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Narang G, Jakhan J, Tamang S, Yadav K, Singh V. Characterization of drug resistance genes in Indian Plasmodium falciparum and Plasmodium vivax field isolates. Acta Trop 2024; 255:107218. [PMID: 38636585 DOI: 10.1016/j.actatropica.2024.107218] [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: 11/14/2023] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
One of the major challenges for malaria control and elimination is the spread and emergence of antimalarial drug resistance. Mutations in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) field isolates for five drug resistance genes viz. crt, mdr1, dhps, dhfr and kelch known to confer resistance to choloroquine (CQ), sulfadoxine-pyrimethamine (SP) and artemisinin (ART) and its derivatives were analyzed. A total of 342 symptomatic isolates of P. falciparum (Pf) and P. vivax (Pv) from 1993 to 2014 were retrieved from malaria parasite repository at National Institute of Malaria Research (NIMR). Sample DNA was extracted from dried blood spots and various targeted single nucleotide polymorphisms (SNPs) associated with antimalarial drug resistance were analysed for these isolates. 72S (67.7%) and 76T (83.8%) mutations along with SVMNT haplotype (67.7%) predominated the study population for Pfcrt. The most prevalent SNPs were 108N (73.2%) and 437G (24.8%) and the most prevalent haplotypes were ACNRNI (51.9%) and SAKAA (74.5%) in Pfdhfr and Pfdhps respectively. Only two mutations in Pfmdr1, 86Y (26.31%) and 184F (56.26%), were seen frequently in our study population. No mutations associated with Pfk13 were observed. For Pv, all the studied isolates showed two Pvdhps mutations, 383G and 553G, and two Pfdhfr mutations, 58R and 117N. Similarly, three mutations, viz. 958M, 908L and 1076L were found in Pvmdr1. No variations were observed in Pvcrt-o and Pvk12 genes. Overall, our study demonstrates an increase in mutations associated with SP resistance in both Pf and Pv, however, no single nucleotide polymorphisms (SNPs) associated with ART resistance have been observed for either species. Various SNPs associated with CQ resistance were seen in Pf; whereas only Pvmdr1 associated resistant SNPs were observed in Pv. Therefore, molecular characterization of drug resistance genes is essential for timely monitoring and prevention of malaria by identifying the circulating drug resistant parasites in the country.
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Affiliation(s)
- Geetika Narang
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Jahnvi Jakhan
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Suman Tamang
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Karmveer Yadav
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India
| | - Vineeta Singh
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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Acharya A, Naskar A, Chaudhury A, Sardar AA, Samanta A, Guha SK, Maji AK, Bera DK, Saha P. Prevalence of polymorphisms in marker genes associated with antimalarial drug resistance in Plasmodium falciparum following 10 years of artemisinin-based combination therapy implementation in urban Kolkata. Trop Parasitol 2024; 14:23-29. [PMID: 38444799 PMCID: PMC10911185 DOI: 10.4103/tp.tp_43_23] [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: 07/06/2023] [Revised: 09/05/2023] [Accepted: 10/19/2023] [Indexed: 03/07/2024] Open
Abstract
Context Resistance to antimalarial drugs is one of the major challenges for malaria elimination. In India, artemisinin combination therapy (artesunate-sulfadoxin pyrimethamine) was introduced in place of chloroquine (CQ) for the treatment of uncomplicated falciparum malaria in 2010. Periodical monitoring of polymorphisms in antimalarial drug resistance marker genes will be useful for assessing drug pressure, mapping and monitoring of drug resistance status; and will be helpful for searching alternative treatments. Objectives This study was conducted to study the polymorphisms in antimalarial drug resistance marker genes among clinical Plasmodium falciparum isolates collected from Kolkata after 10 years of artemisinin-based combination therapie (ACT) implementation. Materials and Methods Blood samples were collected from P. falciparum mono-infected patients and polymorphisms in P. falciparum CQ resistance transporter (pfcrt), P. falciparum multidrug resistance (pfmdr-1), P. falciparum dihydrofolate reductase (pfdhfr), P. falciparum dihydropteroate synthetase (pfdhps), pfATPase6 and pfK-13 propeller genes were analysed by polymerase chain reaction and DNA sequencing. Results In pfcrt gene, C72S, and K76T mutation was recorded in 100% isolates and no mutations was detected in any of the targeted codons of pfmdr-1 gene. A double mutant pfcrt haplotype SVMNT and wildtype haplotype NYD in pfmdr-1 were prevalent in 100% of study isolates. Triple mutant pfdhfr-pfdhps haplotype ANRNI-SGKAA was recorded. No polymorphism in pfK13 gene was documented in any of the isolates. Conclusions Observed wild codon N86 along with Y184 and D1246 of pfmdr-1 gene might be an indication of the reappearance of CQ sensitivity. The absence of quadruple and quintuple haplotypes in pfdhfr-pfdhps gene along with the wild haplotype of pfK13 is evidence of ACT effectivity. Hence, similar studies with large sample size are highly suggested for monitoring the drug resistance status of P. falciparum.
