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Pilling OA, Sundararaman SA, Brisson D, Beiting DP. Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment. PLoS Pathog 2024; 20:e1012418. [PMID: 39264872 PMCID: PMC11392400 DOI: 10.1371/journal.ppat.1012418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionized microbiology, but many microbes exist at low abundance in their natural environment and/or are difficult, if not impossible, to culture in the laboratory. This makes it challenging to use HTS to study the genomes of many important microbes and pathogens. In this review, we discuss the development and application of selective whole genome amplification (SWGA) to allow whole or partial genomes to be sequenced for low abundance microbes directly from complex biological samples. We highlight ways in which genomic data generated by SWGA have been used to elucidate the population dynamics of important human pathogens and monitor development of antimicrobial resistance and the emergence of potential outbreaks. We also describe the limitations of this method and propose some potential innovations that could be used to improve the quality of SWGA and lower the barriers to using this method across a wider range of infectious pathogens.
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Affiliation(s)
- Olivia A Pilling
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sesh A Sundararaman
- Department of Pediatrics, Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Pennsylvania, United States of America
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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2
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Crispim M, Verdaguer IB, Hernández A, Kronenberger T, Fenollar À, Yamaguchi LF, Alberione MP, Ramirez M, de Oliveira SS, Katzin AM, Izquierdo L. Beyond the MEP Pathway: A novel kinase required for prenol utilization by malaria parasites. PLoS Pathog 2024; 20:e1011557. [PMID: 38277417 PMCID: PMC10849223 DOI: 10.1371/journal.ppat.1011557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/07/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
A proposed treatment for malaria is a combination of fosmidomycin and clindamycin. Both compounds inhibit the methylerythritol 4-phosphate (MEP) pathway, the parasitic source of farnesyl and geranylgeranyl pyrophosphate (FPP and GGPP, respectively). Both FPP and GGPP are crucial for the biosynthesis of several essential metabolites such as ubiquinone and dolichol, as well as for protein prenylation. Dietary prenols, such as farnesol (FOH) and geranylgeraniol (GGOH), can rescue parasites from MEP inhibitors, suggesting the existence of a missing pathway for prenol salvage via phosphorylation. In this study, we identified a gene in the genome of P. falciparum, encoding a transmembrane prenol kinase (PolK) involved in the salvage of FOH and GGOH. The enzyme was expressed in Saccharomyces cerevisiae, and its FOH/GGOH kinase activities were experimentally validated. Furthermore, conditional knockout parasites (Δ-PolK) were created to investigate the biological importance of the FOH/GGOH salvage pathway. Δ-PolK parasites were viable but displayed increased susceptibility to fosmidomycin. Their sensitivity to MEP inhibitors could not be rescued by adding prenols. Additionally, Δ-PolK parasites lost their capability to utilize prenols for protein prenylation. Experiments using culture medium supplemented with whole/delipidated human plasma in transgenic parasites revealed that human plasma has components that can diminish the effectiveness of fosmidomycin. Mass spectrometry tests indicated that both bovine supplements used in culture and human plasma contain GGOH. These findings suggest that the FOH/GGOH salvage pathway might offer an alternate source of isoprenoids for malaria parasites when de novo biosynthesis is inhibited. This study also identifies a novel kind of enzyme related to isoprenoid metabolism.
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Affiliation(s)
- Marcell Crispim
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ignasi Bofill Verdaguer
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Agustín Hernández
- Center for Biological and Health Sciences, Integrated Unit for Research in Biodiversity (BIOTROP-CCBS), Federal University of São Carlos, São Carlos, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany
| | - Àngel Fenollar
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | - María Pía Alberione
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Miriam Ramirez
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | - Alejandro Miguel Katzin
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Luis Izquierdo
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
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Dwivedi-Yu JA, Oppler ZJ, Mitchell MW, Song YS, Brisson D. A fast machine-learning-guided primer design pipeline for selective whole genome amplification. PLoS Comput Biol 2023; 19:e1010137. [PMID: 37068103 PMCID: PMC10138271 DOI: 10.1371/journal.pcbi.1010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 04/27/2023] [Accepted: 03/23/2023] [Indexed: 04/18/2023] Open
Abstract
Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales-precisely the scales at which these processes occur-microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluation strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluate the novel swga2.0 pipeline by designing primer sets that successfully amplify Prevotella melaninogenica, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.
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Affiliation(s)
- Jane A. Dwivedi-Yu
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Facebook AI Research, 1 Rathbone Square, London, England
| | - Zachary J. Oppler
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew W. Mitchell
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Yun S. Song
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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4
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Pilling OA, Reis-Cunha JL, Grace CA, Berry ASF, Mitchell MW, Yu JA, Malekshahi CR, Krespan E, Go CK, Lombana C, Song YS, Amorim CF, Lago AS, Carvalho LP, Carvalho EM, Brisson D, Scott P, Jeffares DC, Beiting DP. Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies. PLoS Pathog 2023; 19:e1011230. [PMID: 36940219 PMCID: PMC10063166 DOI: 10.1371/journal.ppat.1011230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 03/30/2023] [Accepted: 02/22/2023] [Indexed: 03/21/2023] Open
Abstract
In Brazil, Leishmania braziliensis is the main causative agent of the neglected tropical disease, cutaneous leishmaniasis (CL). CL presents on a spectrum of disease severity with a high rate of treatment failure. Yet the parasite factors that contribute to disease presentation and treatment outcome are not well understood, in part because successfully isolating and culturing parasites from patient lesions remains a major technical challenge. Here we describe the development of selective whole genome amplification (SWGA) for Leishmania and show that this method enables culture-independent analysis of parasite genomes obtained directly from primary patient skin samples, allowing us to circumvent artifacts associated with adaptation to culture. We show that SWGA can be applied to multiple Leishmania species residing in different host species, suggesting that this method is broadly useful in both experimental infection models and clinical studies. SWGA carried out directly on skin biopsies collected from patients in Corte de Pedra, Bahia, Brazil, showed extensive genomic diversity. Finally, as a proof-of-concept, we demonstrated that SWGA data can be integrated with published whole genome data from cultured parasite isolates to identify variants unique to specific geographic regions in Brazil where treatment failure rates are known to be high. SWGA provides a relatively simple method to generate Leishmania genomes directly from patient samples, unlocking the potential to link parasite genetics with host clinical phenotypes.
