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Martinez-Vega R, Mbacham WF, Ali I, Nji A, Mousa A, Beshir KB, Chopo-Pizarro A, Kaur H, Okell L, Hansson H, Hocke EF, Alifrangis M, Gosling R, Roper C, Sutherland C, Chico RM. Parasite clearance and protection from Plasmodium falciparum infection (PCPI): a three-arm, parallel, double-blinded, placebo-controlled, randomised trial of presumptive sulfadoxine-pyrimethamine versus sulfadoxine-pyrimethamine plus amodiaquine versus artesunate monotherapy among asymptomatic children 3-5 years of age in Cameroon. BMC Infect Dis 2024; 24:1028. [PMID: 39327613 PMCID: PMC11425934 DOI: 10.1186/s12879-024-09868-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/28/2024] Open
Abstract
BACKGROUND The World Health Organization 2022 malaria chemoprevention guidelines recommend providing a full course of antimalarial treatment at pre-defined intervals, regardless of malaria status to prevent illness among children resident in moderate to high perennial malaria transmission settings as perennial malaria chemoprevention (PMC) with sulfadoxine-pyrimethamine (SP). The dhps I431V mutation circulating in West Africa has unknown effect on SP protective efficacy. METHODS This protocol is for a three-arm, parallel, double-blinded, placebo-controlled, randomised trial in Cameroon among children randomly assigned to one of three directly-observed treatment groups: (i) Group 1 (n = 450) receives daily artesunate (AS) placebo on days - 7 to -1, then active SP plus placebo amodiaquine (AQ) on day 0, and placebo AQ on days 1 and 2; (ii) Group 2 (n = 250) receives placebo AS on days - 7 to -1, then active SP and AQ on day 0, and active AQ on days 1 and 2; and (iii) Group 3 (n = 200) receives active AS on days - 7 to -1, then placebo SP on day 0 and placebo AQ on days 0 to 2. On days 0, 2, 5, 7, and thereafter weekly until day 28, children provide blood for thick smear slides. Dried blood spots are collected on the same days and weekly from day 28 to day 63 for quantitative polymerase chain reaction (qPCR) and genotype analyses. DISCUSSION Our aim is to quantify the chemopreventive efficacy of SP, and SP plus AQ, and measure the effect of the parasite genotypes associated with SP resistance on parasite clearance and protection from infection when exposed to SP chemoprevention. We will report unblinded results including: (i) time-to-parasite clearance among SP and SP plus AQ recipients who were positive on day 0 by qPCR and followed to day 63; (ii) mean duration of SP and SP plus AQ protection against infection, and (iii) mean duration of symptom-free status among SP and SP plus AQ recipients who were parasite free on day 0 by qPCR. Our study is designed to compare the 28-day follow-up of the new WHO malaria chemoprevention efficacy study protocol with extended follow-up to day 63. TRIAL REGISTRATION ClinicalTrials.gov NCT06173206; 15/12/2023.
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Affiliation(s)
- Rosario Martinez-Vega
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Wilfred Fon Mbacham
- Fobang Institute for Innovation in Science and Technology, 14 Missionary Road, Simbok, Yaounde, Cameroon
- Department of Biochemistry, Faculty of Sciences, The University of Yaounde I, Yaounde, Cameroon
| | - Innocent Ali
- Department of Biochemistry, Faculty of Science, University of Dschang, BP 67, Dschang, Cameroon
- The Biotechnology Center, The University of Yaounde I, Yaounde, Cameroon
| | - Akindeh Nji
- Fobang Institute for Innovation in Science and Technology, 14 Missionary Road, Simbok, Yaounde, Cameroon
- The Biotechnology Center, The University of Yaounde I, Yaounde, Cameroon
| | - Andria Mousa
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W12 0BZ, United Kingdom
| | - Khalid B Beshir
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Ana Chopo-Pizarro
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Harparkash Kaur
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Lucy Okell
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W12 0BZ, United Kingdom
| | - Helle Hansson
- Department of Immunology and Microbiology, Centre for translational Medicine and Parasitology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Emma Filtenborg Hocke
- Department of Immunology and Microbiology, Centre for translational Medicine and Parasitology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michael Alifrangis
- Department of Immunology and Microbiology, Centre for translational Medicine and Parasitology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Roland Gosling
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Cally Roper
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Colin Sutherland
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - R Matthew Chico
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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Zhu H, Zhu D, Wu K, He W, Li L, Li T, Liu L, Liu Z, Song X, Cheng W, Mo J, Yao Y, Li J. Establishment and evaluation of a qPCR method for the detection of pfmdr1 mutations in Plasmodium falciparum, the causal agent of fatal malaria. Diagn Microbiol Infect Dis 2024; 110:116400. [PMID: 38909426 DOI: 10.1016/j.diagmicrobio.2024.116400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
Drug resistance surveillance is a major integral part of malaria control programs. Molecular methods play a pivotal role in drug resistance detection and related molecular research. This study aimed to develop a rapid and accurate detection method for drug resistance of Plasmodium falciparum (P. falciparum). A quantitative real-time PCR (qPCR) assay has been developed that identifies the mutation at locus A256T in the P.falciparum multi-drug resistance(pfmdr1) gene producing amino acid change at position 86. The results of 198 samples detected by qPCR were consistent with nested PCR and sequencing, giving an accuracy of 94.3%. The sensitivity, specificity, positive and negative predictive value of qPCR were 85.7%, 97.6%, 90.0% and 96.4%, respectively. The results of qPCR are basically consistent with the nested PCR, which is expected to replace the nested PCR as a new molecular biological method for drug resistance detection, providing reliable technical support for global malaria prevention and control.
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Affiliation(s)
- Huiyin Zhu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China; Department of Pediatrics, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, PR China
| | - Daiqian Zhu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Kai Wu
- Wuhan Centers for Disease Prevention and Control, Wuhan 430024, PR China
| | - Wei He
- Jiangnan University, Wuxi 442000, PR China
| | - Liugen Li
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Tongfei Li
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Long Liu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Zhixin Liu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Xiaonan Song
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Weijia Cheng
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Jinyu Mo
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Yi Yao
- Department of Pediatrics, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, PR China
| | - Jian Li
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China.
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3
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Kraft FLH, Crino OL, Adeniran-Obey SO, Moraney RA, Clayton DF, George JM, Buchanan KL. Parental developmental experience affects vocal learning in offspring. Sci Rep 2024; 14:13787. [PMID: 38877207 PMCID: PMC11178867 DOI: 10.1038/s41598-024-64520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Cultural and genetic inheritance combine to enable rapid changes in trait expression, but their relative importance in determining trait expression across generations is not clear. Birdsong is a socially learned cognitive trait that is subject to both cultural and genetic inheritance, as well as being affected by early developmental conditions. We sought to test whether early-life conditions in one generation can affect song acquisition in the next generation. We exposed one generation (F1) of nestlings to elevated corticosterone (CORT) levels, allowed them to breed freely as adults, and quantified their son's (F2) ability to copy the song of their social father. We also quantified the neurogenetic response to song playback through immediate early gene (IEG) expression in the auditory forebrain. F2 males with only one corticosterone-treated parent copied their social father's song less accurately than males with two control parents. Expression of ARC in caudomedial nidopallium (NCM) correlated with father-son song similarity, and patterns of expression levels of several IEGs in caudomedial mesopallium (CMM) in response to father song playback differed between control F2 sons and those with a CORT-treated father only. This is the first study to demonstrate that developmental conditions can affect social learning and neurogenetic responses in a subsequent generation.
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Affiliation(s)
- Fanny-Linn H Kraft
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Ondi L Crino
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | | | - Raven A Moraney
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - David F Clayton
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Julia M George
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Katherine L Buchanan
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
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4
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Hosch S, Wagner P, Giger JN, Dubach N, Saavedra E, Perno CF, Gody JC, Pagonendji MS, Ngoagouni C, Ndoua C, Nsanzabana C, Vickos U, Daubenberger C, Schindler T. PHARE: a bioinformatics pipeline for compositional profiling of multiclonal Plasmodium falciparum infections from long-read Nanopore sequencing data. J Antimicrob Chemother 2024; 79:987-996. [PMID: 38502783 PMCID: PMC11062946 DOI: 10.1093/jac/dkae060] [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: 09/25/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND The emergence of drug-resistant clones of Plasmodium falciparum is a major public health concern, and the ability to detect and track the spread of these clones is crucial for effective malaria control and treatment. However, in endemic settings, malaria infected people often carry multiple P. falciparum clones simultaneously making it likely to miss drug-resistant clones using traditional molecular typing methods. OBJECTIVES Our goal was to develop a bioinformatics pipeline for compositional profiling in multiclonal P. falciparum samples, sequenced using the Oxford Nanopore Technologies MinION platform. METHODS We developed the 'Finding P. falciparum haplotypes with resistance mutations in polyclonal infections' (PHARE) pipeline using existing bioinformatics tools and custom scripts written in python. PHARE was validated on three control datasets containing P. falciparum DNA of four laboratory strains at varying mixing ratios. Additionally, the pipeline was tested on clinical samples from children admitted to a paediatric hospital in the Central African Republic. RESULTS The PHARE pipeline achieved high recall and accuracy rates in all control datasets. The pipeline can be used on any gene and was tested with amplicons of the P. falciparum drug resistance marker genes pfdhps, pfdhfr and pfK13. CONCLUSIONS The PHARE pipeline helps to provide a more complete picture of drug resistance in the circulating P. falciparum population and can help to guide treatment recommendations. PHARE is freely available under the GNU Lesser General Public License v.3.0 on GitHub: https://github.com/Fippu/PHARE.