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Affiliation(s)
| | - Arindam Naskar
- Department of Tropical Medicine, Kolkata, West Bengal, India
| | - Abhijit Chaudhury
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences and Sri Padmavathi Medical College (Women), Tirupati, Andhra Pradesh, India
| | | | | | | | | | | | - Pabitra Saha
- Department of Microbiology, Kolkata, West Bengal, India
- Department of Zoology, P. R. Thakur Government College, North 24 Parganas, West Bengal, India
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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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Kojom Foko LP, Narang G, Jakhan J, Tamang S, Moun A, Singh V. Nationwide spatiotemporal drug resistance genetic profiling from over three decades in Indian Plasmodium falciparum and Plasmodium vivax isolates. Malar J 2023; 22:236. [PMID: 37582796 PMCID: PMC10428610 DOI: 10.1186/s12936-023-04651-x] [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: 03/09/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND Drug resistance is a serious impediment to efficient control and elimination of malaria in endemic areas. METHODS This study aimed at analysing the genetic profile of molecular drug resistance in Plasmodium falciparum and Plasmodium vivax parasites from India over a ~ 30-year period (1993-2019). Blood samples of P. falciparum and/or P. vivax-infected patients were collected from 14 regions across India. Plasmodial genome was extracted and used for PCR amplification and sequencing of drug resistance genes in P. falciparum (crt, dhps, dhfr, mdr1, k13) and P. vivax (crt-o, dhps, dhfr, mdr1, k12) field isolates. RESULTS The double mutant pfcrt SVMNT was highly predominant across the country over three decades, with restricted presence of triple mutant CVIET from Maharashtra in 2012. High rates of pfdhfr-pfdhps quadruple mutants were observed with marginal presence of "fully resistant" quintuple mutant ACIRNI-ISGEAA. Also, resistant pfdhfr and pfdhps haplotype has significantly increased in Delhi between 1994 and 2010. For pfmdr1, only 86Y and 184F mutations were present while no pfk13 mutations associated with artemisinin resistance were observed. Regarding P. vivax isolates, the pvcrt-o K10 "AAG" insertion was absent in all samples collected from Delhi in 2017. Pvdhps double mutant SGNAV was found only in Goa samples of year 2008 for the first time. The pvmdr1 908L, 958M and 1076L mutations were highly prevalent in Delhi and Haryana between 2015 and 2019 at complete fixation. One nonsynonymous novel pvk12 polymorphism was identified (K264R) in Goa. CONCLUSIONS These findings support continuous surveillance and characterization of P. falciparum and P. vivax populations as proxy for effectiveness of anti-malarial drugs in India, especially for independent emergence of artemisinin drug resistance as recently seen in Africa.
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Affiliation(s)
- Loick P Kojom Foko
- Parasite & Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, Sector 8, New Delhi, 110077, India
| | - Geetika Narang
- Parasite & Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, Sector 8, New Delhi, 110077, India
| | - Jahnvi Jakhan
- Parasite & Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, Sector 8, New Delhi, 110077, India
| | - Suman Tamang
- Parasite & Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, Sector 8, New Delhi, 110077, India
| | - Amit Moun
- Parasite & Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, Sector 8, New Delhi, 110077, India
| | - Vineeta Singh
- Parasite & Host Biology Group, ICMR-National Institute of Malaria Research, Dwarka, Sector 8, New Delhi, 110077, India.
