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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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Bakari C, Mandara CI, Madebe RA, Seth MD, Ngasala B, Kamugisha E, Ahmed M, Francis F, Bushukatale S, Chiduo M, Makene T, Kabanywanyi AM, Mahende MK, Kavishe RA, Muro F, Mkude S, Mandike R, Molteni F, Chacky F, Bishanga DR, Njau RJA, Warsame M, Kabula B, Nyinondi SS, Lucchi NW, Talundzic E, Venkatesan M, Moriarty LF, Serbantez N, Kitojo C, Reaves EJ, Halsey ES, Mohamed A, Udhayakumar V, Ishengoma DS. Trends of Plasmodium falciparum molecular markers associated with resistance to artemisinins and reduced susceptibility to lumefantrine in Mainland Tanzania from 2016 to 2021. Malar J 2024; 23:71. [PMID: 38461239 PMCID: PMC10924419 DOI: 10.1186/s12936-024-04896-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/28/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Therapeutic efficacy studies (TESs) and detection of molecular markers of drug resistance are recommended by the World Health Organization (WHO) to monitor the efficacy of artemisinin-based combination therapy (ACT). This study assessed the trends of molecular markers of artemisinin resistance and/or reduced susceptibility to lumefantrine using samples collected in TES conducted in Mainland Tanzania from 2016 to 2021. METHODS A total of 2,015 samples were collected during TES of artemether-lumefantrine at eight sentinel sites (in Kigoma, Mbeya, Morogoro, Mtwara, Mwanza, Pwani, Tabora, and Tanga regions) between 2016 and 2021. Photo-induced electron transfer polymerase chain reaction (PET-PCR) was used to confirm presence of malaria parasites before capillary sequencing, which targeted two genes: Plasmodium falciparum kelch 13 propeller domain (k13) and P. falciparum multidrug resistance 1 (pfmdr1). RESULTS Sequencing success was ≥ 87.8%, and 1,724/1,769 (97.5%) k13 wild-type samples were detected. Thirty-seven (2.1%) samples had synonymous mutations and only eight (0.4%) had non-synonymous mutations in the k13 gene; seven of these were not validated by the WHO as molecular markers of resistance. One sample from Morogoro in 2020 had a k13 R622I mutation, which is a validated marker of artemisinin partial resistance. For pfmdr1, all except two samples carried N86 (wild-type), while mutations at Y184F increased from 33.9% in 2016 to about 60.5% in 2021, and only four samples (0.2%) had D1246Y mutations. pfmdr1 haplotypes were reported in 1,711 samples, with 985 (57.6%) NYD, 720 (42.1%) NFD, and six (0.4%) carrying minor haplotypes (three with NYY, 0.2%; YFD in two, 0.1%; and NFY in one sample, 0.1%). Between 2016 and 2021, NYD decreased from 66.1% to 45.2%, while NFD increased from 38.5% to 54.7%. CONCLUSION This is the first report of the R622I (k13 validated mutation) in Tanzania. N86 and D1246 were nearly fixed, while increases in Y184F mutations and NFD haplotype were observed between 2016 and 2021. Despite the reports of artemisinin partial resistance in Rwanda and Uganda, this study did not report any other validated mutations in these study sites in Tanzania apart from R622I suggesting that intensified surveillance is urgently needed to monitor trends of drug resistance markers and their impact on the performance of ACT.
