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Baltrušis P, Doyle SR, Halvarsson P, Höglund J. Genome-wide analysis of the response to ivermectin treatment by a Swedish field population of Haemonchus contortus. Int J Parasitol Drugs Drug Resist 2022; 18:12-19. [PMID: 34959200 PMCID: PMC8718930 DOI: 10.1016/j.ijpddr.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022]
Abstract
Haemonchus contortus is a pathogenic gastrointestinal nematode of small ruminants and, in part due to its capacity to develop resistance to drugs, contributes to significant losses in the animal production sector worldwide. Despite decades of research, comparatively little is known about the specific mechanism(s) driving resistance to drugs such as ivermectin in this species. Here we describe a genome-wide approach to detect evidence of selection by ivermectin treatment in a field population of H. contortus from Sweden, using parasites sampled from the same animals before and seven days after ivermectin exposure followed by whole-genome sequencing. Despite an 89% reduction in parasites recovered after treatment measured by the fecal egg count reduction test, the surviving population was highly genetically similar to the population before treatment, suggesting that resistance has likely evolved over time and that resistance alleles are present on diverse haplotypes. Pairwise gene and SNP frequency comparisons indicated the highest degree of differentiation was found at the terminal end of chromosome 4, whereas the most striking difference in nucleotide diversity was observed in a region on chromosome 5 previously reported to harbor a major quantitative trait locus involved in ivermectin resistance. These data provide novel insight into the genome-wide effect of ivermectin selection in a field population as well as confirm the importance of the previously established quantitative trait locus in the development of resistance to ivermectin.
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Affiliation(s)
- Paulius Baltrušis
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, P.O. Box 7036, Uppsala, Sweden.
| | - Stephen R Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Peter Halvarsson
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, P.O. Box 7036, Uppsala, Sweden
| | - Johan Höglund
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, P.O. Box 7036, Uppsala, Sweden
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2
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Aydemir O, Mensah B, Marsh PW, Abuaku B, Myers-Hansen JL, Bailey JA, Ghansah A. Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations. PeerJ 2021; 9:e11794. [PMID: 34820155 PMCID: PMC8588852 DOI: 10.7717/peerj.11794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/25/2021] [Indexed: 12/03/2022] Open
Abstract
Antimalarial resistance surveillance in sub-Saharan Africa is often constrained by logistical and financial challenges limiting its breadth and frequency. At two sites in Ghana, we have piloted a streamlined sample pooling process created immediately by sequential addition of positive malaria cases at the time of diagnostic testing. This streamlined process involving a single tube minimized clinical and laboratory work and provided accurate frequencies of all known drug resistance mutations after high-throughput targeted sequencing using molecular inversion probes. Our study validates this method as a cost-efficient, accurate and highly-scalable approach for drug resistance mutation monitoring that can potentially be applied to other infectious diseases such as tuberculosis.
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Affiliation(s)
- Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Brown University, Providence, RI, United States of America
| | - Benedicta Mensah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Patrick W Marsh
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Brown University, Providence, RI, United States of America
| | - Benjamin Abuaku
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - James Leslie Myers-Hansen
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Brown University, Providence, RI, United States of America
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
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3
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Toukam LL, Tatsinkou Fossi B, Taiwe GS, Bila RB, Feugaing Sofeu DD, Ivo EP, Achidi EA. In vivo antimalarial activity of a probiotic bacterium Lactobacillus sakei isolated from traditionally fermented milk in BALB/c mice infected with Plasmodium berghei ANKA. JOURNAL OF ETHNOPHARMACOLOGY 2021; 280:114448. [PMID: 34303805 DOI: 10.1016/j.jep.2021.114448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/10/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Milk production, processing and consumption are integral part of traditional practices in Fulani tribe of Cameroon. It has been observed that Fulani are resistant to malaria. Dairy products traditionally processed by Fulani are intensively used in the ritual treatment of malarial, inflammations and behavioural disorders. Many studies have demonstrated that fermented milk is a rich source of probiotic bacteria. However, the antimalarial activity of probiotics isolated from this natural source has not been experimentally tested. AIM OF THE STUDY Hence, this study was therefore aimed at evaluating the antimalarial activity of a probiotic bacterium Lactobacillus sakei isolated from traditionally fermented milk in mice infected with chloroquine sensitive Plasmodium berghei ANKA. MATERIALS AND METHODS The probiotic bacterium was isolated from the Cameroonian Mborro Fulani's traditionally fermented milk and identified using the 16S r RNA gene sequencing. The schizontocidal activity of Lactobacillus sakei on established malaria infection was evaluated. Eighty-four healthy young adult Balb/c mice infected with Plasmodium berghei parasite were randomly divided into two sets of seven group of six mice each, and were given three different doses of Lactobacillus sakei, chloroquine and sulfadoxine/pyrimethamine for seven and fourteen days respectively. The level of parasitaemia, body temperature, survival time and haematological parameters were evaluated. RESULTS The parasite growth inhibition was observed to increase with increasing dose of probiotic bacterium with maximum suppression being 100 % at dose 3 on day 20. Also, the probiotic bacterium significantly prevented body weight loss and was associated with body temperature reduction and prevented (p<0.05) a decrease in haematological parameters compared to that untreated malaria infected mice. CONCLUSION The results obtained suggest that Lactobacillus sakei is a probiotic bacterium with antimalarial activity in mice infected with chloroquine sensitive Plasmodium berghei.
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Affiliation(s)
- Liliane Laure Toukam
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Bertrand Tatsinkou Fossi
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon.
| | - Germain Sotoing Taiwe
- Department of Zoology and Animal Physiology, Faculty of Science, University of Buea, Cameroon
| | - Raymond Bess Bila
- Department of Zoology and Animal Physiology, Faculty of Science, University of Buea, Cameroon
| | | | - Enyong Peter Ivo
- Research Foundation for Tropical Diseases and Environment (REFOTDE) , Cameroon
| | - Eric Akum Achidi
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Cameroon
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4
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Oberstaller J, Zoungrana L, Bannerman CD, Jahangiri S, Dwivedi A, Silva JC, Adams JH, Takala-Harrison S. Integration of population and functional genomics to understand mechanisms of artemisinin resistance in Plasmodium falciparum. Int J Parasitol Drugs Drug Resist 2021; 16:119-128. [PMID: 34102588 PMCID: PMC8187163 DOI: 10.1016/j.ijpddr.2021.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/05/2021] [Accepted: 05/21/2021] [Indexed: 11/05/2022]
Abstract
Resistance to antimalarial drugs, and in particular to the artemisinin derivatives and their partner drugs, threatens recent progress toward regional malaria elimination and eventual global malaria eradication. Population-level studies utilizing whole-genome sequencing approaches have facilitated the identification of regions of the parasite genome associated with both clinical and in vitro drug-resistance phenotypes. However, the biological relevance of genes identified in these analyses and the establishment of a causal relationship between genotype and phenotype requires functional characterization. Here we examined data from population genomic and transcriptomic studies in the context of data generated from recent functional studies, using a new population genetic approach designed to identify potential favored mutations within the region of a selective sweep (iSAFE). We identified several genes functioning in pathways now known to be associated with artemisinin resistance that were supported in early population genomic studies, as well as potential new drug targets/pathways for further validation and consideration for treatment of artemisinin-resistant Plasmodium falciparum. In addition, we establish the utility of iSAFE in identifying positively-selected mutations in population genomic studies, potentially accelerating the time to functional validation of candidate genes.
