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Oyebola KM, Idowu ET, Olukosi YA, Awolola TS, Amambua-Ngwa A. Pooled-DNA sequencing identifies genomic regions of selection in Nigerian isolates of Plasmodium falciparum. Parasit Vectors 2017; 10:320. [PMID: 28662682 PMCID: PMC5492182 DOI: 10.1186/s13071-017-2260-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/22/2017] [Indexed: 01/22/2023] Open
Abstract
Background The burden of falciparum malaria is especially high in sub-Saharan Africa. Differences in pressure from host immunity and antimalarial drugs lead to adaptive changes responsible for high level of genetic variations within and between the parasite populations. Population-specific genetic studies to survey for genes under positive or balancing selection resulting from drug pressure or host immunity will allow for refinement of interventions. Methods We performed a pooled sequencing (pool-seq) of the genomes of 100 Plasmodium falciparum isolates from Nigeria. We explored allele-frequency based neutrality test (Tajima’s D) and integrated haplotype score (iHS) to identify genes under selection. Results Fourteen shared iHS regions that had at least 2 SNPs with a score > 2.5 were identified. These regions code for genes that were likely to have been under strong directional selection. Two of these genes were the chloroquine resistance transporter (CRT) on chromosome 7 and the multidrug resistance 1 (MDR1) on chromosome 5. There was a weak signature of selection in the dihydrofolate reductase (DHFR) gene on chromosome 4 and MDR5 genes on chromosome 13, with only 2 and 3 SNPs respectively identified within the iHS window. We observed strong selection pressure attributable to continued chloroquine and sulfadoxine-pyrimethamine use despite their official proscription for the treatment of uncomplicated malaria. There was also a major selective sweep on chromosome 6 which had 32 SNPs within the shared iHS region. Tajima’s D of circumsporozoite protein (CSP), erythrocyte-binding antigen (EBA-175), merozoite surface proteins - MSP3 and MSP7, merozoite surface protein duffy binding-like (MSPDBL2) and serine repeat antigen (SERA-5) were 1.38, 1.29, 0.73, 0.84 and 0.21, respectively. Conclusion We have demonstrated the use of pool-seq to understand genomic patterns of selection and variability in P. falciparum from Nigeria, which bears the highest burden of infections. This investigation identified known genomic signatures of selection from drug pressure and host immunity. This is evidence that P. falciparum populations explore common adaptive strategies that can be targeted for the development of new interventions. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2260-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kolapo M Oyebola
- Medical Research Council Unit The Gambia, Atlantic Road, Fajara, Gambia.,Parasitology and Bioinformatics, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria.,Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Emmanuel T Idowu
- Parasitology and Bioinformatics, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
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Abstract
The increasing prevalence of infections involving intracellular apicomplexan parasites such as Plasmodium, Toxoplasma, and Cryptosporidium (the causative agents of malaria, toxoplasmosis, and cryptosporidiosis, respectively) represent a significant global healthcare burden. Despite their significance, few treatments are available; a situation that is likely to deteriorate with the emergence of new resistant strains of parasites. To lay the foundation for programs of drug discovery and vaccine development, genome sequences for many of these organisms have been generated, together with large-scale expression and proteomic datasets. Comparative analyses of these datasets are beginning to identify the molecular innovations supporting both conserved processes mediating fundamental roles in parasite survival and persistence, as well as lineage-specific adaptations associated with divergent life-cycle strategies. The challenge is how best to exploit these data to derive insights into parasite virulence and identify those genes representing the most amenable targets. In this review, we outline genomic datasets currently available for apicomplexans and discuss biological insights that have emerged as a consequence of their analysis. Of particular interest are systems-based resources, focusing on areas of metabolism and host invasion that are opening up opportunities for discovering new therapeutic targets.
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Affiliation(s)
| | - John Parkinson
- a Program in Molecular Structure and Function , Hospital for Sick Children , Toronto , Ontario , Canada
- b Departments of Biochemistry, Molecular Genetics and Computer Science , University of Toronto , Toronto , Ontario , Canada
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Selective sweep suggests transcriptional regulation may underlie Plasmodium vivax resilience to malaria control measures in Cambodia. Proc Natl Acad Sci U S A 2016; 113:E8096-E8105. [PMID: 27911780 DOI: 10.1073/pnas.1608828113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cambodia, in which both Plasmodium vivax and Plasmodium falciparum are endemic, has been the focus of numerous malaria-control interventions, resulting in a marked decline in overall malaria incidence. Despite this decline, the number of P vivax cases has actually increased. To understand better the factors underlying this resilience, we compared the genetic responses of the two species to recent selective pressures. We sequenced and studied the genomes of 70 P vivax and 80 P falciparum isolates collected between 2009 and 2013. We found that although P falciparum has undergone population fracturing, the coendemic P vivax population has grown undisrupted, resulting in a larger effective population size, no discernable population structure, and frequent multiclonal infections. Signatures of selection suggest recent, species-specific evolutionary differences. Particularly, in contrast to P falciparum, P vivax transcription factors, chromatin modifiers, and histone deacetylases have undergone strong directional selection, including a particularly strong selective sweep at an AP2 transcription factor. Together, our findings point to different population-level adaptive mechanisms used by P vivax and P falciparum parasites. Although population substructuring in P falciparum has resulted in clonal outgrowths of resistant parasites, P vivax may use a nuanced transcriptional regulatory approach to population maintenance, enabling it to preserve a larger, more diverse population better suited to facing selective threats. We conclude that transcriptional control may underlie P vivax's resilience to malaria control measures. Novel strategies to target such processes are likely required to eradicate P vivax and achieve malaria elimination.
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Carpi G, Walter KS, Mamoun CB, Krause PJ, Kitchen A, Lepore TJ, Dwivedi A, Cornillot E, Caccone A, Diuk-Wasser MA. Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States. BMC Genomics 2016; 17:888. [PMID: 27821055 PMCID: PMC5100190 DOI: 10.1186/s12864-016-3225-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 10/27/2016] [Indexed: 11/16/2022] Open
Abstract
Background Babesia microti is an emerging tick-borne apicomplexan parasite with increasing geographic range and incidence in the United States. The rapid expansion of B. microti into its current distribution in the northeastern USA has been due to the range expansion of the tick vector, Ixodes scapularis, upon which the causative agent is dependent for transmission to humans. Results To reconstruct the history of B. microti in the continental USA and clarify the evolutionary origin of human strains, we used multiplexed hybrid capture of 25 B. microti isolates obtained from I. scapularis and human blood. Despite low genomic variation compared with other Apicomplexa, B. microti was strongly structured into three highly differentiated genetic clusters in the northeastern USA. Bayesian analyses of the apicoplast genomes suggest that the origin of the current diversity of B. microti in northeastern USA dates back 46 thousand years with a signature of recent population expansion in the last 1000 years. Human-derived samples belonged to two rarely intermixing clusters, raising the possibility of highly divergent infectious phenotypes in humans. Conclusions Our results validate the multiplexed hybrid capture strategy for characterizing genome-wide diversity and relatedness of B. microti from ticks and humans. We find strong population structure in B. microti samples from the Northeast indicating potential barriers to gene flow. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3225-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giovanna Carpi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.,Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Katharine S Walter
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Peter J Krause
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA.,Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA, 52242, USA
| | | | - Ankit Dwivedi
- Institut de Biologie Computationnelle, University de Montpellier, 34095, Montpellier, Cedex 5, France
| | - Emmanuel Cornillot
- Institut de Biologie Computationnelle, University de Montpellier, 34095, Montpellier, Cedex 5, France
| | - Adalgisa Caccone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Maria A Diuk-Wasser
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA. .,Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA.
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Volkman SK, Herman J, Lukens AK, Hartl DL. Genome-Wide Association Studies of Drug-Resistance Determinants. Trends Parasitol 2016; 33:214-230. [PMID: 28179098 DOI: 10.1016/j.pt.2016.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/26/2016] [Accepted: 10/06/2016] [Indexed: 02/07/2023]
Abstract
Population genetic strategies that leverage association, selection, and linkage have identified drug-resistant loci. However, challenges and limitations persist in identifying drug-resistance loci in malaria. In this review we discuss the genetic basis of drug resistance and the use of genome-wide association studies, complemented by selection and linkage studies, to identify and understand mechanisms of drug resistance and response. We also discuss the implications of nongenetic mechanisms of drug resistance recently reported in the literature, and present models of the interplay between nongenetic and genetic processes that contribute to the emergence of drug resistance. Throughout, we examine artemisinin resistance as an example to emphasize challenges in identifying phenotypes suitable for population genetic studies as well as complications due to multiple-factor drug resistance.
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Affiliation(s)
- Sarah K Volkman
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Disease, Boston, MA, USA; The Broad Institute of MIT and Harvard, Infectious Disease Initiative, Cambridge, MA, USA; Simmons College, School of Nursing and Health Science, Boston, MA, USA.
| | - Jonathan Herman
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Disease, Boston, MA, USA; Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Amanda K Lukens
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Disease, Boston, MA, USA; The Broad Institute of MIT and Harvard, Infectious Disease Initiative, Cambridge, MA, USA
| | - Daniel L Hartl
- The Broad Institute of MIT and Harvard, Infectious Disease Initiative, Cambridge, MA, USA; Harvard University, Organismic and Evolutionary Biology, Cambridge, MA, USA
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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Singh GP, Sharma A. South-East Asian strains of Plasmodium falciparum display higher ratio of non-synonymous to synonymous polymorphisms compared to African strains. F1000Res 2016; 5:1964. [PMID: 27853513 PMCID: PMC5089136 DOI: 10.12688/f1000research.9372.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/19/2016] [Indexed: 11/20/2022] Open
Abstract
Resistance to frontline anti-malarial drugs, including artemisinin, has repeatedly arisen in South-East Asia, but the reasons for this are not understood. Here we test whether evolutionary constraints on
Plasmodium falciparum strains from South-East Asia differ from African strains. We find a significantly higher ratio of non-synonymous to synonymous polymorphisms in
P. falciparum from South-East Asia compared to Africa, suggesting differences in the selective constraints on
P. falciparum genome in these geographical regions. Furthermore, South-East Asian strains showed a higher proportion of non-synonymous polymorphism at conserved positions, suggesting reduced negative selection. There was a lower rate of mixed infection by multiple genotypes in samples from South-East Asia compared to Africa. We propose that a lower mixed infection rate in South-East Asia reduces intra-host competition between the parasite clones, reducing the efficiency of natural selection. This might increase the probability of fixation of fitness-reducing mutations including drug resistant ones.
