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Hashemi M, Schneider KA. Estimating multiplicity of infection, allele frequencies, and prevalences accounting for incomplete data. PLoS One 2024; 19:e0287161. [PMID: 38512826 PMCID: PMC10956774 DOI: 10.1371/journal.pone.0287161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Molecular surveillance of infectious diseases allows the monitoring of pathogens beyond the granularity of traditional epidemiological approaches and is well-established for some of the most relevant infectious diseases such as malaria. The presence of genetically distinct pathogenic variants within an infection, referred to as multiplicity of infection (MOI) or complexity of infection (COI) is common in malaria and similar infectious diseases. It is an important metric that scales with transmission intensities, potentially affects the clinical pathogenesis, and a confounding factor when monitoring the frequency and prevalence of pathogenic variants. Several statistical methods exist to estimate MOI and the frequency distribution of pathogen variants. However, a common problem is the quality of the underlying molecular data. If molecular assays fail not randomly, it is likely to underestimate MOI and the prevalence of pathogen variants. METHODS AND FINDINGS A statistical model is introduced, which explicitly addresses data quality, by assuming a probability by which a pathogen variant remains undetected in a molecular assay. This is different from the assumption of missing at random, for which a molecular assay either performs perfectly or fails completely. The method is applicable to a single molecular marker and allows to estimate allele-frequency spectra, the distribution of MOI, and the probability of variants to remain undetected (incomplete information). Based on the statistical model, expressions for the prevalence of pathogen variants are derived and differences between frequency and prevalence are discussed. The usual desirable asymptotic properties of the maximum-likelihood estimator (MLE) are established by rewriting the model into an exponential family. The MLE has promising finite sample properties in terms of bias and variance. The covariance matrix of the estimator is close to the Cramér-Rao lower bound (inverse Fisher information). Importantly, the estimator's variance is larger than that of a similar method which disregards incomplete information, but its bias is smaller. CONCLUSIONS Although the model introduced here has convenient properties, in terms of the mean squared error it does not outperform a simple standard method that neglects missing information. Thus, the new method is recommendable only for data sets in which the molecular assays produced poor-quality results. This will be particularly true if the model is extended to accommodate information from multiple molecular markers at the same time, and incomplete information at one or more markers leads to a strong depletion of sample size.
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Affiliation(s)
- Meraj Hashemi
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Kristan A. Schneider
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
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Nkemngo FN, Raissa LW, Nguete DN, Ndo C, Fru-Cho J, Njiokou F, Wanji S, Wondji CS. Geographical emergence of sulfadoxine-pyrimethamine drug resistance-associated P. falciparum and P. malariae alleles in co-existing Anopheles mosquito and asymptomatic human populations across Cameroon. Antimicrob Agents Chemother 2023; 67:e0058823. [PMID: 37947766 PMCID: PMC10720508 DOI: 10.1128/aac.00588-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/28/2023] [Indexed: 11/12/2023] Open
Abstract
Malaria molecular surveillance remains critical in detecting and tracking emerging parasite resistance to anti-malarial drugs. The current study employed molecular techniques to determine Plasmodium species prevalence and characterize the genetic diversity of Plasmodium falciparum and Plasmodium malariae molecular markers of sulfadoxine-pyrimethamine resistance in humans and wild Anopheles mosquito populations in Cameroon. Anopheles mosquito collections and parasitological survey were conducted in villages to determine Plasmodium species infection, and genomic phenotyping of anti-folate resistance was accomplished by sequencing the dihydrofolate-reductase (dhfr) and dihydropteroate-synthase (dhps) genes of naturally circulating P. falciparum and P. malariae isolates. The malaria prevalence in Elende was 73.5% with the 5-15 years age group harboring significant P. falciparum (27%) and P. falciparum + P. malariae (19%) infections. The polymorphism breadth of the pyrimethamine-associated Pfdhfr marker revealed a near fixation (94%) of the triple-mutant -A16I51R59N108I164. The Pfdhps backbone mediating sulfadoxine resistance reveals a high frequency of the V431A436G437K540A581A613 alleles (20.8%). Similarly, the Pmdhfr N50K55L57R58S59S114F168I170 haplotype (78.4%) was predominantly detected in the asexual blood stage. In contrast, the Pmdhps- S436A437occured at 37.2% frequency. The combined quadruple N50K55L57R58S59S114F168I170_ S436G437K540A581A613 (31.9%) was the major circulating haplotype with similar frequency in humans and mosquitoes. This study highlights the increasing frequency of the P. malariae parasite mostly common in asymptomatic individuals with apparent P. falciparum infection. Interventions directed at reducing malaria transmission such as the scaling-up of SP are favoring the emergence and spread of multiple drug-resistant alleles between the human and mosquito host systems.
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Affiliation(s)
- Francis N. Nkemngo
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Lymen W. Raissa
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
| | - Daniel N. Nguete
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
| | - Cyrille Ndo
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala, Cameroon
| | - Jerome Fru-Cho
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment, Buea, Cameroon
- Centre for Infection Biology and Translational Research, Forzi Institute, Buea, Cameroon
| | - Flobert Njiokou
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
| | - Samuel Wanji
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment, Buea, Cameroon
| | - Charles S. Wondji
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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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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Schneider KA, Salas CJ. Evolutionary genetics of malaria. Front Genet 2022; 13:1030463. [DOI: 10.3389/fgene.2022.1030463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
Many standard-textbook population-genetic results apply to a wide range of species. Sometimes, however, population-genetic models and principles need to be tailored to a particular species. This is particularly true for malaria, which next to tuberculosis and HIV/AIDS ranks among the economically most relevant infectious diseases. Importantly, malaria is not one disease—five human-pathogenic species of Plasmodium exist. P. falciparum is not only the most severe form of human malaria, but it also causes the majority of infections. The second most relevant species, P. vivax, is already considered a neglected disease in several endemic areas. All human-pathogenic species have distinct characteristics that are not only crucial for control and eradication efforts, but also for the population-genetics of the disease. This is particularly true in the context of selection. Namely, fitness is determined by so-called fitness components, which are determined by the parasites live-history, which differs between malaria species. The presence of hypnozoites, i.e., dormant liver-stage parasites, which can cause disease relapses, is a distinct feature of P. vivax and P. ovale sp. In P. malariae inactivated blood-stage parasites can cause a recrudescence years after the infection was clinically cured. To properly describe population-genetic processes, such as the spread of anti-malarial drug resistance, these features must be accounted for appropriately. Here, we introduce and extend a population-genetic framework for the evolutionary dynamics of malaria, which applies to all human-pathogenic malaria species. The model focuses on, but is not limited to, the spread of drug resistance. The framework elucidates how the presence of dormant liver stage or inactivated blood stage parasites that act like seed banks delay evolutionary processes. It is shown that, contrary to standard population-genetic theory, the process of selection and recombination cannot be decoupled in malaria. Furthermore, we discuss the connection between haplotype frequencies, haplotype prevalence, transmission dynamics, and relapses or recrudescence in malaria.
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Schneider KA, Tsoungui Obama HCJ, Kamanga G, Kayanula L, Adil Mahmoud Yousif N. The many definitions of multiplicity of infection. FRONTIERS IN EPIDEMIOLOGY 2022; 2:961593. [PMID: 38455332 PMCID: PMC10910904 DOI: 10.3389/fepid.2022.961593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/06/2022] [Indexed: 03/09/2024]
Abstract
The presence of multiple genetically different pathogenic variants within the same individual host is common in infectious diseases. Although this is neglected in some diseases, it is well recognized in others like malaria, where it is typically referred to as multiplicity of infection (MOI) or complexity of infection (COI). In malaria, with the advent of molecular surveillance, data is increasingly being available with enough resolution to capture MOI and integrate it into molecular surveillance strategies. The distribution of MOI on the population level scales with transmission intensities, while MOI on the individual level is a confounding factor when monitoring haplotypes of particular interests, e.g., those associated with drug-resistance. Particularly, in high-transmission areas, MOI leads to a discrepancy between the likelihood of a haplotype being observed in an infection (prevalence) and its abundance in the pathogen population (frequency). Despite its importance, MOI is not universally defined. Competing definitions vary from verbal ones to those based on concise statistical frameworks. Heuristic approaches to MOI are popular, although they do not mine the full potential of available data and are typically biased, potentially leading to misinferences. We introduce a formal statistical framework and suggest a concise definition of MOI and its distribution on the host-population level. We show how it relates to alternative definitions such as the number of distinct haplotypes within an infection or the maximum number of alleles detectable across a set of genetic markers. It is shown how alternatives can be derived from the general framework. Different statistical methods to estimate the distribution of MOI and pathogenic variants at the population level are discussed. The estimates can be used as plug-ins to reconstruct the most probable MOI of an infection and set of infecting haplotypes in individual infections. Furthermore, the relation between prevalence of pathogenic variants and their frequency (relative abundance) in the pathogen population in the context of MOI is clarified, with particular regard to seasonality in transmission intensities. The framework introduced here helps to guide the correct interpretation of results emerging from different definitions of MOI. Especially, it excels comparisons between studies based on different analytical methods.
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Tsoungui Obama HCJ, Schneider KA. A maximum-likelihood method to estimate haplotype frequencies and prevalence alongside multiplicity of infection from SNP data. FRONTIERS IN EPIDEMIOLOGY 2022; 2:943625. [PMID: 38455338 PMCID: PMC10911023 DOI: 10.3389/fepid.2022.943625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/26/2022] [Indexed: 03/09/2024]
Abstract
The introduction of genomic methods facilitated standardized molecular disease surveillance. For instance, SNP barcodes in Plasmodium vivax and Plasmodium falciparum malaria allows the characterization of haplotypes, their frequencies and prevalence to reveal temporal and spatial transmission patterns. A confounding factor is the presence of multiple genetically distinct pathogen variants within the same infection, known as multiplicity of infection (MOI). Disregarding ambiguous information, as usually done in ad-hoc approaches, leads to less confident and biased estimates. We introduce a statistical framework to obtain maximum-likelihood estimates (MLE) of haplotype frequencies and prevalence alongside MOI from malaria SNP data, i.e., multiple biallelic marker loci. The number of model parameters increases geometrically with the number of genetic markers considered and no closed-form solution exists for the MLE. Therefore, the MLE needs to be derived numerically. We use the Expectation-Maximization (EM) algorithm to derive the maximum-likelihood estimates, an efficient and easy-to-implement algorithm that yields a numerically stable solution. We also derive expressions for haplotype prevalence based on either all or just the unambiguous genetic information and compare both approaches. The latter corresponds to a biased ad-hoc estimate of prevalence. We assess the performance of our estimator by systematic numerical simulations assuming realistic sample sizes and various scenarios of transmission intensity. For reasonable sample sizes, and number of loci, the method has little bias. As an example, we apply the method to a dataset from Cameroon on sulfadoxine-pyrimethamine resistance in P. falciparum malaria. The method is not confined to malaria and can be applied to any infectious disease with similar transmission behavior. An easy-to-use implementation of the method as an R-script is provided.