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Affiliation(s)
- Jenna Oberstaller
- Center for Global Health and Infectious Disease Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
| | - Linda Zoungrana
- Center for Global Health and Infectious Disease Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
| | - Carl D Bannerman
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Samira Jahangiri
- Center for Global Health and Infectious Disease Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - John H Adams
- Center for Global Health and Infectious Disease Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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Button-Simons KA, Kumar S, Carmago N, Haile MT, Jett C, Checkley LA, Kennedy SY, Pinapati RS, Shoue DA, McDew-White M, Li X, Nosten FH, Kappe SH, Anderson TJC, Romero-Severson J, Ferdig MT, Emrich SJ, Vaughan AM, Cheeseman IH. The power and promise of genetic mapping from Plasmodium falciparum crosses utilizing human liver-chimeric mice. Commun Biol 2021; 4:734. [PMID: 34127785 PMCID: PMC8203791 DOI: 10.1038/s42003-021-02210-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 04/30/2021] [Indexed: 12/30/2022] Open
Abstract
Genetic crosses are most powerful for linkage analysis when progeny numbers are high, parental alleles segregate evenly and numbers of inbred progeny are minimized. We previously developed a novel genetic crossing platform for the human malaria parasite Plasmodium falciparum, an obligately sexual, hermaphroditic protozoan, using mice carrying human hepatocytes (the human liver-chimeric FRG NOD huHep mouse) as the vertebrate host. We report on two genetic crosses-(1) an allopatric cross between a laboratory-adapted parasite (NF54) of African origin and a recently patient-derived Asian parasite, and (2) a sympatric cross between two recently patient-derived Asian parasites. We generated 144 unique recombinant clones from the two crosses, doubling the number of unique recombinant progeny generated in the previous 30 years. The allopatric African/Asian cross has minimal levels of inbreeding and extreme segregation distortion, while in the sympatric Asian cross, inbred progeny predominate and parental alleles segregate evenly. Using simulations, we demonstrate that these progeny provide the power to map small-effect mutations and epistatic interactions. The segregation distortion in the allopatric cross slightly erodes power to detect linkage in several genome regions. We greatly increase the power and the precision to map biomedically important traits with these new large progeny panels.
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Affiliation(s)
- Katrina A Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nelly Carmago
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Meseret T Haile
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Catherine Jett
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Lisa A Checkley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Spencer Y Kennedy
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Douglas A Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Marina McDew-White
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - François H Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Stefan H Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Timothy J C Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Michael T Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Ashley M Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ian H Cheeseman
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA.
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6
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Kayiba NK, Yobi DM, Tshibangu-Kabamba E, Tuan VP, Yamaoka Y, Devleesschauwer B, Mvumbi DM, Okitolonda Wemakoy E, De Mol P, Mvumbi GL, Hayette MP, Rosas-Aguirre A, Speybroeck N. Spatial and molecular mapping of Pfkelch13 gene polymorphism in Africa in the era of emerging Plasmodium falciparum resistance to artemisinin: a systematic review. THE LANCET. INFECTIOUS DISEASES 2020; 21:e82-e92. [PMID: 33125913 DOI: 10.1016/s1473-3099(20)30493-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 03/29/2020] [Accepted: 04/21/2020] [Indexed: 12/19/2022]
Abstract
The spread of Plasmodium falciparum isolates carrying mutations in the kelch13 (Pfkelch13) gene associated with artemisinin resistance (PfART-R) in southeast Asia threatens malaria control and elimination efforts. Emergence of PfART-R in Africa would result in a major public health problem. In this systematic review, we investigate the frequency and spatial distribution of Pfkelch13 mutants in Africa, including mutants linked to PfART-R in southeast Asia. Seven databases were searched (PubMed, Embase, Scopus, African Journal Online, African Index Medicus, Bioline, and Web of Science) for relevant articles about polymorphisms of the Pfkelch13 gene in Africa before January, 2019. Following PRISMA guidelines, 53 studies that sequenced the Pfkelch13 gene of 23 100 sample isolates in 41 sub-Saharan African countries were included. The Pfkelch13 sequence was highly polymorphic (292 alleles, including 255 in the Pfkelch13-propeller domain) but with mutations occurring at very low relative frequencies. Non-synonymous mutations were found in only 626 isolates (2·7%) from west, central, and east Africa. According to WHO, nine different mutations linked to PfART-R in southeast Asia (Phe446Ile, Cys469Tyr, Met476Ile, Arg515Lys, Ser522Cys, Pro553Leu, Val568Gly, Pro574Leu, and Ala675Val) were detected, mainly in east Africa. Several other Pfkelch13 mutations, such as those structurally similar to southeast Asia PfART-R mutations, were also identified, but their relevance for drug resistance is still unknown. This systematic review shows that Africa, thought to not have established PfART-R, reported resistance-related mutants in the past 5 years. Surveillance using PfART-R molecular markers can provide valuable decision-making information to sustain the effectiveness of artemisinin in Africa.
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Affiliation(s)
- Nadine K Kayiba
- Institute of Health and Society, Université catholique de Louvain, Brussels, Belgium; Department of Public Health, University of Mbujimayi, Mbujimayi, DR Congo; Department of Epidemiology and Biostatistics, University of Kinshasa, Kinshasa, DR Congo
| | - Doudou M Yobi
- Department of Basic Sciences, University of Kinshasa, Kinshasa, DR Congo
| | - Evariste Tshibangu-Kabamba
- Department of Basic Sciences, University of Mbujimayi, Mbujimayi, DR Congo; Department of Environmental and Preventive Medicine, Oita University, Yufu, Japan
| | - Vo P Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam; Department of Environmental and Preventive Medicine, Oita University, Yufu, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University, Yufu, Japan
| | - Brecht Devleesschauwer
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium; Department of Veterinary Public Health and Food Safety, Ghent University, Merelbeke, Belgium
| | - Dieudonné M Mvumbi
- Department of Basic Sciences, University of Kinshasa, Kinshasa, DR Congo
| | | | - Patrick De Mol
- Department of Parasitology and Mycology, University Hospital of Liège, Liège, Belgium
| | - Georges L Mvumbi
- Department of Basic Sciences, University of Kinshasa, Kinshasa, DR Congo
| | - Marie-Pierre Hayette
- Department of Parasitology and Mycology, University Hospital of Liège, Liège, Belgium
| | - Angel Rosas-Aguirre
- Institute of Health and Society, Université catholique de Louvain, Brussels, Belgium
| | - Niko Speybroeck
- Institute of Health and Society, Université catholique de Louvain, Brussels, Belgium.