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Affiliation(s)
- Gajinder Pal Singh
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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Amambua-Ngwa A, Danso B, Worwui A, Ceesay S, Davies N, Jeffries D, D'Alessandro U, Conway D. Exceptionally long-range haplotypes in Plasmodium falciparum chromosome 6 maintained in an endemic African population. Malar J 2016; 15:515. [PMID: 27769292 PMCID: PMC5073846 DOI: 10.1186/s12936-016-1560-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 10/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous genome-wide analyses of single nucleotide variation in Plasmodium falciparum identified evidence of an extended haplotype region on chromosome 6 in West Africa, suggesting recent positive selection. Such a pattern is not seen in samples from East Africa or South East Asia, so it could be marking a selective process specific to West Africa. Analyses of the haplotype structure in samples taken at different times could give clues to possible causes of selection. METHODS This study investigates chromosome 6 extended haplotypes in The Gambia by analysing alleles at multiple microsatellite loci using genome sequence data previously obtained from clinical isolates collected in 2008, followed by genotyping of 13 loci in 439 isolates from 1984, 1991, 2008 and 2014. Temporal changes in haplotype structure and frequencies were determined. RESULTS A region of high linkage disequilibrium spanning over 170 kilobases (kb) was identified with both NGS and laboratory determined microsatellite alleles. Multiple long haplotypes were found in all temporal populations from The Gambia. Two of the haplotypes were detected in samples from 1984 and 1991. The frequency of long-range haplotypes increased in 2008 and 2014 populations. There was higher Fst between older and more recent populations at loci in proximity to genes involved in drug metabolism pathways. CONCLUSIONS The occurrence of several long haplotypes at intermediate frequencies suggests an unusual mode of selection in chromosome 6, possibly combined with recombination suppression on specific haplotypes. Such selection apparently occurred before the emergence of known anti-malarial drug resistance alleles, and could be due to effects of other drugs or unknown processes that have long been operating in this endemic region.
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Affiliation(s)
- Alfred Amambua-Ngwa
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia.
| | - Bakary Danso
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Archibald Worwui
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Sukai Ceesay
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Nwakanma Davies
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - David Jeffries
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia
| | - Umberto D'Alessandro
- Medical Research Council, Gambia Unit, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia.,London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - David Conway
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
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Pattaradilokrat S, Sawaswong V, Simpalipan P, Kaewthamasorn M, Siripoon N, Harnyuttanakorn P. Genetic diversity of the merozoite surface protein-3 gene in Plasmodium falciparum populations in Thailand. Malar J 2016; 15:517. [PMID: 27769257 PMCID: PMC5073822 DOI: 10.1186/s12936-016-1566-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/07/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND An effective malaria vaccine is an urgently needed tool to fight against human malaria, the most deadly parasitic disease of humans. One promising candidate is the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum. This antigenic protein, encoded by the merozoite surface protein (msp-3) gene, is polymorphic and classified according to size into the two allelic types of K1 and 3D7. A recent study revealed that both the K1 and 3D7 alleles co-circulated within P. falciparum populations in Thailand, but the extent of the sequence diversity and variation within each allelic type remains largely unknown. METHODS The msp-3 gene was sequenced from 59 P. falciparum samples collected from five endemic areas (Mae Hong Son, Kanchanaburi, Ranong, Trat and Ubon Ratchathani) in Thailand and analysed for nucleotide sequence diversity, haplotype diversity and deduced amino acid sequence diversity. The gene was also subject to population genetic analysis (F st ) and neutrality tests (Tajima's D, Fu and Li D* and Fu and Li' F* tests) to determine any signature of selection. RESULTS The sequence analyses revealed eight unique DNA haplotypes and seven amino acid sequence variants, with a haplotype and nucleotide diversity of 0.828 and 0.049, respectively. Neutrality tests indicated that the polymorphism detected in the alanine heptad repeat region of MSP-3 was maintained by positive diversifying selection, suggesting its role as a potential target of protective immune responses and supporting its role as a vaccine candidate. Comparison of MSP-3 variants among parasite populations in Thailand, India and Nigeria also inferred a close genetic relationship between P. falciparum populations in Asia. CONCLUSION This study revealed the extent of the msp-3 gene diversity in P. falciparum in Thailand, providing the fundamental basis for the better design of future blood stage malaria vaccines against P. falciparum.
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Affiliation(s)
| | - Vorthon Sawaswong
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Phumin Simpalipan
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Morakot Kaewthamasorn
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Napaporn Siripoon
- College of Public Health Sciences, Chulalongkorn University, Bangkok, 10330 Thailand
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Molina-Cruz A, Zilversmit MM, Neafsey DE, Hartl DL, Barillas-Mury C. Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria. Annu Rev Genet 2016; 50:447-465. [PMID: 27732796 DOI: 10.1146/annurev-genet-120215-035211] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plasmodium falciparum malaria remains a devastating public health problem. Recent discoveries have shed light on the origin and evolution of Plasmodium parasites and their interactions with their vertebrate and mosquito hosts. P. falciparum malaria originated in Africa from a single horizontal transfer between an infected gorilla and a human, and became global as the result of human migration. Today, P. falciparum malaria is transmitted worldwide by more than 70 different anopheline mosquito species. Recent studies indicate that the mosquito immune system can be a barrier to malaria transmission and that the P. falciparum Pfs47 gene allows the parasite to evade mosquito immune detection. Here, we review the origin and globalization of P. falciparum and integrate this history with analysis of the biology, evolution, and dispersal of the main mosquito vectors. This new perspective broadens our understanding of P. falciparum population structure and the dispersal of important parasite genetic traits.
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Affiliation(s)
- Alvaro Molina-Cruz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
| | - Martine M Zilversmit
- Richard Guilder Graduate School and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
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Loy DE, Liu W, Li Y, Learn GH, Plenderleith LJ, Sundararaman SA, Sharp PM, Hahn BH. Out of Africa: origins and evolution of the human malaria parasites Plasmodium falciparum and Plasmodium vivax. Int J Parasitol 2016; 47:87-97. [PMID: 27381764 DOI: 10.1016/j.ijpara.2016.05.008] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/25/2016] [Accepted: 05/28/2016] [Indexed: 12/22/2022]
Abstract
Plasmodium falciparum and Plasmodium vivax account for more than 95% of all human malaria infections, and thus pose a serious public health challenge. To control and potentially eliminate these pathogens, it is important to understand their origins and evolutionary history. Until recently, it was widely believed that P. falciparum had co-evolved with humans (and our ancestors) over millions of years, whilst P. vivax was assumed to have emerged in southeastern Asia following the cross-species transmission of a parasite from a macaque. However, the discovery of a multitude of Plasmodium spp. in chimpanzees and gorillas has refuted these theories and instead revealed that both P. falciparum and P. vivax evolved from parasites infecting wild-living African apes. It is now clear that P. falciparum resulted from a recent cross-species transmission of a parasite from a gorilla, whilst P. vivax emerged from an ancestral stock of parasites that infected chimpanzees, gorillas and humans in Africa, until the spread of the protective Duffy-negative mutation eliminated P. vivax from human populations there. Although many questions remain concerning the biology and zoonotic potential of the P. falciparum- and P. vivax-like parasites infecting apes, comparative genomics, coupled with functional parasite and vector studies, are likely to yield new insights into ape Plasmodium transmission and pathogenesis that are relevant to the treatment and prevention of human malaria.
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Affiliation(s)
- Dorothy E Loy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sesh A Sundararaman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Vembar SS, Seetin M, Lambert C, Nattestad M, Schatz MC, Baybayan P, Scherf A, Smith ML. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Res 2016; 23:339-51. [PMID: 27345719 PMCID: PMC4991835 DOI: 10.1093/dnares/dsw022] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/10/2016] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging due to the skewed AT-richness [∼80.6% (A + T)] of its genome and the lack of technology to assemble highly polymorphic subtelomeric regions that contain clonally variant, multigene virulence families (Ex: var and rifin). To address this, we performed amplification-free, single molecule, real-time sequencing of P. falciparum genomic DNA and generated reads of average length 12 kb, with 50% of the reads between 15.5 and 50 kb in length. Next, using the Hierarchical Genome Assembly Process, we assembled the P. falciparum genome de novo and successfully compiled all 14 nuclear chromosomes telomere-to-telomere. We also accurately resolved centromeres [∼90–99% (A + T)] and subtelomeric regions and identified large insertions and duplications that add extra var and rifin genes to the genome, along with smaller structural variants such as homopolymer tract expansions. Overall, we show that amplification-free, long-read sequencing combined with de novo assembly overcomes major challenges inherent to studying the P. falciparum genome. Indeed, this technology may not only identify the polymorphic and repetitive subtelomeric sequences of parasite populations from endemic areas but may also evaluate structural variation linked to virulence, drug resistance and disease transmission.