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Mahamar A, Sumner KM, Levitt B, Freedman B, Traore A, Barry A, Issiaka D, Dembele AB, Kanoute MB, Attaher O, Diarra BN, Sagara I, Djimde A, Duffy PE, Fried M, Taylor SM, Dicko A. Effect of three years' seasonal malaria chemoprevention on molecular markers of resistance of Plasmodium falciparum to sulfadoxine-pyrimethamine and amodiaquine in Ouelessebougou, Mali. Malar J 2022; 21:39. [PMID: 35135546 PMCID: PMC8822718 DOI: 10.1186/s12936-022-04059-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/21/2022] [Indexed: 11/11/2022] Open
Abstract
Background In 2012, seasonal malaria chemoprevention (SMC) was recommended as policy for malaria control by the World Health Organization (WHO) in areas of highly seasonal malaria transmission across the Sahel sub-region in Africa along with monitoring of drug resistance. We assessed the long-term impact of SMC on Plasmodium falciparum resistance to sulfadoxine-pyrimethamine (SP) and amodiaquine (AQ) over a 3-year period of SMC implementation in the health district of Ouelessebougou, Mali. Methods In 8 randomly selected sub-districts of Ouelessebougou, Mali, children aged 0–5 years were randomly selected during cross-sectional surveys at baseline (August 2014) and 1, 2 and 3 years post-SMC, at the beginning and end of the malaria transmission season. Blood smears and blood spots on filter paper were obtained and frequencies of mutation in P. falciparum genes related to resistance to SP and AQ (Pfdhfr, Pfdhps, Pfmdr1, and Pfcrt) were assessed by PCR amplification on individual samples and PCR amplification followed by deep sequencing on pooled (by site and year) samples. Results At each survey, approximately 50–100 individual samples were analysed by PCR amplification and a total of 1,164 samples were analysed by deep sequencing with an average read depth of 18,018–36,918 after pooling by site and year. Most molecular markers of resistance did not increase in frequency over the period of study (2014–2016). After 3 years of SMC, the frequencies of Pfdhps 540E, Pfdhps 437G and Pfcrt K76T remained similar compared to baseline (4.0 vs 1.4%, p = 0.41; 74.5 vs 64.6%, p = 0.22; 71.3 vs 67.4%, p = 0.69). Nearly all samples tested carried Pfdhfr 59R, and this proportion remained similar 3 years after SMC implementation (98.8 vs 100%, p = 1). The frequency of Pfmdr1 N86Y increased significantly over time from 5.6% at baseline to 18.6% after 3 years of SMC (p = 0.016). Results of pooled analysis using deep sequencing were consistent with those by individual analysis with standard PCR, but also indicated for the first time the presence of mutations at the Pfdhps A581G allele at a frequency of 11.7% after 2 years of SMC, as well as the Pfdhps I431V allele at frequencies of 1.6–9.3% following 1 and 2 years of SMC, respectively. Conclusion Two and 3 years of SMC implementation were associated with increased frequency of the Pfmdr1 N86Y mutation but not Pfdhps 540E, Pfdhps 437G and Pfcrt K76T. The first-time detection of the Pfdhps haplotype bearing the I431V and A581G mutations in Mali, even at low frequency, warrants further long-term surveillance.
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Affiliation(s)
- Almahamoudou Mahamar
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali.
| | - Kelsey M Sumner
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA.,Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Brandt Levitt
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Betsy Freedman
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Aliou Traore
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Amadou Barry
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Djibrilla Issiaka
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Adama B Dembele
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Moussa B Kanoute
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Oumar Attaher
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | | | - Issaka Sagara
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Abdoulaye Djimde
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
| | - Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology (LMIV), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Michal Fried
- Laboratory of Malaria Immunology and Vaccinology (LMIV), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Steve M Taylor
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Alassane Dicko
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Science, Techniques and Technologies (USTT), Bamako, Mali
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Han J, Munro JE, Kocoski A, Barry AE, Bahlo M. Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species. PLoS Genet 2022; 18:e1009604. [PMID: 35007277 PMCID: PMC8782505 DOI: 10.1371/journal.pgen.1009604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/21/2022] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).
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Affiliation(s)
- Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Anthony Kocoski
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail:
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Whitlock AOB, Juliano JJ, Mideo N. Immune selection suppresses the emergence of drug resistance in malaria parasites but facilitates its spread. PLoS Comput Biol 2021; 17:e1008577. [PMID: 34280179 PMCID: PMC8321109 DOI: 10.1371/journal.pcbi.1008577] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/29/2021] [Accepted: 06/04/2021] [Indexed: 12/23/2022] Open
Abstract
Although drug resistance in Plasmodium falciparum typically evolves in regions of low transmission, resistance spreads readily following introduction to regions with a heavier disease burden. This suggests that the origin and the spread of resistance are governed by different processes, and that high transmission intensity specifically impedes the origin. Factors associated with high transmission, such as highly immune hosts and competition within genetically diverse infections, are associated with suppression of resistant lineages within hosts. However, interactions between these factors have rarely been investigated and the specific relationship between adaptive immunity and selection for resistance has not been explored. Here, we developed a multiscale, agent-based model of Plasmodium parasites, hosts, and vectors to examine how host and parasite dynamics shape the evolution of resistance in populations with different transmission intensities. We found that selection for antigenic novelty (“immune selection”) suppressed the evolution of resistance in high transmission settings. We show that high levels of population immunity increased the strength of immune selection relative to selection for resistance. As a result, immune selection delayed the evolution of resistance in high transmission populations by allowing novel, sensitive lineages to remain in circulation at the expense of the spread of a resistant lineage. In contrast, in low transmission settings, we observed that resistant strains were able to sweep to high population prevalence without interference. Additionally, we found that the relationship between immune selection and resistance changed when resistance was widespread. Once resistance was common enough to be found on many antigenic backgrounds, immune selection stably maintained resistant parasites in the population by allowing them to proliferate, even in untreated hosts, when resistance was linked to a novel epitope. Our results suggest that immune selection plays a role in the global pattern of resistance evolution. Drug resistance in the malaria parasite, Plasmodium falciparum, presents an ongoing public health challenge, but aspects of its evolution are poorly understood. Although antimalarial resistance is common worldwide, it can typically be traced to just a handful of evolutionary origins. Counterintuitively, although Sub Saharan Africa bears 90% of the global malaria burden, resistance typically originates in regions where transmission intensity is low. In high transmission regions, infections are genetically diverse, and hosts have significant standing adaptive immunity, both of which are known to suppress the frequency of resistance within infections. However, interactions between immune-driven selection, transmission intensity, and resistance have not been investigated. Using a multiscale, agent-based model, we found that high transmission intensity slowed the evolution of resistance via its effect on host population immunity. High host immunity strengthened selection for antigenic novelty, interfering with selection for resistance and allowing sensitive lineages to suppress resistant lineages in untreated hosts. However, once resistance was common in the circulating parasite population, immune selection maintained it in the population at a high prevalence. Our findings provide a novel explanation for observations about the origin of resistance and suggest that adaptive immunity is a critical component of selection.
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Affiliation(s)
| | - Jonathan J. Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Canada
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Pacheco MA, Schneider KA, Cheng Q, Munde EO, Ndege C, Onyango C, Raballah E, Anyona SB, Ouma C, Perkins DJ, Escalante AA. Changes in the frequencies of Plasmodium falciparum dhps and dhfr drug-resistant mutations in children from Western Kenya from 2005 to 2018: the rise of Pfdhps S436H. Malar J 2020; 19:378. [PMID: 33092587 PMCID: PMC7583259 DOI: 10.1186/s12936-020-03454-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/18/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Sulfadoxine-pyrimethamine (SP) is the only anti-malarial drug formulation approved for intermittent preventive treatment in pregnancy (IPTp). However, mutations in the Plasmodium falciparum dhfr (Pfdhfr) and dhps (Pfdhps) genes confer resistance to pyrimethamine and sulfadoxine, respectively. Here, the frequencies of SP resistance-associated mutations from 2005 to 2018 were compared in samples from Kenyan children with malaria residing in a holoendemic transmission region. METHODS Partial sequences of the Pfdhfr and Pfdhps genes were amplified and sequenced from samples collected in 2005 (n = 81), 2010 (n = 95), 2017 (n = 43), and 2018 (n = 55). The frequency of known mutations conferring resistance to pyrimethamine and sulfadoxine were estimated and compared. Since artemisinin-based combination therapy (ACT) is the current first-line treatment for malaria, the presence of mutations in the propeller domain of P. falciparum kelch13 gene (Pfk13) linked to ACT-delayed parasite clearance was studied in the 2017/18 samples. RESULTS Among other changes, the point mutation of Pfdhps S436H increased in frequency from undetectable in 2005 to 28% in 2017/18. Triple Pfdhfr mutant allele (CIRNI) increased in frequency from 84% in 2005 to 95% in 2017/18, while the frequency of Pfdhfr double mutant alleles declined (allele CICNI from 29% in 2005 to 6% in 2017/18, and CNRNI from 9% in 2005 to undetectable in 2010 and 2017/18). Thus, a multilocus Pfdhfr/Pfdhps genotype with six mutations (HGEAA/CIRNI), including Pfdhps S436H, increased in frequency from 2010 to 2017/18. Although none of the mutations associated with ACT-delayed parasite clearance was observed, the Pfk13 mutation A578S, the most widespread Pfk13 SNP found in Africa, was detected in low frequency (2.04%). CONCLUSIONS There were changes in SP resistance mutant allele frequencies, including an increase in the Pfdhps S436H. Although these patterns seem consistent with directional selection due to drug pressure, there is a lack of information to determine the actual cause of such changes. These results suggest incorporating molecular surveillance of Pfdhfr/Pfdhps mutations in the context of SP efficacy studies for intermittent preventive treatment in pregnancy (IPTp).
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Affiliation(s)
- M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, USA
| | - Kristan A Schneider
- Department of Applied Computer and Biosciences, University of Applied Sciences Mittweida, Technikumplatz, Mittweida, Germany
| | - Qiuying Cheng
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Elly O Munde
- University of New Mexico-Kenya Global Health Programs, Kisumu, Siaya, Kenya
- Department of Clinical Medicine, School of Health Sciences, Kirinyaga University, Kerugoya, Kenya
| | - Caroline Ndege
- University of New Mexico-Kenya Global Health Programs, Kisumu, Siaya, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Clinton Onyango
- University of New Mexico-Kenya Global Health Programs, Kisumu, Siaya, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Evans Raballah
- University of New Mexico-Kenya Global Health Programs, Kisumu, Siaya, Kenya
- Department of Medical Laboratory Sciences, School of Public Health, Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Samuel B Anyona
- University of New Mexico-Kenya Global Health Programs, Kisumu, Siaya, Kenya
- Department of Medical Biochemistry, School of Medicine, Maseno University, Maseno, Kenya
| | - Collins Ouma
- University of New Mexico-Kenya Global Health Programs, Kisumu, Siaya, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Douglas J Perkins
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
- University of New Mexico-Kenya Global Health Programs, Kisumu, Siaya, Kenya.
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, USA.
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Escobar DF, Lucchi NW, Abdallah R, Valenzuela MT, Udhayakumar V, Jercic MI, Chenet SM. Molecular and epidemiological characterization of imported malaria cases in Chile. Malar J 2020; 19:289. [PMID: 32792011 PMCID: PMC7427082 DOI: 10.1186/s12936-020-03353-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022] Open
Abstract
Background Chile is one of the South American countries certified as malaria-free since 1945. However, the recent increase of imported malaria cases and the presence of the vector Anopheles pseudopunctipennis in previously endemic areas in Chile require an active malaria surveillance programme. Methods Specimens from 268 suspected malaria cases—all imported—collected between 2015 and 2018 at the Public Health Institute of Chile (ISP), were diagnosed by microscopy and positive cases were included for epidemiological analysis. A photo-induced electron transfer fluorogenic primer real-time PCR (PET-PCR) was used to confirm the presence of malaria parasites in available blood samples. Sanger sequencing of drug resistance molecular markers (pfk13, pfcrt and pfmdr1) and microsatellite (MS) analysis were performed in confirmed Plasmodium falciparum samples and results were related to origin of infection. Results Out of the 268 suspected cases, 65 were Plasmodium spp. positive by microscopy. A total of 63% of the malaria patients were male and 37% were female; 43/65 of the patients acquired infections in South American endemic countries. Species confirmation of available blood samples by PET-PCR revealed that 15 samples were positive for P. falciparum, 27 for Plasmodium vivax and 4 were mixed infections. The P. falciparum samples sequenced contained four mutant pfcrt genotypes (CVMNT, CVMET, CVIET and SVMNT) and three mutant pfmdr1 genotypes (Y184F/S1034C/N1042D/D1246Y, Y184F/N1042D/D1246Y and Y184F). MS analysis confirmed that all P. falciparum samples presented different haplotypes according to the suspected country of origin. Four patients with P. vivax infection returned to the health facilities due to relapses. Conclusion The timely detection of polymorphisms associated with drug resistance will contribute to understanding if current drug policies in the country are appropriate for treatment of imported malaria cases and provide information about the most frequent resistant genotypes entering Chile.
