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Coonahan E, Gage H, Chen D, Noormahomed EV, Buene TP, Mendes de Sousa I, Akrami K, Chambal L, Schooley RT, Winzeler EA, Cowell AN. Whole-genome surveillance identifies markers of Plasmodium falciparum drug resistance and novel genomic regions under selection in Mozambique. mBio 2023; 14:e0176823. [PMID: 37750720 PMCID: PMC10653802 DOI: 10.1128/mbio.01768-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Malaria is a devastating disease caused by Plasmodium parasites. The evolution of parasite drug resistance continues to hamper progress toward malaria elimination, and despite extensive efforts to control malaria, it remains a leading cause of death in Mozambique and other countries in the region. The development of successful vaccines and identification of molecular markers to track drug efficacy are essential for managing the disease burden. We present an analysis of the parasite genome in Mozambique, a country with one of the highest malaria burdens globally and limited available genomic data, revealing current selection pressure. We contribute additional evidence to limited prior studies supporting the effectiveness of SWGA in producing reliable genomic data from complex clinical samples. Our results provide the identity of genomic loci that may be associated with current antimalarial drug use, including artemisinin and lumefantrine, and reveal selection pressure predicted to compromise the efficacy of current vaccine candidates.
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Affiliation(s)
- Erin Coonahan
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Hunter Gage
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Daisy Chen
- Department of Pediatrics, University of California San Diego (UCSD), La Jolla, California, USA
| | - Emilia Virginia Noormahomed
- School of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Microbiology, Parasitology Laboratory, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
| | - Titos Paulo Buene
- Department of Microbiology, Parasitology Laboratory, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
| | - Irina Mendes de Sousa
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
- Biological Sciences Department, Faculty of Sciences, Eduardo Mondlane University, Maputo, Mozambique
| | - Kevan Akrami
- School of Medicine, University of California San Diego, La Jolla, California, USA
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - Lucia Chambal
- Mozambique Institute of Health Education and Research (MIHER), Maputo, Mozambique
- Department of Internal Medicine, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
- Maputo Central Hospital, Maputo, Mozambique
| | - Robert T. Schooley
- School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Elizabeth A. Winzeler
- Department of Pediatrics, University of California San Diego (UCSD), La Jolla, California, USA
| | - Annie N. Cowell
- School of Medicine, University of California San Diego, La Jolla, California, USA
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Rawat M, Kanyal A, Choubey D, Deshmukh B, Malhotra R, Mamatharani DV, Rao AG, Karmodiya K. Identification of Co-Existing Mutations and Gene Expression Trends Associated With K13-Mediated Artemisinin Resistance in Plasmodium falciparum. Front Genet 2022; 13:824483. [PMID: 35464842 PMCID: PMC9019836 DOI: 10.3389/fgene.2022.824483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Plasmodium falciparum infects millions and kills thousands of people annually the world over. With the emergence of artemisinin and/or multidrug resistant strains of the pathogen, it has become even more challenging to control and eliminate the disease. Multiomics studies of the parasite have started to provide a glimpse into the confounding genetics and mechanisms of artemisinin resistance and identified mutations in Kelch13 (K13) as a molecular marker of resistance. Over the years, thousands of genomes and transcriptomes of artemisinin-resistant/sensitive isolates have been documented, supplementing the search for new genes/pathways to target artemisinin-resistant isolates. This meta-analysis seeks to recap the genetic landscape and the transcriptional deregulation that demarcate artemisinin resistance in the field. To explore the genetic territory of artemisinin resistance, we use genomic single-nucleotide polymorphism (SNP) datasets from 2,517 isolates from 15 countries from the MalariaGEN Network (The Pf3K project, pilot data release 4, 2015) to dissect the prevalence, geographical distribution, and co-existing patterns of genetic markers associated with/enabling artemisinin resistance. We have identified several mutations which co-exist with the established markers of artemisinin resistance. Interestingly, K13-resistant parasites harbor α-ß hydrolase and putative HECT domain-containing protein genes with the maximum number of SNPs. We have also explored the multiple, publicly available transcriptomic datasets to identify genes from key biological pathways whose consistent deregulation may be contributing to the biology of resistant parasites. Surprisingly, glycolytic and pentose phosphate pathways were consistently downregulated in artemisinin-resistant parasites. Thus, this meta-analysis highlights the genetic and transcriptomic features of resistant parasites to propel further exploratory studies in the community to tackle artemisinin resistance.