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Affiliation(s)
- Olivia A. Pilling
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - João L. Reis-Cunha
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Cooper A. Grace
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Alexander S. F. Berry
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew W. Mitchell
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jane A. Yu
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
| | - Clara R. Malekshahi
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Elise Krespan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christina K. Go
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Cláudia Lombana
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yun S. Song
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Camila F. Amorim
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexsandro S. Lago
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Lucas P. Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Edgar M. Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Dustin Brisson
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Phillip Scott
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel C. Jeffares
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Daniel P. Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Bofill Verdaguer I, Sussmann RAC, Santiago VF, Palmisano G, Moura GC, Mesquita JT, Yamaguchi LF, Kato MJ, Katzin AM, Crispim M. Isoprenoid alcohols utilization by malaria parasites. Front Chem 2022; 10:1035548. [PMID: 36531309 PMCID: PMC9751614 DOI: 10.3389/fchem.2022.1035548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/15/2022] [Indexed: 05/14/2024] Open
Abstract
Plasmodium falciparum is the etiological agent of human malaria, one of the most widespread diseases in tropical and subtropical regions. Drug resistance is one of the biggest problems in controlling the disease, which leads to the need to discover new antimalarial compounds. One of the most promissory drugs purposed is fosmidomycin, an inhibitor of the biosynthesis of isoprene units by the methylerythritol 4-phosphate (MEP) pathway, which in some cases failed in clinical studies. Once formed, isoprene units are condensed to form longer structures such as farnesyl and geranylgeranyl pyrophosphate, which are necessary for Heme O and A formation, ubiquinone, and dolichyl phosphate biosynthesis as well as for protein isoprenylation. Even though the natural substrates of polyprenyl transferases and synthases are polyprenyl pyrophosphates, it was already demonstrated that isoprenoid alcohols (polyprenols) such as farnesol (FOH) and geranylgeraniol (GGOH) can rescue parasites from fosmidomycin. This study better investigated how this rescue phenomenon occurs by performing drug-rescue assays. Similarly, to FOH and GGOH, it was observed that phytol (POH), a 20-carbon plant isoprenoid, as well as unsaponifiable lipid extracts from foods rescue parasites from the antimalarial effect of fosmidomycin. Contrarily, neither dolichols nor nonaprenol rescue parasites from fosmidomycin. Considering this, here we characterized the transport of FOH, GGOH, and POH. Once incorporated, it was observed that these substances are phosphorylated, condensed into longer isoprenoid alcohols, and incorporated into proteins and dolichyl phosphates. Through proteomic and radiolabelling approaches, it was found that prenylated proteins are naturally attached to several isoprenoids, derived from GGOH, dolichol, and POH if exogenously added. Furthermore, the results suggest the presence of at least two promiscuous protein prenyltransferases in the parasite: one enzyme which can use FPP among other unidentified substrates and another enzyme that can use GGPP, phytyl pyrophosphate (PPP), and dolichols, among other substrates not identified here. Thus, further evidence was obtained for dolichols and other isoprenoid products attached to proteins. This study helps to better understand the apicoplast-targeting antimalarial mechanism of action and a novel post-translational modification of proteins in P. falciparum.
