletions detected. Continued molecular surveillance in this region and surrounding areas is needed to follow artemisinin resistance and provide early detection of partner drug resistance, which would likely compromise control and increase malaria morbidity and mortality in East Africa.
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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 : THE PREPRINT SERVER FOR HEALTH SCIENCES 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] [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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Zupko RJ, Nguyen TD, Ngabonziza JCS, Kabera M, Li H, Tran TNA, Tran KT, Uwimana A, Boni MF. Modeling policy interventions for slowing the spread of artemisinin-resistant pfkelch R561H mutations in Rwanda. Nat Med 2023; 29:2775-2784. [PMID: 37735560 PMCID: PMC10667088 DOI: 10.1038/s41591-023-02551-w] [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: 12/20/2022] [Accepted: 08/18/2023] [Indexed: 09/23/2023]
Abstract
Artemisinin combination therapies (ACTs) are highly effective at treating uncomplicated Plasmodium falciparum malaria, but the emergence of the new pfkelch13 R561H mutation in Rwanda, associated with delayed parasite clearance, suggests that interventions are needed to slow its spread. Using a Rwanda-specific spatial calibration of an individual-based malaria model, we evaluate 26 strategies aimed at minimizing treatment failures and delaying the spread of R561H after 3, 5 and 10 years. Lengthening ACT courses and deploying multiple first-line therapies (MFTs) reduced treatment failures after 5 years when compared to the current approach of a 3-d course of artemether-lumefantrine. The best among these options (an MFT policy) resulted in median treatment failure counts that were 49% lower and a median R561H allele frequency that was 0.15 lower than under baseline. New approaches to resistance management, such as triple ACTs or sequential courses of two different ACTs, were projected to have a larger impact than longer ACT courses or MFT; these were associated with median treatment failure counts in 5 years that were 81-92% lower than the current approach. A policy response to currently circulating artemisinin-resistant genotypes in Africa is urgently needed to prevent a population-wide rise in treatment failures.
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Affiliation(s)
- Robert J Zupko
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Tran Dang Nguyen
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - J Claude S Ngabonziza
- Research, Innovation and Data Science Division, Rwanda Biomedical Center (RBC), Kigali, Rwanda
- Department of Clinical Biology, University of Rwanda, Kigali, Rwanda
| | - Michee Kabera
- Malaria and Other Parasitic Diseases Division, Rwanda Biomedical Centre (RBC), Kigali, Rwanda
| | - Haojun Li
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
- Department of Computer Science, Columbia University, New York City, NY, USA
| | - Thu Nguyen-Anh Tran
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Kien Trung Tran
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Aline Uwimana
- Malaria and Other Parasitic Diseases Division, Rwanda Biomedical Centre (RBC), Kigali, Rwanda
- Louvain Drug Research Institute, Université Catholique de Louvain, Ottignies-Louvain-la-Neuve, Belgium
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Modeling to guide drug policy response to artemisinin-resistant malaria in Rwanda. Nat Med 2023; 29:2716-2717. [PMID: 37821688 DOI: 10.1038/s41591-023-02619-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
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da Silva C, Matias D, Dias B, Cancio B, Silva M, Viegas R, Chivale N, Luis S, Salvador C, Duarte D, Arnaldo P, Enosse S, Nogueira F. Anti-malarial resistance in Mozambique: Absence of Plasmodium falciparum Kelch 13 (K13) propeller domain polymorphisms associated with resistance to artemisinins. Malar J 2023; 22:160. [PMID: 37208708 DOI: 10.1186/s12936-023-04589-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Malaria remains one of the most serious public health problems in sub-Saharan Africa and Mozambique is the world's fourth largest contributor, with 4.7% of disease cases and 3.6% of total deaths due to malaria. Its control relies on the fight against the vector and treatment of confirmed cases with anti-malarial drugs. Molecular surveillance is an important tool for monitoring the spread of anti-malarial drug resistance. METHODS A cross-sectional study recruited 450 participants with malaria infection detected by Rapid Diagnostic Tests, from three different study sites (Niassa, Manica and Maputo) between April and August 2021. Correspondent blood samples were collected on filter paper (Whatman® FTA® cards), parasite DNA extracted and pfk13 gene sequenced using Sanger method. SIFT software (Sorting Intolerant From Tolerant) was used, predict whether an amino acid substitution affects protein function. RESULTS No pfkelch13-mediated artemisinin resistance gene mutation was detected in this study settings. However, non-synonymous mutations were detected at prevalence of 10.2%, 6% and 5% in Niassa, Manica and Maputo, respectively. Most (56.3%) of the reported non-synonymous mutations were due to substitution at the first base of the codon, 25% at the second base and 18.8% at the third base. Additionally, 50% of non-synonymous mutations showed a SIFTscore bellow cut off value of 0.05, therefore, they were predicted to be deleterious. CONCLUSION These results do not show an emergence of artemisinin resistance cases in Mozambique. However, the increased number of novel non-synonymous mutations highlights the relevance of increasing the number of studies focused on the molecular surveillance of artemisinin resistance markers, for its early detection.
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Affiliation(s)
- Clemente da Silva
- Global Health and Tropical Medicine (GHTM), Department of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira Nº100, 1349-008, Lisbon, Portugal.
| | - Daniela Matias
- Global Health and Tropical Medicine (GHTM), Department of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira Nº100, 1349-008, Lisbon, Portugal
| | - Brigite Dias
- Global Health and Tropical Medicine (GHTM), Department of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira Nº100, 1349-008, Lisbon, Portugal
| | - Beatriz Cancio
- Global Health and Tropical Medicine (GHTM), Department of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira Nº100, 1349-008, Lisbon, Portugal
| | - Miguel Silva
- Global Health and Tropical Medicine (GHTM), Department of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira Nº100, 1349-008, Lisbon, Portugal
| | - Ruben Viegas
- Global Health and Tropical Medicine (GHTM), Department of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira Nº100, 1349-008, Lisbon, Portugal
| | - Nordino Chivale
- Instituto Nacional de Saúde (INS), Av. Eduardo Mondlane Nº 1008, Caixa Postal 264, Maputo, Mozambique
| | - Sonia Luis
- Hospital Provincial de Matola, 2CPV+55, Matola, Mozambique
| | - Crizolgo Salvador
- Instituto Nacional de Saúde (INS), Av. Eduardo Mondlane Nº 1008, Caixa Postal 264, Maputo, Mozambique
| | - Denise Duarte
- Global Health and Tropical Medicine (GHTM), Department of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira Nº100, 1349-008, Lisbon, Portugal
| | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Av. Eduardo Mondlane Nº 1008, Caixa Postal 264, Maputo, Mozambique
| | - Sonia Enosse
- Malaria Consortium, Av. Lucas Elias Kumato, Nº 118. Bairro da Sommershield, Maputo, Mozambique
| | - Fatima Nogueira
- Global Health and Tropical Medicine (GHTM), Department of Medical Parasitology, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira Nº100, 1349-008, Lisbon, Portugal
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