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Affiliation(s)
- Salome Hosch
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Philipp Wagner
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Johanna Nouria Giger
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Nina Dubach
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Elis Saavedra
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Carlo Federico Perno
- Department of Microbiology, Ospedale Pediatrico Bambino Gesù, Piazza di Sant’Onofrio, 4, 00165 Roma, Italy
| | - Jean-Chrysostome Gody
- Department of Intensive Care, Pediatric University Hospital Centre of Bangui, Bangui, Central African Republic
| | | | - Carine Ngoagouni
- Medical Entomology Unit, Institut Pasteur of Bangui, Bangui, Central African Republic
| | - Christophe Ndoua
- National Malaria Control Program, Ministry of Health, Bangui, Central African Republic
| | - Christian Nsanzabana
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Ulrich Vickos
- Department of Microbiology, Ospedale Pediatrico Bambino Gesù, Piazza di Sant’Onofrio, 4, 00165 Roma, Italy
| | - Claudia Daubenberger
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Tobias Schindler
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
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5
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Moss S, Pretorius E, Ceesay S, Hutchins H, da Silva ET, Ndiath MO, Jones RT, Vasileva H, Phelan J, Acford-Palmer H, Collins E, Rodrigues A, Krishna S, Clark TG, Last A, Campino S. Genomic surveillance of Anopheles mosquitoes on the Bijagós Archipelago using custom targeted amplicon sequencing identifies mutations associated with insecticide resistance. Parasit Vectors 2024; 17:10. [PMID: 38178249 PMCID: PMC10768400 DOI: 10.1186/s13071-023-06085-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Insecticide resistance is reducing the efficacy of vector control interventions, consequently threatening efforts to control vector-borne diseases, including malaria. Investigating the prevalence of molecular markers of resistance is a useful tool for monitoring the spread of insecticide resistance in disease vectors. The Bijagós Archipelago (Bijagós) in Guinea-Bissau is a region of stable malaria transmission where insecticide-treated nets are the mainstay for malaria control. However, the prevalence of molecular markers of insecticide resistance in malaria vectors is not well understood. METHODS A total of 214 Anopheles mosquitoes were analysed from 13 islands across the Bijagós. These mosquitoes were collected using CDC light traps in November 2019, during the peak malaria transmission season. High-throughput multiplex amplicon sequencing was used to investigate the prevalence of 17 different molecular markers associated with insecticide resistance in four genes: vgsc, rdl, ace1 and gste2. RESULTS Of the 17 screened mutations, four were identified in mosquitoes from the Bijagós: vgsc L995F (12.2%), N1570Y (6.2%) and A1746S (0.7%) and rdl A269G (1.1%). This study is the first to report the L995F knock-down resistance (kdr)-west allele in Anopheles melas on the Archipelago. An additional eight non-synonymous single-nucleotide polymorphisms were identified across the four genes which have not been described previously. The prevalences of the vgsc L995F and N1570Y mutations were higher on Bubaque Island than on the other islands in this study; Bubaque is the most populous island in the archipelago, with the greatest population mobility and connection to continental Guinea-Bissau. CONCLUSIONS This study provides the first surveillance data for genetic markers present in malaria vectors from islands across the Bijagós Archipelago. Overall prevalence of insecticide resistance mutations was found to be low. However, the identification of the vgsc L995F and N1570Y mutations associated with pyrethroid resistance warrants further monitoring. This is particularly important as the mainstay of malaria control on the islands is the use of pyrethroid insecticide-treated nets.
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Affiliation(s)
- Sophie Moss
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Elizabeth Pretorius
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Sainey Ceesay
- Medical Research Council, The Gambia (MRCG), Fajara, Gambia
| | - Harry Hutchins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Eunice Teixeira da Silva
- Ministério de Saúde Pública, Bissau, Guinea-Bissau
- Projecto de Saúde Bandim, Bissau, Guinea-Bissau
| | | | - Robert T Jones
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Hristina Vasileva
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Sanjeev Krishna
- Clinical Academic Group, Institute for Infection and Immunity, St. George's University Hospitals NHS Foundation Trust-St. George's University of London, London, UK
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon
- Institut Für Tropenmedizin Universitätsklinikum Tübingen, Tübingen, Germany
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Anna Last
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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6
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Girgis ST, Adika E, Nenyewodey FE, Senoo Jnr DK, Ngoi JM, Bandoh K, Lorenz O, van de Steeg G, Harrott AJR, Nsoh S, Judge K, Pearson RD, Almagro-Garcia J, Saiid S, Atampah S, Amoako EK, Morang'a CM, Asoala V, Adjei ES, Burden W, Roberts-Sengier W, Drury E, Pierce ML, Gonçalves S, Awandare GA, Kwiatkowski DP, Amenga-Etego LN, Hamilton WL. Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana. Nat Microbiol 2023; 8:2365-2377. [PMID: 37996707 PMCID: PMC10686832 DOI: 10.1038/s41564-023-01516-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/06/2023] [Indexed: 11/25/2023]
Abstract
Malaria results in over 600,000 deaths annually, with the highest burden of deaths in young children living in sub-Saharan Africa. Molecular surveillance can provide important information for malaria control policies, including detection of antimalarial drug resistance. However, genome sequencing capacity in malaria-endemic countries is limited. We designed and implemented an end-to-end workflow to detect Plasmodium falciparum antimalarial resistance markers and diversity in the vaccine target circumsporozoite protein (csp) using nanopore sequencing in Ghana. We analysed 196 clinical samples and showed that our method is rapid, robust, accurate and straightforward to implement. Importantly, our method could be applied to dried blood spot samples, which are readily collected in endemic settings. We report that P. falciparum parasites in Ghana are mostly susceptible to chloroquine, with persistent sulfadoxine-pyrimethamine resistance and no evidence of artemisinin resistance. Multiple single nucleotide polymorphisms were identified in csp, but their significance is uncertain. Our study demonstrates the feasibility of nanopore sequencing for malaria genomic surveillance in endemic countries.
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Affiliation(s)
- Sophia T Girgis
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Edem Adika
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Felix E Nenyewodey
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Dodzi K Senoo Jnr
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Joyce M Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Kukua Bandoh
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Oliver Lorenz
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Guus van de Steeg
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Sebastian Nsoh
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Kim Judge
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Samirah Saiid
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Solomon Atampah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Enock K Amoako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Collins M Morang'a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Victor Asoala
- Navrongo Health Research Centre (NHRC), Ghana Health Service, Navrongo, Upper East Region, Ghana
| | - Elrmion S Adjei
- Ledzokuku Krowor Municipal Assembly (LEKMA) Hospital, Accra, Ghana
| | - William Burden
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Eleanor Drury
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Megan L Pierce
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sónia Gonçalves
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | | | - Lucas N Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.
| | - William L Hamilton
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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7
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Osborne A, Phelan JE, Vanheer LN, Manjurano A, Gitaka J, Drakeley CJ, Kaneko A, Kita K, Campino S, Clark TG. High throughput human genotyping for variants associated with malarial disease outcomes using custom targeted amplicon sequencing. Sci Rep 2023; 13:12062. [PMID: 37495620 PMCID: PMC10371994 DOI: 10.1038/s41598-023-39233-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Malaria has exhibited the strongest known selective pressure on the human genome in recent history and is the evolutionary driving force behind genetic conditions, such as sickle-cell disease, glucose-6-phosphatase deficiency, and some other erythrocyte defects. Genomic studies (e.g., The 1000 Genomes project) have provided an invaluable baseline for human genetics, but with an estimated two thousand ethno-linguistic groups thought to exist across the African continent, our understanding of the genetic differences between indigenous populations and their implications on disease is still limited. Low-cost sequencing-based approaches make it possible to target specific molecular markers and genes of interest, leading to potential insights into genetic diversity. Here we demonstrate the versatility of custom dual-indexing technology and Illumina next generation sequencing to generate a genetic profile of human polymorphisms associated with malaria pathology. For 100 individuals diagnosed with severe malaria in Northeast Tanzania, variants were successfully characterised on the haemoglobin subunit beta (HBB), glucose-6-phosphate dehydrogenase (G6PD), atypical chemokine receptor 1 (ACKR1) genes, and the intergenic Dantu genetic blood variant, then validated using pre-existing genotyping data. High sequencing coverage was observed across all amplicon targets in HBB, G6PD, ACKR1, and the Dantu blood group, with variants identified at frequencies previously observed within this region of Tanzania. Sequencing data exhibited high concordance rates to pre-existing genotyping data (> 99.5%). Our work demonstrates the potential utility of amplicon sequencing for applications in human genetics, including to personalise medicine and understand the genetic diversity of loci linked to important host phenotypes, such as malaria susceptibility.
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Affiliation(s)
- Ashley Osborne
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Leen N Vanheer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Alphaxard Manjurano
- Mwanza Medical Research Centre, National Institute for Medical Research, Mwanza, Tanzania
- Joint Malaria Program, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Christopher J Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Akira Kaneko
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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8
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Osborne A, Phelan JE, Kaneko A, Kagaya W, Chan C, Ngara M, Kongere J, Kita K, Gitaka J, Campino S, Clark TG. Drug resistance profiling of asymptomatic and low-density Plasmodium falciparum malaria infections on Ngodhe island, Kenya, using custom dual-indexing next-generation sequencing. Sci Rep 2023; 13:11416. [PMID: 37452073 PMCID: PMC10349106 DOI: 10.1038/s41598-023-38481-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
Malaria control initiatives require rapid and reliable methods for the detection and monitoring of molecular markers associated with antimalarial drug resistance in Plasmodium falciparum parasites. Ngodhe island, Kenya, presents a unique malaria profile, with lower P. falciparum incidence rates than the surrounding region, and a high proportion of sub-microscopic and low-density infections. Here, using custom dual-indexing and Illumina next generation sequencing, we generate resistance profiles on seventy asymptomatic and low-density P. falciparum infections from a mass drug administration program implemented on Ngodhe island between 2015 and 2016. Our assay encompasses established molecular markers on the Pfcrt, Pfmdr1, Pfdhps, Pfdhfr, and Pfk13 genes. Resistance markers for sulfadoxine-pyrimethamine were identified at high frequencies, including a quintuple mutant haplotype (Pfdhfr/Pfdhps: N51I, C59R, S108N/A437G, K540E) identified in 62.2% of isolates. The Pfdhps K540E biomarker, used to inform decision making for intermittent preventative treatment in pregnancy, was identified in 79.2% of isolates. Several variants on Pfmdr1, associated with reduced susceptibility to quinolones and lumefantrine, were also identified (Y184F 47.1%; D1246Y 16.0%; N86 98%). Overall, we have presented a low-cost and extendable approach that can provide timely genetic profiles to inform clinical and surveillance activities, especially in settings with abundant low-density infections, seeking malaria elimination.