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Affiliation(s)
- Ignasi Bofill Verdaguer
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Rodrigo A C Sussmann
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
- Center for Environmental Sciences, Institute of Humanities, Arts and Sciences, Federal University of Southern Bahia, Bahia, Brazil
| | - Verônica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Gabriel Cândido Moura
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Juliana Tonini Mesquita
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Lydia Fumiko Yamaguchi
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Massuo Jorge Kato
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Alejandro Miguel Katzin
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Marcell Crispim
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
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Coppée R, Mama A, Sarrasin V, Kamaliddin C, Adoux L, Palazzo L, Ndam NT, Letourneur F, Ariey F, Houzé S, Clain J. 5WBF: a low-cost and straightforward whole blood filtration method suitable for whole-genome sequencing of Plasmodium falciparum clinical isolates. Malar J 2022; 21:51. [PMID: 35172825 PMCID: PMC8848818 DOI: 10.1186/s12936-022-04073-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/31/2022] [Indexed: 11/21/2022] Open
Abstract
Background Whole-genome sequencing (WGS) is becoming increasingly helpful to assist malaria control programmes. A major drawback of this approach is the large amount of human DNA compared to parasite DNA extracted from unprocessed whole blood. As red blood cells (RBCs) have a diameter of about 7–8 µm and exhibit some deformability, it was hypothesized that cheap and commercially available 5 µm filters might retain leukocytes but much less of Plasmodium falciparum-infected RBCs. This study aimed to test the hypothesis that such a filtration method, named 5WBF (for 5 µm Whole Blood Filtration), may provide highly enriched parasite material suitable for P. falciparum WGS. Methods Whole blood was collected from five patients experiencing a P. falciparum malaria episode (ring-stage parasitaemia range: 0.04–5.5%) and from mock samples obtained by mixing synchronized, ring-stage cultured P. falciparum 3D7 parasites with uninfected human whole blood (final parasitaemia range: 0.02–1.1%). These whole blood samples (50 to 400 µL) were diluted in RPMI 1640 medium or PBS 1× buffer and filtered with a syringe connected to a 5 µm commercial filter. DNA was extracted from 5WBF-treated and unfiltered counterpart blood samples using a commercial kit. The 5WBF method was evaluated on the ratios of parasite:human DNA assessed by qPCR and by sequencing depth and percentages of coverage from WGS data (Illumina NextSeq 500). As a comparison, the popular selective whole-genome amplification (sWGA) method, which does not rely on blood filtration, was applied to the unfiltered counterpart blood samples. Results After applying 5WBF, qPCR indicated an average of twofold loss in the amount of parasite template DNA (Pf ARN18S gene) and from 4096- to 65,536-fold loss of human template DNA (human β actin gene). WGS analyses revealed that > 95% of the parasite nuclear and organellar genomes were all covered at ≥ 10× depth for all samples tested. In sWGA counterparts, the organellar genomes were poorly covered and from 47.7 to 82.1% of the nuclear genome was covered at ≥ 10× depth depending on parasitaemia. Sequence reads were homogeneously distributed across gene sequences for 5WBF-treated samples (n = 5460 genes; mean coverage: 91×; median coverage: 93×; 5th percentile: 70×; 95th percentile: 103×), allowing the identification of gene copy number variations such as for gch1. This later analysis was not possible for sWGA-treated samples, as a much more heterogeneous distribution of reads across gene sequences was observed (mean coverage: 80×; median coverage: 51×; 5th percentile: 7×; 95th percentile: 245×). Conclusions The novel 5WBF leucodepletion method is simple to implement and based on commercially available, standardized 5 µm filters which cost from 1.0 to 1.7€ per unit depending on suppliers. 5WBF permits extensive genome-wide analysis of P. falciparum ring-stage isolates from minute amounts of whole blood even with parasitaemias as low as 0.02%. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04073-1.
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Affiliation(s)
- Romain Coppée
- Université de Paris, IRD, MERIT, 75006, Paris, France. .,Université de Paris, Infection Modelisation Antimicrobial Evolution (IAME), Inserm UMR1137, 75018, Paris, France.
| | - Atikatou Mama
- Université de Paris, IRD, MERIT, 75006, Paris, France
| | - Véronique Sarrasin
- Université de Paris, IRD, MERIT, 75006, Paris, France.,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, 75018, Paris, France
| | - Claire Kamaliddin
- Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, 75018, Paris, France.,Cumming School of Medicine, Pathology and Laboratory Medicine, The University of Calgary, Calgary, AB, Canada
| | - Lucie Adoux
- Cochin Institute, INSERM U1016, UMR CNRS 8104, Genomic Platform, 75014, Paris, France
| | | | | | - Franck Letourneur
- Cochin Institute, INSERM U1016, UMR CNRS 8104, Genomic Platform, 75014, Paris, France
| | - Frédéric Ariey
- Université de Paris, INSERM 1016, Service de Parasitologie-Mycologie Hôpital Cochin, 75014, Paris, France
| | - Sandrine Houzé
- Université de Paris, IRD, MERIT, 75006, Paris, France.,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, 75018, Paris, France
| | - Jérôme Clain
- Université de Paris, IRD, MERIT, 75006, Paris, France. .,Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, 75018, Paris, France.
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Franssen SU, Takele Y, Adem E, Sanders MJ, Müller I, Kropf P, Cotton JA. Diversity and Within-Host Evolution of Leishmania donovani from Visceral Leishmaniasis Patients with and without HIV Coinfection in Northern Ethiopia. mBio 2021; 12:e0097121. [PMID: 34182785 PMCID: PMC8262925 DOI: 10.1128/mbio.00971-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/16/2021] [Indexed: 12/20/2022] Open
Abstract
Visceral leishmaniasis (VL) is a fatal disease and a growing public health problem in East Africa, where Ethiopia has one of the highest VL burdens. The largest focus of VL in Ethiopia is driven by high prevalence in migrant agricultural workers and associated with a high rate of coinfection with HIV. This coinfection makes VL more difficult to treat successfully and is associated with a high rate of relapse, with VL/HIV patients frequently experiencing many relapses of VL before succumbing to this infection. We present genome-wide data on Leishmania donovani isolates from a longitudinal study of cohorts of VL and VL/HIV patients reporting to a single clinic in Ethiopia. Extensive clinical data allow us to investigate the influence of coinfection and relapse on the populations of parasites infecting these patients. We find that the same parasite population is responsible for both VL and VL/HIV infections and that, in most cases, disease relapse is caused by recrudescence of the population of parasites that caused primary VL. Complex, multiclonal infections are present in both primary and relapse cases, but the infrapopulation of parasites within a patient loses genetic diversity between primary disease presentation and subsequent relapses, presumably due to a population bottleneck induced by treatment. These data suggest that VL/HIV relapses are not caused by genetically distinct parasite infections or by reinfection. Treatment of VL does not lead to sterile cure, and in VL/HIV, the infecting parasites are able to reestablish after clinically successful treatment, leading to repeated relapse of VL. IMPORTANCE Visceral leishmaniasis (VL) is the second largest cause of deaths due to parasite infections and a growing problem in East Africa. In Ethiopia, it is particularly associated with migrant workers moving from regions of nonendemicity for seasonal agricultural work and is frequently found as a coinfection with HIV, which leads to frequent VL relapse following treatment. Insight into the process of relapse in these patients is thus key to controlling the VL epidemic in Ethiopia. We show that there is little genetic differentiation between the parasites infecting HIV-positive and HIV-negative VL patients. Moreover, we provide evidence that relapses are caused by the initially infecting parasite population and that treatment induces a loss of genetic diversity in this population. We propose that restoring functioning immunity and improving antiparasitic treatment may be key in breaking the cycle of relapsing VL in VL/HIV patients.