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7
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Davis SZ, Singh PP, Vendrely KM, Shoue DA, Checkley LA, McDew-White M, Button-Simons KA, Cassady Z, Sievert MAC, Foster GJ, Nosten FH, Anderson TJC, Ferdig MT. The extended recovery ring-stage survival assay provides a superior association with patient clearance half-life and increases throughput. Malar J 2020; 19:54. [PMID: 32005233 PMCID: PMC6995136 DOI: 10.1186/s12936-020-3139-6] [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: 12/09/2019] [Accepted: 01/24/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Tracking and understanding artemisinin resistance is key for preventing global setbacks in malaria eradication efforts. The ring-stage survival assay (RSA) is the current gold standard for in vitro artemisinin resistance phenotyping. However, the RSA has several drawbacks: it is relatively low throughput, has high variance due to microscopy readout, and correlates poorly with the current benchmark for in vivo resistance, patient clearance half-life post-artemisinin treatment. Here a modified RSA is presented, the extended Recovery Ring-stage Survival Assay (eRRSA), using 15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives, including parasite isolates with and without kelch13 mutations. METHODS Plasmodium falciparum cultures were synchronized with single layer Percoll during the schizont stage of the intraerythrocytic development cycle. Cultures were left to reinvade to early ring-stage and parasitaemia was quantified using flow cytometry. Cultures were diluted to 2% haematocrit and 0.5% parasitaemia in a 96-well plate to start the assay, allowing for increased throughput and decreased variability between biological replicates. Parasites were treated with 700 nM of dihydroartemisinin or 0.02% dimethyl sulfoxide (DMSO) for 6 h, washed three times in drug-free media, and incubated for 66 or 114 h, when samples were collected and frozen for PCR amplification. A SYBR Green-based quantitative PCR method was used to quantify the fold-change between treated and untreated samples. RESULTS 15 cloned patient isolates from Southeast Asia with a range of patient clearance half-lives were assayed using the eRRSA. Due to the large number of pyknotic and dying parasites at 66 h post-exposure (72 h sample), parasites were grown for an additional cell cycle (114 h post-exposure, 120 h sample), which drastically improved correlation with patient clearance half-life compared to the 66 h post-exposure sample. A Spearman correlation of - 0.8393 between fold change and patient clearance half-life was identified in these 15 isolates from Southeast Asia, which is the strongest correlation reported to date. CONCLUSIONS eRRSA drastically increases the efficiency and accuracy of in vitro artemisinin resistance phenotyping compared to the traditional RSA, which paves the way for extensive in vitro phenotyping of hundreds of artemisinin resistant parasites.
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Affiliation(s)
- Sage Z Davis
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.,Molecular, Cell, and Systems Biology Department, University of California Riverside, Riverside, CA, USA
| | - Puspendra P Singh
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Katelyn M Vendrely
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Douglas A Shoue
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Lisa A Checkley
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Katrina A Button-Simons
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Zione Cassady
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Mackenzie A C Sievert
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Gabriel J Foster
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - François H Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | | | - Michael T Ferdig
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
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8
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McDew-White M, Li X, Nkhoma SC, Nair S, Cheeseman I, Anderson TJC. Mode and Tempo of Microsatellite Length Change in a Malaria Parasite Mutation Accumulation Experiment. Genome Biol Evol 2020; 11:1971-1985. [PMID: 31273388 PMCID: PMC6644851 DOI: 10.1093/gbe/evz140] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2019] [Indexed: 12/12/2022] Open
Abstract
Malaria parasites have small extremely AT-rich genomes: microsatellite repeats (1–9 bp) comprise 11% of the genome and genetic variation in natural populations is dominated by repeat changes in microsatellites rather than point mutations. This experiment was designed to quantify microsatellite mutation patterns in Plasmodium falciparum. We established 31 parasite cultures derived from a single parasite cell and maintained these for 114–267 days with frequent reductions to a single cell, so parasites accumulated mutations during ∼13,207 cell divisions. We Illumina sequenced the genomes of both progenitor and end-point mutation accumulation (MA) parasite lines in duplicate to validate stringent calling parameters. Microsatellite calls were 99.89% (GATK), 99.99% (freeBayes), and 99.96% (HipSTR) concordant in duplicate sequence runs from independent sequence libraries, whereas introduction of microsatellite mutations into the reference genome revealed a low false negative calling rate (0.68%). We observed 98 microsatellite mutations. We highlight several conclusions: microsatellite mutation rates (3.12 × 10−7 to 2.16 × 10−8/cell division) are associated with both repeat number and repeat motif like other organisms studied. However, 41% of changes resulted from loss or gain of more than one repeat: this was particularly true for long repeat arrays. Unlike other eukaryotes, we found no insertions or deletions that were not associated with repeats or homology regions. Overall, microsatellite mutation rates are among the lowest recorded and comparable to those in another AT-rich protozoan (Dictyostelium). However, a single infection (>1011 parasites) will still contain over 2.16 × 103 to 3.12 × 104 independent mutations at any single microsatellite locus.
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Affiliation(s)
| | - Xue Li
- Texas Biomedical Research Institute, San Antonio, Texas
| | - Standwell C Nkhoma
- Texas Biomedical Research Institute, San Antonio, Texas.,Malaria Research and Reference Reagent Resource Center (MR4), BEI Resources, American Type Culture Collection, 10801 University Boulevard, Manassas, VA
| | - Shalini Nair
- Texas Biomedical Research Institute, San Antonio, Texas
| | - Ian Cheeseman
- Texas Biomedical Research Institute, San Antonio, Texas
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9
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Calarco L, Barratt J, Ellis J. Detecting sequence variants in clinically important protozoan parasites. Int J Parasitol 2019; 50:1-18. [PMID: 31857072 DOI: 10.1016/j.ijpara.2019.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/29/2019] [Accepted: 10/01/2019] [Indexed: 02/06/2023]
Abstract
Second and third generation sequencing methods are crucial for population genetic studies, and variant detection is a popular approach for exploiting this sequence data. While mini- and microsatellites are historically useful markers for studying important Protozoa such as Toxoplasma and Plasmodium spp., detecting non-repetitive variants such as those found in genes can be fundamental to investigating a pathogen's biology. These variants, namely single nucleotide polymorphisms and insertions and deletions, can help elucidate the genetic basis of an organism's pathogenicity, identify selective pressures, and resolve phylogenetic relationships. They also have the added benefit of possessing a comparatively low mutation rate, which contributes to their stability. However, there is a plethora of variant analysis tools with nuanced pipelines and conflicting recommendations for best practise, which can be confounding. This lack of standardisation means that variant analysis requires careful parameter optimisation, an understanding of its limitations, and the availability of high quality data. This review explores the value of variant detection when applied to non-model organisms such as clinically important protozoan pathogens. The limitations of current methods are discussed, including special considerations that require the end-users' attention to ensure that the results generated are reproducible, and the biological conclusions drawn are valid.