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Affiliation(s)
- Ashley Osborne
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Jody E Phelan
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Akira Kaneko
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Wataru Kagaya
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Chim Chan
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Mtakai Ngara
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - James Kongere
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
- Centre for Research in Tropical Medicine and Community Development (CRTMCD), Hospital Road Next to Kenyatta National Hospital, Nairobi, Kenya
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Susana Campino
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
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9
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Hutchins H, Bradley J, Pretorius E, Teixeira da Silva E, Vasileva H, Jones RT, Ndiath MO, Dit Massire Soumare H, Mabey D, Nante EJ, Martins C, Logan JG, Slater H, Drakeley C, D'Alessandro U, Rodrigues A, Last AR. Protocol for a cluster randomised placebo-controlled trial of adjunctive ivermectin mass drug administration for malaria control on the Bijagós Archipelago of Guinea-Bissau: the MATAMAL trial. BMJ Open 2023; 13:e072347. [PMID: 37419638 PMCID: PMC10335573 DOI: 10.1136/bmjopen-2023-072347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
INTRODUCTION As malaria declines, innovative tools are required to further reduce transmission and achieve elimination. Mass drug administration (MDA) of artemisinin-based combination therapy (ACT) is capable of reducing malaria transmission where coverage of control interventions is already high, though the impact is short-lived. Combining ACT with ivermectin, an oral endectocide shown to reduce vector survival, may increase its impact, while also treating ivermectin-sensitive co-endemic diseases and minimising the potential impact of ACT resistance in this context. METHODS AND ANALYSIS MATAMAL is a cluster-randomised placebo-controlled trial. The trial is being conducted in 24 clusters on the Bijagós Archipelago, Guinea-Bissau, where the peak prevalence of Plasmodium falciparum (Pf) parasitaemia is approximately 15%. Clusters have been randomly allocated to receive MDA with dihydroartemisinin-piperaquine and either ivermectin or placebo. The primary objective is to determine whether the addition of ivermectin MDA is more effective than dihydroartemisinin-piperaquine MDA alone in reducing the prevalence of P. falciparum parasitaemia, measured during peak transmission season after 2 years of seasonal MDA. Secondary objectives include assessing prevalence after 1 year of MDA; malaria incidence monitored through active and passive surveillance; age-adjusted prevalence of serological markers indicating exposure to P. falciparum and anopheline mosquitoes; vector parous rates, species composition, population density and sporozoite rates; prevalence of vector pyrethroid resistance; prevalence of artemisinin resistance in P. falciparum using genomic markers; ivermectin's impact on co-endemic diseases; coverage estimates; and the safety of combined MDA. ETHICS AND DISSEMINATION The trial has been approved by the London School of Hygiene and Tropical Medicine's Ethics Committee (UK) (19156) and the Comite Nacional de Eticas de Saude (Guinea-Bissau) (084/CNES/INASA/2020). Results will be disseminated in peer-reviewed publications and in discussion with the Bissau-Guinean Ministry of Public Health and participating communities. TRIAL REGISTRATION NUMBER NCT04844905.
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Affiliation(s)
- Harry Hutchins
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - John Bradley
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Elizabeth Pretorius
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK
| | - Eunice Teixeira da Silva
- Projecto de Saúde Bandim, Bissau, Guinea-Bissau
- Ministério de Saúde Pública, Bissau, Guinea-Bissau
| | - Hristina Vasileva
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Robert T Jones
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - David Mabey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Ernesto Jose Nante
- Programa Nacional de Luta Contra o Paludismo, Ministério de Saúde, Bissau, Guinea-Bissau
| | | | - James G Logan
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK
- Arctech Innovation, London, UK
| | | | - Chris Drakeley
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Amabelia Rodrigues
- Projecto de Saúde Bandim, Bissau, Guinea-Bissau
- Ministério de Saúde Pública, Bissau, Guinea-Bissau
| | - Anna R Last
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
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10
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Holzschuh A, Lerch A, Gerlovina I, Fakih BS, Al-Mafazy AWH, Reaves EJ, Ali A, Abbas F, Ali MH, Ali MA, Hetzel MW, Yukich J, Koepfli C. Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania. Nat Commun 2023; 14:3699. [PMID: 37349311 PMCID: PMC10287761 DOI: 10.1038/s41467-023-39417-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Zanzibar has made significant progress toward malaria elimination, but recent stagnation requires novel approaches. We developed a highly multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug-resistance loci, and successfully sequenced 290 samples from five districts covering both main islands. Here, we elucidate fine-scale Plasmodium falciparum population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. Despite high genetic diversity, we observe pronounced fine-scale spatial and temporal parasite genetic structure. Clusters of near-clonal infections on Pemba indicate persistent local transmission with limited parasite importation, presenting an opportunity for local elimination efforts. Furthermore, we observe an admixed parasite population on Unguja and detect a substantial fraction (2.9%) of significantly related infection pairs between Zanzibar and the mainland, suggesting recent importation. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and provides actionable insights for prioritizing malaria elimination efforts.
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Affiliation(s)
- Aurel Holzschuh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA.
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
| | - Anita Lerch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA
| | - Inna Gerlovina
- EPPIcenter Research Program, Division of HIV, ID and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Bakar S Fakih
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | | | - Erik J Reaves
- U.S. Centers for Disease Control and Prevention, President's Malaria Initiative, Dar es Salaam, United Republic of Tanzania
| | - Abdullah Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Faiza Abbas
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Mohamed Haji Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Mohamed Ali Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Manuel W Hetzel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Joshua Yukich
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA.
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11
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Pati SK, Gupta MK, Banerjee A, Shai R, Shivakumara P. Drug discovery through Covid-19 genome sequencing with siamese graph convolutional neural network. MULTIMEDIA TOOLS AND APPLICATIONS 2023; 83:1-35. [PMID: 37362739 PMCID: PMC10170456 DOI: 10.1007/s11042-023-15270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 09/23/2022] [Accepted: 04/06/2023] [Indexed: 06/28/2023]
Abstract
After several waves of COVID-19 led to a massive loss of human life worldwide due to the changes in its variants and the vast explosion. Several researchers proposed neural network-based drug discovery techniques to fight against the pandemic; utilizing neural networks has limitations (Exponential time complexity, Non-Convergence, Mode Collapse, and Diminished Gradient). To overcome those difficulties, this paper proposed a hybrid architecture that will help to repurpose the most appropriate medicines for the treatment of COVID-19. A brief investigation of the sequences has been made to discover the gene density and noncoding proportion through the next gene sequencing. The paper tracks the exceptional locales in the virus DNA sequence as a Drug Target Region (DTR). Then the variable DNA neighborhood search is applied to this DTR to obtain the DNA interaction network to show how the genes are correlated. A drug database has been obtained based on the ontological property of the genomes with advanced D3Similarity so that all the chemical components of the drug database have been identified. Other methods obtained hydroxychloroquine as an effective drug which was rejected by WHO. However, The experimental results show that Remdesivir and Dexamethasone are the most effective drugs, with 97.41 and 97.93%, respectively.
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Affiliation(s)
- Soumen Kumar Pati
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal 741249 India
| | - Manan Kumar Gupta
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal 741249 India
| | - Ayan Banerjee
- Department of Computer Science & Engineering, Jalpaiguri Governmemt Engineering College, Jalpaiguri, West Bengal 735102 India
| | - Rinita Shai
- Department of Mathematics, Behala College, Calcutta University, Kolkata, West Bengal 700060 India
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12
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Acford-Palmer H, Phelan JE, Tadesse FG, Kristan M, Collins E, Spadar A, Walker T, Bousema T, Messenger LA, Clark TG, Campino S. Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay. Sci Rep 2023; 13:5612. [PMID: 37019918 PMCID: PMC10076309 DOI: 10.1038/s41598-023-32336-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/26/2023] [Indexed: 04/07/2023] Open
Abstract
Since its first detection in 2012 in Djibouti, Anopheles stephensi has invaded and established in the Horn of Africa, and more recently Nigeria. The expansion of this vector poses a significant threat to malaria control and elimination efforts. Integrated vector management is the primary strategy used to interrupt disease transmission; however, growing insecticide resistance is threatening to reverse gains in global malaria control. We present a next-generation amplicon-sequencing approach, for high-throughput monitoring of insecticide resistance genes (ace1, GSTe2, vgsc and rdl), species identification and characterization of genetic diversity (its2 and cox1) in An. stephensi. Ninety-five An. stephensi mosquitoes, collected in Ethiopia, were screened, identifying 104 SNPs, including the knock-down mutation L958F (L1014F in Musca domestica), and for the first time in this vector species, the A296S substitution (A301S in Drosophila melanogaster) in the rdl locus. Two other amino acid substitutions (ace1-N177D, GSTe2-V189L) were also identified but have not been previously implicated in insecticide resistance. Genetic diversity in the mitochondrial cox1 gene revealed shared haplotypes between Ethiopian An. stephensi with samples from Pakistan, Sudan, and Djibouti. Overall, we present a reliable, cost-effective strategy using amplicon-sequencing to monitor known insecticide resistance mutations, with the potential to identify new genetic variants, to assist in the high-throughput surveillance of insecticide resistance in An. stephensi populations.
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Affiliation(s)
- Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Fitsum G Tadesse
- Malaria and NTD Directorate, Armauer Hansen Research Institute, ALERT Hospital Compound, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Mojca Kristan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Thomas Walker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Louisa A Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Environmental and Occupational Health, School of Public Health, University of Nevada, Las Vegas, Las Vegas, USA
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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13
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Leski TA, Taitt CR, Colston SM, Bangura U, Holtz A, Yasuda CY, Reynolds ND, Lahai J, Lamin JM, Baio V, Ansumana R, Stenger DA, Vora GJ. Prevalence of malaria resistance-associated mutations in Plasmodium falciparum circulating in 2017–2018, Bo, Sierra Leone. Front Microbiol 2022; 13:1059695. [DOI: 10.3389/fmicb.2022.1059695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
IntroductionIn spite of promising medical, sociological, and engineering strategies and interventions to reduce the burden of disease, malaria remains a source of significant morbidity and mortality, especially among children in sub-Saharan Africa. In particular, progress in the development and administration of chemotherapeutic agents is threatened by evolved resistance to most of the antimalarials currently in use, including artemisinins.MethodsThis study analyzed the prevalence of mutations associated with antimalarial resistance in Plasmodium falciparum from 95 clinical samples collected from individuals with clinically confirmed malaria at a hospital in Bo, Sierra Leone between May 2017 and December 2018. The combination of polymerase chain reaction amplification and subsequent high throughput DNA sequencing was used to determine the presence of resistance-associated mutations in five P. falciparum genes – pfcrt, pfmdr1, pfdhfr, pfdhps and pfkelch13. The geographic origin of parasites was assigned using mitochondrial sequences.ResultsRelevant mutations were detected in the pfcrt (22%), pfmdr1 (>58%), pfdhfr (100%) and pfdhps (>80%) genes while no resistance-associated mutations were found in the pfkelch13 gene. The mitochondrial barcodes were consistent with a West African parasite origin with one exception indicating an isolate imported from East Africa.DiscussionDetection of the pfmdr1 NFSND haplotype in 50% of the samples indicated the increasing prevalence of strains with elevated tolerance to artemeter + lumefantrine (AL) threatening the combination currently used to treat uncomplicated malaria in Sierra Leone. The frequency of mutations linked to resistance to antifolates suggests widespread resistance to the drug combination used for intermittent preventive treatment during pregnancy.