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Barman L, Sharma A, Kakati S, Sarma DK, Hussain E, Saikia L. Molecular detection of drug-resistant Plasmodium falciparum mutants in Assam. Indian J Med Res 2023; 158:55-65. [PMID: 37602587 PMCID: PMC10550066 DOI: 10.4103/ijmr.ijmr_2976_20] [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: 07/09/2020] [Indexed: 08/22/2023] Open
Abstract
Background & objectives The spread of drug-resistant Plasmodium falciparum (Pf) poses a serious threat to the control and elimination of malaria. The objective of this study was to detect the molecular biomarkers of antimalarial drug resistance in Pf in patients visiting a tertiary care hospital in Assam. Methods Malaria was first detected in fever cases using microscopy and a rapid diagnostic test (RDT), and then confirmed using PCR. Pf chloroquine resistance transporter (Pfcrt), Pf multidrug resistance-1 (Pfmdr-1), and single-nucleotide polymorphisms linked to delayed parasite clearance after treatment with artemisinin MAL 10-688956 and MAL 13-1718319 and Kelch-13 propeller (PfK-13) genes were evaluated by PCR-restriction fragment length polymorphism (RFLP). Results Sixty nine cases of malaria were found among 300 cases of fever. Of these, 54 were positive for Pf, 47 of which were confirmed by PCR. Pfcrt-K76T mutation was seen in 96.6 per cent and Pfmdr1-N86Y mutation in 84.2 per cent of cases. Mutation was not detected in MAL10 and MAL13 genes. Sequence analysis of Kelch-13 gene showed the presence of a novel mutation at amino acid position 675. Statistically, no significant association was found between the molecular biomarkers and demographic profile, clinical presentation and outcome of the cases. Interpretation & conclusions Molecular surveillance is essential to assess the therapeutic efficacy of the drugs against circulating Pf isolates in Assam which are found to be highly resistant to CQ. The role of the new mutation found in the Kelch-13 gene in the development of artemisinin resistance in Assam needs to be thoroughly monitored in future research.
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Affiliation(s)
- Lipika Barman
- Department of Microbiology, Apollo Excelcare Hospital, Guwahati, India
| | - Ajanta Sharma
- Department of Microbiology, Gauhati Medical College, Guwahati, India
| | - Sanjeeb Kakati
- Department of Medicine, Assam Medical College, Dibrugarh, Assam, India
| | - Devojit Kr. Sarma
- Department of Regional Medical Research Centre, Dibrugarh, Assam, India
| | - Ezaz Hussain
- Department of Statistics, Assam Medical College, Dibrugarh, Assam, India
| | - Lahari Saikia
- Department of Microbiology, Gauhati Medical College, Guwahati, India
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Nadeem MF, Zeeshan N, Khattak AA, Awan UA, Yaqoob A. Fixation of pfcrt chloroquine resistance alleles in Plasmodium falciparum clinical isolates collected from unrest tribal agencies of Pakistan. BRAZ J BIOL 2021; 83:e247422. [PMID: 34431917 DOI: 10.1590/1519-6984.247422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/04/2021] [Indexed: 11/21/2022] Open
Abstract
Plasmodium falciparum resistance to Chloroquine (CQ) is a significant cause of mortality and morbidity worldwide. There is a paucity of documented data on the prevalence of CQ-resistant mutant haplotypes of Pfcrt and Pfmdr1 genes from malaria-endemic war effected Federally Administered Tribal Areas of Pakistan. The objective of this study was to investigate the prevalence of P. falciparum CQ-resistance in this area. Clinical isolates were collected between May 2017 and May 2018 from North Waziristan and South Waziristan agencies of Federally Administrated Trial Area. Subsequently, Giemsa-stained blood smears were examined to detect Plasmodium falciparum. Extraction of malarial DNA was done from microscopy positive P. falciparum samples, and P. falciparum infections were confirmed by nested PCR (targeting Plasmodium small subunit ribosomal ribonucleic acid (ssrRNA) genes). All PCR confirmed P. falciparum samples were sequenced by pyrosequencing to find out mutation in Pfcrt gene at codon K76T and in pfmdr1 at codons N86Y, Y184F, N1042D, and D1246Y. Out of 121 microscopies positive P. falciparum cases, 109 samples were positive for P. falciparum by nested PCR. Pfcrt K76T mutation was found in 96% of isolates, Pfmdr1 N86Y mutation was observed in 20%, and 11% harboured Y184F mutation. All samples were wild type for Pfmdr1 codon N1042D and D1246Y. In the FATA, Pakistan, the frequency of resistant allele 76T remained high despite the removal of CQ. However, current findings of the study suggest complete fixation of P. falciparum CQ-resistant genotype in the study area.