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Affiliation(s)
- Mukul Rawat
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Abhishek Kanyal
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Deepak Choubey
- Life Science Research Unit, Persistent Systems Limited, Pune, India
| | - Bhagyashree Deshmukh
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Rashim Malhotra
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - D V Mamatharani
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Anjani Gopal Rao
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
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3
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Fontecha G, Pinto A, Archaga O, Betancourth S, Escober L, Henríquez J, Valdivia HO, Montoya A, Mejía RE. Assessment of Plasmodium falciparum anti-malarial drug resistance markers in pfcrt and pfmdr1 genes in isolates from Honduras and Nicaragua, 2018-2021. Malar J 2021; 20:465. [PMID: 34906144 PMCID: PMC8670165 DOI: 10.1186/s12936-021-03977-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 12/04/2022] Open
Abstract
Background Central America and the island of Hispaniola have set out to eliminate malaria by 2030. However, since 2014 a notable upturn in the number of cases has been reported in the Mosquitia region shared by Nicaragua and Honduras. In addition, the proportion of Plasmodium falciparum malaria cases has increased significantly relative to vivax malaria. Chloroquine continues to be the first-line drug to treat uncomplicated malaria in the region. The objective of this study was to evaluate the emergence of chloroquine resistant strains of P. falciparum using a genetic approach. Plasmodium vivax populations are not analysed in this study. Methods 205 blood samples from patients infected with P. falciparum between 2018 and 2021 were analysed. The pfcrt gene fragment encompassing codons 72–76 was analysed. Likewise, three fragments of the pfmdr1 gene were analysed in 51 samples by nested PCR and sequencing. Results All samples revealed the CVMNK wild phenotype for the pfcrt gene and the N86, Y184F, S1034C, N1042D, D1246 phenotype for the pfmdr1 gene. Conclusions The increase in falciparum malaria cases in Nicaragua and Honduras cannot be attributed to the emergence of chloroquine-resistant mutants. Other possibilities should be investigated further. This is the first study to report the genotype of pfmdr1 for five loci of interest in Central America. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03977-8.
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Affiliation(s)
- Gustavo Fontecha
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa, Honduras.
| | - Alejandra Pinto
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa, Honduras
| | - Osman Archaga
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa, Honduras
| | - Sergio Betancourth
- Microbiology Research Institute, National Autonomous University of Honduras, Tegucigalpa, Honduras
| | - Lenin Escober
- National Malaria Laboratory, National Department of Surveillance, Ministry of Health of Honduras, Tegucigalpa, Honduras
| | - Jessica Henríquez
- National Malaria Laboratory, National Department of Surveillance, Ministry of Health of Honduras, Tegucigalpa, Honduras
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit No, 6 (NAMRU-6), Lima, Peru
| | - Alberto Montoya
- National Center for Diagnosis and Reference, Health Ministry, Managua, Nicaragua
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Nadeem MF, Khattak AA, Zeeshan N, Zahid H, Awan UA, Yaqoob A, Ashraf NM, Gul S, Alam S, Ahmed W. Surveillance of molecular markers of antimalarial drug resistance in Plasmodium falciparum and Plasmodium vivax in Federally Administered Tribal Area (FATA), Pakistan. Rev Inst Med Trop Sao Paulo 2021; 63:e59. [PMID: 34407160 PMCID: PMC8323834 DOI: 10.1590/s1678-9946202163059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/16/2021] [Indexed: 11/22/2022] Open
Abstract
This molecular epidemiological study was designed to determine the antimalarial
drug resistance pattern, and the genetic diversity of malaria isolates collected
from a war-altered Federally Administered Tribal Area (FATA), in Pakistan.