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14
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Zheng S, Liang Y, Wang Z, Liu M, Chen Y, Ai Y, Guo W, Li G, Yuan Y, Xu Z, Wu W, Huang X, Wu Z, Xu Q, Song J, Deng C. Polymorphisms in the K13-Propeller Gene in Artemisinin-Resistant Plasmodium in Mice. Infect Drug Resist 2022; 15:6533-6544. [DOI: 10.2147/idr.s383127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
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15
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Campos M, Phelan J, Spadar A, Collins E, Gonçalves A, Pelloquin B, Vaselli NM, Meiwald A, Clark E, Stica C, Orsborne J, Sylla M, Edi C, Camara D, Mohammed AR, Afrane YA, Kristan M, Walker T, Gomez LF, Messenger LA, Clark TG, Campino S. High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors. Sci Rep 2022; 12:13893. [PMID: 35974073 PMCID: PMC9381500 DOI: 10.1038/s41598-022-17822-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/01/2022] [Indexed: 12/30/2022] Open
Abstract
Surveillance of malaria vector species and the monitoring of insecticide resistance are essential to inform malaria control strategies and support the reduction of infections and disease. Genetic barcoding of mosquitoes is a useful tool to assist the high-throughput surveillance of insecticide resistance, discriminate between sibling species and to detect the presence of Plasmodium infections. In this study, we combined multiplex PCR, custom designed dual indexing, and Illumina next generation sequencing for high throughput single nucleotide polymorphism (SNP)-profiling of four species from the Anopheles (An.) gambiae complex (An. gambiae sensu stricto, An. coluzzii, An. arabiensis and An. melas). By amplifying and sequencing only 14 genetic fragments (500 bp each), we were able to simultaneously detect Plasmodium infection; insecticide resistance-conferring SNPs in ace1, gste2, vgsc and rdl genes; the partial sequences of nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and intergenic spacers (IGS), Short INterspersed Elements (SINE), as well as mitochondrial genes (cox1 and nd4) for species identification and genetic diversity. Using this amplicon sequencing approach with the four selected An. gambiae complex species, we identified a total of 15 non-synonymous mutations in the insecticide target genes, including previously described mutations associated with resistance and two new mutations (F1525L in vgsc and D148E in gste2). Overall, we present a reliable and cost-effective high-throughput panel for surveillance of An. gambiae complex mosquitoes in malaria endemic regions.
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Affiliation(s)
- Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adéritow Gonçalves
- Laboratório de Entomologia Médica, Instituto Nacional de Saúde Pública, Praia, 719, Cabo Verde
| | - Bethanie Pelloquin
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, University of Nagasaki, Nagasaki, Japan
| | - Natasha Marcella Vaselli
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anne Meiwald
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Emma Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Caleb Stica
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James Orsborne
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Moussa Sylla
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland
| | - Constant Edi
- Centre Suisse de Recherches Scientifiques en Cote d'Ivoire, Abidjan, Côte d'Ivoire
| | - Denka Camara
- Programme National de Lutte Contre le Paludisme, Ministère de la Santé, BP. 595, Conakry, Guinea
| | - Abdul Rahim Mohammed
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Yaw Asare Afrane
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Mojca Kristan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Thomas Walker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Louisa A Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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Lyimo BM, Popkin-Hall ZR, Giesbrecht DJ, Mandara CI, Madebe RA, Bakari C, Pereus D, Seth MD, Ngamba RM, Mbwambo RB, MacInnis B, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey J, Ishengoma DS. Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa. Front Cell Infect Microbiol 2022; 12:757844. [PMID: 35909968 PMCID: PMC9326448 DOI: 10.3389/fcimb.2022.757844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent.
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Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | - David J. Giesbrecht
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | | | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Ruth B. Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Bronwyn MacInnis
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute, Boston, MA, United States
| | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha Njau
- World Health Organization, Country Office, Dar es Salaam, Tanzania
| | - Jane A. Cunningham
- Global Malaria Programme, World Health Organization, Headquarters, Geneva, Switzerland
| | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jonathan J. Juliano
- School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey A. Bailey
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
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17
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Genetic Diversity of Plasmodium falciparum and Distribution of Antimalarial Drug Resistance Mutations in Symptomatic and Asymptomatic Infections. Antimicrob Agents Chemother 2022; 66:e0018822. [DOI: 10.1128/aac.00188-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malaria control relies on passive case detection, and this strategy fails detecting asymptomatic infections. In addition, infections in endemic areas harbor multiple parasite genotypes that could affect case management and malaria epidemiology.
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18
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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19
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Kunasol C, Dondorp AM, Batty EM, Nakhonsri V, Sinjanakhom P, Day NPJ, Imwong M. Comparative analysis of targeted next-generation sequencing for Plasmodium falciparum drug resistance markers. Sci Rep 2022; 12:5563. [PMID: 35365711 PMCID: PMC8974807 DOI: 10.1038/s41598-022-09474-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/11/2022] [Indexed: 11/09/2022] Open
Abstract
Well-defined molecular resistance markers are available for a range of antimalarial drugs, and molecular surveillance is increasingly important for monitoring antimalarial drug resistance. Different genotyping platforms are available, but these have not been compared in detail. We compared Targeted Amplicon Deep sequencing (TADs) using Ion Torrent PGM with Illumina MiSeq for the typing of antimalarial drug resistance genes. We developed and validated protocols to type the molecular resistance markers pfcrt, pfdhfr, pfdhps, pfmdr1, pfkelch, and pfcytochrome b, in Plasmodium falciparum for the Ion Torrent PGM and Illumina MiSeq sequencing platforms. With P. falciparum 3D7 and K1 as reference strains, whole blood samples (N = 20) and blood spots from Rapid Diagnostic Test (RDT) samples (N = 5) from patients with uncomplicated falciparum malaria from Ubon Ratchathani were assessed on both platforms and compared for coverage (average reads per amplicon), sequencing accuracy, variant accuracy, false positive rate, false negative rate, and alternative allele detection, with conventional Sanger sequencing as the reference method for SNP calling. Both whole blood and RDT samples could be successfully sequenced using the Ion Torrent PGM and Illumina MiSeq platforms. Coverage of reads per amplicon was higher with Illumina MiSeq (28,886 reads) than with Ion Torrent PGM (1754 reads). In laboratory generated artificial mixed infections, the two platforms could detect the minor allele down to 1% density at 500X coverage. SNPs calls from both platforms were in complete agreement with conventional Sanger sequencing. The methods can be multiplexed with up to 96 samples per run, which reduces cost by 86% compared to conventional Sanger sequencing. Both platforms, using the developed TAD protocols, provide an accurate method for molecular surveillance of drug resistance markers in P. falciparum, but Illumina MiSeq provides higher coverage than Ion Torrent PGM.
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Affiliation(s)
- Chanon Kunasol
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Rd., Bangkok, 10400, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth M Batty
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Vorthunju Nakhonsri
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), 144 Innovation Cluster 2 Building (INC) Tower A, Thailand Science Park, Khlong Nueng, Khlong Luang District, Pathum Thani, Thailand
| | - Puritat Sinjanakhom
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Rd., Bangkok, 10400, Thailand
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Rd., Bangkok, 10400, Thailand.
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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20
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Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance. Malar J 2022; 21:88. [PMID: 35292038 PMCID: PMC8922754 DOI: 10.1186/s12936-022-04122-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/07/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Molecular and genomic surveillance is becoming increasingly used to track malaria control and elimination efforts. Blood samples can be collected as whole blood and stored at - 20 °C until DNA extraction, or as dried blood spots (DBS), circumventing the need for a cold chain. Despite the wide use of either method, systematic comparisons of how the method of blood sample preservation affects the limit of detection (LOD) of molecular diagnosis and the proportion of DNA recovered for downstream applications are lacking. METHODS Extractions based on spin columns, magnetic beads, Tween-Chelex, and direct PCR without prior extraction were compared for whole blood and dried blood spots (DBS) using dilution series of Plasmodium falciparum culture samples. Extracted DNA was quantified by qPCR and droplet digital PCR (ddPCR). RESULTS DNA recovery was 5- to 10-fold higher for whole blood compared to DBS, resulting in a 2- to 3-fold lower LOD for both extraction methods compared to DBS. For whole blood, a magnetic bead-based method resulted in a DNA recovery rate of 88-98% when extracting from whole blood compared to 17-33% for a spin-column based method. For extractions from DBS, the magnetic bead-based method resulted in 8-20% DNA recovery, while the spin-column based method resulted in only 2% DNA recovery. The Tween-Chelex method was superior to other methods with 15-21% DNA recovery, and even more sensitive than extractions from whole blood samples. The direct PCR method was found to have the lowest LOD overall for both, whole blood and DBS. CONCLUSIONS Pronounced differences in LOD and DNA yield need to be considered when comparing prevalence estimates based on molecular methods and when selecting sampling protocols for other molecular surveillance applications.
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21
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Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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22
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Hansson H, Saidi Q, Alifrangis M. Preservation and Extraction of Malaria Parasite DNA from Dried Blood Spots. Methods Mol Biol 2022; 2470:27-36. [PMID: 35881336 DOI: 10.1007/978-1-0716-2189-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molecular studies related to diagnosis and research rely on collection of blood samples and extraction of high-quality DNA. In Africa, where the populations carried 94% of the total burden of cases and deaths due to malaria in 2019, collection of samples is often challenged by remote study areas and lack of a cold chain to transport and store samples. Collection of blood on filter paper is a technique that is less invasive and has simpler requirements regarding training of staff, storage, and transport of samples than collection of venous blood samples. Dried blood spots (DBS) are therefore commonly used in many research projects. However, DNA quality can be affected by duration and conditions of storage. The quality of the DNA for molecular analyses also depends on a DNA extraction methodology that provides high-quality DNA with high purity and yield. Several protocols for DNA extraction have been described, and many comparative studies have analyzed and optimized the different methodologies to find an alternative to the more costly commercial extraction kits. This chapter describes recommendations for storage and preservation of DBS, and a Chelex-based protocol for extraction of DNA from DBS.