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Affiliation(s)
- M F Nadeem
- Department of Biochemistry & Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
| | - N Zeeshan
- Department of Biochemistry & Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
| | - A A Khattak
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - U A Awan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - A Yaqoob
- Department of Biochemistry & Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
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Ompad DC, Kessler A, Van Eijk AM, Padhan TK, Haque MA, Sullivan SA, Tozan Y, Rocklöv J, Mohanty S, Pradhan MM, Sahu PK, Carlton JM. The effectiveness of malaria camps as part of the Durgama Anchalare Malaria Nirakaran (DAMaN) program in Odisha, India: study protocol for a cluster-assigned quasi-experimental study. Glob Health Action 2021; 14:1886458. [PMID: 33866961 PMCID: PMC8183513 DOI: 10.1080/16549716.2021.1886458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Indian state of Odisha has a longstanding battle with forest malaria. Many remote and rural villages have poor access to health care, a problem that is exacerbated during the rainy season when malaria transmission is at its peak. Approximately 62% of the rural population consists of tribal groups who are among the communities most negatively impacted by malaria. To address the persistently high rates of malaria in these remote regions, the Odisha State Malaria Control Program introduced 'malaria camps' in 2017 where teams of health workers visit villages to educate the population, enhance vector control methods, and perform village-wide screening and treatment. Malaria rates declined statewide, particularly in forested areas, following the introduction of the malaria camps, but the impact of the intervention is yet to be externally evaluated. This study protocol describes a cluster-assigned quasi-experimental stepped-wedge study with a pretest-posttest control group design that evaluates if malaria camps reduce the prevalence of malaria, compared to control villages which receive the usual malaria control interventions (e.g. IRS, ITNs), as detected by PCR.
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Affiliation(s)
- Danielle C. Ompad
- School of Global Public Health, New York University, New York, NY, USA,CONTACT Danielle C. Ompad NYU School of Global Public Health, 715 Broadway, Room 1011, New York, NY10003USA
| | - Anne Kessler
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Anna Maria Van Eijk
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Timir K. Padhan
- Department of Molecular & Infectious Diseases, Community Welfare Society Hospital, Rourkela, Odisha, India
| | - Mohammed A. Haque
- Department of Molecular & Infectious Diseases, Community Welfare Society Hospital, Rourkela, Odisha, India
| | - Steven A. Sullivan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Yesim Tozan
- School of Global Public Health, New York University, New York, NY, USA
| | - Joacim Rocklöv
- Department of Public Health and Clinical Medicine, Umea University, Umea, Sweden
| | - Sanjib Mohanty
- Department of Molecular & Infectious Diseases, Community Welfare Society Hospital, Rourkela, Odisha, India
| | - Madan M. Pradhan
- Department of Health & Family Welfare, State Vector Borne Disease Control Programme, Bhubaneswar, Odisha, India
| | - Praveen K. Sahu
- Department of Molecular & Infectious Diseases, Community Welfare Society Hospital, Rourkela, Odisha, India
| | - Jane M. Carlton
- School of Global Public Health, New York University, New York, NY, USA,Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
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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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Chatterjee M, Ganguly S, Saha P, Guha SK, Basu N, Bera DK, Maji AK. Polymorphisms in Pfcrt and Pfmdr-1 genes after five years withdrawal of chloroquine for the treatment of Plasmodium falciparum malaria in West Bengal, India. INFECTION GENETICS AND EVOLUTION 2016; 44:281-285. [PMID: 27448953 DOI: 10.1016/j.meegid.2016.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/11/2016] [Accepted: 07/19/2016] [Indexed: 12/29/2022]
Abstract
BACKGROUND The emergence of resistant power against different antimalarial agents particularly by Plasmodium falciparum is a challenge to combat malaria. Regular monitoring is essential not only to determine the efficacy and development of resistance by the parasite but also to detect early sign of regaining sensitivity to any anti-malarial agent that has been withdrawn for a long period. Studies on molecular markers associated with antimalarial drug resistance of prevailing Plasmodium population play an important role in this aspect. The present protocol was designed to study the polymorphisms in pfcrt and pfmdr-1 gene to determine any sign of regaining sensitivity to chloroquine among P. falciparum after five years of artemisinin combination therapy (ACT) implementation. METHODS Clinical isolates were collected from P. falciparum positive patients attending the malaria clinic of Calcutta School of Tropical Medicine during December 2014 to December 2015. Genomic parasitic DNA was extracted and subjected to sequencing of pfcrt and pfmdr-1 gene directly from purified PCR products. RESULTS A total of 89 isolates were sequenced for pfcrt and 73 isolates for pfmdr-1 genes. In pfcrt gene mutant K76T was detected in all isolates and all were SVMNT haplotype. Out of three important polymorphisms in pfmdr-1 gene mutant Y184F was detected among all isolates. One synonymous G182G and one non-synonymous S232F/Y, mutation were detected in 99% isolates. CONCLUSION All isolates carrying mutant K76T in pfcrt gene, considered as hall mark for CQ resistance, indicate that there is no sign of regaining CQ sensitivity among the prevailing P. falciparum population of the study area after five years of ACT implementation.
