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Sadler JM, Simkin A, Tchuenkam VPK, Gerdes Gyuricza I, Fola AA, Wamae K, Assefa A, Niaré K, Thwai K, White SJ, Moss WJ, Dinglasan RR, Nsango S, Tume CB, Parr JB, Ali IM, Bailey JA, Juliano JJ. Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.10.03.24314715. [PMID: 39417120 PMCID: PMC11482863 DOI: 10.1101/2024.10.03.24314715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Background Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires open-source protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing. Methods P lasmodium falciparum S treamlined M ultiplex A ntimalarial R esistance and R elatedness T esting ( Pf -SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach. Results We evaluated Pf -SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. We then piloted Pf -SMARRT to genotype 100 parasite isolates collected from uncomplicated malaria cases at three health facilities in Dschang, Western Cameroon. Antimalarial resistance genotyping showed high levels of sulfadoxine-pyrimethamine resistance mutations, including 31% prevalence of the DHPS A613S mutation. No K13 candidate or validated artemisinin partial resistance mutations were detected, but one low-level non-synonymous change was observed. Pf -SMARRT's hypervariable targets, used to assess complexity of infections and parasite diversity and relatedness, showed similar levels and patterns compared to molecular inversion probe (MIP) sequencing. While there was strong concordance of antimalarial resistance mutations between individual samples and pools, low-frequency variants in the pooled samples were often missed. Conclusion Overall, Pf -SMARRT is a robust tool for assessing parasite relatedness and antimalarial drug resistance markers from both individual and pooled samples. Control samples support that accurate genotyping as low as 1 parasite per microliter is routinely possible. SCOPE STATEMENT 200 Malaria remains a critical global public health problem. Antimalarial drug resistance has repeatedly undermined control and the emergence of artemisinin partial resistance in Africa is the latest major challenge. Malaria molecular surveillance (MMS) has emerged as a powerful tool to monitor molecular markers of resistance and changes in the parasite population. Streamlined methods are needed that can be readily adopted in endemic countries. We developed P lasmodium falciparum S treamlined M ultiplex A ntimalarial R esistance and R elatedness T esting ( Pf -SMARRT), a multiplex amplicon deep sequencing approach that uses easily accessible products without proprietary steps and can be sequenced on any Illumina sequencer. We validated this tool using controls, including mocked dried blood spots, and then implemented it to evaluate resistance and parasite relatedness among 100 samples from Cameroon. The assay was able to reliably assess the within-sample allele frequency of antimalarial resistance markers and discriminate strains within and between individuals. We also evaluated a more cost-effective surveillance approach for antimalarial resistance polymorphisms using pooled samples. While within-pool frequencies of mutations were accurate in pools with higher numbers of samples, this resulted in the loss of the ability to detect variants uncommon in the pool. Overall Pf- SMARRT provides a new protocol for conducting MMS that is easily implementable in Africa.
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Kucharski M, Nayak S, Gendrot M, Dondorp AM, Bozdech Z. Peeling the onion: how complex is the artemisinin resistance genetic trait of malaria parasites? Trends Parasitol 2024:S1471-4922(24)00245-9. [PMID: 39358163 DOI: 10.1016/j.pt.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 09/02/2024] [Accepted: 09/09/2024] [Indexed: 10/04/2024]
Abstract
The genetics of Plasmodium as an intracellular, mostly haploid, sexually reproducing, eukaryotic organism with a complex life cycle, presents unprecedented challenges in studying drug resistance. This article summarizes current knowledge on the genetic basis of artemisinin resistance (AR) - a main component of current drug therapies for falciparum malaria. Although centered on nonsynonymous single-nucleotide polymorphisms (nsSNPs), we describe multifaceted resistance mechanisms as part of a complex, cumulative genetic trait that involves regulation of expression by a wide array of polymorphisms in noncoding regions. These genetic variations alter transcriptome profiles linked to Plasmodium's development and population dynamics, ultimately influencing the emergence and spread of the resistance.