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Affiliation(s)
- Larissa Calarco
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia.
| | - Joel Barratt
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - John Ellis
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
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10
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Tirrell AR, Vendrely KM, Checkley LA, Davis SZ, McDew-White M, Cheeseman IH, Vaughan AM, Nosten FH, Anderson TJC, Ferdig MT. Pairwise growth competitions identify relative fitness relationships among artemisinin resistant Plasmodium falciparum field isolates. Malar J 2019; 18:295. [PMID: 31462253 PMCID: PMC6714446 DOI: 10.1186/s12936-019-2934-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/23/2019] [Indexed: 02/08/2023] Open
Abstract
Background Competitive outcomes between co-infecting malaria parasite lines can reveal fitness disparities in blood stage growth. Blood stage fitness costs often accompany the evolution of drug resistance, with the expectation that relatively fitter parasites will be more likely to spread in populations. With the recent emergence of artemisinin resistance, it is important to understand the relative competitive fitness of the metabolically active asexual blood stage parasites. Genetically distinct drug resistant parasite clones with independently evolved sets of mutations are likely to vary in asexual proliferation rate, contributing to their chance of transmission to the mosquito vector. Methods An optimized in vitro 96-well plate-based protocol was used to quantitatively measure-head-to-head competitive fitness during blood stage development between seven genetically distinct field isolates from a hotspot of emerging artemisinin resistance and the laboratory strain, NF54. These field isolates were isolated from patients in Southeast Asia carrying different alleles of kelch13 and included both artemisinin-sensitive and artemisinin-resistant isolates. Fluorescent labeled microsatellite markers were used to track the relative densities of each parasite throughout the co-growth period of 14–60 days. All-on-all competitions were conducted for the panel of eight parasite lines (28 pairwise competitions) to determine their quantitative competitive fitness relationships. Results Twenty-eight pairwise competitive growth outcomes allowed for an unambiguous ranking among a set of seven genetically distinct parasite lines isolated from patients in Southeast Asia displaying a range of both kelch13 alleles and clinical clearance times and a laboratory strain, NF54. This comprehensive series of assays established the growth relationships among the eight parasite lines. Interestingly, a clinically artemisinin resistant parasite line that carries the wild-type form of kelch13 outcompeted all other parasites in this study. Furthermore, a kelch13 mutant line (E252Q) was competitively more fit without drug than lines with other resistance-associated kelch13 alleles, including the C580Y allele that has expanded to high frequencies under drug pressure in Southeast Asian resistant populations. Conclusions This optimized competitive growth assay can be employed for assessment of relative growth as an index of fitness during the asexual blood stage growth between natural lines carrying different genetic variants associated with artemisinin resistance. Improved understanding of the fitness costs of different parasites proliferating in human blood and the role different resistance mutations play in the context of specific genetic backgrounds will contribute to an understanding of the potential for specific mutations to spread in populations, with the potential to inform targeted strategies for malaria therapy.
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Affiliation(s)
- Abigail R Tirrell
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Katelyn M Vendrely
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Lisa A Checkley
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Sage Z Davis
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | | | | | - François H Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | | | - Michael T Ferdig
- Eck Institute for Global Health, Dept. of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
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Genome-wide Approaches to Investigate Anthelmintic Resistance. Trends Parasitol 2019; 35:289-301. [DOI: 10.1016/j.pt.2019.01.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 01/09/2023]
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12
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Doyle SR, Illingworth CJR, Laing R, Bartley DJ, Redman E, Martinelli A, Holroyd N, Morrison AA, Rezansoff A, Tracey A, Devaney E, Berriman M, Sargison N, Cotton JA, Gilleard JS. Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus. BMC Genomics 2019; 20:218. [PMID: 30876405 PMCID: PMC6420744 DOI: 10.1186/s12864-019-5592-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infect livestock and companion animals, and there are growing concerns regarding the reduced efficacy in some human-infective helminths. Understanding the mechanisms by which resistance evolves is the focus of increasing interest; robust genetic analysis of helminths is challenging, and although many candidate genes have been proposed, the genetic basis of resistance remains poorly resolved. RESULTS Here, we present a genome-wide analysis of two genetic crosses between ivermectin resistant and sensitive isolates of the parasitic nematode Haemonchus contortus, an economically important gastrointestinal parasite of small ruminants and a model for anthelmintic research. Whole genome sequencing of parental populations, and key stages throughout the crosses, identified extensive genomic diversity that differentiates populations, but after backcrossing and selection, a single genomic quantitative trait locus (QTL) localised on chromosome V was revealed to be associated with ivermectin resistance. This QTL was common between the two geographically and genetically divergent resistant populations and did not include any leading candidate genes, suggestive of a previously uncharacterised mechanism and/or driver of resistance. Despite limited resolution due to low recombination in this region, population genetic analyses and novel evolutionary models supported strong selection at this QTL, driven by at least partial dominance of the resistant allele, and that large resistance-associated haplotype blocks were enriched in response to selection. CONCLUSIONS We have described the genetic architecture and mode of ivermectin selection, revealing a major genomic locus associated with ivermectin resistance, the most conclusive evidence to date in any parasitic nematode. This study highlights a novel genome-wide approach to the analysis of a genetic cross in non-model organisms with extreme genetic diversity, and the importance of a high-quality reference genome in interpreting the signals of selection so identified.
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Affiliation(s)
| | - Christopher J. R. Illingworth
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
- Department of Applied Maths and Theoretical Physics, Wilberforce Road, Cambridge, CB3 0WA UK
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G61 1QH UK
| | - David J. Bartley
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ UK
| | - Elizabeth Redman
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta Canada
| | - Axel Martinelli
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA UK
- Present Address: Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
- Present Address: Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nancy Holroyd
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Alison A. Morrison
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ UK
| | - Andrew Rezansoff
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta Canada
| | - Alan Tracey
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G61 1QH UK
| | | | - Neil Sargison
- University of Edinburgh, Royal (Dick) School of Veterinary Studies, Edinburgh, EH25 9RG UK
| | - James A. Cotton
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA UK
| | - John S. Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta Canada
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Association of mutations in the Plasmodium falciparum Kelch13 gene (Pf3D7_1343700) with parasite clearance rates after artemisinin-based treatments-a WWARN individual patient data meta-analysis. BMC Med 2019; 17:1. [PMID: 30651111 PMCID: PMC6335805 DOI: 10.1186/s12916-018-1207-3] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/01/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Plasmodium falciparum infections with slow parasite clearance following artemisinin-based therapies are widespread in the Greater Mekong Subregion. A molecular marker of the slow clearance phenotype has been identified: single genetic changes within the propeller region of the Kelch13 protein (pfk13; Pf3D7_1343700). Global searches have identified almost 200 different non-synonymous mutant pfk13 genotypes. Most mutations occur at low prevalence and have uncertain functional significance. To characterize the impact of different pfk13 mutations on parasite clearance, we conducted an individual patient data meta-analysis of the associations between parasite clearance half-life (PC1/2) and pfk13 genotype based on a large set of individual patient records from Asia and Africa. METHODS A systematic literature review following the PRISMA protocol was conducted to identify studies published between 2000 and 2017 which included frequent parasite counts and pfk13 genotyping. Four databases (Ovid Medline, PubMed, Ovid Embase, and Web of Science Core Collection) were searched. Eighteen studies (15 from Asia, 2 from Africa, and one multicenter study with sites on both continents) met inclusion criteria and were shared. Associations between the log transformed PC1/2 values and pfk13 genotype were assessed using multivariable regression models with random effects for study site. RESULTS Both the pfk13 genotypes and the PC1/2 were available from 3250 (95%) patients (n = 3012 from Asia (93%), n = 238 from Africa (7%)). Among Asian isolates, all pfk13 propeller region mutant alleles observed in five or more specific isolates were associated with a 1.5- to 2.7-fold longer geometric mean PC1/2 compared to the PC1/2 of wild type isolates (all p ≤ 0.002). In addition, mutant allele E252Q located in the P. falciparum region of pfk13 was associated with 1.5-fold (95%CI 1.4-1.6) longer PC1/2. None of the isolates from four countries in Africa showed a significant difference between the PC1/2 of parasites with or without pfk13 propeller region mutations. Previously, the association of six pfk13 propeller mutant alleles with delayed parasite clearance had been confirmed. This analysis demonstrates that 15 additional pfk13 alleles are associated strongly with the slow-clearing phenotype in Southeast Asia. CONCLUSION Pooled analysis associated 20 pfk13 propeller region mutant alleles with the slow clearance phenotype, including 15 mutations not confirmed previously.