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Affiliation(s)
- Moytrey Chatterjee
- Protozoology Unit, Department of Microbiology, Calcutta School of Tropical Medicine, 108, C. R. Avenue, Kolkata 700 073, India.
| | - Swagata Ganguly
- Department of Microbiology, NRS Medical College, 138 AJC Bose Road, Kolkata 700 014, India.
| | - Pabitra Saha
- Department of Zoology, APC Roy Government College, Himachal Bihar, Matigara, Siliguri 734 010, West Bengal, India.
| | - Subhasish Kamal Guha
- Department of Tropical Medicine, Calcutta School of Tropical Medicine, 108, C. R. Avenue, Kolkata 700 073, India.
| | - Nandita Basu
- Calcutta School of Tropical Medicine, 108, C. R. Avenue, Kolkata 700 073, India.
| | - Dilip K Bera
- Protozoology Unit, Department of Microbiology, Calcutta School of Tropical Medicine, 108, C. R. Avenue, Kolkata 700 073, India.
| | - Ardhendu Kumar Maji
- Protozoology Unit, Department of Microbiology, Calcutta School of Tropical Medicine, 108, C. R. Avenue, Kolkata 700 073, India.
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A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India. J Clin Microbiol 2016; 54:1500-1511. [PMID: 27008882 PMCID: PMC4879288 DOI: 10.1128/jcm.00235-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/20/2016] [Indexed: 11/20/2022] Open
Abstract
A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy.
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Gabryszewski SJ, Modchang C, Musset L, Chookajorn T, Fidock DA. Combinatorial Genetic Modeling of pfcrt-Mediated Drug Resistance Evolution in Plasmodium falciparum. Mol Biol Evol 2016; 33:1554-70. [PMID: 26908582 PMCID: PMC4868112 DOI: 10.1093/molbev/msw037] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The emergence of drug resistance continuously threatens global control of infectious diseases, including malaria caused by the protozoan parasite Plasmodium falciparum. A critical parasite determinant is the P. falciparum chloroquine resistance transporter (PfCRT), the primary mediator of chloroquine (CQ) resistance (CQR), and a pleiotropic modulator of susceptibility to several first-line artemisinin-based combination therapy partner drugs. Aside from the validated CQR molecular marker K76T, P. falciparum parasites have acquired at least three additional pfcrt mutations, whose contributions to resistance and fitness have been heretofore unclear. Focusing on the quadruple-mutant Ecuadorian PfCRT haplotype Ecu1110 (K76T/A220S/N326D/I356L), we genetically modified the pfcrt locus of isogenic, asexual blood stage P. falciparum parasites using zinc-finger nucleases, producing all possible combinations of intermediate pfcrt alleles. Our analysis included the related quintuple-mutant PfCRT haplotype 7G8 (Ecu1110 + C72S) that is widespread throughout South America and the Western Pacific. Drug susceptibilities and in vitro growth profiles of our combinatorial pfcrt-modified parasites were used to simulate the mutational trajectories accessible to parasites as they evolved CQR. Our results uncover unique contributions to parasite drug resistance and growth for mutations beyond K76T and predict critical roles for the CQ metabolite monodesethyl-CQ and the related quinoline-type drug amodiaquine in driving mutant pfcrt evolution. Modeling outputs further highlight the influence of parasite proliferation rates alongside gains in drug resistance in dictating successful trajectories. Our findings suggest that P. falciparum parasites have navigated constrained pfcrt adaptive landscapes by means of probabilistically rare mutational bursts that led to the infrequent emergence of pfcrt alleles in the field.