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Affiliation(s)
- Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris 75015, France CNRS, ERL 9195, Paris 75015, France INSERM, Unit U1201, Paris 75015, France
| | | | | | | | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris 75015, France CNRS, ERL 9195, Paris 75015, France INSERM, Unit U1201, Paris 75015, France
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Allain J, Assennato SM, Osei EN, Owusu‐Ofori AK, Marschner S, Goodrich RP, Owusu‐Ofori S. Characterization of posttransfusionPlasmodium falciparuminfection in semi‐immune nonparasitemic patients. Transfusion 2016; 56:2374-83. [DOI: 10.1111/trf.13706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/10/2016] [Accepted: 05/24/2016] [Indexed: 01/14/2023]
Affiliation(s)
| | | | - Eric N. Osei
- Transfusion Medicine Unit, Komfo Anokye Teaching Hospital
| | - Alex K. Owusu‐Ofori
- Department of Clinical MicrobiologyKwame Nkrumah University of Science and TechnologyKumasi Ghana
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Allain JP, Owusu-Ofori AK, Assennato SM, Marschner S, Goodrich RP, Owusu-Ofori S. Effect of Plasmodium inactivation in whole blood on the incidence of blood transfusion-transmitted malaria in endemic regions: the African Investigation of the Mirasol System (AIMS) randomised controlled trial. Lancet 2016; 387:1753-61. [PMID: 27116282 DOI: 10.1016/s0140-6736(16)00581-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Transfusion-transmitted malaria is a frequent but neglected adverse event in Ghana. We did a randomised controlled clinical trial to assess the efficacy and safety of a whole blood pathogen reduction technology at preventing transfusion transmission of Plasmodium spp parasites. METHODS For this randomised, double-blind, parallel-group clinical trial, eligible adult patients (aged ≥ 18 years) with blood group O+, who required up to two whole blood unit transfusions within 3 days of randomisation and were anticipated to remain in hospital for at least 3 consecutive days after initial transfusion, were enrolled from Komfo Anokye Teaching Hospital in Kumasi, Ghana. The main exclusion criteria were symptoms of clinical malaria, antimalaria treatment within 7 days before randomisation, fever, and haemorrhage expected to require transfusion with up to two units of whole blood during the 3 days following study entry. Eligible patients were randomly assigned 1:1 by computer-generated permuted block randomisation (block size four) list to receive transfusion with either pathogen-reduced whole blood (treated) or whole blood prepared and transfused by standard local practice (untreated). Patients, health-care providers, and data collectors were masked to treatment allocation. Patients in both groups received up to two whole blood unit transfusions that were retrospectively tested for parasitaemia. Pre-transfusion and post-transfusion blood samples (taken on days 0, 1, 3, 7, and 28) were tested for presence and amount of parasite genome, and assessed for haematological and biochemical parameters. The primary endpoint was the incidence of transfusion-transmitted malaria in non-parasitaemic recipients exposed to parasitaemic whole blood, defined as two consecutive parasitaemic post-transfusion samples with parasite allelic matching, assessed at 1-7 days after transfusion. Secondary endpoints included haematological parameters and a safety analysis of adverse events in patients. This study is registered with ClinicalTrials.gov, number NCT02118428, and with the Pan African Clinical Trials Registry, number PACTR201406000777310. FINDINGS Between March 12, 2014, and Nov 7, 2014, 227 patients were enrolled into the study, one of whom was subsequently excluded because she did not meet the inclusion criteria. Of the 226 randomised patients, 113 were allocated to receive treated whole blood and 113 to receive standard untreated whole blood. 223 patients (111 treated and 112 untreated) received study-related transfusions, whereas three patients (two treated and one untreated) did not. 214 patients (107 treated and 107 untreated) completed the protocol as planned and comprised the per-protocol population. Overall, 65 non-parasitaemic patients (28 treated and 37 untreated) were exposed to parasitaemic blood. The incidence of transfusion-transmitted malaria was significantly lower for the pathogen-reduced (treated) patients (1 [4%] of 28 patients) than the untreated group (8 [22%] of 37 patients) in this population (p=0.039). Overall, 92 (41%) of 223 patients reported 145 treatment-related emergent adverse events during the conduct of the study, with a similar incidence of adverse events between groups receiving untreated or treated whole blood. No transfusion-related deaths occurred in the trial. INTERPRETATION Treatment of whole blood with the Mirasol pathogen reduction system for whole blood reduced the incidence of transfusion-transmitted malaria. The primary endpoint of the study was achieved in the population of non-parasitaemic patients receiving parasitaemic whole blood. The safety profile and clinical outcomes were similar across the two treatment groups. FUNDING Terumo BCT Inc.
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Affiliation(s)
| | - Alex K Owusu-Ofori
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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65
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Chen JH, Chen SB, Wang Y, Ju C, Zhang T, Xu B, Shen HM, Mo XJ, Molina DM, Eng M, Liang X, Gardner MJ, Wang R, Hu W. An immunomics approach for the analysis of natural antibody responses to Plasmodium vivax infection. MOLECULAR BIOSYSTEMS 2016; 11:2354-63. [PMID: 26091354 DOI: 10.1039/c5mb00330j] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High throughput immunomics is a powerful platform to discover potential targets of host immunity and develop diagnostic tests for infectious diseases. We screened the sera of Plasmodium vivax-exposed individuals to profile the antibody response to blood-stage antigens of P. vivax using a P. vivax protein microarray. A total of 1936 genes encoding the P. vivax proteins were expressed, printed and screened with sera from P. vivax-exposed individuals and normal subjects. Total of 151 (7.8% of the 1936 targets) highly immunoreactive antigens were identified, including five well-characterized antigens of P. vivax (ETRAMP11.2, Pv34, SUB1, RAP2 and MSP4). Among the highly immunoreactive antigens, 5 antigens were predicted as adhesins by MAAP, and 11 antigens were predicted as merozoite invasion-related proteins based on homology with P. falciparum proteins. There are 40 proteins that have serodiagnostic potential for antibody surveillance. These novel Plasmodium antigens identified provide the clues for understanding host immune response to P. vivax infection and the development of antibody surveillance tools.
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Affiliation(s)
- Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health, WHO Collaborating Center for Malaria, Schistosomiasis and Filariasis, Shanghai 200025, People's Republic of China.
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Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria. Nat Commun 2016; 7:11078. [PMID: 27002652 PMCID: PMC4804174 DOI: 10.1038/ncomms11078] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/18/2016] [Indexed: 01/29/2023] Open
Abstract
African apes harbour at least six Plasmodium species of the subgenus Laverania, one of which gave rise to human Plasmodium falciparum. Here we use a selective amplification strategy to sequence the genome of chimpanzee parasites classified as Plasmodium reichenowi and Plasmodium gaboni based on the subgenomic fragments. Genome-wide analyses show that these parasites indeed represent distinct species, with no evidence of cross-species mating. Both P. reichenowi and P. gaboni are 10-fold more diverse than P. falciparum, indicating a very recent origin of the human parasite. We also find a remarkable Laverania-specific expansion of a multigene family involved in erythrocyte remodelling, and show that a short region on chromosome 4, which encodes two essential invasion genes, was horizontally transferred into a recent P. falciparum ancestor. Our results validate the selective amplification strategy for characterizing cryptic pathogen species, and reveal evolutionary events that likely predisposed the precursor of P. falciparum to colonize humans. African apes harbour six Plasmodium species, one of which gave rise to the human malaria parasite. Here, Sundaraman et al. use selective whole-genome amplification to determine genome sequences from two chimpanzee Plasmodium species, shedding light on the evolutionary origin of the human parasite.
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67
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Gunawardena S, Karunaweera ND. Advances in genetics and genomics: use and limitations in achieving malaria elimination goals. Pathog Glob Health 2016; 109:123-41. [PMID: 25943157 DOI: 10.1179/2047773215y.0000000015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Success of the global research agenda towards eradication of malaria will depend on the development of new tools, including drugs, vaccines, insecticides and diagnostics. Genetic and genomic information now available for the malaria parasites, their mosquito vectors and human host, can be harnessed to both develop these tools and monitor their effectiveness. Here we review and provide specific examples of current technological advances and how these genetic and genomic tools have increased our knowledge of host, parasite and vector biology in relation to malaria elimination and in turn enhanced the potential to reach that goal. We then discuss limitations of these tools and future prospects for the successful achievement of global malaria elimination goals.
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68
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Adjalley SH, Scanfeld D, Kozlowski E, Llinás M, Fidock DA. Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1. BMC Genomics 2015; 16:1090. [PMID: 26689807 PMCID: PMC4687325 DOI: 10.1186/s12864-015-2320-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The acquisition of multidrug resistance by Plasmodium falciparum underscores the need to understand the underlying molecular mechanisms so as to counter their impact on malaria control. For the many antimalarials whose mode of action relates to inhibition of heme detoxification inside infected erythrocytes, the digestive vacuole transporters PfCRT and PfMDR1 constitute primary resistance determinants. RESULTS Using gene expression microarrays over the course of the parasite intra-erythrocytic developmental cycle, we compared the transcriptomic profiles between P. falciparum strains displaying mutant or wild-type pfcrt or varying in pfcrt or pfmdr1 expression levels. To account for differences in the time of sampling, we developed a computational method termed Hypergeometric Analysis of Time Series, which combines Fast Fourier Transform with a modified Gene Set Enrichment Analysis. Our analysis revealed coordinated changes in genes involved in protein catabolism, translation initiation and DNA/RNA metabolism. We also observed differential expression of genes with a role in transport or coding for components of the digestive vacuole. Interestingly, a global comparison of all profiled transcriptomes uncovered a tight correlation between the transcript levels of pfcrt and pfmdr1, extending to dozens of other genes, suggesting an intricate regulatory balance in order to maintain optimal physiological processes. CONCLUSIONS This study provides insight into the mechanisms by which P. falciparum adjusts to the acquisition of mutations or gene amplification in key transporter loci that mediate drug resistance. Our results implicate several biological pathways that may be differentially regulated to compensate for impaired transporter function and alterations in parasite vacuole physiology.
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Affiliation(s)
- Sophie H Adjalley
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA. .,Present addresses: Wellcome Trust Sanger Institute, Hinxton, UK.
| | - Daniel Scanfeld
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA. .,Present addresses: Google Inc., New York, NY, 10011, USA.
| | - Elyse Kozlowski
- Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA. .,Present addresses: Pulmonary Center, Boston University School of Medicine, Boston, MA, 02118, USA.
| | - Manuel Llinás
- Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA. .,Department of Biochemistry and Molecular Biology, Department of Chemistry, Center for Malaria Research and Center for Infectious Diseases Dynamics, Pennsylvania State University, University Park, PA, 16802, USA.
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA. .,Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA.
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Daniels R, Hamilton EJ, Durfee K, Ndiaye D, Wirth DF, Hartl DL, Volkman SK. Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria. J Vis Exp 2015:e52839. [PMID: 26575471 PMCID: PMC4692701 DOI: 10.3791/52839] [Citation(s) in RCA: 6] [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] [Indexed: 01/29/2023] Open
Abstract
Despite decades of eradication efforts, malaria remains a global burden. Recent renewed interest in regional elimination and global eradication has been accompanied by increased genomic information about Plasmodium parasite species responsible for malaria, including characteristics of geographical populations as well as variations associated with reduced susceptibility to anti-malarial drugs. One common genetic variation, single-nucleotide polymorphisms (SNPs), offers attractive targets for parasite genotyping. These markers are useful not only for tracking drug resistance markers but also for tracking parasite populations using markers not under drug or other selective pressures. SNP genotyping methods offer the ability to track drug resistance as well as to fingerprint individual parasites for population surveillance, particularly in response to malaria control efforts in regions nearing elimination status. While informative SNPs have been identified that are agnostic to specific genotyping technologies, high-resolution melting (HRM) analysis is particularly suited to field-based studies. Compared to standard fluorescent-probe based methods that require individual SNPs in a single labeled probe and offer at best 10% sensitivity to detect SNPs in samples that contain multiple genomes (polygenomic), HRM offers 2-5% sensitivity. Modifications to HRM, such as blocked probes and asymmetric primer concentrations as well as optimization of amplification annealing temperatures to bias PCR towards amplification of the minor allele, further increase the sensitivity of HRM. While the sensitivity improvement depends on the specific assay, we have increased detection sensitivities to less than 1% of the minor allele. In regions approaching malaria eradication, early detection of emerging or imported drug resistance is essential for prompt response. Similarly, the ability to detect polygenomic infections and differentiate imported parasite types from cryptic local reservoirs can inform control programs. This manuscript describes modifications to high resolution melting technology that further increase its sensitivity to identify polygenomic infections in patient samples.