Clinical isolates were collected from Bajaur, Mohmand, Khyber, Orakzai and
Kurram agencies of FATA region between May 2017 and May 2018, and they underwent
DNA extraction and amplification. The investigation of gene polymorphisms in
drug resistance genes (dhfr, dhps, crt, and
mdr1) of Plasmodium falciparum and
Plasmodium vivax was carried out by pyrosequencing and
Sanger sequencing, respectively. Out of 679 PCR-confirmed malaria samples, 523
(77%) were P. vivax, 121 (18%) P. falciparum,
and 35 (5%) had mixed-species infections. All P. falciparum
isolates had pfdhfr double mutants (C59R+S108N), while
pfdhfr/pfdhps triple mutants (C59R+S108N+A437G) were
detected in 11.5% of the samples. About 97.4% of P. falciparum
isolates contained pfcrt K76T mutation, while
pfmdr1 N86Y and Y184F mutations were present in 18.2% and
10.2% of the samples. P. vivax pvdhfr S58R mutation was present
in 24.9% of isolates and the S117N mutation in 36.2%, while no mutation in the
pvdhps gene was found. Pvmdr1 F1076L
mutation was found in nearly all samples, as it was observed in 98.9% of
isolates. No significant anti-folate and chloroquine resistance was observed in
P. vivax; however, mutations associated with
antifolate-resistance were found, and the chloroquine-resistant gene has been
observed in 100% of P. falciparum isolates. Chloroquine and
sulphadoxine-pyrimethamine resistance were found to be high in P.
falciparum and low in P. vivax. Chloroquine could
still be used for P. vivax infection but need to be tested
in vivo, whereas a replacement of the artemisinin
combination therapy for P. falciparum appears to be
justified.
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Affiliation(s)
- Muhammad Faisal Nadeem
- University of Gujrat, Department of Biochemistry & Biotechnology, Gujrat, Punjab, Pakistan
| | - Aamer Ali Khattak
- The University of Haripur, Department of Medical Laboratory Technology, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Nadia Zeeshan
- University of Gujrat, Department of Biochemistry & Biotechnology, Gujrat, Punjab, Pakistan
| | - Hamza Zahid
- Sandeman Provincial Hospital, Department of Surgery, Quetta, Balochistan, Pakistan
| | - Usman Ayub Awan
- The University of Haripur, Department of Medical Laboratory Technology, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Adnan Yaqoob
- University of Gujrat, Department of Biochemistry & Biotechnology, Gujrat, Punjab, Pakistan
| | - Naeem Mahmood Ashraf
- University of Gujrat, Department of Biochemistry & Biotechnology, Gujrat, Punjab, Pakistan
| | - Sana Gul
- National University of Medical Sciences, Department of Biological Sciences, Rawalpindi, Pujab, Pakistan
| | - Sadia Alam
- The University of Haripur, Department of Microbiology, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Waqas Ahmed
- The University of Haripur, Department of Microbiology, Haripur, Khyber Pakhtunkhwa, Pakistan
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5
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Mulenga MC, Sitali L, Ciubotariu II, Hawela MB, Hamainza B, Chipeta J, Mharakurwa S. Decreased prevalence of the Plasmodium falciparum Pfcrt K76T and Pfmdr1 and N86Y mutations post-chloroquine treatment withdrawal in Katete District, Eastern Zambia. Malar J 2021; 20:329. [PMID: 34320992 PMCID: PMC8317340 DOI: 10.1186/s12936-021-03859-z] [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] [Received: 03/31/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022] Open
Abstract
Background In 2002, Zambia withdrew chloroquine as first-line treatment for Plasmodium falciparum malaria due to increased treatment failure and worldwide spread of chloroquine resistance. The artemisinin combination regimen, artemether–lumefantrine, replaced chloroquine (CQ) as first choice malaria treatment. The present study determined the prevalence of CQ resistance molecular markers in the Pfcrt and Pfmdr1 genes in Eastern Zambia at 9 and 13 years after the removal of drug pressure. Methods Samples collected from Katete District during the drug therapeutic efficacy assessments conducted in 2012 and 2016 were assayed by polymerase chain reaction (PCR) and restriction fragment length polymorphisms (RFLP) to determine the prevalence of genetic mutations, K76T on the Pfcrt gene and N86Y on the Pfmdr1 gene. A total of 204 P. falciparum-positive DBS samples collected at these two time points were further analysed. Results Among the samples analysed for Pfcrt K76T and Pfmdr1 N86Y in the present study, 112 (82.4%) P. falciparum-infected samples collected in 2012 were successfully amplified for Pfcrt and 94 (69.1%) for Pfmdr1, while 69 (65.7%) and 72 (68.6%) samples from 2016 were successfully amplified for Pfcrt and Pfmdr1, respectively. In 2012, the prevalence of Pfcrt 76K (sensitive) was 97.3%, 76T (resistant) was 1.8%, and 0.8% had both 76K and 76T codons (mixed). Similarly in 2012, the prevalence of Pfmdr1 86N (sensitive) was 97.9% and 86Y (resistant) was 2.1%. In the 2016 samples, the prevalence of the respective samples was 100% Pfcrt 76K and Pfmdr1 86N. Conclusion This study shows that there was a complete recovery of chloroquine-sensitive parasites by 2016 in Katete District, Eastern Zambia, 13 years following the withdrawal of CQ in the country. These findings add to the body of evidence for a fitness cost in CQ-resistant P. falciparum in Zambia and elsewhere. Further studies are recommended to monitor resistance countrywide and explore the feasibility of integration of the former best anti-malarial in combination therapy in the future.