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Affiliation(s)
| | - Charin Modchang
- Department of Physics, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Lise Musset
- Laboratoire de Parasitologie, WHO Collaborating Center for Surveillance of Anti-Malarial Drug Resistance, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Thanat Chookajorn
- Genomics and Evolutionary Medicine Unit, Center of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY
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12
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Sharma D, Lather M, Mallick PK, Adak T, Dang AS, Valecha N, Singh OP. Polymorphism in drug resistance genes dihydrofolate reductase and dihydropteroate synthase in Plasmodium falciparum in some states of India. Parasit Vectors 2015; 8:471. [PMID: 26381498 PMCID: PMC4574150 DOI: 10.1186/s13071-015-1080-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sulfadoxine-pyrimethamine (SP) combination drug is currently being used in India for the treatment of Plasmodium falciparum as partner drug in artemisinin-based combination therapy (ACT). Resistance to sulfadoxine and pyrimethamine in P. falciparum is linked with mutations in dihydropteroate synthase (pfdhps) and dihydrofolate reductase (pfdhfr) genes respectively. This study was undertaken to estimate the prevalence of such mutations in pfdhfr and pfdhps genes in four states of India. METHODS Plasmodium falciparum isolates were collected from two states of India with high malaria incidence i.e., Jharkhand and Odisha and two states with low malaria incidence i.e., Andhra Pradesh and Uttar Pradesh between years 2006 to 2012. Part of sulfadoxine-pyrimethamine (SP) drug resistance genes, pfdhfr and pfdhps were PCR-amplified, sequenced and analyzed. RESULTS A total of 217 confirmed P. falciparum isolates were sequenced for both Pfdhfr and pfdhps gene. Two pfdhfr mutations 59R and 108N were most common mutations prevalent in all localities in 77 % of isolates. Additionally, I164L was found in Odisha and Jharkhand only (4/70 and 8/84, respectively). Another mutation 51I was found in Odisha only (3/70). The pfdhps mutations 436A, 437G, 540E and 581G were found in Jharkhand and Odisha only in 13, 26, 14 and 13 % isolates respectively, and was absent in Uttar Pradesh and Andhra Pradesh. Combined together for pfdhps and pfdhfr locus, triple, quadruple, quintuple and sextuple mutations were present in Jharkhand and Odisha while absent in Uttar Pradesh and Andhra Pradesh. CONCLUSION While only double mutants of pfdhfr was present in low transmission area (Uttar Pradesh and Andhra Pradesh) with total absence of pfdhps mutants, up to sextuple mutations were present in high transmission areas (Odisha and Jharkhand) for both the genes combined. Presence of multiple mutations in pfdhfr and pfdhps genes linked to SP resistance in high transmission area may lead to fixation of multiple mutations in presence of high drug pressure and high recombination rate.
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Affiliation(s)
- Divya Sharma
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Manila Lather
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Prashant K Mallick
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Tridibes Adak
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Amita S Dang
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India.
| | - Neena Valecha
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
| | - Om P Singh
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi-110077, India.
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Sahar S, Tanveer A, Ali A, Bilal H, Muhammad Saleem R. Pfcrt Gene in Plasmodium falciparum Field Isolates from Muzaffargarh, Pakistan. J Arthropod Borne Dis 2015; 9:204-14. [PMID: 26623432 PMCID: PMC4662792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 06/22/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The aim of the study was to identify the prevalence of different species of Plasmodium and haplotypes of pfcrt in Plasmodium falciparum from the selected area. METHODS Overall, 10,372 blood films of suspected malarial patients were examined microscopically from rural health center Sinawan, district Muzaffargarh, Pakistan from November 2008 to November 2010. P. falciparum positive samples (both whole blood and FTA blood spotted cards) were used for DNA extraction. Nested PCR was used to amplify the pfcrt (codon 72-76) gene fragment. Sequencing was carried out to find the haplotypes in the amplified fragment of pfcrt gene. RESULT Over all slide positivity rate (SPR), P. vivax and P. falciparum positivity rate was 21.40 %, 19.37 % and 2.03% respectively. FTA blood spotted cards were equally efficient in the blood storage for PCR and sequencing. Analysis of sequencing results of pfcrt showed only one type of haplotype SagtVMNT (AGTGTAATGAATACA) from codon 72-76 in all samples. CONCLUSION The results show high prevalence of CQ resistance and AQ resistant genes. AQ is not recommended to be used as a partner drug in ACT in this locality, so as to ward off future catastrophes.