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Affiliation(s)
- Rachel Daniels
- Department of Organismic and Evolutionary Biology, Harvard University; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health;
| | - Elizabeth J Hamilton
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health
| | - Katelyn Durfee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health
| | - Daouda Ndiaye
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Institute of Infectious Diseases, Broad Institute
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; School of Nursing and Health Sciences, Simmons College
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Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi. Proc Natl Acad Sci U S A 2015; 112:13027-32. [PMID: 26438871 DOI: 10.1073/pnas.1509534112] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Malaria cases caused by the zoonotic parasite Plasmodium knowlesi are being increasingly reported throughout Southeast Asia and in travelers returning from the region. To test for evidence of signatures of selection or unusual population structure in this parasite, we surveyed genome sequence diversity in 48 clinical isolates recently sampled from Malaysian Borneo and in five lines maintained in laboratory rhesus macaques after isolation in the 1960s from Peninsular Malaysia and the Philippines. Overall genomewide nucleotide diversity (π = 6.03 × 10(-3)) was much higher than has been seen in worldwide samples of either of the major endemic malaria parasite species Plasmodium falciparum and Plasmodium vivax. A remarkable substructure is revealed within P. knowlesi, consisting of two major sympatric clusters of the clinical isolates and a third cluster comprising the laboratory isolates. There was deep differentiation between the two clusters of clinical isolates [mean genomewide fixation index (FST) = 0.21, with 9,293 SNPs having fixed differences of FST = 1.0]. This differentiation showed marked heterogeneity across the genome, with mean FST values of different chromosomes ranging from 0.08 to 0.34 and with further significant variation across regions within several chromosomes. Analysis of the largest cluster (cluster 1, 38 isolates) indicated long-term population growth, with negatively skewed allele frequency distributions (genomewide average Tajima's D = -1.35). Against this background there was evidence of balancing selection on particular genes, including the circumsporozoite protein (csp) gene, which had the top Tajima's D value (1.57), and scans of haplotype homozygosity implicate several genomic regions as being under recent positive selection.
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71
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Neglected Tropical Diseases in the Post-Genomic Era. Trends Genet 2015; 31:539-555. [DOI: 10.1016/j.tig.2015.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/01/2015] [Accepted: 06/03/2015] [Indexed: 01/22/2023]
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Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt. Proc Natl Acad Sci U S A 2015; 112:11672-7. [PMID: 26261345 DOI: 10.1073/pnas.1507142112] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In regions with high malaria endemicity, the withdrawal of chloroquine (CQ) as first-line treatment of Plasmodium falciparum infections has typically led to the restoration of CQ susceptibility through the reexpansion of the wild-type (WT) allele K76 of the chloroquine resistance transporter gene (pfcrt) at the expense of less fit mutant alleles carrying the CQ resistance (CQR) marker K76T. In low-transmission settings, such as South America, drug resistance mutations can attain 100% prevalence, thereby precluding the return of WT parasites after the complete removal of drug pressure. In French Guiana, despite the fixation of the K76T allele, the prevalence of CQR isolates progressively dropped from >90% to <30% during 17 y after CQ withdrawal in 1995. Using a genome-wide association study with CQ-sensitive (CQS) and CQR isolates, we have identified a single mutation in pfcrt encoding a C350R substitution that is associated with the restoration of CQ susceptibility. Genome editing of the CQR reference strain 7G8 to incorporate PfCRT C350R caused a complete loss of CQR. A retrospective molecular survey on 580 isolates collected from 1997 to 2012 identified all C350R mutant parasites as being CQS. This mutation emerged in 2002 and rapidly spread throughout the P. falciparum population. The C350R allele is also associated with a significant decrease in piperaquine susceptibility in vitro, suggesting that piperaquine pressure in addition to potential fitness costs associated with the 7G8-type CQR pfcrt allele may have selected for this mutation. These findings have important implications for understanding the evolutionary dynamics of antimalarial drug resistance.
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73
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Carpi G, Walter KS, Bent SJ, Hoen AG, Diuk-Wasser M, Caccone A. Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi. BMC Genomics 2015; 16:434. [PMID: 26048573 PMCID: PMC4458057 DOI: 10.1186/s12864-015-1634-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 05/18/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Rapid and accurate retrieval of whole genome sequences of human pathogens from disease vectors or animal reservoirs will enable fine-resolution studies of pathogen epidemiological and evolutionary dynamics. However, next generation sequencing technologies have not yet been fully harnessed for the study of vector-borne and zoonotic pathogens, due to the difficulty of obtaining high-quality pathogen sequence data directly from field specimens with a high ratio of host to pathogen DNA. RESULTS We addressed this challenge by using custom probes for multiplexed hybrid capture to enrich for and sequence 30 Borrelia burgdorferi genomes from field samples of its arthropod vector. Hybrid capture enabled sequencing of nearly the complete genome (~99.5 %) of the Borrelia burgdorferi pathogen with 132-fold coverage, and identification of up to 12,291 single nucleotide polymorphisms per genome. CONCLUSIONS The proprosed culture-independent method enables efficient whole genome capture and sequencing of pathogens directly from arthropod vectors, thus making population genomic study of vector-borne and zoonotic infectious diseases economically feasible and scalable. Furthermore, given the similarities of invertebrate field specimens to other mixed DNA templates characterized by a high ratio of host to pathogen DNA, we discuss the potential applicabilty of hybrid capture for genomic study across diverse study systems.
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Affiliation(s)
- Giovanna Carpi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA.
| | - Katharine S Walter
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA.
| | - Stephen J Bent
- Robinson Research Institute, University of Adelaide, 5005, Adelaide, SA, Australia.
| | - Anne Gatewood Hoen
- The Geisel School of Medicine, Dartmouth College, 03755, Hanover, NH, USA.
| | - Maria Diuk-Wasser
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. .,Department of Ecology, Evolution and Environmental Biology, Columbia University, 10027, New York, NY, USA.
| | - Adalgisa Caccone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. .,Department of Ecology and Evolutionary Biology, Yale University, 06520, New Haven, CT, USA.
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74
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Petersen I, Gabryszewski SJ, Johnston GL, Dhingra SK, Ecker A, Lewis RE, de Almeida MJ, Straimer J, Henrich PP, Palatulan E, Johnson DJ, Coburn-Flynn O, Sanchez C, Lehane AM, Lanzer M, Fidock DA. Balancing drug resistance and growth rates via compensatory mutations in the Plasmodium falciparum chloroquine resistance transporter. Mol Microbiol 2015; 97:381-95. [PMID: 25898991 DOI: 10.1111/mmi.13035] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2015] [Indexed: 11/28/2022]
Abstract
The widespread use of chloroquine to treat Plasmodium falciparum infections has resulted in the selection and dissemination of variant haplotypes of the primary resistance determinant PfCRT. These haplotypes have encountered drug pressure and within-host competition with wild-type drug-sensitive parasites. To examine these selective forces in vitro, we genetically engineered P. falciparum to express geographically diverse PfCRT haplotypes. Variant alleles from the Philippines (PH1 and PH2, which differ solely by the C72S mutation) both conferred a moderate gain of chloroquine resistance and a reduction in growth rates in vitro. Of the two, PH2 showed higher IC50 values, contrasting with reduced growth. Furthermore, a highly mutated pfcrt allele from Cambodia (Cam734) conferred moderate chloroquine resistance and enhanced growth rates, when tested against wild-type pfcrt in co-culture competition assays. These three alleles mediated cross-resistance to amodiaquine, an antimalarial drug widely used in Africa. Each allele, along with the globally prevalent Dd2 and 7G8 alleles, rendered parasites more susceptible to lumefantrine, the partner drug used in the leading first-line artemisinin-based combination therapy. These data reveal ongoing region-specific evolution of PfCRT that impacts drug susceptibility and relative fitness in settings of mixed infections, and raise important considerations about optimal agents to treat chloroquine-resistant malaria.
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Affiliation(s)
- Ines Petersen
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, 69120, Heidelberg, Germany
| | - Stanislaw J Gabryszewski
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Geoffrey L Johnston
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,School of International and Public Affairs, Columbia University, New York, NY, 10027, USA
| | - Satish K Dhingra
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,Department of Biological Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - Andrea Ecker
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Rebecca E Lewis
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | | | - Judith Straimer
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Philipp P Henrich
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Eugene Palatulan
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - David J Johnson
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Cecilia Sanchez
- Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, 69120, Heidelberg, Germany
| | - Adele M Lehane
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael Lanzer
- Hygiene Institut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, 69120, Heidelberg, Germany
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.,Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
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Pattaradilokrat S, Tiyamanee W, Simpalipan P, Kaewthamasorn M, Saiwichai T, Li J, Harnyuttanakorn P. Molecular detection of the avian malaria parasite Plasmodium gallinaceum in Thailand. Vet Parasitol 2015; 210:1-9. [DOI: 10.1016/j.vetpar.2015.03.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 03/17/2015] [Accepted: 03/23/2015] [Indexed: 01/21/2023]
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Abstract
The development of a highly effective malaria vaccine remains a key goal to aid in the control and eventual eradication of this devastating parasitic disease. The field has made huge strides in recent years, with the first-generation vaccine RTS,S showing modest efficacy in a Phase III clinical trial. The updated 2030 Malaria Vaccine Technology Roadmap calls for a second generation vaccine to achieve 75% efficacy over two years for both Plasmodium falciparum and Plasmodium vivax, and for a vaccine that can prevent malaria transmission. Whole-parasite immunisation approaches and combinations of pre-erythrocytic subunit vaccines are now reporting high-level efficacy, whilst exciting new approaches to the development of blood-stage and transmission-blocking vaccine subunit components are entering clinical development. The development of a highly effective multi-component multi-stage subunit vaccine now appears to be a realistic ambition. This review will cover these recent developments in malaria vaccinology.