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Affiliation(s)
- Mwenda C Mulenga
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia.
| | - Lungowe Sitali
- School of Health Sciences, Biomedical Sciences Department, Ridgeway campus, Lusaka, Zambia.,School of Medicine, University Teaching Hospital Malaria Research Unit (SMUTH-MRU), Lusaka, Zambia
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Moonga B Hawela
- Malaria Elimination Centre, Ministry of Health, Chainama Hospital and College Grounds, Lusaka, Zambia
| | - Busiku Hamainza
- Malaria Elimination Centre, Ministry of Health, Chainama Hospital and College Grounds, Lusaka, Zambia
| | - James Chipeta
- School of Medicine, University Teaching Hospital Malaria Research Unit (SMUTH-MRU), Lusaka, Zambia
| | - Sungano Mharakurwa
- College of Health, Agriculture and Natural Sciences, Africa University, Mutare, Zimbabwe
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6
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Parija SC, Poddar A. Molecular diagnosis of infectious parasites in the post-COVID-19 era. Trop Parasitol 2021; 11:3-10. [PMID: 34195053 PMCID: PMC8213111 DOI: 10.4103/tp.tp_12_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022] Open
Abstract
The endemicity of several parasitic diseases across the globe and recent evidence of distress among COVID-19 patients with preexisting parasitic infections requires strengthening One Health framework and advanced strategies for parasitic detection. Owing to the greater sensitivity and accuracy, molecular technologies such as conventional polymerase chain reaction (PCR), reverse transcription (RT)-PCR, nested PCR, loop-mediated isothermal amplification (LAMP), and xMAP technology have been extensively studied for parasitic diagnosis. Varieties of genes have been targeted for primer development where 18S rRNA, internal transcribed spacer regions, and mitochondrial DNAs coding for cytochrome, and other enzymes have been widely used. More recent, low-cost sequencing and advances in big data management have resulted in a slow but steady rise of next-generation sequencing-based approaches for parasite diagnosis. However, except for few parasites of global concerns such as Plasmodium and Entamoeba, most of the molecular tools and technologies are yet to witness bench to bedside and field translations. This review looks into some of the advancements in the molecular diagnosis of parasites that have potential relevance to clinical purposes and may pave the way toward disease management in an efficient and timely manner.