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Affiliation(s)
- Daniel F Escobar
- Sección de Parasitología, Instituto de Salud Pública de Chile, Santiago, Región Metropolitana, Chile
| | - Naomi W Lucchi
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rispah Abdallah
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - María Isabel Jercic
- Sección de Parasitología, Instituto de Salud Pública de Chile, Santiago, Región Metropolitana, Chile
| | - Stella M Chenet
- Sección de Parasitología, Instituto de Salud Pública de Chile, Santiago, Región Metropolitana, Chile. .,Instituto de Investigación en Ganadería y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza, Amazonas, Peru. .,Instituto de Enfermedades Tropicales, Universidad Nacional Toribio Rodríguez de Mendoza, Amazonas, Peru.
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Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
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Lin LY, Li J, Huang HY, Liang XY, Jiang TT, Chen JT, Ehapo CS, Eyi UM, Zheng YZ, Zha GC, Xie DD, Wang YL, Chen WZ, Liu XZ, Lin M. Trends in Molecular Markers Associated with Resistance to Sulfadoxine-Pyrimethamine (SP) Among Plasmodium falciparum Isolates on Bioko Island, Equatorial Guinea: 2011-2017. Infect Drug Resist 2020; 13:1203-1212. [PMID: 32431521 PMCID: PMC7197940 DOI: 10.2147/idr.s236898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/19/2020] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Antimalarial drug resistance is one of the major challenges in global efforts to control and eliminate malaria. In 2006, sulfadoxine-pyrimethamine (SP) replaced with artemisinin-based combination therapy (ACT) on Bioko Island, Equatorial Guinea, in response to increasing SP resistance, which is associated with mutations in the dihydrofolate reductase (Pfdhfr) and dihydropteroate synthase (Pfdhps) genes. PATIENTS AND METHODS To evaluate the trend of molecular markers associated with SP resistance on Bioko Island from 2011 to 2017, 179 samples collected during active case detection were analysed by PCR and DNA sequencing. RESULTS Pfdhfr and Pfdhps gene sequences were obtained for 90.5% (162/179) and 77.1% (138/179) of the samples, respectively. For Pfdhfr, 97.5% (158/162), 95.7% (155/162) and 98.1% (159/162) of the samples contained N51I, C59R and S108N mutant alleles, respectively. And Pfdhps S436A, A437G, K540E, A581G, and A613S mutations were observed in 25.4% (35/138), 88.4% (122/138), 5.1% (7/138), 1.4% (2/138), and 7.2% (10/138) of the samples, respectively. Two classes of previously described Pfdhfr-Pfdhps haplotypes associated with SP resistance and their frequencies were identified: partial (IRNI-SGKAA, 59.4%) and full (IRNI-SGEAA, 5.5%) resistance. Although no significant difference was observed in different time periods (p>0.05), our study confirmed a slowly increasing trend of the frequencies of these SP-resistance markers in Bioko parasites over the 7 years investigated. CONCLUSION The findings reveal the general existence of SP-resistance markers on Bioko Island even after the replacement of SP as a first-line treatment for uncomplicated malaria. Continuous molecular monitoring and additional control efforts in the region are urgently needed.
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Affiliation(s)
- Li-Yun Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jian Li
- Department of Human Parasitology, School of Basic Medical Sciences; Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei Province, People’s Republic of China
| | - Hui-Ying Huang
- Department of Medical Laboratory, Chaozhou People’s Hospital Affiliated to Shantou University Medical College, Chaozhou, Guangdong Province, People’s Republic of China
- Department of Medical Genetics, Shantou University Medical College, Shantou, Guangdong Province, People’s Republic of China
| | - Xue-Yan Liang
- Department of Medical Laboratory, Chaozhou People’s Hospital Affiliated to Shantou University Medical College, Chaozhou, Guangdong Province, People’s Republic of China
- Department of Medical Genetics, Shantou University Medical College, Shantou, Guangdong Province, People’s Republic of China
| | - Ting-Ting Jiang
- Department of Human Parasitology, School of Basic Medical Sciences; Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei Province, People’s Republic of China
| | - Jiang-Tao Chen
- The Chinese Medical Aid Team to the Republic of Equatorial Guinea, Guangzhou, Guangdong Province, People’s Republic of China
- Department of Medical Laboratory, Huizhou Central Hospital, Huizhou, Guangdong Province, People’s Republic of China
| | - Carlos Salas Ehapo
- Department of Medical Laboratory, Malabo Regional Hospital, Malabo, Equatorial Guinea
| | - Urbano Monsuy Eyi
- Department of Medical Laboratory, Malabo Regional Hospital, Malabo, Equatorial Guinea
| | - Yu-Zhong Zheng
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, People’s Republic of China
| | - Guang-Cai Zha
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, People’s Republic of China
| | - Dong-De Xie
- The Chinese Medical Aid Team to the Republic of Equatorial Guinea, Guangzhou, Guangdong Province, People’s Republic of China
- Department of Medical Laboratory, Huizhou Central Hospital, Huizhou, Guangdong Province, People’s Republic of China
| | - Yu-Ling Wang
- The Chinese Medical Aid Team to the Republic of Equatorial Guinea, Guangzhou, Guangdong Province, People’s Republic of China
- Department of Medical Laboratory, Huizhou Central Hospital, Huizhou, Guangdong Province, People’s Republic of China
| | - Wei-Zhong Chen
- Department of Medical Laboratory, Chaozhou People’s Hospital Affiliated to Shantou University Medical College, Chaozhou, Guangdong Province, People’s Republic of China
- Department of Medical Genetics, Shantou University Medical College, Shantou, Guangdong Province, People’s Republic of China
| | - Xiang-Zhi Liu
- Department of Medical Laboratory, Chaozhou People’s Hospital Affiliated to Shantou University Medical College, Chaozhou, Guangdong Province, People’s Republic of China
- Department of Medical Genetics, Shantou University Medical College, Shantou, Guangdong Province, People’s Republic of China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, People’s Republic of China
- Department of Medical Laboratory, Chaozhou People’s Hospital Affiliated to Shantou University Medical College, Chaozhou, Guangdong Province, People’s Republic of China
- Department of Medical Genetics, Shantou University Medical College, Shantou, Guangdong Province, People’s Republic of China
- Correspondence: Min Lin School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, People’s Republic of China Tel/Fax +86 768-2317422 Email
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Evolution and Genetic Diversity of the k13 Gene Associated with Artemisinin Delayed Parasite Clearance in Plasmodium falciparum. Antimicrob Agents Chemother 2019; 63:AAC.02550-18. [PMID: 31085516 DOI: 10.1128/aac.02550-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/28/2019] [Indexed: 01/19/2023] Open
Abstract
Mutations in the Plasmodium falciparum k13 (Pfk13) gene are linked to delayed parasite clearance in response to artemisinin-based combination therapies (ACTs) in Southeast Asia. To explore the evolutionary rate and constraints acting on this gene, k13 orthologs from species sharing a recent common ancestor with P. falciparum and Plasmodium vivax were analyzed. These comparative studies were followed by genetic polymorphism analyses within P. falciparum using 982 complete Pfk13 sequences from public databases and new data obtained by next-generation sequencing from African and Haitian isolates. Although k13 orthologs evolve at heterogeneous rates, the gene was conserved across the genus, with only synonymous substitutions being found at residues where mutations linked to the delayed parasite clearance phenotype have been reported. This suggests that those residues were under constraint from undergoing nonsynonymous changes during evolution of the genus. No fixed nonsynonymous differences were found between Pfk13 and its orthologs in closely related species found in African apes. This indicates that all nonsynonymous substitutions currently found in Pfk13 are younger than the time of divergence between P. falciparum and its closely related species. At the population level, no mutations linked to delayed parasite clearance were found in our samples from Africa and Haiti. However, there is a high number of single Pfk13 mutations segregating in P. falciparum populations, and two predominant alleles are distributed worldwide. This pattern is discussed in terms of how changes in the efficacy of natural selection, affected by population expansion, may have allowed for the emergence of mutations tolerant to ACTs.
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Muiruri P, Juma DW, Ingasia LA, Chebon LJ, Opot B, Ngalah BS, Cheruiyot J, Andagalu B, Akala HM, Nyambati VCS, Ng'ang'a JK, Kamau E. Selective sweeps and genetic lineages of Plasmodium falciparum multi-drug resistance (pfmdr1) gene in Kenya. Malar J 2018; 17:398. [PMID: 30376843 PMCID: PMC6208105 DOI: 10.1186/s12936-018-2534-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/20/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND There are concerns that resistance to artemisinin-based combination therapy might emerge in Kenya and sub-Saharan Africa (SSA) in the same pattern as was with chloroquine and sulfadoxine-pyrimethamine. Single nucleotide polymorphisms (SNPs) in critical alleles of pfmdr1 gene have been associated with resistance to artemisinin and its partner drugs. Microsatellite analysis of loci flanking genes associated with anti-malarial drug resistance has been used in defining the geographic origins, dissemination of resistant parasites and identifying regions in the genome that have been under selection. METHODS This study set out to investigate evidence of selective sweep and genetic lineages in pfmdr1 genotypes associated with the use of artemether-lumefantrine (AL), as the first-line treatment in Kenya. Parasites (n = 252) from different regions in Kenya were assayed for SNPs at codons 86, 184 and 1246 and typed for 7 neutral microsatellites and 13 microsatellites loci flanking (± 99 kb) pfmdr1 in Plasmodium falciparum infections. RESULTS The data showed differential site and region specific prevalence of SNPs associated with drug resistance in the pfmdr1 gene. The prevalence of pfmdr1 N86, 184F, and D1246 in western Kenya (Kisumu, Kericho and Kisii) compared to the coast of Kenya (Malindi) was 92.9% vs. 66.7%, 53.5% vs. to 24.2% and 96% vs. to 87.9%, respectively. The NFD haplotype which is consistent with AL selection was at 51% in western Kenya compared to 25% in coastal Kenya. CONCLUSION Selection pressures were observed to be different in different regions of Kenya, especially the western region compared to the coastal region. The data showed independent genetic lineages for all the pfmdr1 alleles. The evidence of soft sweeps in pfmdr1 observed varied in direction from one region to another. This is challenging for malaria control programs in SSA which clearly indicate effective malaria control policies should be based on the region and not at a country wide level.
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Affiliation(s)
- Peninah Muiruri
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya
- Department of Biochemistry, School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, 00200, Nairobi, Kenya
| | - Denis W Juma
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya
| | - Luicer A Ingasia
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya
| | - Lorna J Chebon
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya
| | - Benjamin Opot
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya
| | - Bidii S Ngalah
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya
| | - Jelagat Cheruiyot
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya
| | - Ben Andagalu
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya
| | - Hoseah M Akala
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya
| | - Venny C S Nyambati
- Department of Biochemistry, School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, 00200, Nairobi, Kenya
| | - Joseph K Ng'ang'a
- Department of Biochemistry, School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, 00200, Nairobi, Kenya
| | - Edwin Kamau
- Global Emerging Infections Surveillance Program, United States Army Medical Research Directorate-Africa, Kenya Medical Research Institute, P.O. Box 54, 40100, Kisumu, Kenya.
- Walter Reed National Military Medical Center, Bethesda, Maryland, USA.
