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Singh A, Singh MP, Ali NA, Poriya R, Rajvanshi H, Nisar S, Bhandari S, Sahu RS, Jayswar H, Mishra AK, Das A, Kaur H, Anvikar AR, Escalante AA, Lal AA, Bharti PK. Assessment of Plasmodium falciparum drug resistance associated molecular markers in Mandla, Madhya Pradesh, India. Malar J 2023; 22:375. [PMID: 38072967 PMCID: PMC10712044 DOI: 10.1186/s12936-023-04817-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Resistance against artemisinin-based combination therapy is one of the challenges to malaria control and elimination globally. Mutations in different genes (Pfdhfr, Pfdhps, Pfk-13 and Pfmdr1) confer resistance to artesunate and sulfadoxine-pyrimethamine (AS + SP) were analysed from Mandla district, Madhya Pradesh, to assess the effectiveness of the current treatment regimen against uncomplicated Plasmodium falciparum. METHODS Dried blood spots were collected during the active fever survey and mass screening and treatment activities as part of the Malaria Elimination Demonstration Project (MEDP) from 2019 to 2020. Isolated DNA samples were used to amplify the Pfdhfr, Pfdhps, Pfk13 and Pfmdr1 genes using nested PCR and sequenced for mutation analysis using the Sanger sequencing method. RESULTS A total of 393 samples were subjected to PCR amplification, sequencing and sequence analysis; 199, 215, 235, and 141 samples were successfully sequenced for Pfdhfr, Pfdhps, Pfk13, Pfmdr1, respectively. Analysis revealed that the 53.3% double mutation (C59R, S108N) in Pfdhfr, 89.3% single mutation (G437A) in Pfdhps, 13.5% single mutants (N86Y), and 51.1% synonymous mutations in Pfmdr1 in the study area. Five different non-synonymous and two synonymous point mutations found in Pfk13, which were not associated to artemisinin resistance. CONCLUSION The study has found that mutations linked to SP resistance are increasing in frequency, which may reduce the effectiveness of this drug as a future partner in artemisinin-based combinations. No evidence of mutations linked to artemisinin resistance in Pfk13 was found, suggesting that parasites are sensitive to artemisinin derivatives in the study area. These findings are a baseline for routine molecular surveillance to proactively identify the emergence and spread of artemisinin-resistant parasites.
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Affiliation(s)
- Akansha Singh
- Indian Council of Medical Research-National Institute of Research in Tribal Health (ICMR-NIRTH), Jabalpur, Madhya Pradesh, India
- Indian Council of Medical Research-National Institute of Malaria Research (ICMR-NIMR), New Delhi, India
- University of Illinois, Urbana Champaign, Champaign, IL, USA
| | - Mrigendra P Singh
- Malaria Elimination Demonstration Project, Mandla, Madhya Pradesh, India
| | - Nazia Anwar Ali
- Indian Council of Medical Research-National Institute of Research in Tribal Health (ICMR-NIRTH), Jabalpur, Madhya Pradesh, India
| | - Rajan Poriya
- Indian Council of Medical Research-National Institute of Research in Tribal Health (ICMR-NIRTH), Jabalpur, Madhya Pradesh, India
| | - Harsh Rajvanshi
- Malaria Elimination Demonstration Project, Mandla, Madhya Pradesh, India
- Asia Pacific Leaders Malaria Alliance (APLMA), Singapore, Singapore
| | - Sekh Nisar
- Malaria Elimination Demonstration Project, Mandla, Madhya Pradesh, India
- Department of Health and Family Welfare, NHM Raigarh, Chattisgarh, India
| | - Sneha Bhandari
- Indian Council of Medical Research-National Institute of Research in Tribal Health (ICMR-NIRTH), Jabalpur, Madhya Pradesh, India
- Indian Council of Medical Research-National Institute of Research in Environment Health (ICMR-NIREH), Bhopal, Madhya Pradesh, India
| | - Ram S Sahu
- Department of Health Services, Government of Madhya Pradesh, Mandla, Madhya Pradesh, India
| | - Himanshu Jayswar
- Directorate of Health Services, Government of Madhya Pradesh, Bhopal, India
| | - Ashok K Mishra
- Indian Council of Medical Research-National Institute of Research in Tribal Health (ICMR-NIRTH), Jabalpur, Madhya Pradesh, India
| | - Aparup Das
- Indian Council of Medical Research-National Institute of Research in Tribal Health (ICMR-NIRTH), Jabalpur, Madhya Pradesh, India
| | - Harpreet Kaur
- Department of Health Research, Ministry of Health and Family Welfare, Indian Council of Medical Research, New Delhi, India
| | - Anup R Anvikar
- Indian Council of Medical Research-National Institute of Malaria Research (ICMR-NIMR), New Delhi, India
| | - Ananias A Escalante
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Altaf A Lal
- Indian Council of Medical Research-National Institute of Malaria Research (ICMR-NIMR), New Delhi, India
- Foundation for Disease Elimination and Control of India, Mumbai, Maharashtra, India
- Global Health and Pharmaceuticals Inc., Atlanta, USA
| | - Praveen K Bharti
- Indian Council of Medical Research-National Institute of Research in Tribal Health (ICMR-NIRTH), Jabalpur, Madhya Pradesh, India.