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Affiliation(s)
- Michal Kucharski
- School of Biological Sciences, Nanyang Technological University, Singapore; Amsterdam UMC, University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Sourav Nayak
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Mathieu Gendrot
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore; Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Cabrera-Sosa L, Safarpour M, Kattenberg JH, Ramirez R, Vinetz J, Rosanas-Urgell A, Gamboa D, Delgado-Ratto C. Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.611954. [PMID: 39314390 PMCID: PMC11418992 DOI: 10.1101/2024.09.09.611954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv & 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs & Pf: 28 SNPs) and MS panels (Pv: 16 MS & Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He ) was similar across the subpopulations for both makers: He MS = 0.68 - 0.78 (p = 0.23) and He SNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, F ST ) was also comparable: F ST-MS = 0.04 - 0.14 and F ST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends ( He MS = 0 - 0.48 p = 0.03 - 1; He SNP = 0 - 0.09, p = 0.03 - 1) and pairwise F ST comparisons (F ST-MS = 0.14 - 0.65, F ST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.
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Hossain MS, Matin MA, Ferdous NEN, Hasan A, Sazed SA, Neogi AK, Chakma S, Islam MA, Khan AA, Haque ME, Islam S, Islam MN, Khan WA, Islam MA, Haque R, Alam MS. Adherence to Anti-Malarial Treatment in Malaria Endemic Areas of Bangladesh. Pathogens 2023; 12:1392. [PMID: 38133277 PMCID: PMC10745796 DOI: 10.3390/pathogens12121392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Ensuring adherence to antimalarial treatment is crucial for achieving a radical cure and elimination of malaria, especially in hard-to-reach areas. We conducted this study to assess the current scenario of drug adherence in four endemic sub-districts of Bangladesh. Among 110 enrolled participants, 70% were mono-infected with Plasmodium falciparum and the remaining 30% with P. vivax. The overall treatment adherence frequency was 92.7% (95% CI: 83.0-96.3%). A total of eight participants were found to be nonadherent to treatment and all of them were from Bandarban. Level of nonadherence was equally observed in two age groups: 11-17 and 18+ years. However, male participants (n = 6) were found to be more nonadherent than females (n = 2). Among 7.3% with nonadherence to treatment, a single participant with P. falciparum mono-infection refused to take medication and became nonadherent. Remaining participants stated that they were feeling well and going to work, thus leaving treatment course uncompleted. Although overall compliance with malaria medication seems good, a gradual increase in noncompliance to P. vivax malaria treatment suggests that the National Malaria Elimination Program must be enhanced and monitored to fulfil the projected malaria elimination goal before 2030 from Bangladesh.
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Affiliation(s)
- Mohammad Sharif Hossain
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.S.H.); (M.A.M.); (M.A.I.); (W.A.K.); (R.H.)
| | - Mohammad Abdul Matin
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.S.H.); (M.A.M.); (M.A.I.); (W.A.K.); (R.H.)
| | - Nur-E Naznin Ferdous
- Bangladesh Rural Advancement Committee (BRAC) Health Programme, BRAC, Dhaka 1212, Bangladesh (A.K.N.)
| | - Anamul Hasan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.S.H.); (M.A.M.); (M.A.I.); (W.A.K.); (R.H.)
| | - Saiful Arefeen Sazed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.S.H.); (M.A.M.); (M.A.I.); (W.A.K.); (R.H.)
| | - Amit Kumer Neogi
- Bangladesh Rural Advancement Committee (BRAC) Health Programme, BRAC, Dhaka 1212, Bangladesh (A.K.N.)
| | - Sumit Chakma
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.S.H.); (M.A.M.); (M.A.I.); (W.A.K.); (R.H.)
| | - Md. Atiqul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.S.H.); (M.A.M.); (M.A.I.); (W.A.K.); (R.H.)
| | - Afsana Alamgir Khan
- Directorate General of Health Services (DGHS), Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka 1212, Bangladesh (M.N.I.)
| | - Md. Ekramul Haque
- Directorate General of Health Services (DGHS), Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka 1212, Bangladesh (M.N.I.)
| | - Shayla Islam
- Bangladesh Rural Advancement Committee (BRAC) Health Programme, BRAC, Dhaka 1212, Bangladesh (A.K.N.)
| | - Md. Nazmul Islam
- Directorate General of Health Services (DGHS), Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka 1212, Bangladesh (M.N.I.)
| | - Wasif Ali Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.S.H.); (M.A.M.); (M.A.I.); (W.A.K.); (R.H.)
| | - Md. Akramul Islam
- Bangladesh Rural Advancement Committee (BRAC) Health Programme, BRAC, Dhaka 1212, Bangladesh (A.K.N.)
| | - Rashidul Haque
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.S.H.); (M.A.M.); (M.A.I.); (W.A.K.); (R.H.)
| | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (M.S.H.); (M.A.M.); (M.A.I.); (W.A.K.); (R.H.)
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