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Fitness Costs and the Rapid Spread of kelch13-C580Y Substitutions Conferring Artemisinin Resistance. Antimicrob Agents Chemother 2018; 62:AAC.00605-18. [PMID: 29914963 PMCID: PMC6125530 DOI: 10.1128/aac.00605-18] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/13/2018] [Indexed: 01/31/2023] Open
Abstract
Fitness costs are key determinants of whether drug resistance alleles establish and how fast they spread within populations. More than 125 different kelch13 alleles, each containing a different amino acid substitution, have arisen in Southeast Asian malaria parasite (Plasmodium falciparum) populations under artemisinin selection over the past 15 years in a dramatic example of a soft selective event. Fitness costs are key determinants of whether drug resistance alleles establish and how fast they spread within populations. More than 125 different kelch13 alleles, each containing a different amino acid substitution, have arisen in Southeast Asian malaria parasite (Plasmodium falciparum) populations under artemisinin selection over the past 15 years in a dramatic example of a soft selective event. However, just one of these alleles (C580Y) is now outcompeting other alleles in multiple different countries and is spreading toward fixation. Here we examine the fitness consequences of C580Y, relative to another less successful kelch13 mutation (R561H), to try to explain the distinctive dynamics of C580Y. We hypothesized that C580Y will show lower fitness costs than other kelch13 substitutions in the absence of artemisinin treatment. We used CRISPR/Cas9 methods to introduce single mutations (C580Y or R561H) or synonymous control edits into a wild-type parasite isolated on the Thailand-Myanmar border, conducted replicated head-to-head competition assays, and determined the outcome of competition using deep sequencing of kelch13 amplicons. Contrary to our predictions, these experiments reveal that C580Y carries higher fitness costs (s [selection coefficient] = 0.15 ± 0.008 [1 standard error {SE}]) than R561H (s = 0.084 ± 0.005). Furthermore, R561H outcompetes C580Y in direct competition (s = 0.065 ± 0.004). We conclude that fitness costs of C580Y in isolation are unlikely to explain the rapid spread of this substitution.
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15
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Fitness Loss under Amino Acid Starvation in Artemisinin-Resistant Plasmodium falciparum Isolates from Cambodia. Sci Rep 2018; 8:12622. [PMID: 30135481 PMCID: PMC6105667 DOI: 10.1038/s41598-018-30593-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/31/2018] [Indexed: 11/09/2022] Open
Abstract
Artemisinin is the most rapidly effective drug for Plasmodium falciparum malaria treatment currently in clinical use. Emerging artemisinin-resistant parasites pose a great global health risk. At present, the level of artemisinin resistance is still relatively low with evidence pointing towards a trade-off between artemisinin resistance and fitness loss. Here we show that artemisinin-resistant P. falciparum isolates from Cambodia manifested fitness loss, showing fewer progenies during the intra-erythrocytic developmental cycle. The loss in fitness was exacerbated under the condition of low exogenous amino acid supply. The resistant parasites failed to undergo maturation, whereas their drug-sensitive counterparts were able to complete the erythrocytic cycle under conditions of amino acid deprivation. The artemisinin-resistant phenotype was not stable, and loss of the phenotype was associated with changes in the expression of a putative target, Exp1, a membrane glutathione transferase. Analysis of SNPs in haemoglobin processing genes revealed associations with parasite clearance times, suggesting changes in haemoglobin catabolism may contribute to artemisinin resistance. These findings on fitness and protein homeostasis could provide clues on how to contain emerging artemisinin-resistant parasites.
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Doyle SR, Bourguinat C, Nana-Djeunga HC, Kengne-Ouafo JA, Pion SDS, Bopda J, Kamgno J, Wanji S, Che H, Kuesel AC, Walker M, Basáñez MG, Boakye DA, Osei-Atweneboana MY, Boussinesq M, Prichard RK, Grant WN. Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity. PLoS Negl Trop Dis 2017; 11:e0005816. [PMID: 28746337 PMCID: PMC5546710 DOI: 10.1371/journal.pntd.0005816] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/07/2017] [Accepted: 07/19/2017] [Indexed: 12/30/2022] Open
Abstract
Background Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana—exposed to more than a decade of regular ivermectin treatment—have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread. Methodology/Principal findings Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR. Conclusions/Significance This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic drift rather than genetic selection of SOR is the underlying driver of population differentiation, which has significant implications for the emergence and potential spread of SOR within and between these parasite populations. Onchocerciasis is a human parasitic disease endemic across large areas of Sub-Saharan Africa, where more than 99% of the estimated 100 million people globally at-risk live. The microfilarial stage of Onchocerca volvulus causes pathologies ranging from mild itching to visual impairment and ultimately, irreversible blindness. Mass administration of ivermectin kills microfilariae and has an anti-fecundity effect on adult worms by temporarily inhibiting the development in utero and/or release into the skin of new microfilariae, thereby reducing morbidity and transmission. Phenotypic and genetic changes in some parasite populations that have undergone multiple ivermectin treatments in Cameroon and Ghana have raised concern that sub-optimal response to ivermectin's anti-fecundity effect may increase in frequency, reducing the impact of ivermectin-based control measures. We used next generation sequencing of small pools of parasites to define genome-wide genetic differences between phenotypically characterised good and sub-optimal responder parasites from Cameroon and Ghana, and identified multiple regions of the genome that differentiated the response types. These regions were largely different between parasites from these two countries but revealed common molecular pathways that might be involved in determining the extent of response to ivermectin's anti-fecundity effect. These data reveal a more complex than previously described pattern of genetic diversity among O. volvulus populations that differ in their geography and response to ivermectin treatment.