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Schneider KA. Large and finite sample properties of a maximum-likelihood estimator for multiplicity of infection. PLoS One 2018; 13:e0194148. [PMID: 29630605 PMCID: PMC5890990 DOI: 10.1371/journal.pone.0194148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 02/26/2018] [Indexed: 12/30/2022] Open
Abstract
Reliable measures of transmission intensities can be incorporated into metrics for monitoring disease-control interventions. Genetic (molecular) measures like multiplicity of infection (MOI) have several advantages compared with traditional measures, e.g., R0. Here, we investigate the properties of a maximum-likelihood approach to estimate MOI and pathogen-lineage frequencies. By verifying regulatory conditions, we prove asymptotical unbiasedness, consistency and efficiency of the estimator. Finite sample properties concerning bias and variance are evaluated over a comprehensive parameter range by a systematic simulation study. Moreover, the estimator's sensitivity to model violations is studied. The estimator performs well for realistic sample sizes and parameter ranges. In particular, the lineage-frequency estimates are almost unbiased independently of sample size. The MOI estimate's bias vanishes with increasing sample size, but might be substantial if sample size is too small. The estimator's variance matrix agrees well with the Cramér-Rao lower bound, even for small sample size. The numerical and analytical results of this study can be used for study design. This is exemplified by a malaria data set from Venezuela. It is shown how the results can be used to determine the necessary sample size to achieve certain performance goals. An implementation of the likelihood method and a simulation algorithm for study design, implemented as an R script, is available as S1 File alongside a documentation (S2 File) and example data (S3 File).
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Chenet SM, Silva-Flannery L, Lucchi NW, Dragan L, Dirlikov E, Mace K, Rivera-García B, Arguin PM, Udhayakumar V. Molecular Characterization of a Cluster of Imported Malaria Cases in Puerto Rico. Am J Trop Med Hyg 2017; 97:758-760. [PMID: 28749761 DOI: 10.4269/ajtmh.16-0837] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The Caribbean island of Hispaniola is targeted for malaria elimination. Currently, this is the only island with ongoing transmission of malaria in the Caribbean. In 2015, six patients from Puerto Rico and one from Massachusetts, who traveled to Punta Cana, Dominican Republic, were confirmed to be infected with Plasmodium falciparum. Additional molecular analysis was performed at the Centers for Disease Control and Prevention to characterize the drug-resistant alleles and Plasmodium population genetic markers. All specimens carried wildtype genotypes for chloroquine, sulfadoxine-pyrimethamine, and artemisinin resistance genetic markers. A mutation in codon 184 (Y/F) of Pfmdr-1 gene was observed in all samples and they shared an identical genetic lineage as determined by microsatellite analysis. This genetic profile was similar to one previously reported from Hispaniola suggesting that a clonal P. falciparum residual parasite population present in Punta Cana is the source population for these imported malaria cases.
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Affiliation(s)
- Stella M Chenet
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Naomi W Lucchi
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ljolje Dragan
- Atlanta Research and Education Foundation, Decatur, Georgia
| | - Emilio Dirlikov
- Office of Epidemiology and Research, Puerto Rico Department of Health, San Juan, Puerto Rico.,Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kimberly Mace
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Brenda Rivera-García
- Office of Epidemiology and Research, Puerto Rico Department of Health, San Juan, Puerto Rico
| | - Paul M Arguin
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
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Molecular Profile of Malaria Drug Resistance Markers of Plasmodium falciparum in Suriname. Antimicrob Agents Chemother 2017; 61:AAC.02655-16. [PMID: 28438929 DOI: 10.1128/aac.02655-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/27/2017] [Indexed: 11/20/2022] Open
Abstract
In Suriname, an artesunate monotherapy therapeutic efficacy trial was recently conducted to evaluate partial artemisinin resistance emerging in Plasmodium falciparum We genotyped the PfK13 propeller domain of P. falciparum in 40 samples as well as other mutations proposed to be associated with artemisinin-resistant mutants. We did not find any mutations previously associated with artemisinin resistance in Southeast Asia, but we found fixed resistance mutations for chloroquine (CQ) and sulfadoxine-pyrimethamine. Additionally, the PfCRT C350R mutation, associated with reversal of CQ resistance and piperaquine-selective pressure, was present in 62% of the samples. Our results from neutral microsatellite data also confirmed a high parasite gene flow in the Guiana Shield. Although recruiting participants for therapeutic efficacy studies is challenging in areas where malaria endemicity is very low due to the low number of malaria cases reported, conducting these studies along with molecular surveillance remains essential for the monitoring of artemisinin-resistant alleles and for the characterization of the population structure of P. falciparum in areas targeted for malaria elimination.
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Ruizendaal E, Tahita MC, Geskus RB, Versteeg I, Scott S, d'Alessandro U, Lompo P, Derra K, Traore-Coulibaly M, de Jong MD, Schallig HDFH, Tinto H, Mens PF. Increase in the prevalence of mutations associated with sulfadoxine-pyrimethamine resistance in Plasmodium falciparum isolates collected from early to late pregnancy in Nanoro, Burkina Faso. Malar J 2017; 16:179. [PMID: 28454537 PMCID: PMC5410088 DOI: 10.1186/s12936-017-1831-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pregnant women are a high-risk group for Plasmodium falciparum infections, which may result in maternal anaemia and low birth weight newborns, among other adverse birth outcomes. Intermittent preventive treatment with sulfadoxine-pyrimethamine during pregnancy (IPTp-SP) is widely implemented to prevent these negative effects of malaria. However, resistance against SP by P. falciparum may decrease efficacy of IPTp-SP. Combinations of point mutations in the dhps (codons A437, K540) and dhfr genes (codons N51, C59, S108) of P. falciparum are associated with SP resistance. In this study the prevalence of SP resistance mutations was determined among P. falciparum found in pregnant women and the general population (GP) from Nanoro, Burkina Faso and the association of IPTp-SP dosing and other variables with mutations was studied. METHODS Blood spots on filter papers were collected from pregnant women at their first antenatal care visit (ANC booking) and at delivery, from an ongoing trial and from the GP in a cross-sectional survey. The dhps and dhfr genes were amplified by nested PCR and products were sequenced to identify mutations conferring resistance (ANC booking, n = 400; delivery, n = 223; GP, n = 400). Prevalence was estimated with generalized estimating equations and for multivariate analyses mixed effects logistic regression was used. RESULTS The prevalence of the triple dhfr mutation was high, and significantly higher in the GP and at delivery than at ANC booking, but it did not affect birth weight. Furthermore, quintuple mutations (triple dhfr and double dhps mutations) were found for the first time in Burkina Faso. IPTp-SP did not significantly affect the occurrence of any of the mutations, but high transmission season was associated with increased mutation prevalence in delivery samples. It is unclear why the prevalence of mutations was higher in the GP than in pregnant women at ANC booking. CONCLUSION The high number of mutants and the presence of quintuple mutants in Burkina Faso confirm concerns about the efficacy of IPTp-SP in the near future. Other drug combinations to tackle malaria in pregnancy should, therefore, be explored. An increase in mutation prevalence due to IPTp-SP dosing could not be confirmed.
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Affiliation(s)
- Esmée Ruizendaal
- Department of Medical Microbiology, Academic Medical Centre, Amsterdam, The Netherlands.
| | - Marc C Tahita
- Institut de Recherche en Sciences de la Santé-Unité de Recherche Clinique de Nanoro, (IRSS-URCN), Nanoro, Burkina Faso
| | - Ronald B Geskus
- Department of Clinical Epidemiology, Biostatistic and Bioinformatics, Academic Medical Centre, Amsterdam, The Netherlands.,Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Viet Nam
| | - Inge Versteeg
- Koninklijk Instituut voor de Tropen, Amsterdam, The Netherlands
| | - Susana Scott
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Disease Control and Elimination, Medical Research Council Unit, Fajara, Gambia
| | - Umberto d'Alessandro
- Disease Control and Elimination, Medical Research Council Unit, Fajara, Gambia.,Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Palpouguini Lompo
- Institut de Recherche en Sciences de la Santé-Unité de Recherche Clinique de Nanoro, (IRSS-URCN), Nanoro, Burkina Faso
| | - Karim Derra
- Institut de Recherche en Sciences de la Santé-Unité de Recherche Clinique de Nanoro, (IRSS-URCN), Nanoro, Burkina Faso
| | - Maminata Traore-Coulibaly
- Institut de Recherche en Sciences de la Santé-Unité de Recherche Clinique de Nanoro, (IRSS-URCN), Nanoro, Burkina Faso
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Centre, Amsterdam, The Netherlands
| | - Henk D F H Schallig
- Department of Medical Microbiology, Academic Medical Centre, Amsterdam, The Netherlands
| | - Halidou Tinto
- Institut de Recherche en Sciences de la Santé-Unité de Recherche Clinique de Nanoro, (IRSS-URCN), Nanoro, Burkina Faso
| | - Petra F Mens
- Department of Medical Microbiology, Academic Medical Centre, Amsterdam, The Netherlands
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20
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Guerra M, Neres R, Salgueiro P, Mendes C, Ndong-Mabale N, Berzosa P, de Sousa B, Arez AP. Plasmodium falciparum Genetic Diversity in Continental Equatorial Guinea before and after Introduction of Artemisinin-Based Combination Therapy. Antimicrob Agents Chemother 2017; 61:e02556-15. [PMID: 27795385 PMCID: PMC5192141 DOI: 10.1128/aac.02556-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 10/17/2016] [Indexed: 11/20/2022] Open
Abstract
Efforts to control malaria may affect malaria parasite genetic variability and drug resistance, the latter of which is associated with genetic events that promote mechanisms to escape drug action. The worldwide spread of drug resistance has been a major obstacle to controlling Plasmodium falciparum malaria, and thus the study of the origin and spread of associated mutations may provide some insights into the prevention of its emergence. This study reports an analysis of P. falciparum genetic diversity, focusing on antimalarial resistance-associated molecular markers in two socioeconomically different villages in mainland Equatorial Guinea. The present study took place 8 years after a previous one, allowing the analysis of results before and after the introduction of an artemisinin-based combination therapy (ACT), i.e., artesunate plus amodiaquine. Genetic diversity was assessed by analysis of the Pfmsp2 gene and neutral microsatellite loci. Pfdhps and Pfdhfr alleles associated with sulfadoxine-pyrimethamine (SP) resistance and flanking microsatellite loci were investigated, and the prevalences of drug resistance-associated point mutations of the Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps genes were estimated. Further, to monitor the use of ACT, we provide the baseline prevalences of K13 propeller mutations and Pfmdr1 copy numbers. After 8 years, noticeable differences occurred in the distribution of genotypes conferring resistance to chloroquine and SP, and the spread of mutated genotypes differed according to the setting. Regarding artemisinin resistance, although mutations reported as being linked to artemisinin resistance were not present at the time, several single nucleotide polymorphisms (SNPs) were observed in the K13 gene, suggesting that closer monitoring should be maintained to prevent the possible spread of artemisinin resistance in Africa.
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Affiliation(s)
- Mónica Guerra
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Rita Neres
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Patrícia Salgueiro
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Cristina Mendes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Nicolas Ndong-Mabale
- Centro de Referencia para el Control de Endemias, Instituto de Salud Carlos III, Bata, Equatorial Guinea
| | - Pedro Berzosa
- Centro Nacional de Medicina Tropical, Instituto de Salud Carlos III, Madrid, Spain
| | - Bruno de Sousa
- Faculdade de Psicologia e de Ciências da Educação, Universidade de Coimbra, Coimbra, Portugal
| | - Ana Paula Arez
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
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21
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Ravenhall M, Benavente ED, Mipando M, Jensen ATR, Sutherland CJ, Roper C, Sepúlveda N, Kwiatkowski DP, Montgomery J, Phiri KS, Terlouw A, Craig A, Campino S, Ocholla H, Clark TG. Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi. Malar J 2016; 15:575. [PMID: 27899115 PMCID: PMC5129638 DOI: 10.1186/s12936-016-1634-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malawi experienced prolonged use of sulfadoxine/pyrimethamine (SP) as the front-line anti-malarial drug, with early replacement of chloroquine and delayed introduction of artemisinin-based combination therapy. Extended use of SP, and its continued application in pregnancy is impacting the genomic variation of the Plasmodium falciparum population. METHODS Whole genome sequence data of P. falciparum isolates covering 2 years of transmission within Malawi, alongside global datasets, were used. More than 745,000 SNPs were identified, and differences in allele frequencies between countries assessed, as well as genetic regions under positive selection determined. RESULTS Positive selection signals were identified within dhps, dhfr and gch1, all components of the parasite folate pathway associated with SP resistance. Sitting predominantly on a dhfr triple mutation background, a novel copy number increase of ~twofold was identified in the gch1 promoter. This copy number was almost fixed (96.8% frequency) in Malawi samples, but found at less than 45% frequency in other African populations, and distinct from a whole gene duplication previously reported in Southeast Asian parasites. CONCLUSIONS SP resistance selection pressures have been retained in the Malawian population, with known resistance dhfr mutations at fixation, complemented by a novel gch1 promoter duplication. The effects of the duplication on the fitness costs of SP variants and resistance need to be elucidated.