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Affiliation(s)
| | - Yegnasew Takele
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Emebet Adem
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
| | | | - Ingrid Müller
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Pascale Kropf
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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8
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Teyssier NB, Chen A, Duarte EM, Sit R, Greenhouse B, Tessema SK. Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples. Malar J 2021; 20:116. [PMID: 33637093 PMCID: PMC7912882 DOI: 10.1186/s12936-021-03630-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 02/06/2021] [Indexed: 12/22/2022] Open
Abstract
Background Whole-genome sequencing (WGS) is becoming increasingly useful to study the biology, epidemiology, and ecology of malaria parasites. Despite ease of sampling, DNA extracted from dried blood spots (DBS) has a high ratio of human DNA compared to parasite DNA, which poses a challenge for downstream genetic analyses. The effects of multiple methods for DNA extraction, digestion of methylated DNA, and amplification were evaluated on the quality and fidelity of WGS data recovered from DBS. Methods Low parasite density mock DBS samples were created, extracted either with Tween-Chelex or QIAamp, treated with or without McrBC, and amplified with one of three different amplification techniques (two sWGA primer sets and one rWGA). Extraction conditions were evaluated on performance of sequencing depth, percentiles of coverage, and expected SNP concordance. Results At 100 parasites/μL, Chelex-Tween-McrBC samples had higher coverage (5 × depth = 93% genome) than QIAamp extracted samples (5 × depth = 76% genome). The two evaluated sWGA primer sets showed minor differences in overall genome coverage and SNP concordance, with a newly proposed combination of 20 primers showing a modest improvement in coverage over those previously published. Conclusions Overall, Tween-Chelex extracted samples that were treated with McrBC digestion and are amplified using 6A10AD sWGA conditions had minimal dropout rate, higher percentages of coverage at higher depth, and more accurate SNP concordance than QiaAMP extracted samples. These findings extend the results of previously reported methods, making whole genome sequencing accessible to a larger number of low density samples that are commonly encountered in cross-sectional surveys.
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Affiliation(s)
- Noam B Teyssier
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA
| | - Anna Chen
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA
| | - Elias M Duarte
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA
| | - Rene Sit
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Bryan Greenhouse
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Sofonias K Tessema
- Department of Medicine, EPPIcenter, University of California, San Francisco, CA, USA.
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9
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Derilus D, Rahman MZ, Serrano AE, Massey SE. Proteome size reduction in Apicomplexans is linked with loss of DNA repair and host redundant pathways. INFECTION GENETICS AND EVOLUTION 2020; 87:104642. [PMID: 33296723 DOI: 10.1016/j.meegid.2020.104642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 11/29/2022]
Abstract
Apicomplexans are alveolate parasites which include Plasmodium falciparum, the main cause of malaria, one of the world's biggest killers from infectious disease. Apicomplexans are characterized by a reduction in proteome size, which appears to result from metabolic and functional simplification, commensurate with their parasitic lifestyle. However, other factors may also help to explain gene loss such as population bottlenecks experienced during transmission, and the effect of reducing the overall genomic information content. The latter constitutes an 'informational constraint', which is proposed to exert a selective pressure to evolve and maintain genes involved in informational fidelity and error correction, proportional to the quantity of information in the genome (which approximates to proteome size). The dynamics of gene loss was examined in 41 Apicomplexan genomes using orthogroup analysis. We show that loss of genes involved in amino acid metabolism and steroid biosynthesis can be explained by metabolic redundancy with the host. We also show that there is a marked tendency to lose DNA repair genes as proteome size is reduced. This may be explained by a reduction in size of the informational constraint and can help to explain elevated mutation rates in pathogens with reduced genome size. Multiple Sequentially Markovian Coalescent (MSMC) analysis indicates a recent bottleneck, consistent with predictions generated using allele-based population genetics approaches, implying that relaxed selection pressure due to reduced population size might have contributed to gene loss. However, the non-randomness of pathways that are lost challenges this scenario. Lastly, we identify unique orthogroups in malaria-causing Plasmodium species that infect humans, with a high proportion of membrane associated proteins. Thus, orthogroup analysis appears useful for identifying novel candidate pathogenic factors in parasites, when there is a wide sample of genomes available.
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Affiliation(s)
- D Derilus
- Environmental Sciences Department, University of Puerto Rico-Rio Piedras, United States of America
| | - M Z Rahman
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America
| | - A E Serrano
- Department of Microbiology, University of Puerto Rico-School of Medicine, Medical Sciences, United States of America
| | - S E Massey
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America.