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Affiliation(s)
- Sumrin Sahar
- Lab of Parasitology, Zoology Department, University of the Punjab, Lahore, Pakistan,Corresponding author: Dr Sumrin Sahar, E-mail:
| | - Akhtar Tanveer
- Lab of Parasitology, Zoology Department, University of the Punjab, Lahore, Pakistan
| | - Akbar Ali
- Department of Basic Health Sciences, Faculty of Pharmacy, Northern Border University, Rafha, Saudi Arabia
| | - Hazrat Bilal
- Medical Entomology and Disease Vector Control, Health Services Academy, Lahore, Pakistan
| | - Rana Muhammad Saleem
- Medical Entomology and Disease Vector Control, Health Services Academy, Lahore, Pakistan
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Goswami D, Dhiman S, Rabha B, Kumar D, Baruah I, Veer V, Bhola R, Sharma D. High prevalence of pfcrt K76T and mdr1 N86Y mutations in Sonitpur district of Assam, India. J Parasit Dis 2014; 38:250-4. [PMID: 25035579 DOI: 10.1007/s12639-013-0298-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 04/08/2013] [Indexed: 11/28/2022] Open
Abstract
Present study reports the prevalence and distribution of pfcrt K76T and mdr1 N86Y mutations in malaria endemic areas of Sonitpur district of Assam. Out of 163 individuals tested for malaria, 67 (SPR = 41.1 %) were detected positive for malaria infection using rapid detection kit in the field and PCR assay in the laboratory. Nested PCR-RFLP assay was used to amplify pfcrt K76T and mdr1 N86Y genes flanking the K76T and N86Y mutations. P. falciparum was most abundant (91.04 %) among the three Plasmodium species reported and its prevalence was significantly higher as compared to P. vivax and P. malariae (χ(2) = 150.76; p ≤ 0.0001; df = 2). Malaria was equally distributed among all the age groups and both the sexes. Hemoglobin contents in severe anaemic patients had a significant linear decreasing trend among patients with the increase in age (χ(2) = 4.33; p = 0.03), whereas non severe anaemic patients exhibited significant linear increasing trend among the patients with the increase in age (χ(2) = 18.38; p ≤ 0.0001). Pfcrt K76T mutation was recorded in 44 (72.13 %) isolates, whereas mdr1 N86Y mutation could be detected in 28 (41.79 %) isolates only. Only 32.7 % of the samples had both pfcrt K76T and mdr N86Y mutations. Number of pfcrt K76T mutant isolates was significantly higher than the wild type. However no significant difference was observed among the number of isolates with mdr1 N86Y mutant and wild isolates.
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Affiliation(s)
- Diganta Goswami
- Department of Medical Entomology, Defence Research Laboratory, Tezpur, Assam India
| | - Sunil Dhiman
- Department of Medical Entomology, Defence Research Laboratory, Tezpur, Assam India
| | - Bipul Rabha
- Department of Medical Entomology, Defence Research Laboratory, Tezpur, Assam India
| | - Dinesh Kumar
- Department of Medical Entomology, Defence Research Laboratory, Tezpur, Assam India
| | - Indra Baruah
- Department of Medical Entomology, Defence Research Laboratory, Tezpur, Assam India
| | - Vijay Veer
- Department of Medical Entomology, Defence Research Laboratory, Tezpur, Assam India
| | - Rk Bhola
- Department of Zoology, Gauhati University, Guwahati, Assam India
| | - Dk Sharma
- Department of Zoology, Gauhati University, Guwahati, Assam India
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Chauhan K, Pande V, Das A. DNA sequence polymorphisms of the pfmdr1 gene and association of mutations with the pfcrt gene in Indian Plasmodium falciparum isolates. INFECTION GENETICS AND EVOLUTION 2014; 26:213-22. [PMID: 24911283 DOI: 10.1016/j.meegid.2014.05.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 05/29/2014] [Accepted: 05/31/2014] [Indexed: 12/24/2022]
Abstract
Mutations in the Plasmodium falciparum multidrug resistance (pfmdr1) gene are known to provide compensatory fitness benefits to the chloroquine (CQ)-resistant malaria parasites and are often associated with specific mutations in the P. falciparum CQ resistant transporter (pfcrt) gene. Prevalence of the specific mutations in these two genes across different malaria endemic regions was mostly studies. However, reports on mutations in the pfmdr1 gene and their genetic associations with mutations in the pfcrt gene in Indian P. falciparum field isolates are scarce. We have sequenced a 560 bp region of pfmdr1 coding sequence in 64 P. falciparum isolates collected from different malaria endemic populations in India. Twenty out of these 64 isolates were laboratory cultured with known in vitro CQ sensitiveness (10 sensitive and 10 resistant). Three low frequency mutations (two non-synonymous and one synonymous) in the pfmdr1 gene were segregating in Indian isolates in addition to the predominant Y₈₆ and Y₁₈₄ ones, with high haplotype and nucleotide diversity in the field isolates in comparison to the cultured ones. No statistically significant genetic association between the mutations in the pfmdr1 and pfcrt gene could be detected; almost all observed associations were intragenic in nature. The results on the genetic diversity of the pfmdr1 gene were discussed in term of evolutionary perspectives in Indian P. falciparum, with possible future potential of gaining further insights on this gene in view of evolving malaria parasites resistant to artemisinin partner drugs.