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Affiliation(s)
- Matt Ravenhall
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Mwapatsa Mipando
- Department of Physiology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Anja T. R. Jensen
- Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark
| | - Colin J. Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Cally Roper
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Nuno Sepúlveda
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Centre for Statistics and Applications of University of Lisbon, Lisbon, Portugal
| | | | - Jacqui Montgomery
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Kamija S. Phiri
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Anja Terlouw
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Alister Craig
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Harold Ocholla
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
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22
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Kar NP, Chauhan K, Nanda N, Kumar A, Carlton JM, Das A. Comparative assessment on the prevalence of mutations in the Plasmodium falciparum drug-resistant genes in two different ecotypes of Odisha state, India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 41:47-55. [PMID: 26988711 PMCID: PMC4868809 DOI: 10.1016/j.meegid.2016.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/11/2016] [Accepted: 03/12/2016] [Indexed: 01/14/2023]
Abstract
Considering malaria as a local and focal disease, epidemiological understanding of different ecotypes of malaria can help in devising novel control measures. One of the major hurdles in malaria control lies on the evolution and dispersal of the drug-resistant malaria parasite, Plasmodium falciparum. We herewith present data on genetic variation at the Single Nucleotide Polymorphism (SNP) level in four different genes of P. falciparum (Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps) that confer resistance to different antimalarials in two different eco-epidemiological settings, i.e. Hilly-Forest (HF) and Riverine-Plain (RP), in a high malaria endemic district of Odisha state, India. Greater frequency of antimalarial resistance conferring SNPs and haplotypes was observed in all four genes in P. falciparum, and Pfdhps was the most variable gene among the four. No significant genetic differentiation could be observed in isolates from HF and RP ecotypes. Twelve novel, hitherto unreported nucleotide mutations could be observed in the Pfmdr1 and Pfdhps genes. While the Pfdhps gene presented highest haplotype diversity, the Pfcrt gene displayed the highest nucleotide diversity. When the data on all the four genes were complied, the isolates from HF ecotype were found to harbour higher average nucleotide diversity than those coming from RP ecotype. High and positive Tajima's D values were obtained for the Pfcrt and Pfdhfr genes in isolates from both the HF and RP ecotypes, with statistically significant deviation from neutrality in the RP ecotype. Different patterns of Linkage Disequilibrium (LD) among SNPs located in different drug-resistant genes were found in the isolates collected from HF and RP ecotypes. Whereas in the HF ecotype, SNPs in the Pfmdr1 and Pfdhfr were significantly associated, in the RP ecotype, SNPs located in Pfcrt were associated with Pfmdr1, Pfdhfr and Pfdhps. These findings provide a baseline understanding on how different micro eco-epidemiological settings influence evolution and spread of different drug resistance alleles. Our findings further suggest that drug resistance to chloroquine and sulfadoxine-pyrimethamine is approaching fixation level, which requires urgent attention of malaria control programme in India.
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Affiliation(s)
- Narayani Prasad Kar
- National Institute of Malaria Research, Indian Council of Medical Research, Sector-8, Dwarka, New Delhi-110077, India
| | - Kshipra Chauhan
- National Institute of Malaria Research, Indian Council of Medical Research, Sector-8, Dwarka, New Delhi-110077, India
| | - Nutan Nanda
- National Institute of Malaria Research, Indian Council of Medical Research, Sector-8, Dwarka, New Delhi-110077, India
| | - Ashwani Kumar
- National Institute of Malaria Research, DHS Building, Campal, Panaji, Field Unit, Goa-403001, India
| | - Jane M. Carlton
- Department of Biology, New York University, 12 Waverly Place, New York, NY 10009, U.S.A
| | - Aparup Das
- National Institute of Malaria Research, Indian Council of Medical Research, Sector-8, Dwarka, New Delhi-110077, India
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23
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Riley C, Dellicour S, Ouma P, Kioko U, ter Kuile FO, Omar A, Kariuki S, Buff AM, Desai M, Gutman J. Knowledge and Adherence to the National Guidelines for Malaria Case Management in Pregnancy among Healthcare Providers and Drug Outlet Dispensers in Rural, Western Kenya. PLoS One 2016; 11:e0145616. [PMID: 26789638 PMCID: PMC4720358 DOI: 10.1371/journal.pone.0145616] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/07/2015] [Indexed: 02/07/2023] Open
Abstract
Background Although prompt, effective treatment is a cornerstone of malaria control, information on provider adherence to malaria in pregnancy (MIP) treatment guidelines is limited. Incorrect or sub-optimal treatment can adversely affect the mother and fetus. This study assessed provider knowledge of and adherence to national case management guidelines for uncomplicated MIP. Methods We conducted a cross-sectional study from September to November 2013, in 51 health facilities (HF) and a randomly-selected sample of 39 drug outlets (DO) in the KEMRI/CDC Health and Demographic Surveillance System area in western Kenya. Provider knowledge of national treatment guidelines was assessed with standardized questionnaires. Correct practice required adequate diagnosis, pregnancy assessment, and treatment with correct drug and dosage. In HF, we conducted exit interviews in all women of childbearing age assessed for fever. In DO, simulated clients posing as first trimester pregnant women or as relatives of third trimester pregnant women collected standardized information. Results Correct MIP case management knowledge and practice were observed in 45% and 31% of HF and 0% and 3% of DO encounters, respectively. The correct drug and dosage for pregnancy trimester was prescribed in 62% of HF and 42% of DO encounters; correct prescription occurred less often in first than in second/ third trimesters (HF: 24% vs. 65%, p<0.01; DO: 0% vs. 40%, p<0.01). Sulfadoxine-pyrimethamine, which is not recommended for malaria treatment, was prescribed in 3% of HF and 18% of DO encounters. Exposure to artemether-lumefantrine in first trimester, which is contraindicated, occurred in 29% and 49% of HF and DO encounters, respectively. Conclusion This study highlights knowledge inadequacies and incorrect prescribing practices in the treatment of MIP. Particularly concerning is the prescription of contraindicated medications in the first trimester. These issues should be addressed through comprehensive trainings and increased supportive supervision. Additional innovative means to improve care should be explored.
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Affiliation(s)
- Christina Riley
- Rollins School of Public Health, Emory University, Atlanta, United States of America
- * E-mail: (JG); (CR)
| | | | - Peter Ouma
- KEMRI, Centre for Global Health Research, Kisumu, Kenya
| | - Urbanus Kioko
- Malaria Control Unit, Ministry of Health, Nairobi, Kenya
| | | | - Ahmeddin Omar
- Malaria Control Unit, Ministry of Health, Nairobi, Kenya
| | - Simon Kariuki
- KEMRI, Centre for Global Health Research, Kisumu, Kenya
| | - Ann M. Buff
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, US Centers for Disease Control and Prevention, Atlanta, United States of America
- US President’s Malaria Initiative, Nairobi, Kenya
| | - Meghna Desai
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, US Centers for Disease Control and Prevention, Atlanta, United States of America
- Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Julie Gutman
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, US Centers for Disease Control and Prevention, Atlanta, United States of America
- * E-mail: (JG); (CR)
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24
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Winter DJ, Pacheco MA, Vallejo AF, Schwartz RS, Arevalo-Herrera M, Herrera S, Cartwright RA, Escalante AA. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia. PLoS Negl Trop Dis 2015; 9:e0004252. [PMID: 26709695 PMCID: PMC4692395 DOI: 10.1371/journal.pntd.0004252] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/30/2015] [Indexed: 11/24/2022] Open
Abstract
Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. Although P. vivax is not as deadly as the more widely studied P. falciparum, it remains a pressing global health problem. Here we report the results of a whole-genome study of P. vivax from Cordóba, Colombia, in South America. This parasite is the most prevalent in this region. We show that the parasite population is genetically diverse, which is contrary to expectations from earlier studies from the Americas. We also find molecular evidence that resistance to an anti-malarial drug has arisen recently in this region. This selective sweep indicates that the parasite has been exposed to a drug that is not used as first-line treatment for this malaria parasite. In addition to extensive single nucleotide and microsatellite polymorphism, we report 18 new genetic loci that might be helpful for fine-scale studies of this species in the Americas.
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Affiliation(s)
- David J. Winter
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- * E-mail: (DJW); (AAE)
| | - M. Andreína Pacheco
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
| | | | - Rachel S. Schwartz
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Myriam Arevalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia
- Faculty of Health, Universidad del Valle, Cali, Colombia
| | | | - Reed A. Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- The School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Ananias A. Escalante
- The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (DJW); (AAE)
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25
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Papa Mze N, Ndiaye YD, Diedhiou CK, Rahamatou S, Dieye B, Daniels RF, Hamilton EJ, Diallo M, Bei AK, Wirth DF, Mboup S, Volkman SK, Ahouidi AD, Ndiaye D. RDTs as a source of DNA to study Plasmodium falciparum drug resistance in isolates from Senegal and the Comoros Islands. Malar J 2015; 14:373. [PMID: 26415927 PMCID: PMC4587814 DOI: 10.1186/s12936-015-0861-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/23/2015] [Indexed: 11/29/2022] Open
Abstract
Background The World Health Organization has recommended rapid diagnostic tests (RDTs) for use in the diagnosis of suspected malaria cases. In addition to providing quick and accurate detection of Plasmodium parasite proteins in the blood, these tests can be used as sources of DNA for further genetic studies. As sulfadoxine-pyrimethamine is used currently for intermittent presumptive treatment of pregnant women in both Senegal and in the Comoros Islands, resistance mutations in the dhfr and dhps genes were investigated using DNA extracted from RDTs. Methods The proximal portion of the nitrocellulose membrane of discarded RDTs was used for DNA extraction. This genomic DNA was amplified using HRM to genotype the molecular markers involved in resistance to sulfadoxine-pyrimethamine: dhfr (51, 59, 108, and 164) and dhps (436, 437, 540, 581, and 613). Additionally, the msp1 and msp2 genes were amplified to determine the average clonality between Grande-Comore (Comoros) and Thiès (Senegal). Results A total of 201 samples were successfully genotyped at all codons by HRM; whereas, in 200 msp1 and msp2 genes were successfully amplified and genotyped by nested PCR. A high prevalence of resistance mutations were observed in the dhfr gene at codons 51, 59, and 108 as well as in the dhps gene at codons 437 and 436. A novel mutant in dhps at codon positions 436Y/437A was observed. The dhfr I164L codon and dhps K540 and dhps A581G codons had 100 % wild type alleles in all samples. Conclusion The utility of field-collected RDTs was validated as a source of DNA for genetic studies interrogating frequencies of drug resistance mutations, using two different molecular methods (PCR and High Resolution Melting). RDTs should not be discarded after use as they can be a valuable source of DNA for genetic and epidemiological studies in sites where filter paper or venous blood collected samples are nonexistent. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0861-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nasserdine Papa Mze
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Yaye Die Ndiaye
- Laboratoire of Parasitology and Mycology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, 5005, Dakar, Senegal.
| | - Cyrille K Diedhiou
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Silai Rahamatou
- Laboratory of National Malaria Control Programme, Moroni, Comoros.
| | - Baba Dieye
- Laboratoire of Parasitology and Mycology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, 5005, Dakar, Senegal.
| | - Rachel F Daniels
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA.
| | - Elizabeth J Hamilton
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Mouhamadou Diallo
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Amy K Bei
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal. .,Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA.