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Affiliation(s)
- Helle Hansson
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen N, Denmark.
| | - Queen Saidi
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen N, Denmark
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen N, Denmark
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23
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Diagnosing the drug resistance signature in Plasmodium falciparum: a review from contemporary methods to novel approaches. J Parasit Dis 2021; 45:869-876. [PMID: 34475670 DOI: 10.1007/s12639-020-01333-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022] Open
Abstract
The genome sequence project of the human malaria parasite Plasmodium falciparum reveal variations in the parasite DNA sequence. Most of these variations are single nucleotide polymorphism (SNP). A high frequency of single nucleotide polymorphism (SNP) in the Plasmodium falciparum population is usually a benchmark for anti-malarial resistance which allows parasites to be elusive to the chemotherapeutic agents, vaccine and vector control strategies, resulting in the leading cause of morbidity and mortality globally. The high density of drug resistance signature markers such as pfcrt,pfmdr1, pfdhps, pfdhfr, pfkelch13, pfatpase6 and pfmrp1 in the genome opens up a scope for the study of the genetic basis of this elusive parasite. The precise and prompt diagnosis of resistance strains of parasite plays vital role in malaria elimination program.This review probably shed light on contemporary SNP diagnostic tools used in molecular surveillance of Plasmodium falciparum drug resistance in terms of mechanism, reaction modalities, and development with their virtues and shortcomings.
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24
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Chaturvedi R, Chhibber-Goel J, Verma I, Gopinathan S, Parvez S, Sharma A. Geographical spread and structural basis of sulfadoxine-pyrimethamine drug-resistant malaria parasites. Int J Parasitol 2021; 51:505-525. [PMID: 33775670 DOI: 10.1016/j.ijpara.2020.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 12/22/2022]
Abstract
The global spread of sulfadoxine (Sdx, S) and pyrimethamine (Pyr, P) resistance is attributed to increasing number of mutations in DHPS and DHFR enzymes encoded by malaria parasites. The association between drug resistance mutations and SP efficacy is complex. Here we provide an overview of the geographical spread of SP resistance mutations in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) encoded dhps and dhfr genes. In addition, we have collated the mutation data and mapped it on to the three-dimensional structures of DHPS and DHFR which have become available. Data from genomic databases and 286 studies were collated to provide a comprehensive landscape of mutational data from 2005 to 2019. Our analyses show that the Pyr-resistant double mutations are widespread in Pf/PvDHFR (P. falciparum ∼61% in Asia and the Middle East, and in the Indian sub-continent; in P. vivax ∼33% globally) with triple mutations prevailing in Africa (∼66%) and South America (∼33%). For PfDHPS, triple mutations dominate South America (∼44%), Asia and the Middle East (∼34%) and the Indian sub-continent (∼27%), while single mutations are widespread in Africa (∼45%). Contrary to the status for P. falciparum, Sdx-resistant single point mutations in PvDHPS dominate globally. Alarmingly, highly resistant quintuple and sextuple mutations are rising in Africa (PfDHFR-DHPS) and Asia (Pf/PvDHFR-DHPS). Structural analyses of DHFR and DHPS proteins in complexes with substrates/drugs have revealed that resistance mutations map proximal to Sdx and Pyr binding sites. Thus new studies can focus on discovery of novel inhibitors that target the non-substrate binding grooves in these two validated malaria parasite drug targets.
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Affiliation(s)
- Rini Chaturvedi
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; Department of Toxicology, Jamia Hamdard, New Delhi, India
| | - Jyoti Chhibber-Goel
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ishika Verma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sreehari Gopinathan
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Suhel Parvez
- Department of Toxicology, Jamia Hamdard, New Delhi, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; National Institute of Malaria Research, Dwarka, New Delhi, India.
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25
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Wichers JS, Tonkin-Hill G, Thye T, Krumkamp R, Kreuels B, Strauss J, von Thien H, Scholz JAM, Smedegaard Hansson H, Weisel Jensen R, Turner L, Lorenz FR, Schöllhorn A, Bruchhaus I, Tannich E, Fendel R, Otto TD, Lavstsen T, Gilberger TW, Duffy MF, Bachmann A. Common virulence gene expression in adult first-time infected malaria patients and severe cases. eLife 2021; 10:e69040. [PMID: 33908865 PMCID: PMC8102065 DOI: 10.7554/elife.69040] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/18/2021] [Indexed: 12/22/2022] Open
Abstract
Sequestration of Plasmodium falciparum(P. falciparum)-infected erythrocytes to host endothelium through the parasite-derived P. falciparum erythrocyte membrane protein 1 (PfEMP1) adhesion proteins is central to the development of malaria pathogenesis. PfEMP1 proteins have diversified and expanded to encompass many sequence variants, conferring each parasite a similar array of human endothelial receptor-binding phenotypes. Here, we analyzed RNA-seq profiles of parasites isolated from 32 P. falciparum-infected adult travellers returning to Germany. Patients were categorized into either malaria naive (n = 15) or pre-exposed (n = 17), and into severe (n = 8) or non-severe (n = 24) cases. For differential expression analysis, PfEMP1-encoding var gene transcripts were de novo assembled from RNA-seq data and, in parallel, var-expressed sequence tags were analyzed and used to predict the encoded domain composition of the transcripts. Both approaches showed in concordance that severe malaria was associated with PfEMP1 containing the endothelial protein C receptor (EPCR)-binding CIDRα1 domain, whereas CD36-binding PfEMP1 was linked to non-severe malaria outcomes. First-time infected adults were more likely to develop severe symptoms and tended to be infected for a longer period. Thus, parasites with more pathogenic PfEMP1 variants are more common in patients with a naive immune status, and/or adverse inflammatory host responses to first infections favor the growth of EPCR-binding parasites.
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Affiliation(s)
- J Stephan Wichers
- Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | | | - Thorsten Thye
- Epidemiology and Diagnostics, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Ralf Krumkamp
- Epidemiology and Diagnostics, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-RiemsHamburgGermany
| | - Benno Kreuels
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, GermanyHamburgGermany
- Department of Medicine, College of MedicineBlantyreMalawi
- Department of Medicine, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Jan Strauss
- Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Heidrun von Thien
- Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Judith AM Scholz
- Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
| | | | | | | | | | - Anna Schöllhorn
- Institute of Tropical Medicine, University of TübingenTübingenGermany
| | - Iris Bruchhaus
- Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Egbert Tannich
- Epidemiology and Diagnostics, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-RiemsHamburgGermany
| | - Rolf Fendel
- Institute of Tropical Medicine, University of TübingenTübingenGermany
- German Center for Infection Research (DZIF), Partner Site TübingenTübingenGermany
| | - Thomas D Otto
- Institute of Infection, Immunity and Inflammation, University of GlasgowGlasgowUnited Kingdom
| | | | - Tim W Gilberger
- Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
| | - Michael F Duffy
- Department of Microbiology and Immunology, University of MelbourneMelbourneAustralia
| | - Anna Bachmann
- Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical MedicineHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Biology Department, University of HamburgHamburgGermany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-RiemsHamburgGermany
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26
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Hu F, Zou Q, Li Y, Zhu G, Zhou H, Zhang M, Tian F, Liu Y, Lu F. A PCR-Based Technique to Track the Geographic Origin of Plasmodium falciparum With 23-SNP Barcode Analysis. Front Public Health 2021; 9:649170. [PMID: 33937177 PMCID: PMC8085391 DOI: 10.3389/fpubh.2021.649170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/12/2021] [Indexed: 11/28/2022] Open
Abstract
Increased population movement has increased the risk of reintroducing parasites to elimination areas and also dispersing drug-resistant parasites to new regions. Therefore, reliable and repeatable methods to trace back to the source of imported infections are essential. The recently developed 23-single-nucleotide polymorphism (SNP) barcode from organellar genomes of mitochondrion (mt) and apicoplast (apico) provides a valuable tool to locate the geographic origin of Plasmodium falciparum. This study aims to explore the feasibility of using the 23-SNP barcode for tracking P. falciparum by polymerase chain reaction and sequencing, while providing geographical haplotypes of isolates that originated from Central Africa. Based on 23-SNP barcode analysis, SNPs were found at seven loci; 27 isolates were confirmed to have originated in West Africa, and this study also showed four isolates from Central Africa (Equatorial Guinea, 3; Republic of Congo, 1) that originated in East Africa. This study provides the sequence data from Central Africa and fills 23-SNP barcode data gaps of sample origins.
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Affiliation(s)
- Fengyue Hu
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, School of Medicine, Yangzhou University, Yangzhou, China
| | - Qicheng Zou
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, School of Medicine, Yangzhou University, Yangzhou, China
| | - Yinyue Li
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, School of Medicine, Yangzhou University, Yangzhou, China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Institute of Parasitic Diseases, Wuxi, China
- Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Huayun Zhou
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Institute of Parasitic Diseases, Wuxi, China
- Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Meihua Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Institute of Parasitic Diseases, Wuxi, China
- Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Fang Tian
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, School of Medicine, Yangzhou University, Yangzhou, China
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Institute of Parasitic Diseases, Wuxi, China
- Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Feng Lu
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, School of Medicine, Yangzhou University, Yangzhou, China
- Department of Clinical Laboratory, Affiliated Hospital of Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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27
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Slater L, Betson M, Ashraf S, Sargison N, Chaudhry U. Current methods for the detection of antimalarial drug resistance in Plasmodium parasites infecting humans. Acta Trop 2021; 216:105828. [PMID: 33465353 DOI: 10.1016/j.actatropica.2021.105828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/08/2021] [Accepted: 01/10/2021] [Indexed: 12/19/2022]
Abstract
Malaria is the world's deadliest parasitic disease. Great progress has been made in the fight against malaria over the past two decades, but this has recently begun to plateau, in part due to the global development of antimalarial drug resistance. The ability to track drug resistance is necessary to achieve progress in treatment, disease surveillance and epidemiology, which has prompted the development of advanced diagnostic methods. These new methods provide unprecedented access to information that can help to guide public health policies. Development of new technologies increases the potential for high throughput and reduced costs of diagnostic tests; improving the accessibility of tools to investigate the forces driving disease dynamics and, ultimately, clinical outcomes for malaria patients and public health. This literature review provides a summary of the methods currently available for the detection of antimalarial drug resistance from the examination of patients' blood samples. While no single method is perfect for every application, many of the newly developed methods give promise for more reliable and efficient characterisation of Plasmodium resistance in a range of settings. By exploiting the strengths of the tools available, we can develop a deeper understanding of the evolutionary and spatiotemporal dynamics of this disease. This will translate into more effective disease control, better-informed policy, and more timely and successful treatment for malaria patients.