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Affiliation(s)
- Stephen R. Doyle
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- * E-mail: (SRD); (RKP); (WNG)
| | - Catherine Bourguinat
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Québec, Canada
| | - Hugues C. Nana-Djeunga
- Parasitology and Ecology Laboratory, Department of Animal Biology and Physiology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
- Centre for Research on Filariasis and other Tropical Diseases (CRFilMT), Yaoundé, Cameroon
| | - Jonas A. Kengne-Ouafo
- Research Foundation in Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Sébastien D. S. Pion
- Institut de Recherche pour le Développement (IRD), IRD UMI 233 TransVIHMI – Université Montpellier – INSERM U1175, Montpellier, France
| | - Jean Bopda
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Joseph Kamgno
- Centre for Research on Filariasis and other Tropical Diseases (CRFilMT), Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Samuel Wanji
- Research Foundation in Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Hua Che
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Québec, Canada
| | - Annette C. Kuesel
- UNICEF/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (WHO/TDR), World Health Organization, Geneva, Switzerland
| | - Martin Walker
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, United Kingdom
| | - Maria-Gloria Basáñez
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Faculty of Medicine, School of Public Health, Imperial College London, United Kingdom
| | - Daniel A. Boakye
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Mike Y. Osei-Atweneboana
- Department of Environmental Biology and Health Water Research Institute, Council for Scientific and Industrial Research (CSIR), Accra, Ghana
| | - Michel Boussinesq
- Institut de Recherche pour le Développement (IRD), IRD UMI 233 TransVIHMI – Université Montpellier – INSERM U1175, Montpellier, France
| | - Roger K. Prichard
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Québec, Canada
- * E-mail: (SRD); (RKP); (WNG)
| | - Warwick N. Grant
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
- * E-mail: (SRD); (RKP); (WNG)
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Wit J, Gilleard JS. Resequencing Helminth Genomes for Population and Genetic Studies. Trends Parasitol 2017; 33:388-399. [DOI: 10.1016/j.pt.2017.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 10/20/2022]
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Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya. Sci Rep 2017; 7:41108. [PMID: 28117350 PMCID: PMC5259759 DOI: 10.1038/srep41108] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/15/2016] [Indexed: 12/23/2022] Open
Abstract
Large-scale molecular epidemiologic studies of Plasmodium falciparum parasites have provided insights into parasite biology and transmission, can identify the spread of drug resistance, and are useful in assessing vaccine targets. The polyclonal nature infections in high transmission settings is problematic for traditional genotyping approaches. Next-generation sequencing (NGS) approaches to parasite genotyping allow sensitive detection of minority variants, disaggregation of complex parasite mixtures, and scalable processing of large samples sets. Therefore, we designed, validated, and applied to field parasites an approach that leverages sequencing of individually barcoded samples in a multiplex manner. We utilize variant barcodes, invariant linker sequences and modular template-specific primers to allow for the simultaneous generation of high-dimensional sequencing data of multiple gene targets. This modularity permits a cost-effective and reproducible way to query many genes at once. In mixtures of reference parasite genomes, we quantitatively detected unique haplotypes comprising as little as 2% of a polyclonal infection. We applied this genotyping approach to field-collected parasites collected in Western Kenya in order to simultaneously obtain parasites genotypes at three unlinked loci. In summary, we present a rapid, scalable, and flexible method for genotyping individual parasites that enables molecular epidemiologic studies of parasite evolution, population structure and transmission.
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Luo X, Shi X, Yuan C, Ai M, Ge C, Hu M, Feng X, Yang X. Genome-wide SNP analysis using 2b-RAD sequencing identifies the candidate genes putatively associated with resistance to ivermectin in Haemonchus contortus. Parasit Vectors 2017; 10:31. [PMID: 28095895 PMCID: PMC5240194 DOI: 10.1186/s13071-016-1959-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/27/2016] [Indexed: 01/15/2023] Open
Abstract
Background The excessive and uncontrolled use of anthelmintics, e.g. ivermectin (IVM) for the treatment of livestock parasites has led to widespread resistance in gastrointestinal nematodes, such as Haemonchus contortus. There is an urgent need for better management of drug-use in nematode control and development of novel anthelmintics. Discovery and identification of anthelmintic resistance-associate molecules/markers can provide a basis for rational anthelmintics-use and development of novel drugs. Recent studies have shown that ivermectin resistance in H. contortus is likely to be multi-genic in nature except for several genes coding for IVM target and efflux pump. However, no other IVM resistance-associated genes were characterized by conventional methods or strategies. In the present study we adopted a new strategy, i.e. using genome-wide single nucleotide polymorphism (SNP) analysis based on 2b-RAD sequencing, for discovering SNPs markers across the genomes in both IVM susceptible and resistant isolates of H. contortus and identifying potential IVM resistance-associated genes. Results We discovered 2962 and 2667 SNPs within both susceptible and resistant strains of H. contortus, respectively. A relative lower and similar genetic variations were observed within both resistant and susceptible strains (average π values were equal to 0.1883 and 0.1953, respectively); whereas a high genetic variation was found across both strains (average π value was equal to 0.3899). A significant differentiation across 2b-RAD tags nucleotide sites was also observed between the two strains (average FST value was equal to 0.3076); the larger differences in average FST were observed at SNPs loci between coding and noncoding (including intronic) regions. Comparison between resistant and susceptible strains revealed that 208 SNPs loci exhibited significantly elevated FST values, 24 SNPs of those loci were located in the CDS regions of the nine genes and were likely to have signature of IVM directional selection. Seven of the nine candidate genes were predicted to code for some functional proteins such as potential IVM target and/or efflux pump proteins, component proteins of receptor complex in membrane on neuromuscular cells, and transcriptional regulation proteins. Those genes might be involved in resistance to IVM. Conclusions Our data suggest that candidate genes putatively associated with resistance to IVM in H. contortus may be identified by genome-wide SNP analysis using 2b-RAD sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1959-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoping Luo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.,College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010010, Inner Mongolia Nationality Autonomous, People's Republic of China
| | - Xiaona Shi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.,College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 250014, People's Republic of China
| | - Chunxiu Yuan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, Jiangsu Province, People's Republic of China
| | - Min Ai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China
| | - Cheng Ge
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.,College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 250014, People's Republic of China
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Xingang Feng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai, 200241, People's Republic of China.
| | - Xiaoye Yang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010010, Inner Mongolia Nationality Autonomous, People's Republic of China.
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Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data. G3-GENES GENOMES GENETICS 2016; 6:3507-3515. [PMID: 27613752 PMCID: PMC5100849 DOI: 10.1534/g3.116.034488] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and widespread use of this method for many research questions, ranging from unraveling the genetic basis of complex traits, to the clonal evolution of cancer cells. Because the accuracy of Pool-Seq could be affected by many potential sources of error, several studies have determined, for example, the influence of sequencing technology, the library preparation protocol, and mapping parameters. Nevertheless, the impact of the mapping tools has not yet been evaluated. Using simulated and real Pool-Seq data, we demonstrate a substantial impact of the mapping tools, leading to characteristic false positives in genome-wide scans. The problem of false positives was particularly pronounced when data with different read lengths and insert sizes were compared. Out of 14 evaluated algorithms novoalign, bwa mem and clc4 are most suitable for mapping Pool-Seq data. Nevertheless, no single algorithm is sufficient for avoiding all false positives. We show that the intersection of the results of two mapping algorithms provides a simple, yet effective, strategy to eliminate false positives. We propose that the implementation of a consistent Pool-Seq bioinformatics pipeline, building on the recommendations of this study, can substantially increase the reliability of Pool-Seq results, in particular when libraries generated with different protocols are being compared.