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Samad H, Coll F, Preston MD, Ocholla H, Fairhurst RM, Clark TG. Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites. PLoS Genet 2015; 11:e1005131. [PMID: 25928499 PMCID: PMC4415759 DOI: 10.1371/journal.pgen.1005131] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 03/06/2015] [Indexed: 11/19/2022] Open
Abstract
Whole-genome sequencing technologies are being increasingly applied to Plasmodium falciparum clinical isolates to identify genetic determinants of malaria pathogenesis. However, genome-wide discovery methods, such as haplotype scans for signatures of natural selection, are hindered by missing genotypes in sequence data. Poor correlation between single nucleotide polymorphisms (SNPs) in the P. falciparum genome complicates efforts to apply established missing-genotype imputation methods that leverage off patterns of linkage disequilibrium (LD). The accuracy of state-of-the-art, LD-based imputation methods (IMPUTE, Beagle) was assessed by measuring allelic r2 for 459 P. falciparum samples from malaria patients in 4 countries: Thailand, Cambodia, Gambia, and Malawi. In restricting our analysis to 86 k high-quality SNPs across the populations, we found that the complete-case analysis was restricted to 21k SNPs (24.5%), despite no single SNP having more than 10% missing genotypes. The accuracy of Beagle in filling in missing genotypes was consistently high across all populations (allelic r2, 0.87-0.96), but the performance of IMPUTE was mixed (allelic r2, 0.34-0.99) depending on reference haplotypes and population. Positive selection analysis using Beagle-imputed haplotypes identified loci involved in resistance to chloroquine (crt) in Thailand, Cambodia, and Gambia, sulfadoxine-pyrimethamine (dhfr, dhps) in Cambodia, and artemisinin (kelch13) in Cambodia. Tajima's D-based analysis identified genes under balancing selection that encode well-characterized vaccine candidates: apical merozoite antigen 1 (ama1) and merozoite surface protein 1 (msp1). In contrast, the complete-case analysis failed to identify any well-validated drug resistance or candidate vaccine loci, except kelch13. In a setting of low LD and modest levels of missing genotypes, using Beagle to impute P. falciparum genotypes is a viable strategy for conducting accurate large-scale population genetics and association analyses, and supporting global surveillance for drug resistance markers and candidate vaccine antigens.
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Affiliation(s)
- Hanif Samad
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Mark D. Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harold Ocholla
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi and Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Rick M. Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Baniecki ML, Faust AL, Schaffner SF, Park DJ, Galinsky K, Daniels RF, Hamilton E, Ferreira MU, Karunaweera ND, Serre D, Zimmerman PA, Sá JM, Wellems TE, Musset L, Legrand E, Melnikov A, Neafsey DE, Volkman SK, Wirth DF, Sabeti PC. Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections. PLoS Negl Trop Dis 2015; 9:e0003539. [PMID: 25781890 PMCID: PMC4362761 DOI: 10.1371/journal.pntd.0003539] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/15/2015] [Indexed: 12/30/2022] Open
Abstract
Plasmodium vivax, one of the five species of Plasmodium parasites that cause human malaria, is responsible for 25–40% of malaria cases worldwide. Malaria global elimination efforts will benefit from accurate and effective genotyping tools that will provide insight into the population genetics and diversity of this parasite. The recent sequencing of P. vivax isolates from South America, Africa, and Asia presents a new opportunity by uncovering thousands of novel single nucleotide polymorphisms (SNPs). Genotyping a selection of these SNPs provides a robust, low-cost method of identifying parasite infections through their unique genetic signature or barcode. Based on our experience in generating a SNP barcode for P. falciparum using High Resolution Melting (HRM), we have developed a similar tool for P. vivax. We selected globally polymorphic SNPs from available P. vivax genome sequence data that were located in putatively selectively neutral sites (i.e., intergenic, intronic, or 4-fold degenerate coding). From these candidate SNPs we defined a barcode consisting of 42 SNPs. We analyzed the performance of the 42-SNP barcode on 87 P. vivax clinical samples from parasite populations in South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We found that the P. vivax barcode is robust, as it requires only a small quantity of DNA (limit of detection 0.3 ng/μl) to yield reproducible genotype calls, and detects polymorphic genotypes with high sensitivity. The markers are informative across all clinical samples evaluated (average minor allele frequency > 0.1). Population genetic and statistical analyses show the barcode captures high degrees of population diversity and differentiates geographically distinct populations. Our 42-SNP barcode provides a robust, informative, and standardized genetic marker set that accurately identifies a genomic signature for P. vivax infections. Plasmodium vivax malaria is a major global public health problem, with nearly 2.5 billion people at risk for infection and approximately 132–391 million clinical infections annually. It has a wide geographical range, with a high disease burden in Asia, Central and South America, the Middle East, Oceania, and East Africa. Advances in sequencing technology and sample processing have made it possible to characterize the genetic diversity of P. vivax populations. This genetic variation provides a means to identify parasites by unique genetic signatures, or “barcodes.” We developed such a genetic barcode for P. vivax, composed of 42 robust and informative variants. Here we report its development and validation based on 87 clinical samples identified by microscopy to contain P. vivax from geographically diverse parasite populations from South America (Brazil, French Guiana), Africa (Ethiopia) and Asia (Sri Lanka). We show that the SNP barcode provides a genotyping tool that can be performed at low cost, providing a means to uniquely identify parasite infections and distinguish geographic origins, and that barcode data may offer new insights into P. vivax population structure and diversity.
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Affiliation(s)
- Mary Lynn Baniecki
- Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
| | - Aubrey L. Faust
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Daniel J. Park
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Kevin Galinsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Rachel F. Daniels
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Elizabeth Hamilton
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | | | - Nadira D. Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - David Serre
- Department of Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Peter A. Zimmerman
- Department of International Health, Biology and Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Juliana M. Sá
- Laboratory of Malaria and Vector Research, Malaria Genetics Section, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Thomas E. Wellems
- Laboratory of Malaria and Vector Research, Malaria Genetics Section, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Lise Musset
- Department of Parasitology, Institute Pasteur de la Guyane, Cayenne, French Guiana
| | - Eric Legrand
- Department of Parasitology, Institute Pasteur de la Guyane, Cayenne, French Guiana
| | | | | | - Sarah K. Volkman
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- School of Nursing and Health Sciences, Simmons College, Boston, Massachusetts, United States of America
| | - Dyann F. Wirth
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Pardis C. Sabeti
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Brown TS, Jacob CG, Silva JC, Takala-Harrison S, Djimdé A, Dondorp AM, Fukuda M, Noedl H, Nyunt MM, Kyaw MP, Mayxay M, Hien TT, Plowe CV, Cummings MP. Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:318-322. [PMID: 25514047 PMCID: PMC4316729 DOI: 10.1016/j.meegid.2014.12.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/04/2014] [Accepted: 12/07/2014] [Indexed: 11/30/2022]
Abstract
Multiple transcontinental waves of drug resistance in Plasmodium falciparum have originated in Southeast Asia before spreading westward, first into the rest of Asia and then to sub-Saharan Africa. In vitro studies have suggested that hypermutator P. falciparum parasites may exist in Southeast Asia and that an increased rate of acquisition of new mutations in these parasites may explain the repeated emergence of drug resistance in Southeast Asia. This study is the first to test the hypermutator hypothesis using field isolates. Using genome-wide SNP data from human P. falciparum infections in Southeast Asia and West Africa and a test for relative rate differences we found no evidence of increased relative substitution rates in P. falciparum isolates from Southeast Asia. Instead, we found significantly increased substitution rates in Mali and Bangladesh populations relative to those in populations from Southeast Asia. Additionally we found no association between increased relative substitution rates and parasite clearance following treatment with artemisinin derivatives.
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Affiliation(s)
- Tyler S Brown
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Christopher G Jacob
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Abdoulaye Djimdé
- Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, Faculty of Medicine and Pharmacy, University of Science, Techniques and Technology of Bamako, Bamako, Mali
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Center for Tropical Medicine, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Mark Fukuda
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Harald Noedl
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Austria and Malaria Research Initiative Bandarban, Bandarban, Bangladesh
| | - Myaing Myaing Nyunt
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Myat Phone Kyaw
- Department of Medical Research (Lower Myanmar), Yangon, Myanmar
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic; Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao Democratic People's Republic
| | - Tran Tinh Hien
- Centre for Tropical Medicine Oxford University Clinical Research Unit Vietnam (OUCRU), Ho Chi Minh City, Viet Nam
| | - Christopher V Plowe
- Howard Hughes Medical Institute/Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael P Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
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80
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Pimenta PFP, Orfano AS, Bahia AC, Duarte APM, Ríos-Velásquez CM, Melo FF, Pessoa FAC, Oliveira GA, Campos KMM, Villegas LM, Rodrigues NB, Nacif-Pimenta R, Simões RC, Monteiro WM, Amino R, Traub-Cseko YM, Lima JBP, Barbosa MGV, Lacerda MVG, Tadei WP, Secundino NFC. An overview of malaria transmission from the perspective of Amazon Anopheles vectors. Mem Inst Oswaldo Cruz 2015; 110:23-47. [PMID: 25742262 PMCID: PMC4371216 DOI: 10.1590/0074-02760140266] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/18/2014] [Indexed: 02/07/2023] Open
Abstract
In the Americas, areas with a high risk of malaria transmission are mainly located in the Amazon Forest, which extends across nine countries. One keystone step to understanding the Plasmodium life cycle in Anopheles species from the Amazon Region is to obtain experimentally infected mosquito vectors. Several attempts to colonise Anopheles species have been conducted, but with only short-lived success or no success at all. In this review, we review the literature on malaria transmission from the perspective of its Amazon vectors. Currently, it is possible to develop experimental Plasmodium vivax infection of the colonised and field-captured vectors in laboratories located close to Amazonian endemic areas. We are also reviewing studies related to the immune response to P. vivax infection of Anopheles aquasalis, a coastal mosquito species. Finally, we discuss the importance of the modulation of Plasmodium infection by the vector microbiota and also consider the anopheline genomes. The establishment of experimental mosquito infections with Plasmodium falciparum, Plasmodium yoelii and Plasmodium berghei parasites that could provide interesting models for studying malaria in the Amazonian scenario is important. Understanding the molecular mechanisms involved in the development of the parasites in New World vectors is crucial in order to better determine the interaction process and vectorial competence.