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Affiliation(s)
- Catherine Bakari
- National Institute for Medical Research, Dar Es Salaam, Tanzania
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Celine I Mandara
- 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
| | - Billy Ngasala
- Department of Parasitology, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Erasmus Kamugisha
- Catholic University of Health and Allied Sciences, Bugando Medical Centre, Mwanza, Tanzania
| | - Maimuna Ahmed
- Catholic University of Health and Allied Sciences, Bugando Medical Centre, Mwanza, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Samwel Bushukatale
- Department of Parasitology, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Mercy Chiduo
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Twilumba Makene
- Department of Parasitology, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | | | - Muhidin K Mahende
- Ifakara Health Institute, Dar Es Salaam Office, Dar Es Salaam, Tanzania
| | | | - Florida Muro
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | | | - Fabrizio Molteni
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- National Malaria Control Program, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Program, Dodoma, Tanzania
| | - Dunstan R Bishanga
- Ifakara Health Institute, Dar Es Salaam Office, Dar Es Salaam, Tanzania
- Maternal and Child Survival Program, Jhpiego, Dar Es Salaam, Tanzania
- School of Public Health and Social Sciences, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Ritha J A Njau
- Malariologist and Public Health Specialist, Dar Es Salaam, Tanzania
| | | | - Bilali Kabula
- PMI/Okoa Maisha Dhibiti Malaria, RTI International, Dar Es Salaam, Tanzania
- National Institute for Medical Research, Amani Research Centre, Muheza, Tanga, Tanzania
| | - Ssanyu S Nyinondi
- PMI/Okoa Maisha Dhibiti Malaria, RTI International, Dar Es Salaam, Tanzania
| | - Naomi W Lucchi
- Malaria Branch, U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
- Division of Global Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Eldin Talundzic
- Malaria Branch, U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Leah F Moriarty
- Malaria Branch, U.S. President's Malaria Initiative, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Naomi Serbantez
- U.S. President's Malaria Initiative, USAID, Dar Es Salaam, Tanzania
| | - Chonge Kitojo
- U.S. President's Malaria Initiative, USAID, Dar Es Salaam, Tanzania
| | - Erik J Reaves
- U.S. President's Malaria Initiative, US Centers for Disease Control and Prevention, Dar Es Salaam, Tanzania
| | - Eric S Halsey
- Malaria Branch, U.S. President's Malaria Initiative, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ally Mohamed
- National Malaria Control Program, Dodoma, Tanzania
| | - Venkatachalam Udhayakumar
- Malaria Branch, U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
- Independenant Consultant, Decatur, Georgia
| | - 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.
- Department of Biochemistry, Kampala International University, Dar Es Salaam, Tanzania.
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Canavati SE, Quintero CE, Haller B, Lek D, Yok S, Richards JS, Whittaker MA. Maximizing research study effectiveness in malaria elimination settings: a mixed methods study to capture the experiences of field-based staff. Malar J 2017; 16:362. [PMID: 28893264 PMCID: PMC5594431 DOI: 10.1186/s12936-017-2016-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 09/06/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In a drug-resistant, malaria elimination setting like Western Cambodia, field research is essential for the development of novel anti-malarial regimens and the public health solutions necessary to monitor the spread of resistance and eliminate infection. Such field studies often face a variety of similar implementation challenges, but these are rarely captured in a systematic way or used to optimize future study designs that might overcome similar challenges. Field-based research staff often have extensive experience and can provide valuable insight regarding these issues, but their perspectives and experiences are rarely documented and seldom integrated into future research protocols. This mixed-methods analysis sought to gain an understanding of the daily challenges encountered by research field staff in the artemisinin-resistant, malaria elimination setting of Western Cambodia. In doing so, this study seeks to understand how the experiences and opinions of field staff can be captured, and used to inform future study designs. METHODS Twenty-two reports from six field-based malaria studies conducted in Western Cambodia were reviewed using content analysis to identify challenges to conducting the research. Informal Interviews, Focus Group Discussions and In-depth Interviews were also conducted among field research staff. Thematic analysis of the data was undertaken using Nvivo 9® software. Triangulation and critical case analysis was also used. RESULTS There was a lack of formalized avenues through which field workers could report challenges experienced when conducting the malaria studies. Field research staff faced significant logistical barriers to participant recruitment and data collection, including a lack of available transportation to cover long distances, and the fact that mobile and migrant populations (MMPs) are usually excluded from studies because of challenges in follow-up. Cultural barriers to communication also hindered participant recruitment and created unexpected delays. Field staff often paid a physical, emotional and financial cost, going beyond their duty in order to keep the study running. CONCLUSIONS Formal monthly reports filled out by field study staff could be a key tool for capturing field study staff experiences effectively, but require specific report fields to encourage staff to outline their challenges and to propose potential solutions. Forging strong bonds with communities and their leaders may improve communication, and decrease barriers to participant recruitment. Study designs that make it feasible for MMPs to participate should be pursued; in addition to increasing the potential participant pool, this will ensure that the most malaria-endemic demographic is taken into account in research studies. Overlaps between clinical care and research create ethical dilemmas for study staff, a fact that warrants careful consideration. Lessons learned from study field staff should be used to create a set of locally-relevant recommendations to inform future study designs.
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Affiliation(s)
- Sara E. Canavati
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Vysnova Partners Inc., Washington, DC USA
| | - Cesia E. Quintero
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | | | - Dysoley Lek
- The National Centre for Parasitology, Entomology and Malaria Control, Ministry of Health, Phnom Penh, Cambodia
| | - Sovann Yok
- Provincial Health Department, Pailin City, Pailin Province Cambodia
| | - Jack S. Richards
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Medicine, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Department of Infectious Diseases, Monash University, Melbourne, Australia
| | - Maxine Anne Whittaker
- College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Australia
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