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10
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Brown AC, Guler JL. From Circulation to Cultivation: Plasmodium In Vivo versus In Vitro. Trends Parasitol 2020; 36:914-926. [DOI: 10.1016/j.pt.2020.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022]
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11
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Palmer LD, Minor KE, Mettlach JA, Rivera ES, Boyd KL, Caprioli RM, Spraggins JM, Dalebroux ZD, Skaar EP. Modulating Isoprenoid Biosynthesis Increases Lipooligosaccharides and Restores Acinetobacter baumannii Resistance to Host and Antibiotic Stress. Cell Rep 2020; 32:108129. [PMID: 32905776 PMCID: PMC7519801 DOI: 10.1016/j.celrep.2020.108129] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/19/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
Acinetobacter baumannii is a leading cause of ventilator-associated pneumonia and a critical threat due to multidrug resistance. The A. baumannii outer membrane is an asymmetric lipid bilayer composed of inner leaflet glycerophospholipids and outer leaflet lipooligosaccharides. Deleting mlaF of the maintenance of lipid asymmetry (Mla) system causes A. baumannii to become more susceptible to pulmonary surfactants and antibiotics and decreases bacterial survival in the lungs of mice. Spontaneous suppressor mutants isolated from infected mice contain an ISAba11 insertion upstream of the ispB initiation codon, an essential isoprenoid biosynthesis gene. The insertion restores antimicrobial resistance and virulence to ΔmlaF. The suppressor strain increases lipooligosaccharides, suggesting that the mechanism involves balancing the glycerophospholipids/lipooligosaccharides ratio on the bacterial surface. An identical insertion exists in an extensively drug-resistant A. baumannii isolate, demonstrating its clinical relevance. These data show that the stresses bacteria encounter during infection select for genomic rearrangements that increase resistance to antimicrobials.
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Affiliation(s)
- Lauren D Palmer
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Keaton E Minor
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Joshua A Mettlach
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Emilio S Rivera
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Kelli L Boyd
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Zachary D Dalebroux
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA.
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12
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Mombo-Ngoma G, Remppis J, Sievers M, Zoleko Manego R, Endamne L, Kabwende L, Veletzky L, Nguyen TT, Groger M, Lötsch F, Mischlinger J, Flohr L, Kim J, Cattaneo C, Hutchinson D, Duparc S, Moehrle J, Velavan TP, Lell B, Ramharter M, Adegnika AA, Mordmüller B, Kremsner PG. Efficacy and Safety of Fosmidomycin-Piperaquine as Nonartemisinin-Based Combination Therapy for Uncomplicated Falciparum Malaria: A Single-Arm, Age De-escalation Proof-of-Concept Study in Gabon. Clin Infect Dis 2019; 66:1823-1830. [PMID: 29293893 PMCID: PMC5982710 DOI: 10.1093/cid/cix1122] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/23/2017] [Indexed: 12/03/2022] Open
Abstract
Background Fosmidomycin–piperaquine is being developed as nonartemisinin-based combination therapy to meet the challenge of emerging artemisinin resistance. Methods The study was a phase 2, single-arm, proof-of-concept study of the efficacy, tolerability, and safety of fosmidomycin–piperaquine for the treatment of uncomplicated Plasmodium falciparum monoinfection in Gabon. Adults and children of both sexes with initial parasite counts between 1000 and 150000/µL received oral treatment with fosmidomycin (twice daily doses of 30 mg/kg) and piperaquine (once daily dose of 16 mg/kg) for 3 days and followed-up for 63 days. The primary efficacy endpoint was the per-protocol polymerase chain reaction (PCR)–corrected day 28 adequate clinical and parasitological response (ACPR). Results One hundred patients were enrolled. The PCR-corrected day 28 ACPR rate was 83/83, or 100% (95% confidence interval, 96–100). Fourteen patients had asexual parasitaemia between day 28 and day 63; all were typed by PCR as new infections. Fosmidomycin–piperaquine therapy led to rapid parasite clearance (median, 36 hours; interquartile range [IQR], 6–60) and fever clearance time (median, 12 hours; IQR, 6–48). The electrocardiogram assessments showed 2 patients with prolonged QT interval >500 msec following study drug administration. The majority of adverse events affected the gastrointestinal and respiratory tracts and were transient and mild to moderate in severity. Conclusions This is the first report of the use of the combination fosmidomycin–piperaquine. The combination appeared to have high efficacy and be safe and well tolerated despite observed transient changes in electrocardiogram with prolongation of the QT interval. Clinical Trials Registration. NCT02198807.