- Indian Council of Medical Research-National Institute of Malaria Research (ICMR-NIMR), New Delhi, India.
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Ozarkar A, Kanyal A, Dass S, Deshpande P, Deobagkar D, Karmodiya K. Analysis of drug resistance marker genes of Plasmodium falciparum after implementation of artemisinin-based combination therapy in Pune district, India. J Biosci 2021. [DOI: 10.1007/s12038-021-00200-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zomuanpuii R, Hmar CL, Lallawmzuala K, Hlimpuia L, Balabaskaran Nina P, Senthil Kumar N. Epidemiology of malaria and chloroquine resistance in Mizoram, northeastern India, a malaria-endemic region bordering Myanmar. Malar J 2020; 19:95. [PMID: 32103751 PMCID: PMC7045395 DOI: 10.1186/s12936-020-03170-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 02/17/2020] [Indexed: 11/30/2022] Open
Abstract
Background Mizoram, a northeastern state in India, shares international borders with Myanmar and Bangladesh and is considered to be one of the key routes through which drug-resistant parasites of Southeast Asia enter mainland India. Despite its strategic location and importance, malaria epidemiology and molecular status of chloroquine resistance had not been well documented, and since chloroquine (CQ), as the first-line treatment in Plasmodium falciparum infection was discontinued since 2008, it was expected that CQ-sensitive haplotype would be more abundant. Methods Malaria epidemiology data for the period 2010 to 2018 was collected from the office of State Vector Disease Control Programme. Plasmodium falciparum-positive blood samples were collected from government district hospitals, community health centres, primary health centres, sub-centres, and diagnostic centres from six malaria-prone districts. The samples were processed and analysed using genes–P. falciparum chloroquine-resistant transporter (pfcrt) and P. falciparum multidrug resistance 1 (pfmdr1) via sequencing of PCR amplicon from 2015 to 2017. Results Malaria occurred throughout the year and P. falciparum accounted for > 89% of total malaria cases. During 2010–2018, the highest number of malaria incidence was recorded in Lawngtlai (36% of total malaria cases; average API2010–2018 of 34.8) while Champhai remained consistently low (0.4%; average API2010–2018 of 0.04). Males of ≥ 15 years old contributed maximum (35.7%) among gender and age malarial distribution recorded during 2014–2018. Death due to malaria gradually decreased over the years. A higher abundance of mutated pfcrt (58.5% of the total sample analysed) and a lower prevalence of mutated pfmdr1 (48.7%) were observed. All mutations identified for pfcrt belong to the Southeast Asian CVIET haplotype. Only a single point mutation was observed at 86 (N → Y) position in pfmdr1 (48.7%). The key N86Y mutation in pfmdr1 that had been shown to modulate CQR was found in 67.1% of the samples positive for the CVIET haplotype. Conclusions This is the first report that details malaria epidemiology and also the molecular status of CQ-resistance in P. falciparum population of the region. The efforts of the State Vector Borne Disease Control Programme have proved to be quite effective in controlling the malaria burden in the state. Despite the discontinuation of CQ for a decade, local P. falciparum is observed with decreased CQ-sensitive haplotype. It is believed that the present findings will form a basis for further studies on genetic diversity in P. falciparum, which could confer better understanding of the complexity of the disease in Southeast Asia.