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Affiliation(s)
- Paulo FP Pimenta
- Centro de Pesquisas René Rachou-Fiocruz, Belo Horizonte, MG,
Brasil
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, AM,
Brasil
| | | | - Ana C Bahia
- Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Ana PM Duarte
- Centro de Pesquisas René Rachou-Fiocruz, Belo Horizonte, MG,
Brasil
| | | | - Fabrício F Melo
- Centro de Pesquisas René Rachou-Fiocruz, Belo Horizonte, MG,
Brasil
| | | | | | - Keillen MM Campos
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, AM,
Brasil
| | | | | | | | - Rejane C Simões
- Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brasil
| | - Wuelton M Monteiro
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, AM,
Brasil
| | - Rogerio Amino
- Unité de Biologie et Génétique du Paludisme, Institut Pasteur, Paris,
France
| | | | - José BP Lima
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, AM,
Brasil
- Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Maria GV Barbosa
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, AM,
Brasil
| | - Marcus VG Lacerda
- Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, AM,
Brasil
- Instituto Leônidas e Maria Deane-Fiocruz, Manaus, AM, Brasil
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COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data. Malar J 2015; 14:4. [PMID: 25599890 PMCID: PMC4417311 DOI: 10.1186/1475-2875-14-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/16/2014] [Indexed: 12/15/2022] Open
Abstract
Background Complex malaria infections are defined as those containing more than one genetically distinct lineage of Plasmodium parasite. Complexity of infection (COI) is a useful parameter to estimate from patient blood samples because it is associated with clinical outcome, epidemiology and disease transmission rate. This manuscript describes a method for estimating COI using likelihood, called COIL, from a panel of bi-allelic genotyping assays. Methods COIL assumes that distinct parasite lineages in complex infections are unrelated and that genotyped loci do not exhibit significant linkage disequilibrium. Using the population minor allele frequency (MAF) of the genotyped loci, COIL uses the binomial distribution to estimate the likelihood of a COI level given the prevalence of observed monomorphic or polymorphic genotypes within each sample. Results COIL reliably estimates COI up to a level of three or five with at least 24 or 96 unlinked genotyped loci, respectively, as determined by in silico simulation and empirical validation. Evaluation of COI levels greater than five in patient samples may require a very large collection of genotype data, making sequencing a more cost-effective approach for evaluating COI under conditions when disease transmission is extremely high. Performance of the method is positively correlated with the MAF of the genotyped loci. COI estimates from existing SNP genotype datasets create a more detailed portrait of disease than analyses based simply on the number of polymorphic genotypes observed within samples. Conclusions The capacity to reliably estimate COI from a genome-wide panel of SNP genotypes provides a potentially more accurate alternative to methods relying on PCR amplification of a small number of loci for estimating COI. This approach will also increase the number of applications of SNP genotype data, providing additional motivation to employ SNP barcodes for studies of disease epidemiology or control measure efficacy. The COIL program is available for download from GitHub, and users may also upload their SNP genotype data to a web interface for simple and efficient determination of sample COI. Electronic supplementary material The online version of this article (doi:10.1186/1475-2875-14-4) contains supplementary material, which is available to authorized users.
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82
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Awasthi G, Das A. Genetics of chloroquine-resistant malaria: a haplotypic view. Mem Inst Oswaldo Cruz 2015; 108:947-61. [PMID: 24402147 PMCID: PMC4005552 DOI: 10.1590/0074-0276130274] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 09/26/2013] [Indexed: 02/05/2023] Open
Abstract
The development and rapid spread of chloroquine resistance (CQR) in
Plasmodium falciparum have triggered the identification of
several genetic target(s) in the P. falciparum genome. In
particular, mutations in the Pfcrt gene, specifically, K76T and
mutations in three other amino acids in the region adjoining K76 (residues 72, 74, 75
and 76), are considered to be highly related to CQR. These various mutations form
several different haplotypes and Pfcrt gene polymorphisms and the
global distribution of the different CQR- Pfcrt haplotypes in
endemic and non-endemic regions of P. falciparum malaria have been
the subject of extensive study. Despite the fact that the Pfcrt gene
is considered to be the primary CQR gene in P. falciparum , several
studies have suggested that this may not be the case. Furthermore, there is a poor
correlation between the evolutionary implications of the Pfcrt
haplotypes and the inferred migration of CQR P. falciparum based on
CQR epidemiological surveillance data. The present paper aims to clarify the existing
knowledge on the genetic basis of the different CQR- Pfcrt
haplotypes that are prevalent in worldwide populations based on the published
literature and to analyse the data to generate hypotheses on the genetics and
evolution of CQR malaria.
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83
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Abstract
A key part of the life cycle of an organism is reproduction. For a number of important protist parasites that cause human and animal disease, their sexuality has been a topic of debate for many years. Traditionally, protists were considered to be primitive relatives of the ‘higher’ eukaryotes, which may have diverged prior to the evolution of sex and to reproduce by binary fission. More recent views of eukaryotic evolution suggest that sex, and meiosis, evolved early, possibly in the common ancestor of all eukaryotes. However, detecting sex in these parasites is not straightforward. Recent advances, particularly in genome sequencing technology, have allowed new insights into parasite reproduction. Here, we review the evidence on reproduction in parasitic protists. We discuss protist reproduction in the light of parasitic life cycles and routes of transmission among hosts.
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Abstract
Although efforts to understand the basis for inter-strain phenotypic variation in the most virulent malaria species, Plasmodium falciparum, have benefited from advances in genomic technologies, there have to date been few metabolomic studies of this parasite. Using 1H-NMR spectroscopy, we have compared the metabolite profiles of red blood cells infected with different P. falciparum strains. These included both chloroquine-sensitive and chloroquine-resistant strains, as well as transfectant lines engineered to express different isoforms of the chloroquine-resistance-conferring pfcrt (P. falciparum chloroquine resistance transporter). Our analyses revealed strain-specific differences in a range of metabolites. There was marked variation in the levels of the membrane precursors choline and phosphocholine, with some strains having >30-fold higher choline levels and >5-fold higher phosphocholine levels than others. Chloroquine-resistant strains showed elevated levels of a number of amino acids relative to chloroquine-sensitive strains, including an approximately 2-fold increase in aspartate levels. The elevation in amino acid levels was attributable to mutations in pfcrt. Pfcrt-linked differences in amino acid abundance were confirmed using alternate extraction and detection (HPLC) methods. Mutations acquired to withstand chloroquine exposure therefore give rise to significant biochemical alterations in the parasite. The metabolite profiles of red blood cells infected with different malaria parasite strains were compared. Amino acid profiles varied with the chloroquine resistance status of the strain, and this was linked specifically to mutations in the parasite's chloroquine resistance transporter.
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85
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Hupalo DN, Bradic M, Carlton JM. The impact of genomics on population genetics of parasitic diseases. Curr Opin Microbiol 2014; 23:49-54. [PMID: 25461572 DOI: 10.1016/j.mib.2014.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022]
Abstract
Parasites, defined as eukaryotic microbes and parasitic worms that cause global diseases of human and veterinary importance, span many lineages in the eukaryotic Tree of Life. Historically challenging to study due to their complicated life-cycles and association with impoverished settings, their inherent complexities are now being elucidated by genome sequencing. Over the course of the last decade, projects in large sequencing centers, and increasingly frequently in individual research labs, have sequenced dozens of parasite reference genomes and field isolates from patient populations. This 'tsunami' of genomic data is answering questions about parasite genetic diversity, signatures of evolution orchestrated through anti-parasitic drug and host immune pressure, and the characteristics of populations. This brief review focuses on the state of the art of parasitic protist genomics, how the peculiar genomes of parasites are driving creative methods for their sequencing, and the impact that next-generation sequencing is having on our understanding of parasite population genomics and control of the diseases they cause.
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Affiliation(s)
- Daniel N Hupalo
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States
| | - Martina Bradic
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States
| | - Jane M Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States.
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Akala HM, Achieng AO, Eyase FL, Juma DW, Ingasia L, Cheruiyot AC, Okello C, Omariba D, Owiti EA, Muriuki C, Yeda R, Andagalu B, Johnson JD, Kamau E. Five-year tracking of Plasmodium falciparum allele frequencies in a holoendemic area with indistinct seasonal transitions. J Multidiscip Healthc 2014; 7:515-23. [PMID: 25395861 PMCID: PMC4227620 DOI: 10.2147/jmdh.s67252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The renewed malaria eradication efforts require an understanding of the seasonal patterns of frequency of polymorphic variants in order to focus limited funds productively. Although cross-sectional studies in holoendemic areas spanning a single year could be useful in describing parasite genotype status at a given point, such information is inadequate in describing temporal trends in genotype polymorphisms. For Plasmodium falciparum isolates from Kisumu District Hospital, Plasmodium falciparum chloroquine-resistance transporter gene (Pfcrt-K76T) and P. falciparum multidrug resistance gene 1 (PfMDR1-N86Y), were analyzed for polymorphisms and parasitemia changes in the 53 months from March 2008 to August 2012. Observations were compared with prevailing climatic factors, including humidity, rainfall, and temperature. METHODS Parasitemia (the percentage of infected red blood cells per total red blood cells) was established by microscopy for P. falciparum malaria-positive samples. P. falciparum DNA was extracted from whole blood using a Qiagen DNA Blood Mini Kit. Single nucleotide polymorphism identification at positions Pfcrt-K76T and PfMDR1-N86Y was performed using real-time polymerase chain reaction and/or sequencing. Data on climatic variables were obtained from http://www.tutiempo.net/en/. RESULTS A total of 895 field isolates from 2008 (n=169), 2009 (n=161), 2010 (n=216), 2011 (n=223), and 2012 (n=126) showed large variations in monthly frequency of PfMDR1-N86Y and Pfcrt-K76T as the mutant genotypes decreased from 68.4%±15% and 38.1%±13% to 29.8%±18% and 13.3%±9%, respectively. The mean percentage of parasitemia was 2.61%±1.01% (coefficient of variation 115.86%; n=895). There was no correlation between genotype or parasitemia and climatic factors. CONCLUSION This study shows variability in the frequency of Pfcrt-K76T and PfMDR1-N86Y polymorphisms during the study period, bringing into focus the role of cross-sectional studies in describing temporal genotype trends. The lack of correlation between genotypes and climatic changes, especially precipitation, emphasizes the cost of investment in genotype change.
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Affiliation(s)
- Hoseah M Akala
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Angela O Achieng
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Fredrick L Eyase
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Dennis W Juma
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Luiser Ingasia
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Agnes C Cheruiyot
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Charles Okello
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Duke Omariba
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Eunice A Owiti
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Catherine Muriuki
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Redemptah Yeda
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Ben Andagalu
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Jacob D Johnson
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
| | - Edwin Kamau
- Global Emerging Infections Surveillance Program, United States Army Medical Research Unit-Kenya, Kenya Medical Research Institute, Walter Reed Project, Kisumu and Nairobi, Kenya
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Doolan DL, Apte SH, Proietti C. Genome-based vaccine design: the promise for malaria and other infectious diseases. Int J Parasitol 2014; 44:901-13. [PMID: 25196370 DOI: 10.1016/j.ijpara.2014.07.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 01/08/2023]
Abstract
Vaccines are one of the most effective interventions to improve public health, however, the generation of highly effective vaccines for many diseases has remained difficult. Three chronic diseases that characterise these difficulties include malaria, tuberculosis and HIV, and they alone account for half of the global infectious disease burden. The whole organism vaccine approach pioneered by Jenner in 1796 and refined by Pasteur in 1857 with the "isolate, inactivate and inject" paradigm has proved highly successful for many viral and bacterial pathogens causing acute disease but has failed with respect to malaria, tuberculosis and HIV as well as many other diseases. A significant advance of the past decade has been the elucidation of the genomes, proteomes and transcriptomes of many pathogens. This information provides the foundation for new 21st Century approaches to identify target antigens for the development of vaccines, drugs and diagnostic tests. Innovative genome-based vaccine strategies have shown potential for a number of challenging pathogens, including malaria. We advocate that genome-based rational vaccine design will overcome the problem of poorly immunogenic, poorly protective vaccines that has plagued vaccine developers for many years.