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Ahouidi A, Oliveira R, Lobo L, Diedhiou C, Mboup S, Nogueira F. Prevalence of pfk13 and pfmdr1 polymorphisms in Bounkiling, Southern Senegal. PLoS One 2021; 16:e0249357. [PMID: 33770151 PMCID: PMC7996989 DOI: 10.1371/journal.pone.0249357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 03/17/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Delayed Plasmodium falciparum parasite clearance has been associated with Single Nucleotide Polymorphisms (SNPs) in the kelch protein propeller domain (coded by pfk13 gene). SNPs in the Plasmodium falciparum multidrug resistance gene 1 (pfmdr1) are associated with multi-drug resistance including the combination artemether-lumefantrine. To our knowledge, this is the first work providing information on the prevalence of k13-propeller and pfmdr1 mutations from Sédhiou, a region in the south of Senegal. METHODS 147 dried blood spots on filter papers were collected from symptomatic patients attending a hospital located in Bounkiling City, Sédhiou Region, Southern Senegal. All samples were collected between 2015-2017 during the malaria transmission season. Specific regions of the gene pfk13 and pfmdr1 were analyzed using PCR amplification and Sanger sequencing. RESULTS The majority of parasites (92.9%) harboured the pfk13 wild type sequence and 6 samples harboured synonymous changes. Regarding pfmdr1, wild-type alleles represented the majority except at codon 184. Overall, prevalence of 86Y was 11.9%, 184F was 56.3% and 1246Y was 1.5%. The mutant allele 184F decreased from 73.7% in 2015 to 40.7% in 2017. The prevalence of haplotype NFD decreased from 71.4% in 2015 to 20.8% in 2017. CONCLUSIONS This study provides the first description of pfk13 and pfmdr1 genes variations in Bounkiling, a city in the Sédhiou Region of Senegal, contributing to closing the gap of information on anti-malaria drug resistance molecular markers in southern Senegal.
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Affiliation(s)
- Ambroise Ahouidi
- Laboratory of Bacteriology and Virology, Hospital Aristide Le Dantec, Dakar, Senegal
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Rafael Oliveira
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisboa, Portugal
| | - Lis Lobo
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisboa, Portugal
| | - Cyrille Diedhiou
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Souleymane Mboup
- Institute for Health Research, Epidemiological Surveillance and Training (IRESSEF), Dakar, Senegal
| | - Fatima Nogueira
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisboa, Portugal
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Ippolito MM, Moser KA, Kabuya JBB, Cunningham C, Juliano JJ. Antimalarial Drug Resistance and Implications for the WHO Global Technical Strategy. CURR EPIDEMIOL REP 2021; 8:46-62. [PMID: 33747712 PMCID: PMC7955901 DOI: 10.1007/s40471-021-00266-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2021] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW Five years have passed since the World Health Organization released its Global Technical Strategy for Malaria (GTS). In that time, progress against malaria has plateaued. This review focuses on the implications of antimalarial drug resistance for the GTS and how interim progress in parasite genomics and antimalarial pharmacology offer a bulwark against it. RECENT FINDINGS For the first time, drug resistance-conferring genes have been identified and validated before their global expansion in malaria parasite populations. More efficient methods for their detection and elaboration have been developed, although low-density infections and polyclonality remain a nuisance to be solved. Clinical trials of alternative regimens for multidrug-resistant malaria have delivered promising results. New agents continue down the development pipeline, while a nascent infrastructure in sub-Saharan Africa for conducting phase I trials and trials of transmission-blocking agents has come to fruition after years of preparation. SUMMARY These and other developments can help inform the GTS as the world looks ahead to the next two decades of its implementation. To remain ahead of the threat that drug resistance poses, wider application of genomic-based surveillance and optimization of existing and forthcoming antimalarial drugs are essential.
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Affiliation(s)
- Matthew M. Ippolito
- Divisions of Clinical Pharmacology and Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- The Johns Hopkins Malaria Research Institute, Johns Hopkins University School of Public Health, Baltimore, MD USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Kara A. Moser
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC USA
| | | | - Clark Cunningham
- School of Medicine, University of North Carolina, Chapel Hill, NC USA
| | - Jonathan J. Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina, CB#7030, 130 Mason Farm Rd, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA
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Schwabl P, Maiguashca Sánchez J, Costales JA, Ocaña-Mayorga S, Segovia M, Carrasco HJ, Hernández C, Ramírez JD, Lewis MD, Grijalva MJ, Llewellyn MS. Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity. PLoS Genet 2020; 16:e1009170. [PMID: 33326438 PMCID: PMC7743988 DOI: 10.1371/journal.pgen.1009170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/02/2020] [Indexed: 12/30/2022] Open
Abstract
Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective 'genome-wide locus sequence typing' (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research.
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Affiliation(s)
- Philipp Schwabl
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Jalil Maiguashca Sánchez
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jaime A. Costales
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Maikell Segovia
- Laboratorio de Biología Molecular de Protozoarios, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Hernán J. Carrasco
- Laboratorio de Biología Molecular de Protozoarios, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Carolina Hernández
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Michael D. Lewis
- London School of Hygiene & Tropical Medicine, Keppel Street, London, United Kingdom
| | - Mario J. Grijalva
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Infectious and Tropical Disease Institute, Biomedical Sciences Department, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States of America
| | - Martin S. Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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Tessema SK, Hathaway NJ, Teyssier NB, Murphy M, Chen A, Aydemir O, Duarte EM, Simone W, Colborn J, Saute F, Crawford E, Aide P, Bailey JA, Greenhouse B. Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome. J Infect Dis 2020; 225:1227-1237. [PMID: 32840625 PMCID: PMC8974853 DOI: 10.1093/infdis/jiaa527] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/24/2020] [Indexed: 01/28/2023] Open
Abstract
Background Targeted next-generation sequencing offers the potential for consistent, deep coverage of information-rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited. Methods A bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, whole-genome sequencing data were generated for the same controls. Results Using publicly available genomes, 4465 high-diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median expected heterozygosity = 0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%), and sensitivity (90% for haplotypes with 5% within sample frequency in dried blood spots with 100 parasites/µL). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic single-nucleotide polymorphism barcodes. Conclusions The bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high-throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.
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Affiliation(s)
- Sofonias K Tessema
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Nicholas J Hathaway
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Noam B Teyssier
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Maxwell Murphy
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Anna Chen
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Elias M Duarte
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Wilson Simone
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - James Colborn
- Clinton Health Access Initiative, Maputo, Mozambique
| | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Bryan Greenhouse
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, California, United States
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Makenga G, Baraka V, Francis F, Nakato S, Gesase S, Mtove G, Madebe R, Kyaruzi E, Minja DT, Lusingu JP, Van geertruyden JP. Effectiveness and safety of intermittent preventive treatment for malaria using either dihydroartemisinin-piperaquine or artesunate-amodiaquine in reducing malaria related morbidities and improving cognitive ability in school-aged children in Tanzania: A study protocol for a controlled randomised trial. Contemp Clin Trials Commun 2020; 17:100546. [PMID: 32382685 PMCID: PMC7201189 DOI: 10.1016/j.conctc.2020.100546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND In high transmission settings, up to 70% of school-aged children harbour malaria parasites without showing any clinical symptoms. Thus, epidemiologically, school aged children act as a substantial reservoir for malaria transmission. Asymptomatic Plasmodium infections induce inflammation leading to iron deficiency anaemia. Consequently, anaemia retards child growth, predisposes children to other diseases and reduces cognitive potential that could lead to poor academic performance. School aged children become increasingly more vulnerable as compared to those aged less than five years due to delayed acquisition of protective immunity. None of the existing Intermittent Preventive Treatment (IPT) strategies is targeting school-aged children. Here, we describe the study protocol of a clinical trial conducted in north-eastern Tanzania to expand the IPT by assessing the effectiveness and safety of two antimalarial drugs, Dihydroartemisinin-Piperaquine (DP) and Artesunate-Amodiaquine (ASAQ) in preventing malaria related morbidities in school-aged children (IPTsc) living in a high endemic area. METHODS/DESIGN The trial is a phase IIIb, individual randomized, open label, controlled trial enrolling school children aged 5-15 years, who receive either DP or ASAQ or control (no drug), using a "balanced block design" with the "standard of care" arm as reference. The interventional treatments are given three times a year for the first year. A second non-interventional year will assess possible rebound effects. Sample size was estimated to 1602 school children (534 per group) from selected primary schools in an area with high malaria endemicity. Thick and thin blood smears (to measure malaria parasitaemia using microscope) were obtained prior to treatment at baseline, and will be obtained again at month 12 and 20 from all participants. Haemoglobin concentration using a haemoglobinometer (HemoCue AB, Sweden) will be measured four monthly. Finger-prick blood (dried bloodspot-DBS) prepared on Whatman 3 M filter paper, will be used for sub-microscopic malaria parasite detection usingPCR, detect markers of drug resistance (using next generation sequencing (NGS) technology), and malaria serological assays (using enzyme-linked immunosorbent assay, ELISA). To determine the benefit of IPTsc on cognitive and psychomotor ability test of everyday attention for children (TEA-Ch) and a '20 m Shuttle run' respectively, will be conducted at baseline, month 12 and 20. The primary endpoints are change in mean haemoglobin from baseline concentration and reduction in clinical malaria incidence at month 12 and 20 of follow up. Mixed design methods are used to assess the acceptability, cost-effectiveness and feasibility of IPTsc as part of a more comprehensive school children health package. Statistical analysis will be in the form of multilevel modelling, owing to repeated measurements and clustering effect of participants. DISCUSSION Malaria intervention using IPTsc strategy may be integrated in the existing national school health programme. However, there is limited systematic evidence to assess the effectiveness and operational feasibility of this approach. School-aged children are easily accessible in most endemic malaria settings. The evidence from this study will guide the implementation of the strategy to provide complementary approach to reduce malaria related morbidity, anaemia and contribute to the overall burden reduction. TRIAL REGISTRATION Clinicaltrials.gov: NCT03640403, registered on Aug 21, 2018, prospectively registered.Url https://www.clinicaltrials.gov/ct2/show/NCT03640403?term=NCT03640403&rank=1.