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Affiliation(s)
- Ghyslain Mombo-Ngoma
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Département de Parasitologie-Mycologie, Université des Sciences de la Santé, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Jonathan Remppis
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Moritz Sievers
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Rella Zoleko Manego
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Lilian Endamne
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Lumeka Kabwende
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon
| | - Luzia Veletzky
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - The Trong Nguyen
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Mirjam Groger
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Felix Lötsch
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Johannes Mischlinger
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Lena Flohr
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Johanna Kim
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Chiara Cattaneo
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - David Hutchinson
- DMG Deutsche Malaria GmbH, formerly Jomaa Pharma GmbH, Hamburg, Germany
| | | | | | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany.,Vietnamese-German Center for Medical Research, Hanoi and Faculty of Medicine, Duy Tan University DaNang, Vietnam
| | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Michael Ramharter
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany.,Bernhard Nocht Hospital for Tropical Diseases, Bernhard Nocht Institute for Tropical Medicine and University Medical Center Hamburg-Eppendorf, Germany
| | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Benjamin Mordmüller
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
| | - Peter G Kremsner
- Centre de Recherches Médicales de Lambaréné, Libreville, Gabon.,Institute of Tropical Medicine, University of Tübingen, and German Centre for Infection Research, Hamburg, Germany
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13
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Li X, Kumar S, McDew-White M, Haile M, Cheeseman IH, Emrich S, Button-Simons K, Nosten F, Kappe SHI, Ferdig MT, Anderson TJC, Vaughan AM. Genetic mapping of fitness determinants across the malaria parasite Plasmodium falciparum life cycle. PLoS Genet 2019; 15:e1008453. [PMID: 31609965 PMCID: PMC6821138 DOI: 10.1371/journal.pgen.1008453] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/30/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
Determining the genetic basis of fitness is central to understanding evolution and transmission of microbial pathogens. In human malaria parasites (Plasmodium falciparum), most experimental work on fitness has focused on asexual blood stage parasites, because this stage can be easily cultured, although the transmission of malaria requires both female Anopheles mosquitoes and vertebrate hosts. We explore a powerful approach to identify the genetic determinants of parasite fitness across both invertebrate and vertebrate life-cycle stages of P. falciparum. This combines experimental genetic crosses using humanized mice, with selective whole genome amplification and pooled sequencing to determine genome-wide allele frequencies and identify genomic regions under selection across multiple lifecycle stages. We applied this approach to genetic crosses between artemisinin resistant (ART-R, kelch13-C580Y) and ART-sensitive (ART-S, kelch13-WT) parasites, recently isolated from Southeast Asian patients. Two striking results emerge: we observed (i) a strong genome-wide skew (>80%) towards alleles from the ART-R parent in the mosquito stage, that dropped to ~50% in the blood stage as selfed ART-R parasites were selected against; and (ii) repeatable allele specific skews in blood stage parasites with particularly strong selection (selection coefficient (s) ≤ 0.18/asexual cycle) against alleles from the ART-R parent at loci on chromosome 12 containing MRP2 and chromosome 14 containing ARPS10. This approach robustly identifies selected loci and has strong potential for identifying parasite genes that interact with the mosquito vector or compensatory loci involved in drug resistance.
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Affiliation(s)
- Xue Li
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Marina McDew-White
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Meseret Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Ian H. Cheeseman
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Scott Emrich
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Katie Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Stefan H. I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Tim J. C. Anderson
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- * E-mail: (TJCA); (AMV)
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- * E-mail: (TJCA); (AMV)
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14
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Aninagyei E, Smith-Graham S, Boye A, Egyir-Yawson A, Acheampong DO. Evaluating 18s-rRNA LAMP and selective whole genome amplification (sWGA) assay in detecting asymptomatic Plasmodium falciparum infections in blood donors. Malar J 2019; 18:214. [PMID: 31234871 PMCID: PMC6591871 DOI: 10.1186/s12936-019-2850-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/19/2019] [Indexed: 11/18/2022] Open
Abstract
Background Undesirable consequences of donor Plasmodium falciparum parasitaemia on stored donor blood have been reported. Therefore, it is imperative that all prospective blood donors are screened for P. falciparum infections using sensitive techniques. In this study, the sensitivities of microscopy, rapid diagnostic test (RDT), loop-mediated isothermal amplification (LAMP) assay and selective whole genome amplification (sWGA) technique in detecting P. falciparum infections in blood donors was assessed. Methods Randomly selected blood donors from 5 districts in Greater Accra Region of Ghana were screened for asymptomatic P. falciparum infections. Each donor sample was screened with SD Bioline RDT kit for P. falciparum histidine rich protein 2 and Plasmodium lactate dehydrogenase antigens, sWGA and 18s-rRNA LAMP. Crude DNA LAMP (crDNA-LAMP) was compared to purified DNA LAMP (pDNA-LAMP). Results A total of 771 blood donors were screened. The respective overall prevalence of P. falciparum in Ghana by microscopy, RDT, crDNA-LAMP, pDNA-LAMP and sWGA was 7.4%, 11.8%, 16.9%, 17.5% and 18.0%. Using sWGA as the reference test, the sensitivities of microscopy, RDT, crDNA-LAMP and pDNA-LAMP were 41.0% (95% CI 32.7–49.7), 65.5% (95% CI 56.9–73.3), 82.6% (95% CI 75.8–88.3) and 95.7% (95% CI 90.1–98.4), respectively. There was near perfect agreement between LAMP and sWGA (sWGA vs. crDNA-LAMP, κ = 0.87; sWGA vs. pDNA-LAMP, κ = 0.96), while crDNA-LAMP and pDNA-LAMP agreed perfectly (κ = 0.91). Goodness of fit test indicated non-significant difference between the performance of LAMP and sWGA (crDNA-LAMP vs. sWGA: x2 = 0.71, p = 0.399 and pDNA-LAMP vs. sWGA: x2 = 0.14, p = 0.707). Finally, compared to sWGA, the performance of LAMP did not differ in detecting sub-microscopic parasitaemia (sWGA vs. crDNA-LAMP: x2 = 1.12, p = 0.290 and sWGA vs. pDNA-LAMP: x2 = 0.22, p = 0.638). Conclusions LAMP assay agreed near perfectly with sWGA with non-significant differences in their ability to detect asymptomatic P. falciparum parasitaemia in blood donors. Therefore, it is recommended that LAMP based assays are employed to detect P. falciparum infections in blood donors due to its high sensitivity, simplicity, cost-effectiveness and user-friendliness.