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Affiliation(s)
- Denise L Doolan
- Infectious Diseases Programme, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia.
| | - Simon H Apte
- Infectious Diseases Programme, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Carla Proietti
- Infectious Diseases Programme, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
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88
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Jacob CG, Tan JC, Miller BA, Tan A, Takala-Harrison S, Ferdig MT, Plowe CV. A microarray platform and novel SNP calling algorithm to evaluate Plasmodium falciparum field samples of low DNA quantity. BMC Genomics 2014; 15:719. [PMID: 25159520 PMCID: PMC4153902 DOI: 10.1186/1471-2164-15-719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 08/11/2014] [Indexed: 01/07/2023] Open
Abstract
Background Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In areas with adequate cold chain facilities, large volumes of leukocyte-depleted patient blood can be frozen for use in parasite genomic analyses. In more remote endemic areas smaller volumes of infected blood are taken by finger prick, and dried and stored on filter paper. These dried blood spots do not generally yield enough concentrated parasite DNA for whole-genome sequencing. Results A DNA microarray was designed for use on field samples to type a genome-wide set of SNPs which prior sequencing had shown to be variable in Africa, Southeast Asia, and Papua New Guinea. An algorithm was designed to call SNPs in samples with low parasite DNA. With this new algorithm SNP-calling accuracy of 98% was measured by hybridizing purified DNA from malaria lab strains and comparing calls with SNPs called from full genome sequences. An average accuracy of >98% was likewise obtained for DNA extracted from malaria field samples collected in studies in Southeast Asia, with an average call rate of > 82%. Conclusion This new high-density microarray provided high quality SNP calls from a wide range of parasite DNA quantities, and represents a robust tool for genome-wide analysis of malaria parasites in diverse settings.
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Affiliation(s)
| | | | | | | | | | | | - Christopher V Plowe
- Malaria Group, Howard Hughes Medical Institute / Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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89
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The revolution of whole genome sequencing to study parasites. Mol Biochem Parasitol 2014; 195:77-81. [PMID: 25111965 DOI: 10.1016/j.molbiopara.2014.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 12/14/2022]
Abstract
Genome sequencing has revolutionized the way in which we approach biological research from fundamental molecular biology to ecology and epidemiology. In the last 10 years the field of genomics has changed enormously as technology has improved and the tools for genomic sequencing have moved out of a few dedicated centers and now can be performed on bench-top instruments. In this review we will cover some of the key discoveries that were catalyzed by some of the first genome projects and discuss how this field is developing, what the new challenges are and how this may impact on research in the near future.
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90
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Yamagishi J, Natori A, Tolba MEM, Mongan AE, Sugimoto C, Katayama T, Kawashima S, Makalowski W, Maeda R, Eshita Y, Tuda J, Suzuki Y. Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum. Genome Res 2014; 24:1433-44. [PMID: 25091627 PMCID: PMC4158759 DOI: 10.1101/gr.158980.113] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To understand the molecular mechanisms of parasitism in vivo, it is essential to elucidate how the transcriptomes of the human hosts and the infecting parasites affect one another. Here we report the RNA-seq analysis of 116 Indonesian patients infected with the malaria parasite Plasmodium falciparum (Pf). We extracted RNAs from their peripheral blood as a mixture of host and parasite transcripts and mapped the RNA-seq tags to the human and Pf reference genomes to separate the respective tags. We were thus able to simultaneously analyze expression patterns in both humans and parasites. We identified human and parasite genes and pathways that correlated with various clinical data, which may serve as primary targets for drug developments. Of particular importance, we revealed characteristic expression changes in the human innate immune response pathway genes including TLR2 and TICAM2 that correlated with the severity of the malaria infection. We also found a group of transcription regulatory factors, JUND, for example, and signaling molecules, TNFAIP3, for example, that were strongly correlated in the expression patterns of humans and parasites. We also identified several genetic variations in important anti-malaria drug resistance-related genes. Furthermore, we identified the genetic variations which are potentially associated with severe malaria symptoms both in humans and parasites. The newly generated data should collectively lay a unique foundation for understanding variable behaviors of the field malaria parasites, which are far more complex than those observed under laboratory conditions.
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Affiliation(s)
- Junya Yamagishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8579, Japan; Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Anna Natori
- Department of Medical Genome Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | | | - Arthur E Mongan
- Department of Medicine, Sam Ratulangi University, Kampus Unsrat, Bahu Manado, 95115, Indonesia
| | - Chihiro Sugimoto
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Toshiaki Katayama
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), The University of Tokyo Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shuichi Kawashima
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), The University of Tokyo Bunkyo-ku, Tokyo 113-0032, Japan
| | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, 48149 Munster, Germany
| | - Ryuichiro Maeda
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Yuki Eshita
- Oita University, School of Medicine, Yufushi, Oita 879-5593, Japan
| | - Josef Tuda
- Department of Medicine, Sam Ratulangi University, Kampus Unsrat, Bahu Manado, 95115, Indonesia
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan;
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91
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Ocholla H, Preston MD, Mipando M, Jensen ATR, Campino S, MacInnis B, Alcock D, Terlouw A, Zongo I, Oudraogo JB, Djimde AA, Assefa S, Doumbo OK, Borrmann S, Nzila A, Marsh K, Fairhurst RM, Nosten F, Anderson TJC, Kwiatkowski DP, Craig A, Clark TG, Montgomery J. Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates. J Infect Dis 2014; 210:1991-2000. [PMID: 24948693 PMCID: PMC4241944 DOI: 10.1093/infdis/jiu349] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. Methods We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used population genetics approaches to investigate genetic diversity and population structure and identify loci under selection. Results High genetic diversity (π = 2.4 × 10−4), moderately high multiplicity of infection (2.7), and low linkage disequilibrium (500-bp) were observed in Chikhwawa District, Malawi, an area of high malaria transmission. Allele frequency–based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically dispersed countries (Kenya, Burkina Faso, Mali, Cambodia, and Thailand) detected population genetic differences between Africa and Asia, within Southeast Asia, and within Africa. Haplotype-based tests of selection to sequence data from all 6 populations identified signals of directional selection at known drug-resistance loci, including pfcrt, pfdhps, pfmdr1, and pfgch1. Conclusions The sequence variations observed at drug-resistance loci reflect differences in each country's historical use of antimalarial drugs and may be useful in formulating local malaria treatment guidelines.
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Affiliation(s)
- Harold Ocholla
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme Liverpool School of Tropical Medicine, Pembroke Place, Liverpool
| | - Mark D Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Mwapatsa Mipando
- Department of Physiology, College of Medicine, University of Malawi, Blantyre
| | - Anja T R Jensen
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, University of Copenhagen Department of Infectious Diseases, Copenhagen University Hospital, Denmark
| | | | | | | | - Anja Terlouw
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme Liverpool School of Tropical Medicine, Pembroke Place, Liverpool
| | - Issaka Zongo
- Institut de Recherche en Sciences de la Sant, Bobo-Dioulasso, Burkina Faso
| | | | - Abdoulaye A Djimde
- Wellcome Trust Sanger Institute, Hinxton Malaria Research and Training Centre, Faculty of Medicine, Pharmacy and Dentistry, University of Bamako, Mali
| | - Samuel Assefa
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, Faculty of Medicine, Pharmacy and Dentistry, University of Bamako, Mali
| | | | - Alexis Nzila
- Department of Biology, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Francois Nosten
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
| | - Alister Craig
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Jacqui Montgomery
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme Liverpool School of Tropical Medicine, Pembroke Place, Liverpool
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92
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Nair S, Nkhoma SC, Serre D, Zimmerman PA, Gorena K, Daniel BJ, Nosten F, Anderson TJC, Cheeseman IH. Single-cell genomics for dissection of complex malaria infections. Genome Res 2014; 24:1028-38. [PMID: 24812326 PMCID: PMC4032849 DOI: 10.1101/gr.168286.113] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Most malaria infections contain complex mixtures of distinct parasite lineages. These multiple-genotype infections (MGIs) impact virulence evolution, drug resistance, intra-host dynamics, and recombination, but are poorly understood. To address this we have developed a single-cell genomics approach to dissect MGIs. By combining cell sorting and whole-genome amplification (WGA), we are able to generate high-quality material from parasite-infected red blood cells (RBCs) for genotyping and next-generation sequencing. We optimized our approach through analysis of >260 single-cell assays. To quantify accuracy, we decomposed mixtures of known parasite genotypes and obtained highly accurate (>99%) single-cell genotypes. We applied this validated approach directly to infections of two major malaria species, Plasmodium falciparum, for which long term culture is possible, and Plasmodium vivax, for which no long-term culture is feasible. We demonstrate that our single-cell genomics approach can be used to generate parasite genome sequences directly from patient blood in order to unravel the complexity of P. vivax and P. falciparum infections. These methods open the door for large-scale analysis of within-host variation of malaria infections, and reveal information on relatedness and drug resistance haplotypes that is inaccessible through conventional sequencing of infections.
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Affiliation(s)
- Shalini Nair
- Texas Biomedical Research Institute, San Antonio, Texas 78227-5301, USA
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Chichiri, Blantyre 3, Malawi
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195, USA
| | - Peter A Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Karla Gorena
- University of Texas Health Science Center San Antonio, San Antonio, Texas 78229, USA
| | - Benjamin J Daniel
- University of Texas Health Science Center San Antonio, San Antonio, Texas 78229, USA
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak 63110, Thailand; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford 0X3 7LJ, United Kingdom
| | | | - Ian H Cheeseman
- Texas Biomedical Research Institute, San Antonio, Texas 78227-5301, USA
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93
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Tibayrenc M, Ayala FJ. New insights into clonality and panmixia in Plasmodium and toxoplasma. ADVANCES IN PARASITOLOGY 2014; 84:253-68. [PMID: 24480316 DOI: 10.1016/b978-0-12-800099-1.00005-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Until the 1990s, Plasmodium and Toxoplasma were widely considered to be potentially panmictic species, because they both undergo a meiotic sexual cycle in their definitive hosts. We have proposed that both parasites are able of clonal (nonrecombining) propagation, at least in some cycles. Toxoplasma was soon shown to be a paradigmatic case of clonal population structure in North American and in European cycles. But the proposal provoked an outcry in the case of Plasmodium and still appears as doubtful to many scientists. However, the existence of Plasmodium nonrecombining lines has been fully confirmed, although the origin of these lines is debatable. We discuss the current state of knowledge concerning the population structure of both parasites in the light of the recent developments of pathogen clonal evolution proposed by us and of new hypotheses presented here.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), IRD Center, Montpellier, France.
| | - Francisco J Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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94
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Chelo IM, Nédli J, Gordo I, Teotónio H. An experimental test on the probability of extinction of new genetic variants. Nat Commun 2014; 4:2417. [PMID: 24030070 PMCID: PMC3778522 DOI: 10.1038/ncomms3417] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 08/08/2013] [Indexed: 11/09/2022] Open
Abstract
In 1927, J.B.S. Haldane reasoned that the probability of fixation of new beneficial alleles is twice their fitness effect. This result, later generalized by M. Kimura, has since become the cornerstone of modern population genetics. There is no experimental test of Haldane's insight that new beneficial alleles are lost with high probability. Here we demonstrate that extinction rates decrease with increasing initial numbers of beneficial alleles, as expected, by performing invasion experiments with inbred lines of the nematode Caenorhabditis elegans. We further show that the extinction rates of deleterious alleles are higher than those of beneficial alleles, also as expected. Interestingly, we also find that for these inbred lines, when at intermediate frequencies, the fate of invaders might not result in their ultimate fixation or loss but on their maintenance. Our study confirms the key results from classical population genetics and highlights that the nature of adaptation can be complex.