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Affiliation(s)
- Rita Zomuanpuii
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, India.
| | - Christopher L Hmar
- Department of Orthopaedics, District Hospital, Government of Mizoram, Serchhip, Aizawl, Mizoram, India
| | - Khawlhring Lallawmzuala
- Department of Medicine, District Hospital, Government of Mizoram, Serchhip, Aizawl, Mizoram, India
| | - Lal Hlimpuia
- State Vector Disease Control Programme, Department of Health and Family Welfare, Government of Mizoram, Aizawl, Mizoram, India
| | - Praveen Balabaskaran Nina
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Tiruvarur, Tamil Nadu, India
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Patel P, Bharti PK, Bansal D, Ali NA, Raman RK, Mohapatra PK, Sehgal R, Mahanta J, Sultan AA, Singh N. Prevalence of mutations linked to antimalarial resistance in Plasmodium falciparum from Chhattisgarh, Central India: A malaria elimination point of view. Sci Rep 2017; 7:16690. [PMID: 29192183 PMCID: PMC5709362 DOI: 10.1038/s41598-017-16866-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/19/2017] [Indexed: 11/09/2022] Open
Abstract
Antimalarial drug resistance is a major global challenge in malaria control and elimination. Mutations in six different genes of Plasmodium falciparum (crt, mdr1, dhfr, dhps, ATPase6 and K-13 propeller) that confer resistance to chloroquine, sulphadoxine-pyrimethamine and artemisinin-based combination therapy were analyzed in samples from Chhattisgarh. Seventy-eight percent of the samples were found to have a pfcrt mutation (53% double, 24% triple and 1% single mutant), and 59% of pfmdr1 genes were found to have an N86Y mutation. Double mutations were recorded in pfdhfr gene among 76% of the samples while only 6% of the samples harbored mutant genotypes in pfdhps. No mutation was found in the K-13 propeller gene, while only one sample showed a mutant genotype for the PfATPase6 gene. The Tajima test confirmed that there is no role of evolutionary natural selection in drug resistance, and gene pairwise linkage of disequilibrium showed significant intragenic association. The high level of pfcrt mutations suggests that parasite resistance to chloroquine is almost at a fixed level, whereas resistance to SP is evolving in the population and parasites remain sensitive to artemisinin derivatives. These findings provide potential information and understanding of the evolution and spread of different drug resistance alleles in Chhattisgarh.
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Affiliation(s)
- Priyanka Patel
- National Institute for Research in Tribal Health, Indian Council of Medical Research, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India.,Symbiosis School of Biomedical Sciences, Symbiosis International University, Lavale, Maharashtra, 412115, India
| | - Praveen K Bharti
- National Institute for Research in Tribal Health, Indian Council of Medical Research, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India
| | - Devendra Bansal
- Department of Microbiology and Immunology, Weill Cornell Medicine - Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | - Nazia A Ali
- National Institute for Research in Tribal Health, Indian Council of Medical Research, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India
| | - Rajive K Raman
- Medical Officer, Community Health Centre Janakpur, District Baikunthpur, Chhattisgarh, India
| | - Pradyumna K Mohapatra
- Regional Medical Research Centre, NE, Indian Council of Medical Research, Post Box no. 105, Dibrugarh, 786 001, Assam, India
| | - Rakesh Sehgal
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, Punjab, India
| | - Jagadish Mahanta
- Regional Medical Research Centre, NE, Indian Council of Medical Research, Post Box no. 105, Dibrugarh, 786 001, Assam, India
| | - Ali A Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine - Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | - Neeru Singh
- National Institute for Research in Tribal Health, Indian Council of Medical Research, Nagpur Road, Garha, Jabalpur, 482003, Madhya Pradesh, India.