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Affiliation(s)
- Geofrey Makenga
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Vito Baraka
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Swabra Nakato
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Samwel Gesase
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - George Mtove
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Rashid Madebe
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - Edna Kyaruzi
- College of Education (DUCE), University of Dar Es Salaam, Dar Es Salaam, Tanzania
| | - Daniel T.R. Minja
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
| | - John P.A. Lusingu
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania
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A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria. PLoS Genet 2020; 16:e1008576. [PMID: 32053607 PMCID: PMC7043780 DOI: 10.1371/journal.pgen.1008576] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/26/2020] [Accepted: 12/19/2019] [Indexed: 11/19/2022] Open
Abstract
Although Plasmodium vivax parasites are the predominant cause of malaria outside of sub-Saharan Africa, they not always prioritised by elimination programmes. P. vivax is resilient and poses challenges through its ability to re-emerge from dormancy in the human liver. With observed growing drug-resistance and the increasing reports of life-threatening infections, new tools to inform elimination efforts are needed. In order to halt transmission, we need to better understand the dynamics of transmission, the movement of parasites, and the reservoirs of infection in order to design targeted interventions. The use of molecular genetics and epidemiology for tracking and studying malaria parasite populations has been applied successfully in P. falciparum species and here we sought to develop a molecular genetic tool for P. vivax. By assembling the largest set of P. vivax whole genome sequences (n = 433) spanning 17 countries, and applying a machine learning approach, we created a 71 SNP barcode with high predictive ability to identify geographic origin (91.4%). Further, due to the inclusion of markers for within population variability, the barcode may also distinguish local transmission networks. By using P. vivax data from a low-transmission setting in Malaysia, we demonstrate the potential ability to infer outbreak events. By characterising the barcoding SNP genotypes in P. vivax DNA sourced from UK travellers (n = 132) to ten malaria endemic countries predominantly not used in the barcode construction, we correctly predicted the geographic region of infection origin. Overall, the 71 SNP barcode outperforms previously published genotyping methods and when rolled-out within new portable platforms, is likely to be an invaluable tool for informing targeted interventions towards elimination of this resilient human malaria.
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Yakubu B, Longdet IY, Jen TH, Davou DT, Obishakin E. High-Complexity Plasmodium falciparum Infections, North Central Nigeria, 2015-2018. Emerg Infect Dis 2019; 25:1330-1338. [PMID: 31211682 PMCID: PMC6590735 DOI: 10.3201/eid2507.181614] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The mass migration that occurred during 2009–2013 and after the insurgency in northeastern Nigeria could have increased malaria incidence and Plasmodium falciparum genetic diversity in North Central Nigeria. To determine P. falciparum sequence diversity in this region, we screened 282 samples collected in regional clinics during 2015–2018 for Plasmodium spp. and, with positive samples, determined P. falciparum infection complexity and allele diversity using PCR. Of 34 P. falciparum–positive samples, 39 msp1, 31 msp2, and 13 glurp alleles were detected, and 88% of infections were polyclonal. We identified trimorphic and dimorphic allele combinations in a high percentage of samples, indicative of a high infection complexity in the study population. High genetic diversity is a catalyst for the evolution of drug-resistant alleles. Improved measures (e.g., better drug quality, diagnostics) are needed to control P. falciparum transmission and reduce the potential for the emergence of drug resistance in Nigeria.
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Calarco L, Barratt J, Ellis J. Detecting sequence variants in clinically important protozoan parasites. Int J Parasitol 2019; 50:1-18. [PMID: 31857072 DOI: 10.1016/j.ijpara.2019.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/29/2019] [Accepted: 10/01/2019] [Indexed: 02/06/2023]
Abstract
Second and third generation sequencing methods are crucial for population genetic studies, and variant detection is a popular approach for exploiting this sequence data. While mini- and microsatellites are historically useful markers for studying important Protozoa such as Toxoplasma and Plasmodium spp., detecting non-repetitive variants such as those found in genes can be fundamental to investigating a pathogen's biology. These variants, namely single nucleotide polymorphisms and insertions and deletions, can help elucidate the genetic basis of an organism's pathogenicity, identify selective pressures, and resolve phylogenetic relationships. They also have the added benefit of possessing a comparatively low mutation rate, which contributes to their stability. However, there is a plethora of variant analysis tools with nuanced pipelines and conflicting recommendations for best practise, which can be confounding. This lack of standardisation means that variant analysis requires careful parameter optimisation, an understanding of its limitations, and the availability of high quality data. This review explores the value of variant detection when applied to non-model organisms such as clinically important protozoan pathogens. The limitations of current methods are discussed, including special considerations that require the end-users' attention to ensure that the results generated are reproducible, and the biological conclusions drawn are valid.
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Affiliation(s)
- Larissa Calarco
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia.
| | - Joel Barratt
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - John Ellis
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
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Smith-Aguasca R, Gupta H, Uberegui E, Maquina M, Saute F, Paaijmans KP, Mayor A, Huijben S. Mosquitoes as a feasible sentinel group for anti-malarial resistance surveillance by Next Generation Sequencing of Plasmodium falciparum. Malar J 2019; 18:351. [PMID: 31623623 PMCID: PMC6796398 DOI: 10.1186/s12936-019-2946-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/03/2019] [Indexed: 12/19/2022] Open
Abstract
Background Plasmodium falciparum drug resistance surveillance is key to successful disease control and eradication. Contemporary methods that only allow determination of prevalence of resistance are expensive, time consuming and require ethical considerations. A newer method involving Next Generation Sequencing (NGS) permits obtaining frequency of resistance while allowing to detect minority variants in mixed infections. Here, NGS was tested for P. falciparum resistance marker detection in mosquito samples as a feasible and suitable alternative for molecular resistance surveillance. Anopheles funestus were collected in southern Mozambique using CDC light traps and manual collections. DNA was extracted from either whole mosquito, head-thorax and abdomen separately or pools of five mosquitoes. These samples were screened for P. falciparum and if positive for k13, pfcrt, pfmdr1, pfdhps and pfdhfr mutations related to anti-malarial drug resistance with Sanger sequencing and NGS. Results Among the 846 samples screened for P. falciparum, 122 were positive by 18S ssrDNA qPCR with an infection rate of 23.6%. No mutations were observed for k13 and pfcrt72-76 and almost zero for pfmdr86, but quintuple pfdhfr/pfdhps mutations were near fixation and about half of the isolates contained the pfmdr184F polymorphism. Similar allele frequencies of resistance markers were estimated with NGS in comparison with the prevalence of markers obtained with the gold standard Sanger sequencing. Conclusions Pooled deep sequencing of P. falciparum isolates extracted from mosquitoes is a promising, efficient and cost-effective method to quantify allele frequencies at population level which allows to detect known and unknown markers of resistance in single and mixed infections in a timelier manner. Using mosquitoes as sentinel group and focusing on allele frequency opposed to prevalence, permits active surveillance across a more homogeneous geographical range.
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Affiliation(s)
- Rebecca Smith-Aguasca
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036, Barcelona, Spain.,Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-1701, USA
| | - Himanshu Gupta
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036, Barcelona, Spain
| | - Estefania Uberegui
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036, Barcelona, Spain
| | - Mara Maquina
- Centro de Investigação em Saúde da Manhiça (CISM), 1929, Manhiça, Mozambique
| | - Francisco Saute
- Centro de Investigação em Saúde da Manhiça (CISM), 1929, Manhiça, Mozambique
| | - Krijn P Paaijmans
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036, Barcelona, Spain.,Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-1701, USA.,Centro de Investigação em Saúde da Manhiça (CISM), 1929, Manhiça, Mozambique.,The Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ, 85287-1701, USA
| | - Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036, Barcelona, Spain.,Centro de Investigação em Saúde da Manhiça (CISM), 1929, Manhiça, Mozambique
| | - Silvie Huijben
- ISGlobal, Hospital Clínic - Universitat de Barcelona, 08036, Barcelona, Spain. .,Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-1701, USA.
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Ghansah A, Kamau E, Amambua-Ngwa A, Ishengoma DS, Maiga-Ascofare O, Amenga-Etego L, Deme A, Yavo W, Randrianarivelojosia M, Ochola-Oyier LI, Helegbe GK, Bailey J, Alifrangis M, Djimde A. Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook. Malar J 2019; 18:324. [PMID: 31547818 PMCID: PMC6757370 DOI: 10.1186/s12936-019-2944-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/29/2019] [Indexed: 11/10/2022] Open
Abstract
Targeted Next Generation Sequencing (TNGS) is an efficient and economical Next Generation Sequencing (NGS) platform and the preferred choice when specific genomic regions are of interest. So far, only institutions located in middle and high-income countries have developed and implemented the technology, however, the efficiency and cost savings, as opposed to more traditional sequencing methodologies (e.g. Sanger sequencing) make the approach potentially well suited for resource-constrained regions as well. In April 2018, scientists from the Plasmodium Diversity Network Africa (PDNA) and collaborators met during the 7th Pan African Multilateral Initiative of Malaria (MIM) conference held in Dakar, Senegal to explore the feasibility of applying TNGS to genetic studies and malaria surveillance in Africa. The group of scientists reviewed the current experience with TNGS platforms in sub-Saharan Africa (SSA) and identified potential roles the technology might play to accelerate malaria research, scientific discoveries and improved public health in SSA. Research funding, infrastructure and human resources were highlighted as challenges that will have to be mitigated to enable African scientists to drive the implementation of TNGS in SSA. Current roles of important stakeholders and strategies to strengthen existing networks to effectively harness this powerful technology for malaria research of public health importance were discussed.
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Affiliation(s)
- Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, P. O. Box LG 581, Legon, Ghana
| | - Edwin Kamau
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate -Africa (USAMR D-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Alfred Amambua-Ngwa
- Parasite Molecular Biology, Disease Control and Elimination, Medical Research Council Unit The Gambia at LSHTM, Atlantic Road Fajara, Banjul, The Gambia
| | | | | | - Lucas Amenga-Etego
- West Africa Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Awa Deme
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - William Yavo
- Faculty of Pharmacy, Department of Parasitology and Mycology, Fe ́lix Houphoue ̈t-Boigny University, BPV 34, Abidjan, Côte d'Ivoire.,Malaria Research and Control Centre, National Institute of Public Health, BPV 47, Abidjan, Côte d'Ivoire
| | | | | | | | - Gideon Kofi Helegbe
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, University for Development Studies, P. O. Box TL1883, Tamale, Northern Region, Ghana
| | - Jeffery Bailey
- Warren Alpert Medical School, Brown University, 55 Claverick St, Rm 314B, Providence, RI, 02903, USA
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali. .,Wellcome Trust Sanger Institute, Hinxton, UK.