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Affiliation(s)
- Enoch Aninagyei
- Department of Biomedical Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana. .,Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
| | | | - Alex Boye
- Department of Medical Laboratory Science, University of Cape Coast, Cape Coast, Ghana
| | - Alexander Egyir-Yawson
- Department of Biomedical Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Desmond Omane Acheampong
- Department of Biomedical Sciences, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana.
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15
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Clarke EL, Sundararaman SA, Seifert SN, Bushman FD, Hahn BH, Brisson D. swga: a primer design toolkit for selective whole genome amplification. Bioinformatics 2018; 33:2071-2077. [PMID: 28334194 PMCID: PMC5870857 DOI: 10.1093/bioinformatics/btx118] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/24/2017] [Indexed: 02/04/2023] Open
Abstract
Motivation Population genomic analyses are often hindered by difficulties in obtaining sufficient numbers of genomes for analysis by DNA sequencing. Selective whole-genome amplification (SWGA) provides an efficient approach to amplify microbial genomes from complex backgrounds for sequence acquisition. However, the process of designing sets of primers for this method has many degrees of freedom and would benefit from an automated process to evaluate the vast number of potential primer sets. Results Here, we present swga, a program that identifies primer sets for SWGA and evaluates them for efficiency and selectivity. We used swga to design and test primer sets for the selective amplification of Wolbachia pipientis genomic DNA from infected Drosophila melanogaster and Mycobacterium tuberculosis from human blood. We identify primer sets that successfully amplify each against their backgrounds and describe a general method for using swga for arbitrary targets. In addition, we describe characteristics of primer sets that correlate with successful amplification, and present guidelines for implementation of SWGA to detect new targets. Availability and Implementation Source code and documentation are freely available on https://www.github.com/eclarke/swga. The program is implemented in Python and C and licensed under the GNU Public License. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erik L Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sesh A Sundararaman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice H Hahn
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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16
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Nag S, Kofoed PE, Ursing J, Lemvigh CK, Allesøe RL, Rodrigues A, Svendsen CA, Jensen JD, Alifrangis M, Lund O, Aarestrup FM. Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots. Malar J 2018; 17:91. [PMID: 29471822 PMCID: PMC5824530 DOI: 10.1186/s12936-018-2232-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/13/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Plasmodium falciparum malaria remains a major health burden and genomic research represents one of the necessary approaches for continued progress towards malaria control and elimination. Sample acquisition for this purpose is troublesome, with the majority of malaria-infected individuals living in rural areas, away from main infrastructure and the electrical grid. The aim of this study was to describe a low-tech procedure to sample P. falciparum specimens for direct whole genome sequencing (WGS), without use of electricity and cold-chain. METHODS Venous blood samples were collected from malaria patients in Bandim, Guinea-Bissau and leukocyte-depleted using Plasmodipur filters, the enriched parasite sample was spotted on Whatman paper and dried. The samples were stored at ambient temperatures and subsequently used for DNA-extraction. Ratios of parasite:human content of the extracted DNA was assessed by qPCR, and five samples with varying parasitaemia, were sequenced. Sequencing data were used to analyse the sample content, as well as sample coverage and depth as compared to the 3d7 reference genome. RESULTS qPCR revealed that 73% of the 199 samples were applicable for WGS, as defined by a minimum ratio of parasite:human DNA of 2:1. WGS revealed an even distribution of sequence data across the 3d7 reference genome, regardless of parasitaemia. The acquired read depths varied from 16 to 99×, and coverage varied from 87.5 to 98.9% of the 3d7 reference genome. SNP-analysis of six genes, for which amplicon sequencing has been performed previously, confirmed the reliability of the WGS-data. CONCLUSION This study describes a simple filter paper based protocol for sampling P. falciparum from malaria patients for subsequent direct WGS, enabling acquisition of samples in remote settings with no access to electricity.
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Affiliation(s)
- Sidsel Nag
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark. .,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.
| | - Poul-Erik Kofoed
- Department of Paediatrics, Kolding Hospital, Kolding, Denmark.,Bandim Health Project, Bissau, Guinea-Bissau
| | - Johan Ursing
- Bandim Health Project, Bissau, Guinea-Bissau.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Danderyds Hospital, Danderyd, Sweden
| | | | | | | | - Christina Aaby Svendsen
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jacob Dyring Jensen
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael Alifrangis
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Ole Lund
- DTU Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Frank M Aarestrup
- Division for Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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17
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Amberg-Johnson K, Hari SB, Ganesan SM, Lorenzi HA, Sauer RT, Niles JC, Yeh E. Small molecule inhibition of apicomplexan FtsH1 disrupts plastid biogenesis in human pathogens. eLife 2017; 6:29865. [PMID: 28826494 PMCID: PMC5576918 DOI: 10.7554/elife.29865] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/17/2017] [Indexed: 12/21/2022] Open
Abstract
The malaria parasite Plasmodium falciparum and related apicomplexan pathogens contain an essential plastid organelle, the apicoplast, which is a key anti-parasitic target. Derived from secondary endosymbiosis, the apicoplast depends on novel, but largely cryptic, mechanisms for protein/lipid import and organelle inheritance during parasite replication. These critical biogenesis pathways present untapped opportunities to discover new parasite-specific drug targets. We used an innovative screen to identify actinonin as having a novel mechanism-of-action inhibiting apicoplast biogenesis. Resistant mutation, chemical-genetic interaction, and biochemical inhibition demonstrate that the unexpected target of actinonin in P. falciparum and Toxoplasma gondii is FtsH1, a homolog of a bacterial membrane AAA+ metalloprotease. PfFtsH1 is the first novel factor required for apicoplast biogenesis identified in a phenotypic screen. Our findings demonstrate that FtsH1 is a novel and, importantly, druggable antimalarial target. Development of FtsH1 inhibitors will have significant advantages with improved drug kinetics and multistage efficacy against multiple human parasites.