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Prevalence of Malaria Infection and Risk Factors Associated with Anaemia among Pregnant Women in Semiurban Community of Hazaribag, Jharkhand, India. BIOMED RESEARCH INTERNATIONAL 2015; 2015:740512. [PMID: 26783526 PMCID: PMC4691455 DOI: 10.1155/2015/740512] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/13/2015] [Indexed: 01/11/2023]
Abstract
The escalating burden, pathogenesis, and clinical sequel of malaria during pregnancy have combinatorial adverse impact on both mother and foetus that further perplexed the situation of diagnosis, treatment, and prevention. This prompted us to evaluate the status of population at risk of MIP in Hazaribag, Jharkhand, India. Cross-sectional study was conducted over a year at Sadar Hospital, Hazaribag. Malaria was screened using blood smear and/or RDT. Anaemia was defined as haemoglobin concentration. Pretested questionnaires were used to gather sociodemographic, clinical, and obstetrical data. The prevalence of MIP was 5.4% and 4.3% at ANC and DU, and 13.2% malaria was in women without pregnancy. Interestingly, majority were asymptomatically infected with P. vivax (over 85%) at ANC and DU. Peripheral parasitemia was significantly associated with fever within past week, rural origin of subjects, and first/second pregnancies in multivariate analysis, with the highest risk factor associated with fever followed by rural residence. Strikingly in cohort, anaemia was prevalent in 86% at ANC as compared to 72% at DU, whereas severe anaemia was 13.6% and 7.8% at ANC and DU. Even more anaemia prevalence was observed in MIP group (88% and 89% at ANC and DU), whereas severe anaemia was 23% and 21%, respectively. In view of observed impact of anaemia, parasitemia and asymptomatic infection of P. vivax during pregnancy and delivery suggest prompt diagnosis regardless of symptoms and comprehensive drug regime should be offered to pregnant women in association with existing measures in clinical spectrum of MIP, delivery, and its outcome.
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Artimovich E, Schneider K, Taylor TE, Kublin JG, Dzinjalamala FK, Escalante AA, Plowe CV, Laufer MK, Takala-Harrison S. Persistence of Sulfadoxine-Pyrimethamine Resistance Despite Reduction of Drug Pressure in Malawi. J Infect Dis 2015; 212:694-701. [PMID: 25672905 DOI: 10.1093/infdis/jiv078] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/15/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND In 2007, Malawi replaced sulfadoxine-pyrimethamine (SP) with an artemisinin-based combination therapy as the first-line treatment for uncomplicated Plasmodium falciparum malaria in response to failing SP efficacy. Here we estimate the effect of reduced SP pressure on the prevalence of SP-resistant parasites and the characteristics of the associated selective sweeps flanking the resistance loci. METHODS Samples obtained from individuals with clinical malaria during a period of high SP use (1999-2001), a transitional period (2007-2008), and a period of low SP use (2012) were genotyped for resistance markers at pfdhfr-ts codons 51, 59, and 108 and pfdhps codons 437, 540, and 581. Expected heterozygosity was estimated to evaluate the genetic diversity flanking pfdhfr-ts and pfdhps. RESULTS An increase in the prevalence of the resistance haplotypes DHFR 51I/59R/108N and DHPS 437G/540E occurred under sustained drug pressure, with no change in haplotype prevalence 5 years after reduction in SP pressure. The DHPS 437G/540E/581G haplotype was observed in 2007 and increased in prevalence during a period of reduced SP pressure. Changes to the sweep characteristics flanking pfdhfr-ts and pfdhps were minimal. CONCLUSIONS In contrast to the rapid and complete return of chloroquine-susceptible falciparum malaria after chloroquine was withdrawn from Malawi, a reemergence of SP efficacy is unlikely in the near future.