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Affiliation(s)
- Ivo M Chelo
- Instituto Gulbenkian de Ciência, Apartado 14, P-2781-901 Oeiras, Portugal
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95
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Manary MJ, Singhakul SS, Flannery EL, Bopp SER, Corey VC, Bright AT, McNamara CW, Walker JR, Winzeler EA. Identification of pathogen genomic variants through an integrated pipeline. BMC Bioinformatics 2014; 15:63. [PMID: 24589256 PMCID: PMC3945619 DOI: 10.1186/1471-2105-15-63] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 02/06/2014] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Whole-genome sequencing represents a powerful experimental tool for pathogen research. We present methods for the analysis of small eukaryotic genomes, including a streamlined system (called Platypus) for finding single nucleotide and copy number variants as well as recombination events. RESULTS We have validated our pipeline using four sets of Plasmodium falciparum drug resistant data containing 26 clones from 3D7 and Dd2 background strains, identifying an average of 11 single nucleotide variants per clone. We also identify 8 copy number variants with contributions to resistance, and report for the first time that all analyzed amplification events are in tandem. CONCLUSIONS The Platypus pipeline provides malaria researchers with a powerful tool to analyze short read sequencing data. It provides an accurate way to detect SNVs using known software packages, and a novel methodology for detection of CNVs, though it does not currently support detection of small indels. We have validated that the pipeline detects known SNVs in a variety of samples while filtering out spurious data. We bundle the methods into a freely available package.
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Affiliation(s)
- Micah J Manary
- Department of Pediatrics, University of California, San Diego, School of Medicine, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
- Biomedical Sciences Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Suriya S Singhakul
- Department of Pediatrics, University of California, San Diego, School of Medicine, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
| | - Erika L Flannery
- Department of Pediatrics, University of California, San Diego, School of Medicine, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
| | - Selina ER Bopp
- Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Victoria C Corey
- Department of Pediatrics, University of California, San Diego, School of Medicine, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
- Biomedical Sciences Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Andrew Taylor Bright
- Department of Pediatrics, University of California, San Diego, School of Medicine, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
- Biomedical Sciences Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Case W McNamara
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
| | - John R Walker
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, School of Medicine, 9500 Gilman Drive 0741, La Jolla, California 92093, USA
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96
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Abstract
Detecting signals of selection in the genome of malaria parasites is a key to identify targets for drug and vaccine development. Malaria parasites have a unique life cycle alternating between vector and host organism with a population bottleneck at each transition. These recurrent bottlenecks could influence the patterns of genetic diversity and the power of existing population genetic tools to identify sites under positive selection. We therefore simulated the site-frequency spectrum of a beneficial mutant allele through time under the malaria life cycle. We investigated the power of current population genetic methods to detect positive selection based on the site-frequency spectrum as well as temporal changes in allele frequency. We found that a within-host selective advantage is difficult to detect using these methods. Although a between-host transmission advantage could be detected, the power is decreased when compared with the classical Wright–Fisher (WF) population model. Using an adjusted null site-frequency spectrum that takes the malaria life cycle into account, the power of tests based on the site-frequency spectrum to detect positive selection is greatly improved. Our study demonstrates the importance of considering the life cycle in genetic analysis, especially in parasites with complex life cycles.
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97
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Sinha R, Pearson LA, Davis TW, Muenchhoff J, Pratama R, Jex A, Burford MA, Neilan BA. Comparative genomics of Cylindrospermopsis raciborskii strains with differential toxicities. BMC Genomics 2014; 15:83. [PMID: 24476316 PMCID: PMC3922686 DOI: 10.1186/1471-2164-15-83] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 01/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cylindrospermopsis raciborskii is an invasive filamentous freshwater cyanobacterium, some strains of which produce toxins. Sporadic toxicity may be the result of gene deletion events, the horizontal transfer of toxin biosynthesis gene clusters, or other genomic variables, yet the evolutionary drivers for cyanotoxin production remain a mystery. Through examining the genomes of toxic and non-toxic strains of C. raciborskii, we hoped to gain a better understanding of the degree of similarity between these strains of common geographical origin, and what the primary differences between these strains might be. Additionally, we hoped to ascertain why some cyanobacteria possess the cylindrospermopsin biosynthesis (cyr) gene cluster and produce toxin, while others do not. It has been hypothesised that toxicity or lack thereof might confer a selective advantage to cyanobacteria under certain environmental conditions. RESULTS In order to examine the fundamental differences between toxic and non-toxic C. raciborskii strains, we sequenced the genomes of two closely related isolates, CS-506 (CYN+) and CS-509 (CYN-) sourced from different lakes in tropical Queensland, Australia. These genomes were then compared to a third (reference) genome from C. raciborskii CS-505 (CYN+). Genome sizes were similar across all three strains and their G + C contents were almost identical. At least 2,767 genes were shared among all three strains, including the taxonomically important rpoc1, ssuRNA, lsuRNA, cpcA, cpcB, nifB and nifH, which exhibited 99.8-100% nucleotide identity. Strains CS-506 and CS-509 contained at least 176 and 101 strain-specific (or non-homologous) genes, respectively, most of which were associated with DNA repair and modification, nutrient uptake and transport, or adaptive measures such as osmoregulation. However, the only significant genetic difference observed between the two strains was the presence or absence of the cylindrospermopsin biosynthesis gene cluster. Interestingly, we also identified a cryptic secondary metabolite gene cluster in strain CS-509 (CYN-) and a second cryptic cluster common to CS-509 and the reference strain, CS-505 (CYN+). CONCLUSIONS Our results confirm that the most important factor contributing to toxicity in C. raciborskii is the presence or absence of the cyr gene cluster. We did not identify any other distally encoded genes or gene clusters that correlate with CYN production. The fact that the additional genomic differences between toxic and non-toxic strains were primarily associated with stress and adaptation genes suggests that CYN production may be linked to these physiological processes.
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Affiliation(s)
- Rati Sinha
- School of Biotechnology and Bimolecular Sciences, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Leanne A Pearson
- School of Biotechnology and Bimolecular Sciences, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Timothy W Davis
- Australian Rivers Institute, Griffith University, 4111 Nathan, Queensland, Australia
| | - Julia Muenchhoff
- School of Biotechnology and Bimolecular Sciences, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Ryanbi Pratama
- School of Biotechnology and Bimolecular Sciences, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Aaron Jex
- Faculty of Veterinary Science, University of Melbourne, Melbourne, Victoria, Australia
| | - Michele A Burford
- Australian Rivers Institute, Griffith University, 4111 Nathan, Queensland, Australia
| | - Brett A Neilan
- School of Biotechnology and Bimolecular Sciences, University of New South Wales, 2052 Sydney, NSW, Australia
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98
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Chen SB, Ju C, Chen JH, Zheng B, Huang F, Xiao N, Zhou X, Ernest T, Zhou XN. Operational research needs toward malaria elimination in China. ADVANCES IN PARASITOLOGY 2014; 86:109-33. [PMID: 25476883 DOI: 10.1016/b978-0-12-800869-0.00005-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Owing to the implementation of a national malaria elimination programme from 2010 to 2020, we performed a systematic review to assess research challenges in the People's Republic of China (P.R. China) and define research priorities in the next few years. A systematic search was conducted for articles published from January 2000 to December 2012 in international journals from PubMed and Chinese journals from the China National Knowledge Infrastructure (CNKI). In total, 2532 articles from CNKI and 308 articles from PubMed published between 2010 and 2012 related to malaria after unrelated references and review or comment were further excluded, and a set of research gaps have been identified that could hinder progress toward malaria elimination in P.R. China. For example, there is a lack of sensitive and specific tests for the diagnosis of malaria cases with low parasitemia, and there is a need for surveillance tools that can evaluate the epidemic status for guiding the elimination strategy. Hence, we argue that malaria elimination will be accelerated in P.R. China through the development of new tests, such as detection of parasite or drug resistance, monitoring glucose-6-phosphate dehydrogenase (G6PD) deficiency, active malaria screening methods, and understanding the effects of the environment and climate variation on vector distribution.
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Affiliation(s)
- Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health; WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, People's Republic of China
| | - Chuan Ju
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health; WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, People's Republic of China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health; WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, People's Republic of China
| | - Bin Zheng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health; WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, People's Republic of China
| | - Fang Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health; WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, People's Republic of China
| | - Ning Xiao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health; WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, People's Republic of China
| | - Xia Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health; WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, People's Republic of China
| | - Tambo Ernest
- Center for Sustainable Malaria Control, Faculty of Natural and Environmental Science; Center for Sustainable Malaria Control, Biochemistry Department, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health; WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, People's Republic of China
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Li J, Yuan J, Cheng KCC, Inglese J, Su XZ. Chemical genomics for studying parasite gene function and interaction. Trends Parasitol 2013; 29:603-11. [PMID: 24215777 DOI: 10.1016/j.pt.2013.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 12/20/2022]
Abstract
With the development of new technologies in genome sequencing, gene expression profiling, genotyping, and high-throughput screening of chemical compound libraries, small molecules are playing increasingly important roles in studying gene expression regulation, gene-gene interaction, and gene function. Here we briefly review and discuss some recent advancements in drug target identification and phenotype characterization using combinations of high-throughput screening of small-molecule libraries and various genome-wide methods such as whole-genome sequencing, genome-wide association studies (GWAS), and genome-wide expression analysis. These approaches can be used to search for new drugs against parasite infections, to identify drug targets or drug resistance genes, and to infer gene function.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, P.R. China
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Jex AR, Koehler AV, Ansell BR, Baker L, Karunajeewa H, Gasser RB. Getting to the guts of the matter: The status and potential of ‘omics’ research of parasitic protists of the human gastrointestinal system. Int J Parasitol 2013; 43:971-82. [DOI: 10.1016/j.ijpara.2013.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/07/2013] [Accepted: 06/07/2013] [Indexed: 11/17/2022]
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