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21
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Auburn S, Barry AE. Dissecting malaria biology and epidemiology using population genetics and genomics. Int J Parasitol 2016; 47:77-85. [PMID: 27825828 DOI: 10.1016/j.ijpara.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 10/20/2022]
Abstract
Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies. Microsatellite genotyping remains a popular approach for both Plasmodium falciparum and Plasmodium vivax. However, with the increasing availability of whole genome sequencing data enabling effective single nucleotide polymorphism-based panels tailored to a given study question and setting, this approach is gaining popularity. The availability of new reference genomes for Plasmodium malariae and Plasmodium ovale should see a surge in similar molecular studies on these currently neglected species. Genomic studies are revealing new insights into important adaptive mechanisms of the parasite including antimalarial drug resistance. The advent of new methodologies such as selective whole genome amplification for dealing with extensive human DNA in low density field isolates should see genome-wide approaches becoming routine for parasite surveillance once the economic costs outweigh the current cost benefits of targeted approaches.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Alyssa E Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia.
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22
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Anderson TJC, Nair S, McDew-White M, Cheeseman IH, Nkhoma S, Bilgic F, McGready R, Ashley E, Pyae Phyo A, White NJ, Nosten F. Population Parameters Underlying an Ongoing Soft Sweep in Southeast Asian Malaria Parasites. Mol Biol Evol 2016; 34:131-144. [PMID: 28025270 PMCID: PMC5216669 DOI: 10.1093/molbev/msw228] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Multiple kelch13 alleles conferring artemisinin resistance (ART-R) are currently spreading through Southeast Asian malaria parasite populations, providing a unique opportunity to observe an ongoing soft selective sweep, investigate why resistance alleles have evolved multiple times and determine fundamental population genetic parameters for Plasmodium. We sequenced kelch13 (n = 1,876), genotyped 75 flanking SNPs, and measured clearance rate (n = 3,552) in parasite infections from Western Thailand (2001–2014). We describe 32 independent coding mutations including common mutations outside the kelch13 propeller associated with significant reductions in clearance rate. Mutations were first observed in 2003 and rose to 90% by 2014, consistent with a selection coefficient of ∼0.079. ART-R allele diversity rose until 2012 and then dropped as one allele (C580Y) spread to high frequency. The frequency with which adaptive alleles arise is determined by the rate of mutation and the population size. Two factors drive this soft sweep: (1) multiple kelch13 amino-acid mutations confer resistance providing a large mutational target—we estimate the target is 87–163 bp. (2) The population mutation parameter (Θ = 2Neμ) can be estimated from the frequency distribution of ART-R alleles and is ∼5.69, suggesting that short term effective population size is 88 thousand to 1.2 million. This is 52–705 times greater than Ne estimated from fluctuation in allele frequencies, suggesting that we have previously underestimated the capacity for adaptive evolution in Plasmodium. Our central conclusions are that retrospective studies may underestimate the complexity of selective events and the Ne relevant for adaptation for malaria is considerably higher than previously estimated.
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Affiliation(s)
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Marina McDew-White
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell Nkhoma
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Fatma Bilgic
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Elizabeth Ashley
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Nicholas J White
- Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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23
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Ménard D, Khim N, Beghain J, Adegnika AA, Shafiul-Alam M, Amodu O, Rahim-Awab G, Barnadas C, Berry A, Boum Y, Bustos MD, Cao J, Chen JH, Collet L, Cui L, Thakur GD, Dieye A, Djallé D, Dorkenoo MA, Eboumbou-Moukoko CE, Espino FECJ, Fandeur T, Ferreira-da-Cruz MF, Fola AA, Fuehrer HP, Hassan AM, Herrera S, Hongvanthong B, Houzé S, Ibrahim ML, Jahirul-Karim M, Jiang L, Kano S, Ali-Khan W, Khanthavong M, Kremsner PG, Lacerda M, Leang R, Leelawong M, Li M, Lin K, Mazarati JB, Ménard S, Morlais I, Muhindo-Mavoko H, Musset L, Na-Bangchang K, Nambozi M, Niaré K, Noedl H, Ouédraogo JB, Pillai DR, Pradines B, Quang-Phuc B, Ramharter M, Randrianarivelojosia M, Sattabongkot J, Sheikh-Omar A, Silué KD, Sirima SB, Sutherland C, Syafruddin D, Tahar R, Tang LH, Touré OA, Tshibangu-wa-Tshibangu P, Vigan-Womas I, Warsame M, Wini L, Zakeri S, Kim S, Eam R, Berne L, Khean C, Chy S, Ken M, Loch K, Canier L, Duru V, Legrand E, Barale JC, Stokes B, Straimer J, Witkowski B, Fidock DA, Rogier C, Ringwald P, Ariey F, Mercereau-Puijalon O. A Worldwide Map of Plasmodium falciparum K13-Propeller Polymorphisms. N Engl J Med 2016; 374:2453-64. [PMID: 27332904 PMCID: PMC4955562 DOI: 10.1056/nejmoa1513137] [Citation(s) in RCA: 396] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Recent gains in reducing the global burden of malaria are threatened by the emergence of Plasmodium falciparum resistance to artemisinins. The discovery that mutations in portions of a P. falciparum gene encoding kelch (K13)-propeller domains are the major determinant of resistance has provided opportunities for monitoring such resistance on a global scale. METHODS We analyzed the K13-propeller sequence polymorphism in 14,037 samples collected in 59 countries in which malaria is endemic. Most of the samples (84.5%) were obtained from patients who were treated at sentinel sites used for nationwide surveillance of antimalarial resistance. We evaluated the emergence and dissemination of mutations by haplotyping neighboring loci. RESULTS We identified 108 nonsynonymous K13 mutations, which showed marked geographic disparity in their frequency and distribution. In Asia, 36.5% of the K13 mutations were distributed within two areas--one in Cambodia, Vietnam, and Laos and the other in western Thailand, Myanmar, and China--with no overlap. In Africa, we observed a broad array of rare nonsynonymous mutations that were not associated with delayed parasite clearance. The gene-edited Dd2 transgenic line with the A578S mutation, which expresses the most frequently observed African allele, was found to be susceptible to artemisinin in vitro on a ring-stage survival assay. CONCLUSIONS No evidence of artemisinin resistance was found outside Southeast Asia and China, where resistance-associated K13 mutations were confined. The common African A578S allele was not associated with clinical or in vitro resistance to artemisinin, and many African mutations appear to be neutral. (Funded by Institut Pasteur Paris and others.).