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Affiliation(s)
- Elena Artimovich
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore
| | - Kristan Schneider
- Department of Fakultät Mathematik/Naturwissenschaften/Informatik, University of Applied Sciences Mittweida, Germany
| | | | - James G Kublin
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | - Christopher V Plowe
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore
| | - Miriam K Laufer
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore
| | - Shannon Takala-Harrison
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore
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Awasthi G, Das A. Genetics of chloroquine-resistant malaria: a haplotypic view. Mem Inst Oswaldo Cruz 2015; 108:947-61. [PMID: 24402147 PMCID: PMC4005552 DOI: 10.1590/0074-0276130274] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 09/26/2013] [Indexed: 02/05/2023] Open
Abstract
The development and rapid spread of chloroquine resistance (CQR) in
Plasmodium falciparum have triggered the identification of
several genetic target(s) in the P. falciparum genome. In
particular, mutations in the Pfcrt gene, specifically, K76T and
mutations in three other amino acids in the region adjoining K76 (residues 72, 74, 75
and 76), are considered to be highly related to CQR. These various mutations form
several different haplotypes and Pfcrt gene polymorphisms and the
global distribution of the different CQR- Pfcrt haplotypes in
endemic and non-endemic regions of P. falciparum malaria have been
the subject of extensive study. Despite the fact that the Pfcrt gene
is considered to be the primary CQR gene in P. falciparum , several
studies have suggested that this may not be the case. Furthermore, there is a poor
correlation between the evolutionary implications of the Pfcrt
haplotypes and the inferred migration of CQR P. falciparum based on
CQR epidemiological surveillance data. The present paper aims to clarify the existing
knowledge on the genetic basis of the different CQR- Pfcrt
haplotypes that are prevalent in worldwide populations based on the published
literature and to analyse the data to generate hypotheses on the genetics and
evolution of CQR malaria.
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Sutton PL. A call to arms: on refining Plasmodium vivax microsatellite marker panels for comparing global diversity. Malar J 2013; 12:447. [PMID: 24330329 PMCID: PMC3878832 DOI: 10.1186/1475-2875-12-447] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microsatellite (MS) markers have become an important tool for studying the population diversity, evolutionary history and multiplicity of infection (MOI) of malaria parasite infections. MS are typically selected on the basis of being highly polymorphic. However, it is known that the polymorphic potential (mutability) of each marker can vary as much as two orders of magnitude, which radically changes how diversity is represented in the genome from one marker to the next. Over the past decade, approximately 240 Plasmodium vivax MS have been published, comprising nine major panels of markers. Inconsistent usage of each panel has resulted in a surfeit of descriptive genetic diversity data that are largely incomparable between populations. The objective of this study was to statistically evaluate the quality of individual MS markers in order to validate a refined panel of markers that will provide a balanced picture of P. vivax population diversity. METHODS All previously published data, including genetic diversity indices, MS parameters, and population parameters, were assembled from 18 different global studies into a flat file to facilitate statistical analysis and modelling using JMP® Genomics 6.0 (SAS Institute Inc, Cary, NC, USA). Statistical modeling was employed to down-select markers with extreme variation among the mean number of alleles, expected heterozygosity, maximum repeat length and/or chromosomal location of the repeat. Individual MS were analysed by step-down whole model linear regression and standard least squares fit models, both stratified by annual parasite incidence to identify MS markers with values significantly different from the mean. RESULTS Of the 42 MS under evaluation in this study, 18 (nine high priority) were identified as ideal candidates for measuring population diversity between global regions, while five (two high priority) additional markers were identified as candidates for MOI studies. CONCLUSIONS MS diversity was found to be a function of endemicity and motif structure. Evaluation of individual MS permitted the assembly of a refined panel of markers that can be reliably utilized in the field to compare population structures between global regions.