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA. .,Broad Institute: The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Souleymane Mboup
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA. .,Broad Institute: The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,School of Nursing and Health Sciences, Simmons College, Boston, MA, 02115, USA.
| | - Ambroise D Ahouidi
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Daouda Ndiaye
- Laboratoire of Parasitology and Mycology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, 5005, Dakar, Senegal.
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Chenet SM, Taylor JE, Blair S, Zuluaga L, Escalante AA. Longitudinal analysis of Plasmodium falciparum genetic variation in Turbo, Colombia: implications for malaria control and elimination. Malar J 2015; 14:363. [PMID: 26395166 PMCID: PMC4578328 DOI: 10.1186/s12936-015-0887-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/02/2015] [Indexed: 11/15/2022] Open
Abstract
Background Malaria programmes estimate changes in prevalence to evaluate their efficacy. In this study, parasite genetic data was used to explore how the demography of the parasite population can inform about the processes driving variation in prevalence. In particular, how changes in treatment and population movement have affected malaria prevalence in an area with seasonal malaria. Methods Samples of Plasmodium falciparum collected over 8 years from a population in Turbo, Colombia were genotyped at nine microsatellite loci and three drug-resistance loci. These data were analysed using several population genetic methods to detect changes in parasite genetic diversity and population structure. In addition, a coalescent-based method was used to estimate substitution rates at the microsatellite loci. Results The estimated mean microsatellite substitution rates varied between 5.35 × 10−3 and 3.77 × 10−2 substitutions/locus/month. Cluster analysis identified six distinct parasite clusters, five of which persisted for the full duration of the study. However, the frequencies of the clusters varied significantly between years, consistent with a small effective population size. Conclusions Malaria control programmes can detect re-introductions and changes in transmission using rapidly evolving microsatellite loci. In this population, the steadily decreasing diversity and the relatively constant effective population size suggest that an increase in malaria prevalence from 2004 to 2007 was primarily driven by local rather than imported cases. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0887-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stella M Chenet
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Jesse E Taylor
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA.
| | - Silvia Blair
- Malaria Group, Universidad de Antioquia, Medellín, Colombia.
| | - Lina Zuluaga
- Malaria Group, Universidad de Antioquia, Medellín, Colombia.
| | - Ananias A Escalante
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.
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Sharma J, Dutta P, Khan SA. Population genetic study of Plasmodium falciparum parasites pertaining to dhps gene sequence in malaria endemic areas of Assam. Indian J Med Microbiol 2015; 33:401-5. [PMID: 26068343 DOI: 10.4103/0255-0857.158565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Plasmodium falciparum malaria parasite had developed resistance to almost all the currently used antimalarial drugs. The purpose of the study was to come across the genetic distances in P. falciparum dhps gene sequences circulating in Assam. A partial fragment of P. falciparum dhps gene containing major single nucleotide polymorphisms associated with sulphadoxine resistance were amplified and sequenced. Thereafter specific bioinformatics tools like BioEdit v7.0.9, ClustalW in Mega 5, DnaSP version v.5.10.01 etc were used for the analysis. A total of 100 P. falciparum positive cases in different malaria endemic areas of Assam were included for the study. Based upon the mutation analysis, a total of seven different P. falciparum dhps genotypes were observed with five variable sites. Maximum five haplotypes were found in the P. falciparum isolates from Jorhat district of Assam. Four polymorphic sites were observed in the P. falciparum dhps gene sequences in Karbi Anglong, NC Hills, Chirang and Jorhat whereas the isolates from other study areas had three polymorphic sites. A statistically significant positive value of Tajima's D were observed among the P. falciparum field isolates in Assam indicating that there is an excess of intermediate frequency alleles and can result from population bottlenecks, structure and/or balancing selection. Extensive gene flow took place among the P. falciparum population of Jorhat with Sivasagar, Chirang with Sivasagar and Chirang with Karbi Anglong. However, large genetic differentiation was observed among the P. falciparum isolates of NC Hills with Lakhimpur, Tinsukia, Dibrugarh and Golaghat and also the parasite population of Karbi Anglong with Lakhimpur and Tinsukia signifying little gene flow among the population. This finding has shown that mutant Pfdhps gene associated with sulphadoxine resistance is circulating in Assam. It is believed that, the parasite population may have undergone high level of breeding.
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Affiliation(s)
- J Sharma
- Entomology and Filariasis Division, Regional Medical Research Centre (ICMR), Dibrugarh, Assam, India
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28
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Increasing prevalence of a novel triple-mutant dihydropteroate synthase genotype in Plasmodium falciparum in western Kenya. Antimicrob Agents Chemother 2015; 59:3995-4002. [PMID: 25896703 DOI: 10.1128/aac.04961-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/14/2015] [Indexed: 11/20/2022] Open
Abstract
The molecular basis of sulfadoxine-pyrimethamine (SP) resistance lies in a combination of single-nucleotide polymorphisms (SNPs) in two genes coding for Plasmodium falciparum dihydrofolate reductase (Pfdhfr) and P. falciparum dihydropteroate synthase (Pfdhps), targeted by pyrimethamine and sulfadoxine, respectively. The continued use of SP for intermittent preventive treatment in pregnant women in many African countries, despite SP's discontinuation as a first-line antimalarial treatment option due to high levels of drug resistance, may further increase the prevalence of SP-resistant parasites and/or lead to the selection of new mutations. An antimalarial drug resistance surveillance study was conducted in western Kenya between 2010 and 2013. A total of 203 clinical samples from children with uncomplicated malaria were genotyped for SNPs associated with SP resistance. The prevalence of the triple-mutant Pfdhfr C50 I51R59N108: I164 genotype and the double-mutant Pfdhps S436 G437E540: A581A613 genotype was high. Two triple-mutant Pfdhps genotypes, S436 G437E540G581: A613 and H436G437E540: A581A613, were found, with the latter thus far being uniquely found in western Kenya. The prevalence of the S436 G437E540G581: A613 genotype was low. However, a steady increase in the prevalence of the Pfdhps triple-mutant H436G437E540: A581A613 genotype has been observed since its appearance in early 2000. Isolates with these genotypes shared substantial microsatellite haplotypes with the most common double-mutant allele, suggesting that this triple-mutant allele may have evolved locally. Overall, these findings show that the prevalence of the H436G437E540: A581A613 triple mutant may be increasing in this population and could compromise the efficacy of SP for intermittent preventive treatment in pregnant women if it increases the resistance threshold further.
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Artimovich E, Schneider K, Taylor TE, Kublin JG, Dzinjalamala FK, Escalante AA, Plowe CV, Laufer MK, Takala-Harrison S. Persistence of Sulfadoxine-Pyrimethamine Resistance Despite Reduction of Drug Pressure in Malawi. J Infect Dis 2015; 212:694-701. [PMID: 25672905 DOI: 10.1093/infdis/jiv078] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/15/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND In 2007, Malawi replaced sulfadoxine-pyrimethamine (SP) with an artemisinin-based combination therapy as the first-line treatment for uncomplicated Plasmodium falciparum malaria in response to failing SP efficacy. Here we estimate the effect of reduced SP pressure on the prevalence of SP-resistant parasites and the characteristics of the associated selective sweeps flanking the resistance loci. METHODS Samples obtained from individuals with clinical malaria during a period of high SP use (1999-2001), a transitional period (2007-2008), and a period of low SP use (2012) were genotyped for resistance markers at pfdhfr-ts codons 51, 59, and 108 and pfdhps codons 437, 540, and 581. Expected heterozygosity was estimated to evaluate the genetic diversity flanking pfdhfr-ts and pfdhps. RESULTS An increase in the prevalence of the resistance haplotypes DHFR 51I/59R/108N and DHPS 437G/540E occurred under sustained drug pressure, with no change in haplotype prevalence 5 years after reduction in SP pressure. The DHPS 437G/540E/581G haplotype was observed in 2007 and increased in prevalence during a period of reduced SP pressure. Changes to the sweep characteristics flanking pfdhfr-ts and pfdhps were minimal. CONCLUSIONS In contrast to the rapid and complete return of chloroquine-susceptible falciparum malaria after chloroquine was withdrawn from Malawi, a reemergence of SP efficacy is unlikely in the near future.
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Affiliation(s)
- Elena Artimovich
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore
| | - Kristan Schneider
- Department of Fakultät Mathematik/Naturwissenschaften/Informatik, University of Applied Sciences Mittweida, Germany
| | | | - James G Kublin
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | - Christopher V Plowe
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore
| | - Miriam K Laufer
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore
| | - Shannon Takala-Harrison
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore
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Carrel M, Patel J, Taylor SM, Janko M, Mwandagalirwa MK, Tshefu AK, Escalante AA, McCollum A, Alam MT, Udhayakumar V, Meshnick S, Emch M. The geography of malaria genetics in the Democratic Republic of Congo: A complex and fragmented landscape. Soc Sci Med 2014; 133:233-41. [PMID: 25459204 DOI: 10.1016/j.socscimed.2014.10.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 08/27/2014] [Accepted: 10/17/2014] [Indexed: 11/28/2022]
Abstract
Understanding how malaria parasites move between populations is important, particularly given the potential for malaria to be reintroduced into areas where it was previously eliminated. We examine the distribution of malaria genetics across seven sites within the Democratic Republic of Congo (DRC) and two nearby countries, Ghana and Kenya, in order to understand how the relatedness of malaria parasites varies across space, and whether there are barriers to the flow of malaria parasites within the DRC or across borders. Parasite DNA was retrieved from dried blood spots from 7 Demographic and Health Survey sample clusters in the DRC. Malaria genetic characteristics of parasites from Ghana and Kenya were also obtained. For each of 9 geographic sites (7 DRC, 1 Ghana and 1 Kenya), a pair-wise RST statistic was calculated, indicating the genetic distance between malaria parasites found in those locations. Mapping genetics across the spatial extent of the study area indicates a complex genetic landscape, where relatedness between two proximal sites may be relatively high (RST > 0.64) or low (RST < 0.05), and where distal sites also exhibit both high and low genetic similarity. Mantel's tests suggest that malaria genetics differ as geographic distances increase. Principal Coordinate Analysis suggests that genetically related samples are not co-located. Barrier analysis reveals no significant barriers to gene flow between locations. Malaria genetics in the DRC have a complex and fragmented landscape. Limited exchange of genes across space is reflected in greater genetic distance between malaria parasites isolated at greater geographic distances. There is, however, evidence for close genetic ties between distally located sample locations, indicating that movement of malaria parasites and flow of genes is being driven by factors other than distance decay. This research demonstrates the contributions that spatial disease ecology and landscape genetics can make to understanding the evolutionary dynamics of infectious diseases.