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Affiliation(s)
- Didier Ménard
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Nimol Khim
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Johann Beghain
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Ayola A Adegnika
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Mohammad Shafiul-Alam
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Olukemi Amodu
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Ghulam Rahim-Awab
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Céline Barnadas
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Antoine Berry
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Yap Boum
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Maria D Bustos
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jun Cao
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jun-Hu Chen
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Louis Collet
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Liwang Cui
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Garib-Das Thakur
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Alioune Dieye
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Djibrine Djallé
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Monique A Dorkenoo
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | | | - Thierry Fandeur
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | - Abebe A Fola
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Hans-Peter Fuehrer
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Abdillahi M Hassan
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Socrates Herrera
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Bouasy Hongvanthong
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sandrine Houzé
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Maman L Ibrahim
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Mohammad Jahirul-Karim
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Lubin Jiang
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Shigeyuki Kano
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Wasif Ali-Khan
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Maniphone Khanthavong
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Peter G Kremsner
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Marcus Lacerda
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Rithea Leang
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Mindy Leelawong
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Mei Li
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Khin Lin
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jean-Baptiste Mazarati
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sandie Ménard
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Isabelle Morlais
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | - Lise Musset
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Kesara Na-Bangchang
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Michael Nambozi
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Karamoko Niaré
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Harald Noedl
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jean-Bosco Ouédraogo
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Dylan R Pillai
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Bruno Pradines
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Bui Quang-Phuc
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Michael Ramharter
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | - Jetsumon Sattabongkot
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Abdiqani Sheikh-Omar
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Kigbafori D Silué
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sodiomon B Sirima
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Colin Sutherland
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Din Syafruddin
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Rachida Tahar
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Lin-Hua Tang
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Offianan A Touré
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | | | - Inès Vigan-Womas
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Marian Warsame
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Lyndes Wini
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sedigheh Zakeri
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Saorin Kim
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Rotha Eam
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Laura Berne
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Chanra Khean
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Sophy Chy
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Malen Ken
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Kaknika Loch
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Lydie Canier
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Valentine Duru
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Eric Legrand
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Jean-Christophe Barale
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Barbara Stokes
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Judith Straimer
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Benoit Witkowski
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - David A Fidock
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Christophe Rogier
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Pascal Ringwald
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
| | - Frederic Ariey
- The authors' affiliations are listed in the Supplementary Appendix , available at NEJM.org
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24
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Limited Polymorphism of the Kelch Propeller Domain in Plasmodium malariae and P. ovale Isolates from Thailand. Antimicrob Agents Chemother 2016; 60:4055-62. [PMID: 27114275 PMCID: PMC4914644 DOI: 10.1128/aac.00138-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/18/2016] [Indexed: 11/20/2022] Open
Abstract
Artemisinin resistance in Plasmodium falciparum, the agent of severe malaria, is currently a major obstacle to malaria control in Southeast Asia. A gene named "kelch13" has been associated with artemisinin resistance in P. falciparum The orthologue of the kelch gene in P. vivax was identified and a small number of mutations were found in previous studies. The kelch orthologues in the other two human malaria parasites, P. malariae and P. ovale, have not yet been studied. Therefore, in this study, the orthologous kelch genes of P. malariae, P. ovale wallikeri, and P. ovale curtisi were isolated and analyzed for the first time. The homologies of the kelch genes of P. malariae and P. ovale were 84.8% and 82.7%, respectively, compared to the gene in P. falciparum kelch polymorphisms were studied in 13 P. malariae and 5 P. ovale isolates from Thailand. There were 2 nonsynonymous mutations found in these samples. One mutation was P533L, which was found in 1 of 13 P. malariae isolates, and the other was K137R, found in 1 isolate of P. ovale wallikeri (n = 4). This result needs to be considered in the context of widespread artemisinin used within the region; their functional consequences for artemisinin sensitivity in P. malariae and P. ovale will need to be elucidated.
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Wilairat P, Kümpornsin K, Chookajorn T. Plasmodium falciparum malaria: Convergent evolutionary trajectories towards delayed clearance following artemisinin treatment. Med Hypotheses 2016; 90:19-22. [PMID: 27063079 DOI: 10.1016/j.mehy.2016.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/26/2016] [Accepted: 02/27/2016] [Indexed: 11/28/2022]
Abstract
Malaria is a major global health challenge with 300million new cases every year. The most effective regimen for treating Plasmodium falciparum malaria is based on artemisinin and its derivatives. The drugs are highly effective, resulting in rapid clearance of parasites even in severe P. falciparum malaria patients. During the last five years, artemisinin-resistant parasites have begun to emerge first in Cambodia and now in Thailand and Myanmar. At present, the level of artemisinin resistance is relatively low with clinical presentation of delayed artemisinin clearance (a longer time to reduce parasite load) and a small decrease in artemisinin sensitivity in cultured isolates. Nevertheless, multiple genetic loci associated with delayed parasite clearance have been reported, but they cannot account for a large portion of cases. Even the most well-studied kelch 13 propeller mutations cannot always predict the outcome of artemisinin treatment in vitro and in vivo. Here we propose that delayed clearance by artemisinin could be the result of convergent evolution, driven by multiple trajectories to overcome artemisinin-induced stress, but precluded to become full blown resistance by high fitness cost. Genetic association studies by several genome-wide approaches reveal linkage disequilibrium between multiple loci and delayed parasite clearance. Genetic manipulations at some of these loci already have resulted in loss in artemisinin sensitivity. The notion presented here is by itself consistent with existing evidence on artemisinin resistance and has the potential to be explored using available genomic data. Most important of all, molecular surveillance of artemisinin resistance based on multi-genic markers could be more informative than relying on any one particular molecular marker.
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Affiliation(s)
- Prapon Wilairat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Krittikorn Kümpornsin
- Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thanat Chookajorn
- Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Wilson BA, Garud NR, Feder AF, Assaf ZJ, Pennings PS. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens. Mol Ecol 2016; 25:42-66. [PMID: 26578204 PMCID: PMC4943078 DOI: 10.1111/mec.13474] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/28/2015] [Accepted: 10/08/2015] [Indexed: 01/09/2023]
Abstract
Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance.
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Affiliation(s)
| | | | | | - Zoe J. Assaf
- Department of GeneticsStanford UniversityStanfordCA94305USA
| | - Pleuni S. Pennings
- Department of BiologySan Francisco State UniversityRoom 520Hensill Hall1600 Holloway AveSan FranciscoCA94132USA
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27
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Mita T, Tachibana SI, Hashimoto M, Hirai M. Plasmodium falciparum kelch 13: a potential molecular marker for tackling artemisinin-resistant malaria parasites. Expert Rev Anti Infect Ther 2015; 14:125-35. [PMID: 26535806 DOI: 10.1586/14787210.2016.1106938] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although artemisinin combination therapies have been deployed as a first-line treatment for uncomplicated malaria in almost all endemic countries, artemisinin-resistant parasites have emerged and have gradually spread across the Greater Mekong subregions. There is growing concern that the resistant parasites may migrate to or emerge indigenously in sub-Saharan Africa, which might provoke a global increase in malaria-associated morbidity and mortality. Therefore, development of molecular markers that enable identification of artemisinin resistance with high sensitivity is urgently required to combat this issue. In 2014, a potential artemisinin-resistance responsible gene, Plasmodium falciparum kelch13, was discovered. Here, we review the genetic features of P. falciparum kelch13 and discuss its related resistant mechanisms and potential as a molecular marker.
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Affiliation(s)
- Toshihiro Mita
- a Department of Molecular and Cellular Parasitology , Juntendo University School of Medicine , Tokyo , Japan
| | - Shin-Ichiro Tachibana
- a Department of Molecular and Cellular Parasitology , Juntendo University School of Medicine , Tokyo , Japan
| | - Muneaki Hashimoto
- a Department of Molecular and Cellular Parasitology , Juntendo University School of Medicine , Tokyo , Japan
| | - Makoto Hirai
- a Department of Molecular and Cellular Parasitology , Juntendo University School of Medicine , Tokyo , Japan
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