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Affiliation(s)
- Patrick L Sutton
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
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Mallick PK, Singh R, Singh OP, Singh AK, Bhasin VK, Valecha N. Reduced heterozygosity at intragenic and flanking microsatellites of pfcrt gene establishes natural selection based molecular evolution of chloroquine-resistant Plasmodium falciparum in India. INFECTION GENETICS AND EVOLUTION 2013; 20:407-12. [DOI: 10.1016/j.meegid.2013.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/24/2013] [Accepted: 10/01/2013] [Indexed: 11/26/2022]
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Chauhan K, Pande V, Das A. Analyses of genetic variations at microsatellite loci present in-and-around the Pfcrt gene in Indian Plasmodium falciparum. INFECTION GENETICS AND EVOLUTION 2013; 20:476-87. [PMID: 24157593 DOI: 10.1016/j.meegid.2013.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/10/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
Evolution and spread of chloroquine resistant (CQR) malaria parasite Plasmodium falciparum have posed great threat in malaria intervention across the globe. The occurrence of K76T mutation in the P. falciparum chloroquine resistance transporter (pfcrt) gene has been widely attributed to CQR with four neighboring mutations providing compensatory fitness benefit to the parasite survival. Understanding evolutionary patterns of the pfcrt gene is of great relevance not only for devising new malaria control measures but also could serve as a model to understand evolution and spread of other human drug-resistant pathogens. Several studies, mainly based on differential patterns of diversities of the microsatellite loci placed in-and-around the pfcrt gene have indicated the role of positive natural selection under the 'hitchhiking' model of molecular evolution. However, the studies were restricted to limited number of microsatellite loci present inside the pfcrt gene. Moreover, comparatively higher level of diversities in microsatellite loci present inside the pfcrt gene than the loci flanking the pfcrt gene are hallmarks of Indian P. falciparum, presenting contrasting evolutionary models to global isolates. With a view to infer evolutionary patterns of the pfcrt gene in Indian P. falciparum, we have adopted a unique sampling scheme of two types of populations (cultured and field collected) and utilized 20 polymorphic microsatellite loci (16 located inside the pfcrt gene and four in the two flanking regions) to disentangle between genetic drift (inbred cultured isolates) and natural selection (field isolates). Data analyses employing different population genetic tests could not straightforwardly explain either the model invoking 'genetic hitchhiking' or 'genetic drift'. However, complex evolutionary models influenced by both demography and natural selection or an alternative model of natural selection (e.g. diversifying/balancing selection) might better explain the observed microsatellite variation in-and-around the pfcrt gene in Indian P. falciparum.
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Affiliation(s)
- Kshipra Chauhan
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi 110077, India
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Khattak AA, Venkatesan M, Jacob CG, Artimovich EM, Nadeem MF, Nighat F, Hombhanje F, Mita T, Malik SA, Plowe CV. A comprehensive survey of polymorphisms conferring anti-malarial resistance in Plasmodium falciparum across Pakistan. Malar J 2013; 12:300. [PMID: 23988011 PMCID: PMC3765786 DOI: 10.1186/1475-2875-12-300] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/26/2013] [Indexed: 11/16/2022] Open
Abstract
Background Few studies have been conducted in Pakistan to determine the efficacy of chloroquine and sulphadoxine-pyrimethamine (SP), which remain in use as treatment for Plasmodium vivax and in combination with artesunate to treat Plasmodium falciparum, respectively. In this study, samples from several sites across Pakistan were characterized to determine prevalence of molecular resistance markers in the P. falciparum chloroquine resistance transporter (pfcrt), multidrug resistance (pfmdr1), dihydrofolate reductase (pfdhfr) and dihydropteroate synthase (pfdhps) genes and the origin of chloroquine-resistant P. falciparum parasites. Methods Microscopy-confirmed malaria parasite-positive blood samples from 801 patients across the country were collected in 2011. Of these, 171 infections were identified by polymerase chain reaction (PCR) as P. falciparum and analysed by pyrosequencing for mutations conferring chloroquine resistance (pfcrt codons 72–76), multidrug resistance (pfmdr1 N86Y, Y184F, S1034C, N1042D and D1246Y), pyrimethamine resistance (pfdhfr, C50R, N51I, C59R, S108N and I164L) and sulphadoxine resistance (pfdhps, S436A, A437G, K540E, A581G and A613T/S). pfmdr1 gene copy number variation was determined by real-time PCR, and microsatellites flanking the pfcrt locus were typed to determine the origin of the chloroquine-resistant haplotype. Results The pfcrt K76T mutation was found in all samples as part of the S72/V73/M74/N75/T76 (SVMNT) haplotype. Microsatellites flanking pfcrt showed high similarity to the signature found in India and Papua New Guinea. pfmdr1 N86Y was found in 20% of samples and all samples harboured a single copy of the pfmdr1 gene. The pfdhfr double mutation C59R + S108N was present in 87% of samples while the pfdhfr triple mutant (N51I + C59R + S108N) was not detected. Pfdhps A437G was found in 60% of samples. Pure pfdhps K540E was rare, at 4%, but mixed genotype 540 K/E was found in 77% of samples. Similarly, pure pfdhps A581G was found in 4% of the isolates while mixed 581A/G was found in 39% of samples. Conclusions These results suggest an emerging problem with multidrug resistant P. falciparum in Pakistan. The chloroquine resistance genotype has reached complete fixation in the population, with a microsatellite pattern indicative of a selective sweep. Moreover, the prevalence of mutations in both pfdhfr and pfdhps, albeit without the presence of the pfdhfr triple mutant, indicates that continued monitoring is warranted to assess whether SP remains efficacious as a partner drug for artesunate for the treatment of P. falciparum.