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Affiliation(s)
| | - Abhijit Poddar
- Scientist, Sri Balaji Vidyapeeth University, Puducherry, India
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7
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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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Nadeem MF, Khattak AA, Zeeshan N, Zahid H, Awan UA, Yaqoob A, Ashraf NM, Gul S, Alam S, Ahmed W. Surveillance of molecular markers of antimalarial drug resistance in Plasmodium falciparum and Plasmodium vivax in Federally Administered Tribal Area (FATA), Pakistan. Rev Inst Med Trop Sao Paulo 2021. [DOI: 10.1590/s1678-994620216305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | - Sana Gul
- National University of Medical Sciences, Pakistan
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9
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Maraka M, Akala HM, Amolo AS, Juma D, Omariba D, Cheruiyot A, Opot B, Okello Okudo C, Mwakio E, Chemwor G, Juma JA, Okoth R, Yeda R, Andagalu B. A seven-year surveillance of epidemiology of malaria reveals travel and gender are the key drivers of dispersion of drug resistant genotypes in Kenya. PeerJ 2020; 8:e8082. [PMID: 32201636 PMCID: PMC7073242 DOI: 10.7717/peerj.8082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/21/2019] [Indexed: 11/20/2022] Open
Abstract
Malaria drug resistance is a global public health concern. Though parasite mutations have been associated with resistance, other factors could influence the resistance. A robust surveillance system is required to monitor and help contain the resistance. This study established the role of travel and gender in dispersion of chloroquine resistant genotypes in malaria epidemic zones in Kenya. A total of 1,776 individuals presenting with uncomplicated malaria at hospitals selected from four malaria transmission zones in Kenya between 2008 and 2014 were enrolled in a prospective surveillance study assessing the epidemiology of malaria drug resistance patterns. Demographic and clinical information per individual was obtained using a structured questionnaire. Further, 2 mL of blood was collected for malaria diagnosis, parasitemia quantification and molecular analysis. DNA extracted from dried blood spots collected from each of the individuals was genotyped for polymorphisms in Plasmodium falciparum chloroquine transporter gene (Pfcrt 76), Plasmodium falciparum multidrug resistant gene 1 (Pfmdr1 86 and Pfmdr1 184) regions that are putative drug resistance genes using both conventional polymerase chain reaction (PCR) and real-time PCR. The molecular and demographic data was analyzed using Stata version 13 (College Station, TX: StataCorp LP) while mapping of cases at the selected geographic zones was done in QGIS version 2.18. Chloroquine resistant (CQR) genotypes across gender revealed an association with chloroquine resistance by both univariate model (p = 0.027) and by multivariate model (p = 0.025), female as reference group in both models. Prior treatment with antimalarial drugs within the last 6 weeks before enrollment was associated with carriage of CQR genotype by multivariate model (p = 0.034). Further, a significant relationship was observed between travel and CQR carriage both by univariate model (p = 0.001) and multivariate model (p = 0.002). These findings suggest that gender and travel are significantly associated with chloroquine resistance. From a gender perspective, males are more likely to harbor resistant strains than females hence involved in strain dispersion. On the other hand, travel underscores the role of transport network in introducing spread of resistant genotypes, bringing in to focus the need to monitor gene flow and establish strategies to minimize the introduction of resistance strains by controlling malaria among frequent transporters.
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Affiliation(s)
- Moureen Maraka
- School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Siaya, Kenya
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Hoseah M. Akala
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Asito S. Amolo
- School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Siaya, Kenya
| | - Dennis Juma
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Duke Omariba
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Agnes Cheruiyot
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Benjamin Opot
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Charles Okello Okudo
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Edwin Mwakio
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Gladys Chemwor
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Jackline A. Juma
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Raphael Okoth
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Redemptah Yeda
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
| | - Ben Andagalu
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa Kenya (USAMRD-A Kenya)/Kenya Medical Research Institute (KEMRI), Kisumu, Kisumu, Kenya
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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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Characterization of drug resistance and genetic diversity of Plasmodium falciparum parasites from Tripura, Northeast India. Sci Rep 2019; 9:13704. [PMID: 31548652 PMCID: PMC6757058 DOI: 10.1038/s41598-019-50152-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 09/06/2019] [Indexed: 01/23/2023] Open
Abstract
Monitoring of anti-malarial drug resistance is vital in Northeast India as this region shares its international border with Southeast Asia. Genetic diversity of Plasmodium parasites regulates transmission dynamics, disease severity and vaccine efficacy. P. falciparum chloroquine resistance transporter (Pfcrt), multidrug resistance-1 (Pfmdr-1) and kelch 13 propeller (PfK-13) genes which govern antimalarial drug resistance and three genetic diversity markers, merozoite surface protein 1 and 2 (Pfmsp-1, Pfmsp-2) and glutamate rich protein (Pfglurp) were evaluated from Tripura, Northeast India using molecular tools. In the Pfcrt gene, 87% isolates showed triple mutations at codons M74I, N75E and K76T. 12.5% isolates in Pfmdr-1 gene showed mutation at N86Y. No polymorphism in PfK-13 propeller was found. Polyclonal infections were observed in 53.85% isolates and more commonly in adults (p = 0.0494). In the Pfmsp-1 locus, the K1 allelic family was predominant (71.2%) followed by the 3D7/IC family (69.2%) in the Pfmsp-2 locus. RII region of Pfglurp exhibited nine alleles with expected heterozygosity of 0.85. The multiplicity of infection for Pfmsp-1, Pfmsp-2 and Pfglurp were 1.56, 1.31 and 1.06 respectively. Overall, the study demonstrated a high level of chloroquine resistance and extensive parasite diversity in the region, necessitating regular surveillance in this population group.