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Affiliation(s)
- Katherine Amberg-Johnson
- Department of Biochemistry, Stanford Medical School, Stanford, United States.,Microbiology and Immunology, Stanford Medical School, Stanford, United States
| | - Sanjay B Hari
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Suresh M Ganesan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Hernan A Lorenzi
- Department of Infectious Disease, The J. Craig Venter Institute, Maryland, United States
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Ellen Yeh
- Department of Biochemistry, Stanford Medical School, Stanford, United States.,Microbiology and Immunology, Stanford Medical School, Stanford, United States.,Department of Pathology, Stanford Medical School, Stanford, United States
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Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples. mBio 2017; 8:mBio.02257-16. [PMID: 28174312 PMCID: PMC5296604 DOI: 10.1128/mbio.02257-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Whole-genome sequencing (WGS) of microbial pathogens from clinical samples is a highly sensitive tool used to gain a deeper understanding of the biology, epidemiology, and drug resistance mechanisms of many infections. However, WGS of organisms which exhibit low densities in their hosts is challenging due to high levels of host genomic DNA (gDNA), which leads to very low coverage of the microbial genome. WGS of Plasmodium vivax, the most widely distributed form of malaria, is especially difficult because of low parasite densities and the lack of an ex vivo culture system. Current techniques used to enrich P. vivax DNA from clinical samples require significant resources or are not consistently effective. Here, we demonstrate that selective whole-genome amplification (SWGA) can enrich P. vivax gDNA from unprocessed human blood samples and dried blood spots for high-quality WGS, allowing genetic characterization of isolates that would otherwise have been prohibitively expensive or impossible to sequence. We achieved an average genome coverage of 24×, with up to 95% of the P. vivax core genome covered by ≥5 reads. The single-nucleotide polymorphism (SNP) characteristics and drug resistance mutations seen were consistent with those of other P. vivax sequences from a similar region in Peru, demonstrating that SWGA produces high-quality sequences for downstream analysis. SWGA is a robust tool that will enable efficient, cost-effective WGS of P. vivax isolates from clinical samples that can be applied to other neglected microbial pathogens. Malaria is a disease caused by Plasmodium parasites that caused 214 million symptomatic cases and 438,000 deaths in 2015. Plasmodium vivax is the most widely distributed species, causing the majority of malaria infections outside sub-Saharan Africa. Whole-genome sequencing (WGS) of Plasmodium parasites from clinical samples has revealed important insights into the epidemiology and mechanisms of drug resistance of malaria. However, WGS of P. vivax is challenging due to low parasite levels in humans and the lack of a routine system to culture the parasites. Selective whole-genome amplification (SWGA) preferentially amplifies the genomes of pathogens from mixtures of target and host gDNA. Here, we demonstrate that SWGA is a simple, robust method that can be used to enrich P. vivax genomic DNA (gDNA) from unprocessed human blood samples and dried blood spots for cost-effective, high-quality WGS.
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Oyola SO, Ariani CV, Hamilton WL, Kekre M, Amenga-Etego LN, Ghansah A, Rutledge GG, Redmond S, Manske M, Jyothi D, Jacob CG, Otto TD, Rockett K, Newbold CI, Berriman M, Kwiatkowski DP. Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malar J 2016; 15:597. [PMID: 27998271 PMCID: PMC5175302 DOI: 10.1186/s12936-016-1641-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/28/2016] [Indexed: 12/05/2022] Open
Abstract
Background Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB. Methods Parasite DNA with high (>95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8–12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparum DNA) and contaminating (human) genomes. Results Using sWGA method, clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB were sequenced. Greater than 18-fold enrichment of P. falciparum DNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5× coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls. Conclusion The sWGA methods described here provide a reliable and scalable way of generating P. falciparum genome sequence data from DBS samples. The current data indicate that it will be possible to get good quality sequence on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor in P. falciparum genome sequencing from field samples, and paves the way for large-scale epidemiological applications. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1641-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel O Oyola
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. .,International Livestock Research Institute, Box 30709, Nairobi, Kenya.
| | | | - William L Hamilton
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Addenbrooke's Hospital, University of Cambridge School of Clinical Medicine, Hills Rd, Cambridge, CB2 0SP, UK
| | - Mihir Kekre
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, P. O. Box LG 581, Legon, Accra, Ghana
| | | | - Seth Redmond
- Broad Institute, 415 Main St, Cambridge, MA, 02142, USA
| | - Magnus Manske
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | | | - Chris G Jacob
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kirk Rockett
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, OX3 7BN, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Chris I Newbold
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | | | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,MRC Centre for Genomics and Global Health, University of Oxford, Oxford, OX3 7BN, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
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