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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
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital 263001, Uttarakhand, India
| | - Aparup Das
- 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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Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite's chloroquine resistance transporter. Proc Natl Acad Sci U S A 2014; 111:E1759-67. [PMID: 24728833 DOI: 10.1073/pnas.1322965111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mutations in the chloroquine resistance transporter (PfCRT) are the primary determinant of chloroquine (CQ) resistance in the malaria parasite Plasmodium falciparum. A number of distinct PfCRT haplotypes, containing between 4 and 10 mutations, have given rise to CQ resistance in different parts of the world. Here we present a detailed molecular analysis of the number of mutations (and the order of addition) required to confer CQ transport activity upon the PfCRT as well as a kinetic characterization of diverse forms of PfCRT. We measured the ability of more than 100 variants of PfCRT to transport CQ when expressed at the surface of Xenopus laevis oocytes. Multiple mutational pathways led to saturable CQ transport via PfCRT, but these could be separated into two main lineages. Moreover, the attainment of full activity followed a rigid process in which mutations had to be added in a specific order to avoid reductions in CQ transport activity. A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity. The finding that diverse PfCRT variants are all limited in their capacity to transport CQ suggests that resistance could be overcome by reoptimizing the CQ dosage.
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17
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Shalini S, Chaudhuri S, Sutton PL, Mishra N, Srivastava N, David JK, Ravindran KJ, Carlton JM, Eapen A. Chloroquine efficacy studies confirm drug susceptibility of Plasmodium vivax in Chennai, India. Malar J 2014; 13:129. [PMID: 24685286 PMCID: PMC4021252 DOI: 10.1186/1475-2875-13-129] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/24/2014] [Indexed: 02/06/2023] Open
Abstract
Background Assessing the Plasmodium vivax burden in India is complicated by the potential threat of an emerging chloroquine (CQ) resistant parasite population from neighbouring countries in Southeast Asia. Chennai, the capital of Tamil Nadu and an urban setting for P. vivax in southern India, was selected as a sentinel site for investigating CQ efficacy and sensitivity in vivax malaria. Methods CQ efficacy was evaluated with a 28-day in vivo therapeutic study, while CQ sensitivity was measured with an in vitro drug susceptibility assay. In both studies, isolates also underwent molecular genotyping to investigate correlations between parasite diversity and drug susceptibility to CQ. Molecular genotyping included sequencing a 604 base pair (bp) fragment of the P. vivax multidrug resistant gene-1 (Pvmdr1) for single nucleotide polymorphisms (SNPs) and also the amplification of eight microsatellite (MS) loci located across the genome on eight different chromosomes. Results In the 28-day in vivo study (N=125), all subjects were aparasitaemic by Day 14. Passive case surveillance continuing beyond Day 28 in 22 subjects exposed 17 recurrent infections, which ranged from 44 to 148 days post-enrollment. Pvmdr1 sequencing of these recurrent infections revealed that 93.3% had identical mutant haplotypes (958M/Y976/1076L) to their baseline Day 0 infection. MS genotyping further revealed that nine infection pairs were related with ≥75% haplotype similarity (same allele at six or more loci). To test the impact of this mutation on CQ efficacy, an in vitro drug assay (N=68) was performed. No correlation between IC50 values and the percentage of ring-stage parasites prior to culture was observed (rsadj: -0.00063, p = 0.3307) and the distribution of alleles among the Pvmdr1 SNPs and MS haplotypes showed no significant associations with IC50 values. Conclusions Plasmodium vivax was found to be susceptible to CQ drug treatment in both the in vivo therapeutic drug study and the in vitro drug assay. Though the mutant 1076L of Pvmdr1 was found in a majority of isolates tested, this single mutation did not associate with CQ resistance. MS haplotypes revealed strong heterogeneity in this population, indicating a low probability of reinfection with highly related haplotypes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alex Eapen
- National Institute of Malaria Research (Indian Council of Medical Research), National Institute of Epidemiology Campus, Second Main Road, Tamil Nadu Housing Board, Ayapakkam, Chennai 600 077, Tamil Nadu, India.
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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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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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