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12
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Polymorphisms in genes associated with drug resistance of Plasmodium vivax in India. Parasitol Int 2019; 70:92-97. [DOI: 10.1016/j.parint.2019.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/24/2019] [Accepted: 03/01/2019] [Indexed: 02/07/2023]
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13
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Human Genetic Markers and Structural Prediction of Plasmodium falciparum Multidrug Resistance Gene (pfmdr1) for Ligand Binding in Pregnant Women Attending General Hospital Minna. JOURNAL OF ENVIRONMENTAL AND PUBLIC HEALTH 2018; 2018:3984316. [PMID: 29861750 PMCID: PMC5976944 DOI: 10.1155/2018/3984316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/17/2018] [Accepted: 04/01/2018] [Indexed: 12/31/2022]
Abstract
The study aims to determine the association of malaria infection with ABO blood groups and genotype and also to detect point mutations at positions 86, 184, 1034, and 1042 of the Plasmodium falciparum multidrug resistance gene (pfmdr1) in blood samples collected from pregnant women attending General Hospital Minna. Out of 250 pregnant women screened, 39 (15.60%) had malaria infection. Prevalence was higher in women, during the third trimester (46.15%), genotype AA (64.10%), and O blood group (53.84%) individuals when compared with others. There was significant (p < 0.05) decrease in Packed Cell Volume (PCV), hemoglobin (HGB), Red Blood Cells (RBC), and platelet (PLC) count in infected group when compared with noninfected group. Although, two of the isolates showed disrupted protein sequence at codon 1034–1042, no mutation was found in any of the P. falciparum isolates. Structural prediction of chemical ligand led to the identification of Neu5Acα2-3Galβ1-3/β1-4Glc/GlcNAc. This compound can theoretically bind and change the functional integrity of the pfmdr1 protein, thus providing a new window for malaria drug target.
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Grzybek M, Golonko A, Górska A, Szczepaniak K, Strachecka A, Lass A, Lisowski P. The CRISPR/Cas9 system sheds new lights on the biology of protozoan parasites. Appl Microbiol Biotechnol 2018; 102:4629-4640. [PMID: 29626235 PMCID: PMC5954013 DOI: 10.1007/s00253-018-8927-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 01/04/2023]
Abstract
The CRISPR/Cas9 system, a natural defence system of bacterial organisms, has recently been used to modify genomes of the most important protozoa parasites. Successful genome manipulations with the CRISPR/Cas9 system are changing the present view of genetics in parasitology. The application of this system offers a major chance to overcome the current restriction in culturing, maintaining and analysing protozoan parasites, and allows dynamic analysis of parasite genes functions, leading to a better understanding of pathogenesis. CRISPR/Cas9 system will have a significant influence on the process of developing novel drugs and treatment strategies against protozoa parasites.
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Affiliation(s)
- Maciej Grzybek
- Department of Tropical Parasitology, Medical University of Gdansk, Powstania Styczniowego 9b, 81-519 Gdynia, Poland
| | - Aleksandra Golonko
- Department of Biotechnology, Bialystok University of Technology, Wiejska 45E, 15-351, Bialystok, Poland
| | - Aleksandra Górska
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Klaudiusz Szczepaniak
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Aneta Strachecka
- Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Anna Lass
- Department of Tropical Parasitology, Medical University of Gdansk, Powstania Styczniowego 9b, 81-519 Gdynia, Poland
| | - Paweł Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding PAS, Postepu 36A, 05-552 Jastrzebiec, Poland
- iPS Cell-Based Disease Modeling Group, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany
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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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