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Affiliation(s)
- Margaret Carrel
- Department of Geographical & Sustainability Sciences, University of Iowa, Iowa City, IA, USA.
| | - Jaymin Patel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina- Chapel Hill Chapel Hill, NC, USA
| | - Steve M Taylor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina- Chapel Hill Chapel Hill, NC, USA; Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, NC, USA; Duke Global Health Institute, Durham, NC, USA
| | - Mark Janko
- Department of Geography, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Melchior Kashamuka Mwandagalirwa
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina- Chapel Hill Chapel Hill, NC, USA
| | - Antoinette K Tshefu
- Ecole de Sante Publique, Faculte de Medecine, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Ananias A Escalante
- Center for Evolutionary Medicine & Informatics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Andrea McCollum
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Md Tauqeer Alam
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Steven Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina- Chapel Hill Chapel Hill, NC, USA
| | - Michael Emch
- Department of Geography, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
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Abdul-Ghani R, Al-Maktari MT, Al-Shibani LA, Allam AF. A better resolution for integrating methods for monitoring Plasmodium falciparum resistance to antimalarial drugs. Acta Trop 2014; 137:44-57. [PMID: 24801884 DOI: 10.1016/j.actatropica.2014.04.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/25/2014] [Accepted: 04/27/2014] [Indexed: 12/16/2022]
Abstract
Effective chemotherapy is the mainstay of malaria control. However, resistance of falciparum malaria to antimalarial drugs compromised the efforts to eliminate the disease and led to the resurgence of malaria epidemics. Three main approaches are used to monitor antimalarial drug efficacy and drug resistance; namely, in vivo trials, in vitro/ex vivo assays and molecular markers of drug resistance. Each approach has its implications of use as well as its advantages and drawbacks. Therefore, there is a need to use an integrated approach that would give the utmost effect to detect resistance as early as its emergence and to track it once spread. Such integration becomes increasingly needed in the era of artemisinin-based combination therapy as a forward action to deter resistance. The existence of regional and global networks for the standardization of methodology, provision of high quality reagents for the assessment of antimalarial drug resistance and dissemination of open-access data would help in approaching an integrated resistance surveillance system on a global scale.
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Kim Y, Escalante AA, Schneider KA. A population genetic model for the initial spread of partially resistant malaria parasites under anti-malarial combination therapy and weak intrahost competition. PLoS One 2014; 9:e101601. [PMID: 25007207 PMCID: PMC4090191 DOI: 10.1371/journal.pone.0101601] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/09/2014] [Indexed: 11/18/2022] Open
Abstract
To develop public-health policies that extend the lifespan of affordable anti-malarial drugs as effective treatment options, it is necessary to understand the evolutionary processes leading to the origin and spread of mutations conferring drug resistance in malarial parasites. We built a population-genetic model for the emergence of resistance under combination drug therapy. Reproductive cycles of parasites are specified by their absolute fitness determined by clinical parameters, thus coupling the evolutionary-genetic with population-dynamic processes. Initial mutations confer only partial drug-resistance. Therefore, mutant parasites rarely survive combination therapy and within-host competition is very weak among parasites. The model focuses on the early phase of such unsuccessful recurrent mutations. This ends in the rare event of mutants enriching in an infected individual from which the successful spread of resistance over the entire population is initiated. By computer simulations, the waiting time until the establishment of resistant parasites is analysed. Resistance spreads quickly following the first appearance of a host infected predominantly by mutant parasites. This occurs either through a rare transmission of a resistant parasite to an uninfected host or through a rare failure of drugs in removing "transient" mutant alleles. The emergence of resistance is delayed with lower mutation rate, earlier treatment, higher metabolic cost of resistance, longer duration of high drug dose, and higher drug efficacy causing a stronger reduction in the sensitive and resistant parasites' fitnesses. Overall, contrary to other studies' proposition, the current model based on absolute fitness suggests that aggressive drug treatment delays the emergence of drug resistance.
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Affiliation(s)
- Yuseob Kim
- Department of Life Science and Division of EcoScience, Ewha Womans University, Seoul, South Korea
- * E-mail:
| | - Ananias A. Escalante
- School of Life Sciences and Center for Evolutionary Medicine and Informatics at the Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
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Schneider KA, Escalante AA. A likelihood approach to estimate the number of co-infections. PLoS One 2014; 9:e97899. [PMID: 24988302 PMCID: PMC4079681 DOI: 10.1371/journal.pone.0097899] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/24/2014] [Indexed: 11/25/2022] Open
Abstract
The number of co-infections of a pathogen (multiplicity of infection or MOI) is a relevant parameter in epidemiology as it relates to transmission intensity. Notably, such quantities can be built into a metric in the context of disease control and prevention. Having applications to malaria in mind, we develop here a maximum-likelihood (ML) framework to estimate the quantities of interest at low computational and no additional costs to study designs or data collection. We show how the ML estimate for the quantities of interest and corresponding confidence-regions are obtained from multiple genetic loci. Assuming specifically that infections are rare and independent events, the number of infections per host follows a conditional Poisson distribution. Under this assumption, we show that a unique ML estimate for the parameter () describing MOI exists which is found by a simple recursion. Moreover, we provide explicit formulas for asymptotic confidence intervals, and show that profile-likelihood-based confidence intervals exist, which are found by a simple two-dimensional recursion. Based on the confidence intervals we provide alternative statistical tests for the MOI parameter. Finally, we illustrate the methods on three malaria data sets. The statistical framework however is not limited to malaria.
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Affiliation(s)
- Kristan A. Schneider
- Department MNI, University of Applied Sciences Mittweida, Mittweida, Germany
- * E-mail:
| | - Ananias A. Escalante
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute at Arizona State University, Tempe, Arizona, United States of America
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Trends in drug resistance codons in Plasmodium falciparum dihydrofolate reductase and dihydropteroate synthase genes in Kenyan parasites from 2008 to 2012. Malar J 2014; 13:250. [PMID: 24989984 PMCID: PMC4094641 DOI: 10.1186/1475-2875-13-250] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/26/2014] [Indexed: 11/28/2022] Open
Abstract
Background Sulphadoxine-pyrimethamine (SP), an antifolate, was replaced by artemether-lumefantrine as the first-line malaria drug treatment in Kenya in 2004 due to the wide spread of resistance. However, SP still remains the recommended drug for intermittent preventive treatment in pregnant women and infants (IPTP/I) owing to its safety profile. This study assessed the prevalence of mutations in dihydrofolate reductase (Pfdhfr) and dihydropteroate synthase (Pfdhps) genes associated with SP resistance in samples collected in Kenya between 2008 and 2012. Methods Field isolates collected from Kisumu, Kisii, Kericho and Malindi district hospitals were assessed for genetic polymorphism at various loci within Pfdhfr and Pfdhps genes by sequencing. Results Among the Pfdhfr mutations, codons N51I, C59R, S108N showed highest prevalence in all the field sites at 95.5%, 84.1% and 98.6% respectively. Pfdhfr S108N prevalence was highest in Kisii at 100%. A temporal trend analysis showed steady prevalence of mutations over time except for codon Pfdhps 581 which showed an increase in mixed genotypes. Triple Pfdhfr N51I/C59R/S108N and double Pfdhps A437G/ K540E had high prevalence rates of 86.6% and 87.9% respectively. The Pfdhfr/Pfdhps quintuple, N51I/C59R/S108N/A437G/K540E mutant which has been shown to be the most clinically relevant marker for SP resistance was observed in 75.7% of the samples. Conclusion SP resistance is still persistently high in western Kenya, which is likely due to fixation of key mutations in the Pfdhfr and Pfdhps genes as well as drug pressure from other antifolate drugs being used for the treatment of malaria and other infections. In addition, there is emergence and increasing prevalence of new mutations in Kenyan parasite population. Since SP is used for IPTP/I, molecular surveillance and in vitro susceptibility assays must be sustained to provide information on the emergence and spread of SP resistance.
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Nwakanma DC, Duffy CW, Amambua-Ngwa A, Oriero EC, Bojang KA, Pinder M, Drakeley CJ, Sutherland CJ, Milligan PJ, Macinnis B, Kwiatkowski DP, Clark TG, Greenwood BM, Conway DJ. Changes in malaria parasite drug resistance in an endemic population over a 25-year period with resulting genomic evidence of selection. J Infect Dis 2013; 209:1126-35. [PMID: 24265439 PMCID: PMC3952670 DOI: 10.1093/infdis/jit618] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background. Analysis of genome-wide polymorphism in many organisms has potential to identify genes under recent selection. However, data on historical allele frequency changes are rarely available for direct confirmation. Methods. We genotyped single nucleotide polymorphisms (SNPs) in 4 Plasmodium falciparum drug resistance genes in 668 archived parasite-positive blood samples of a Gambian population between 1984 and 2008. This covered a period before antimalarial resistance was detected locally, through subsequent failure of multiple drugs until introduction of artemisinin combination therapy. We separately performed genome-wide sequence analysis of 52 clinical isolates from 2008 to prospect for loci under recent directional selection. Results. Resistance alleles increased from very low frequencies, peaking in 2000 for chloroquine resistance-associated crt and mdr1 genes and at the end of the survey period for dhfr and dhps genes respectively associated with pyrimethamine and sulfadoxine resistance. Temporal changes fit a model incorporating likely selection coefficients over the period. Three of the drug resistance loci were in the top 4 regions under strong selection implicated by the genome-wide analysis. Conclusions. Genome-wide polymorphism analysis of an endemic population sample robustly identifies loci with detailed documentation of recent selection, demonstrating power to prospectively detect emerging drug resistance genes.
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Ndiaye D, Dieye B, Ndiaye YD, Van Tyne D, Daniels R, Bei AK, Mbaye A, Valim C, Lukens A, Mboup S, Ndir O, Wirth DF, Volkman S. Polymorphism in dhfr/dhps genes, parasite density and ex vivo response to pyrimethamine in Plasmodium falciparum malaria parasites in Thies, Senegal. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2013; 3:135-42. [PMID: 24533303 PMCID: PMC3862402 DOI: 10.1016/j.ijpddr.2013.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/19/2013] [Accepted: 07/21/2013] [Indexed: 11/14/2022]
Abstract
Prevalence of dhfr/dhps mutations increased significantly between 2003 and 2011. Triple mutant dhfr 51I/59R/108N increased, from 40% in 2003 to 93% in 2011. Quadruple mutant dhfr and dhps 437G increased, from 20% to 66% then down. A strong correlation between ex vivo response to pyrimethamine and dhfr genotype.
Resistance to sulfadoxine–pyrimethamine (SP) in Plasmodium falciparum malaria parasites is associated with mutations in the dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) genes, and these mutations have spread resistance worldwide. SP, used for several years in Senegal, has been recommended for intermittent preventive treatment for malaria in pregnancy (IPTp) and has been widely implemented since 2003 in this country. There is currently limited data on SP resistance from molecular marker genotyping, and no data on pyrimethamine ex vivo sensitivity in Senegal. Molecular markers of SP resistance and pyrimethamine ex vivo sensitivity were investigated in 416 parasite samples collected from the general population, from the Thies region between 2003 and 2011. The prevalence of the N51I/C59R/S108N triple mutation in dhfr increased from 40% in 2003 to 93% in 2011. Furthermore, the prevalence of the dhfr N51I/C59R/S108N and dhps A437G quadruple mutation increased, from 20% to 66% over the same time frame, then down to 44% by 2011. There was a significant increase in the prevalence of the dhfr triple mutation, as well as an association between dhfr genotypes and pyrimethamine response. Conversely, dhps mutations in codons 436 and 437 did not show consistent variation between 2003 and 2011. These findings suggest that regular screening for molecular markers of antifolate resistance and ex vivo drug response monitoring should be incorporated with ongoing in vivo efficacy monitoring in areas where IPTp-SP is implemented and where pyrimethamine and sulfa drugs are still widely administered in the general population.