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Affiliation(s)
- Aamer A Khattak
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA.
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Microsatellite analysis of chloroquine resistance associated alleles and neutral loci reveal genetic structure of Indian Plasmodium falciparum. INFECTION GENETICS AND EVOLUTION 2013; 19:164-75. [PMID: 23871774 DOI: 10.1016/j.meegid.2013.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/03/2013] [Accepted: 07/06/2013] [Indexed: 11/20/2022]
Abstract
Efforts to control malignant malaria caused by Plasmodium falciparum are hampered by the parasite's acquisition of resistance to antimalarial drugs, e.g., chloroquine. This necessitates evaluating the spread of chloroquine resistance in any malaria-endemic area. India displays highly variable malaria epidemiology and also shares porous international borders with malaria-endemic Southeast Asian countries having multi-drug resistant malaria. Malaria epidemiology in India is believed to be affected by two major factors: high genetic diversity and evolving drug resistance in P. falciparum. How transmission intensity of malaria can influence the genetic structure of chloroquine-resistant P. falciparum population in India is unknown. Here, genetic diversity within and among P. falciparum populations is analyzed with respect to their prevalence and chloroquine resistance observed in 13 different locations in India. Microsatellites developed for P. falciparum, including three putatively neutral and seven microsatellites thought to be under a hitchhiking effect due to chloroquine selection were used. Genetic hitchhiking is observed in five of seven microsatellites flanking the gene responsible for chloroquine resistance. Genetic admixture analysis and F-statistics detected genetically distinct groups in accordance with transmission intensity of different locations and the probable use of chloroquine. A large genetic break between the chloroquine-resistant parasite of the Northeast-East-Island group and Southwest group (FST=0.253, P<0.001) suggests a long period of isolation or a possibility of different origin between them. A pattern of significant isolation by distance was observed in low transmission areas (r=0.49, P=0.003, N=83, Mantel test). An unanticipated pattern of spread of hitchhiking suggests genetic structure for Indian P. falciparum population. Overall, the study suggests that transmission intensity can be an efficient driver for genetic differentiation at both neutral and adaptive loci across India.
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Tyagi RK, Das MK, Singh SS, Sharma YD. Discordance in drug resistance-associated mutation patterns in marker genes of Plasmodium falciparum and Plasmodium knowlesi during coinfections. J Antimicrob Chemother 2013; 68:1081-8. [DOI: 10.1093/jac/dks508] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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PfCRT and its role in antimalarial drug resistance. Trends Parasitol 2012; 28:504-14. [PMID: 23020971 DOI: 10.1016/j.pt.2012.08.002] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 08/09/2012] [Accepted: 08/13/2012] [Indexed: 12/15/2022]
Abstract
Plasmodium falciparum resistance to chloroquine, the former gold standard antimalarial drug, is mediated primarily by mutant forms of the chloroquine resistance transporter (PfCRT). These mutations impart upon PfCRT the ability to efflux chloroquine from the intracellular digestive vacuole, the site of drug action. Recent studies reveal that PfCRT variants can also affect parasite fitness, protect immature gametocytes against chloroquine action, and alter P. falciparum susceptibility to current first-line therapies. These results highlight the need to be vigilant in screening for the appearance of novel pfcrt alleles that could contribute to new multi-drug resistance phenotypes.
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