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Affiliation(s)
- Daouda Ndiaye
- Faculty of Medicine and Pharmacy, University Cheikh Anta Diop, Dakar, PO Box 5005, Dakar, Senegal
| | - Baba Dieye
- Faculty of Medicine and Pharmacy, University Cheikh Anta Diop, Dakar, PO Box 5005, Dakar, Senegal
| | - Yaye D Ndiaye
- Faculty of Medicine and Pharmacy, University Cheikh Anta Diop, Dakar, PO Box 5005, Dakar, Senegal
| | - Daria Van Tyne
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Rachel Daniels
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Amy K Bei
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Aminata Mbaye
- Faculty of Medicine and Pharmacy, University Cheikh Anta Diop, Dakar, PO Box 5005, Dakar, Senegal
| | - Clarissa Valim
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Amanda Lukens
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Souleymane Mboup
- Faculty of Medicine and Pharmacy, University Cheikh Anta Diop, Dakar, PO Box 5005, Dakar, Senegal
| | - Omar Ndir
- Faculty of Medicine and Pharmacy, University Cheikh Anta Diop, Dakar, PO Box 5005, Dakar, Senegal
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Sarah Volkman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
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Gadalla NB, Abdallah TM, Atwal S, Sutherland CJ, Adam I. Selection of pfdhfr/pfdhps alleles and declining artesunate/sulphadoxine-pyrimethamine efficacy against Plasmodium falciparum eight years after deployment in eastern Sudan. Malar J 2013; 12:255. [PMID: 23870667 PMCID: PMC3720549 DOI: 10.1186/1475-2875-12-255] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/16/2013] [Indexed: 12/20/2022] Open
Abstract
Background Artesunate/sulphadoxine-pyrimethamine (AS/SP) has been the first-line treatment for falciparum malaria in Sudan since 2004. The impact of this combination on anti-malarial resistance-associated molecular markers has not been investigated. In this study, an evaluation of the efficacy and prevalence of drug resistance alleles (pfcrt, pfmdr1, pfdhfr and pfdhps) eight years after the adoption of AS/SP in eastern Sudan is reported. Methods A 28-day follow-up efficacy trial of AS/SP was conducted in eastern Sudan during the 2012 transmission season. Blood smears were collected from patients on days 0, 1, 2, 3, 7, 14, 21 and 28. Blood spots on filter paper were obtained pre-treatment and on the day the patient was parasite positive by microscopy. Genotyping of alleles was performed by qPCR (pfcrt 72–76 and pfmdr1 copy number) and direct sequencing of pfmdr1, pfdhfr and pfdhps. Results Sixty-three patients out of 68 (93%) completed the 28-day follow-up, adequate clinical, and parasitological response occurred in 90.5% and 85.3% of the patients in the per-protocol and intent-to-treat analyses, respectively. PCR corrected per-protocol efficacy was 93.7%. The enrolment prevalence of pfcrt-CVMNK was 30.2% and pfmdr1-N86 was 40.3%. The pfmdr1 haplotype NFD occurred in 32.8% of pre-treatment samples and was significantly higher than previous reports (Fisher’s exact p = 0.0001). The pfdhfr-51I/108N combination occurred in all sequenced isolates and 59R was observed in a single individual. pfdhps substitutions 436A, 437G, 540E, 581G and 613S were observed at 7.8, 77.3, 76.9%, 33.8% and 0.0%, respectively. Treatment failures were associated with the pfdhps haplotype SGEGA at these five codons (OR 7.3; 95% CI 0.65 - 368; p = 0.048). Conclusion The decrease of CQR associated genotypes reflects the formal policy of complete removal of CQ in Sudan. However, the frequency of markers associated with SP failure is increasing in this study area and may be contributing to the treatment efficacy falling below 90%. Further monitoring of AS/SP efficacy and of post-treatment selection of pfdhfr and pfdhps alleles in vivo is required to inform future treatment guidelines.
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Affiliation(s)
- Nahla B Gadalla
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK.
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Quiliano M, Valdivia-Olarte H, Olivares C, Requena D, Gutiérrez AH, Reyes-Loyola P, Tolentino-Lopez LE, Sheen P, Briz V, Muñoz-Fernández MA, Correa-Basurto J, Zimic M. Molecular distribution of amino acid substitutions on neuraminidase from the 2009 (H1N1) human influenza pandemic virus. Bioinformation 2013; 9:673-9. [PMID: 23930018 PMCID: PMC3732439 DOI: 10.6026/97320630009673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 05/08/2013] [Indexed: 12/11/2022] Open
Abstract
The pandemic influenza AH1N1 (2009) caused an outbreak of human infection that spread to the world. Neuraminidase (NA) is an antigenic surface glycoprotein, which is essential to the influenza infection process, and is the target of anti-flu drugs oseltamivir and zanamivir. Currently, NA inhibitors are the pillar pharmacological strategy against seasonal and global influenza. Although mutations observed after NA-inhibitor treatment are characterized by changes in conserved amino acids of the enzyme catalytic site, it is possible that specific amino acid substitutions (AASs) distant from the active site such as H274Y, could confer oseltamivir or zanamivir resistance. To better understand the molecular distribution pattern of NA AASs, we analyzed NA AASs from all available reported pandemic AH1N1 NA sequences, including those reported from America, Africa, Asia, Europe, Oceania, and specifically from Mexico. The molecular distributions of the AASs were obtained at the secondary structure domain level for both the active and catalytic sites, and compared between geographic regions. Our results showed that NA AASs from America, Asia, Europe, Oceania and Mexico followed similar molecular distribution patterns. The compiled data of this study showed that highly conserved amino acids from the NA active site and catalytic site are indeed being affected by mutations. The reported NA AASs follow a similar molecular distribution pattern worldwide. Although most AASs are distributed distantly from the active site, this study shows the emergence of mutations affecting the previously conserved active and catalytic site. A significant number of unique AASs were reported simultaneously on different continents.
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Affiliation(s)
- MiguelMiguel Quiliano
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía,
Universidad Peruana Cayetano Heredia. Av. Honorio Delgado, 430. SMP. Lima, Peru
- Drug R&D Unit, Center for Applied Pharmacobiology Research, University of Navarra, C/ Irunlarrea s/n, 31008, Pamplona, Spain
| | - Hugo Valdivia-Olarte
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía,
Universidad Peruana Cayetano Heredia. Av. Honorio Delgado, 430. SMP. Lima, Peru
| | - Carlos Olivares
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía,
Universidad Peruana Cayetano Heredia. Av. Honorio Delgado, 430. SMP. Lima, Peru
- Department of Physics, PUC-Rio, Rua Marquês de São Vicente, 225, Gávea - Rio de Janeiro, Brazil
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía,
Universidad Peruana Cayetano Heredia. Av. Honorio Delgado, 430. SMP. Lima, Peru
| | - Andrés H Gutiérrez
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía,
Universidad Peruana Cayetano Heredia. Av. Honorio Delgado, 430. SMP. Lima, Peru
| | - Paola Reyes-Loyola
- Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México.
Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico city, México
| | - Luis E Tolentino-Lopez
- Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México.
Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico city, México
| | - Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía,
Universidad Peruana Cayetano Heredia. Av. Honorio Delgado, 430. SMP. Lima, Peru
| | - Verónica Briz
- Laboratorio de Inmunobiología Molecular, Hospital Universitario Gregorio Marañón, Madrid, España, CIBER BBN, Madrid, Spain
| | - Maria A Muñoz-Fernández
- Laboratorio de Inmunobiología Molecular, Hospital Universitario Gregorio Marañón, Madrid, España, CIBER BBN, Madrid, Spain
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México.
Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico city, México
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía,
Universidad Peruana Cayetano Heredia. Av. Honorio Delgado, 430. SMP. Lima, Peru
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Schneider KA, Kim Y. Genetic hitchhiking under heterogeneous spatial selection pressures. PLoS One 2013; 8:e61742. [PMID: 23637897 PMCID: PMC3634857 DOI: 10.1371/journal.pone.0061742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 03/17/2013] [Indexed: 12/31/2022] Open
Abstract
During adaptive evolutionary processes substantial heterogeneity in selective pressure might act across local habitats in sympatry. Examples are selection for drug resistance in malaria or herbicide resistance in weeds. In such setups standard population-genetic assumptions (homogeneous constant selection pressures, random mating etc.) are likely to be violated. To avoid misinferences on the strength and pattern of natural selection it is therefore necessary to adjust population-genetic theory to meet the specifics driving adaptive processes in particular organisms. We introduce a deterministic model in which selection acts heterogeneously on a population of haploid individuals across different patches over which the population randomly disperses every generation. A fixed proportion of individuals mates exclusively within patches, whereas the rest mates randomly across all patches. We study how the allele frequencies at neutral markers are affected by the spread of a beneficial mutation at a closely linked locus (genetic hitchhiking). We provide an analytical solution for the frequency change and the expected heterozygosity at the neutral locus after a single copy of a beneficial mutation became fixed. We furthermore provide approximations of these solutions which allow for more obvious interpretations. In addition, we validate the results by stochastic simulations. Our results show that the application of standard population-genetic theory is accurate as long as differences across selective environments are moderate. However, if selective differences are substantial, as for drug resistance in malaria, herbicide resistance in weeds, or insecticide resistance in agriculture, it is necessary to adapt available theory to the specifics of particular organisms.
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Affiliation(s)
- Kristan A Schneider
- Department Fakultät Mathematik/Naturwissenschaften/Informatik, University of Applied Sciences Mittweida, Mittweida, Germany.
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Abdul-Ghani R, Farag HF, Allam AF. Sulfadoxine-pyrimethamine resistance in Plasmodium falciparum: a zoomed image at the molecular level within a geographic context. Acta Trop 2013; 125:163-90. [PMID: 23131424 DOI: 10.1016/j.actatropica.2012.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 10/27/2022]
Abstract
Antimalarial chemotherapy is one of the main pillars in the prevention and control of malaria. Following widespread resistance of Plasmodium falciparum to chloroquine, sulfadoxine-pyrimethamine came to the scene as an alternative to the cheap and well-tolerated chloroquine. However, widespread resistance to sulfadoxine-pyrimethamine has been documented. In vivo efficacy tests are the gold standard for assessing drug resistance and treatment failure. However, they have many disadvantages, such as influence of host immunity and drug pharmacokinetics. In vitro tests of antimalarial drug efficacy also have many technical difficulties. Molecular markers of resistance have emerged as epidemiologic tools to investigate antimalarial drug resistance even before becoming clinically evident. Mutations in P. falciparum dihydrofolate reductase and dihydrofolate synthase have been extensively studied as molecular markers for resistance to pyrimethamine and sulfadoxine, respectively. This review highlights the resistance of P. falciparum at the molecular level presenting both supporting and opposing studies on the utility of molecular markers.
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Chenet SM, Schneider KA, Villegas L, Escalante AA. Local population structure of Plasmodium: impact on malaria control and elimination. Malar J 2012; 11:412. [PMID: 23232077 PMCID: PMC3538601 DOI: 10.1186/1475-2875-11-412] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/05/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Regardless of the growing interest in detecting population structures in malarial parasites, there have been limited discussions on how to use this concept in control programmes. In such context, the effects of the parasite population structures will depend on interventions' spatial or temporal scales. This investigation explores the problem of identifying genetic markers, in this case microsatellites, to unveil Plasmodium genetic structures that could affect decisions in the context of elimination. The study was performed in a low-transmission area, which offers a good proxy to better understand problems associated with surveillance at the final stages of malaria elimination. METHODS Plasmodium vivax samples collected in Tumeremo, Venezuela, between March 2003 and November 2004 were analysed. Since Plasmodium falciparum also circulates in many low endemic areas, P. falciparum samples from the same locality and time period were included for comparison. Plasmodium vivax samples were assayed for an original set of 25 microsatellites and P. falciparum samples were assayed for 12 microsatellites. RESULTS Not all microsatellite loci assayed offered reliable local data. A complex temporal-cluster dynamics is found in both P. vivax and P. falciparum. Such dynamics affect the numbers and the type of microsatellites required for identifying individual parasites or parasite clusters when performing cross-sectional studies. The minimum number of microsatellites required to differentiate circulating P. vivax clusters differs from the minimum number of hyper-variable microsatellites required to distinguish individuals within these clusters. Regardless the extended number of microsatellites used in P. vivax, it was not possible to separate all individual infections. CONCLUSIONS Molecular surveillance has great potential; however, it requires preliminary local studies in order to properly interpret the emerging patterns in the context of elimination. Clonal expansions and clusters turnovers need to be taken into account when using molecular markers. Those affect the number and type of microsatellite markers, as well as, the expected genetic patterns in the context of operational investigations. By considering the local dynamics, elimination programmes could cost-effectively use molecular markers. However, population level studies need to consider the local limitations of a given set of loci in terms of providing epidemiologically relevant information.
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Affiliation(s)
- Stella M Chenet
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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