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Ishengoma DS, Saidi Q, Sibley CH, Roper C, Alifrangis M. Deployment and utilization of next-generation sequencing of Plasmodium falciparum to guide anti-malarial drug policy decisions in sub-Saharan Africa: opportunities and challenges. Malar J 2019; 18:267. [PMID: 31477109 PMCID: PMC6719357 DOI: 10.1186/s12936-019-2853-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/22/2019] [Indexed: 01/13/2023] Open
Abstract
Parasite resistance against anti-malarial drugs is a major threat to the ongoing malaria control and elimination strategies. This is especially true since resistance to the currently recommended artemisinins and partner drugs has been confirmed in South East Asia (SEA) and new anti-malarial compounds are not expected to be available in the near future. Spread from SEA or independent emergence of artemisinin resistance in sub-Saharan Africa (SSA) could reverse the achievements in malaria control that have been attained in the past two decades and derail the ongoing elimination strategies. The current surveillance of clinical efficacy and resistance to anti-malarial drugs is based on efficacy trials to assess the clinical performance of anti-malarials, in vivo/ex vivo assessment of parasite susceptibility to anti-malarials and prevalence of known molecular markers of drug resistance. Whereas clinical efficacy trials are restricted by cost and the complex logistics of patient follow-up, molecular detection of genetic mutations associated with resistance or reduced susceptibility to anti-malarials is by contrast a simple and powerful tool for early detection and monitoring of the prevalence of resistant parasites at population level. This provides needed information before clinical failure emerges, allowing policy makers to anticipate problems and respond. The various methods previously used in detection of molecular markers of drug resistance share some limitations: low-throughput, and high costs per sample and demanding infrastructure. However, recent technological advances including next-generation sequencing (NGS) methodologies promise greatly increased throughput and reduced costs, essentially providing unprecedented potential to address different research and operational questions of relevance for drug policy. This review assesses the potential role of NGS to provide comprehensive information that could guide drug policies in malaria endemic countries and looks at the foreseeable challenges facing the establishment of NGS approaches for routine surveillance of parasite resistance to anti-malarials in SSA.
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Affiliation(s)
- Deus S Ishengoma
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania.
| | - Queen Saidi
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Carol H Sibley
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Cally Roper
- London School of Hygiene & Tropical Medicine, London, UK
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
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Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017. Malar J 2019; 18:252. [PMID: 31349834 PMCID: PMC6660714 DOI: 10.1186/s12936-019-2894-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/23/2019] [Indexed: 01/17/2023] Open
Abstract
Background Large-scale surveillance of molecular markers of anti-malarial drug resistance is an attractive method of resistance monitoring, to complement therapeutic efficacy studies in settings where the latter are logistically challenging. Methods Between 2014 and 2017, this study sampled malaria rapid diagnostic tests (RDTs), used in routine clinical care, from two health centres in Bissau, Guinea-Bissau. In order to obtain epidemiological insights, RDTs were collected together with patient data on age and sex. A subset of positive RDTs from one of the two sites (n = 2184) were tested for Plasmodium DNA content. Those testing positive for Plasmodium DNA by PCR (n = 1390) were used for library preparation, custom designed dual indexing and next generation Miseq targeted sequencing of Plasmodium falciparum genes pfcrt, pfmdr1, pfdhfr, pfdhps and pfk13. Results The study found a high frequency of the pfmdr1 codon 86N at 88–97%, a significant decrease of the pfcrt wildtype CVMNK haplotype and elevated levels of the pfdhfr/pfdhps quadruple mutant ranging from 33 to 51% between 2014 and 2017. No polymorphisms indicating artemisinin tolerance were discovered. The demographic data indicate a large proportion of young adults (66%, interquartile range 11–28 years) presenting with P. falciparum infections. While a total of 5532 gene fragments were successfully analysed on a single Illumina Miseq flow cell, PCR-positivity from the library preparation varied considerably from 13 to 87% for different amplicons. Furthermore, pre-screening of samples for Plasmodium DNA content proved necessary prior to library preparation. Conclusions This study serves as a proof of concept for using leftover clinical material (used RDTs) for large-scale molecular surveillance, encompassing the inherent complications regarding to methodology and analysis when doing so. Factors such as RDT storage prior to DNA extraction and parasitaemia of the infection are likely to have an effect on whether or not parasite DNA can be successfully analysed, and are considered part of the reason the data yield is suboptimal. However, given the necessity of molecular surveillance of anti-malarial resistance in settings where poor infrastructure, poor economy, lack of educated staff and even surges of political instability remain major obstacles to performing clinical studies, obtaining the necessary data from used RDTs, despite suboptimal output, becomes a feasible, affordable and hence a justifiable method. Electronic supplementary material The online version of this article (10.1186/s12936-019-2894-8) contains supplementary material, which is available to authorized users.
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Apinjoh TO, Ouattara A, Titanji VPK, Djimde A, Amambua-Ngwa A. Genetic diversity and drug resistance surveillance of Plasmodium falciparum for malaria elimination: is there an ideal tool for resource-limited sub-Saharan Africa? Malar J 2019; 18:217. [PMID: 31242921 PMCID: PMC6595576 DOI: 10.1186/s12936-019-2844-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
The intensification of malaria control interventions has resulted in its global decline, but it remains a significant public health burden especially in sub-Saharan Africa (sSA). Knowledge on the parasite diversity, its transmission dynamics, mechanisms of adaptation to environmental and interventional pressures could help refine or develop new control and elimination strategies. Critical to this is the accurate assessment of the parasite’s genetic diversity and monitoring of genetic markers of anti-malarial resistance across all susceptible populations. Such wide molecular surveillance will require selected tools and approaches from a variety of ever evolving advancements in technology and the changing epidemiology of malaria. The choice of an effective approach for specific endemic settings remains challenging, particularly for countries in sSA with limited access to advanced technologies. This article examines the current strategies and tools for Plasmodium falciparum genetic diversity typing and resistance monitoring and proposes how the different tools could be employed in resource-poor settings. Advanced approaches enabling targeted deep sequencing is valued as a sensitive method for assessing drug resistance and parasite diversity but remains out of the reach of most laboratories in sSA due to the high cost of development and maintenance. It is, however, feasible to equip a limited number of laboratories as Centres of Excellence in Africa (CEA), which will receive and process samples from a network of peripheral laboratories in the continent. Cheaper, sensitive and portable real-time PCR methods can be used in peripheral laboratories to pre-screen and select samples for targeted deep sequence or genome wide analyses at these CEAs.
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Affiliation(s)
- Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | - Amed Ouattara
- School of Medicine, University of Maryland, College Park, Baltimore, USA
| | - Vincent P K Titanji
- Faculty of Science, Engineering and Technology, Cameroon Christian University, Bali, Cameroon
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
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Dalmat R, Naughton B, Kwan-Gett TS, Slyker J, Stuckey EM. Use cases for genetic epidemiology in malaria elimination. Malar J 2019; 18:163. [PMID: 31064369 PMCID: PMC6503548 DOI: 10.1186/s12936-019-2784-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/22/2019] [Indexed: 12/22/2022] Open
Abstract
Background While traditional epidemiological approaches have supported significant reductions in malaria incidence across many countries, higher resolution information about local and regional malaria epidemiology will be needed to efficiently target interventions for elimination. The application of genetic epidemiological methods for the analysis of parasite genetics has, thus far, primarily been confined to research settings. To illustrate how these technical methods can be used to advance programmatic and operational needs of National Malaria Control Programmes (NMCPs), and accelerate global progress to eradication, this manuscript presents seven use cases for which genetic epidemiology approaches to parasite genetic data are informative to the decision-making of NMCPs. Methods The use cases were developed through a highly iterative process that included an extensive review of the literature and global guidance documents, including the 2017 World Health Organization’s Framework for Malaria Elimination, and collection of stakeholder input. Semi-structured interviews were conducted with programmatic and technical experts about the needs and opportunities for genetic epidemiology methods in malaria elimination. Results Seven use cases were developed: Detect resistance, Assess drug resistance gene flow, Assess transmission intensity, Identify foci, Determine connectivity of parasite populations, Identify imported cases, and Characterize local transmission chains. The method currently used to provide the information sought, population unit for implementation, the pre-conditions for using these approaches, and post-conditions intended as a product of the use case were identified for each use case. Discussion This framework of use cases will prioritize research and development of genetic epidemiology methods that best achieve the goals of NMCPs, and ultimately, inform the establishment of normative policy guidance for their uses. With significant engagement of stakeholders from malaria endemic countries and collaboration with local programme experts to ensure strategic implementation, genetic epidemiological approaches have tremendous potential to accelerate global malaria elimination efforts. Electronic supplementary material The online version of this article (10.1186/s12936-019-2784-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ronit Dalmat
- Department of Epidemiology, University of Washington, Seattle, WA, USA.,Strategic Analysis Research and Training Center, University of Washington, Seattle, WA, USA
| | - Brienna Naughton
- Department of Global Health, University of Washington, Seattle, WA, USA.,Strategic Analysis Research and Training Center, University of Washington, Seattle, WA, USA
| | - Tao Sheng Kwan-Gett
- Department of Health Services, University of Washington, Seattle, WA, USA.,Strategic Analysis Research and Training Center, University of Washington, Seattle, WA, USA
| | - Jennifer Slyker
- Department of Epidemiology, University of Washington, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA.,Strategic Analysis Research and Training Center, University of Washington, Seattle, WA, USA
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42
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Binan L, Drobetsky EA, Costantino S. Exploiting Molecular Barcodes in High-Throughput Cellular Assays. SLAS Technol 2019; 24:298-307. [PMID: 30707854 DOI: 10.1177/2472630318824337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Multiplexing strategies, which greatly increase the number of simultaneously measured parameters in single experiments, are now being widely implemented by both the pharmaceutical industry and academic researchers. Color has long been used to identify biological signals and, when combined with molecular barcodes, has substantially enhanced the depth of multiplexed sample characterization. Moreover, the recent advent of DNA barcodes has led to an explosion of innovative cell sequencing approaches. Novel barcoding strategies also show great promise for encoding spatial information in transcriptomic studies, and for precise assessment of molecular abundance. Both color- and DNA-based barcodes can be conveniently analyzed with either a microscope or a cytometer, or via DNA sequencing. Here we review the basic principles of several technologies used to create barcodes and detail the type of samples that can be identified with such tags.
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Affiliation(s)
- Loïc Binan
- 1 Research Center of the Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,2 Department of Ophthalmology, Université de Montréal, Montreal, QC, Canada
| | - Elliot A Drobetsky
- 1 Research Center of the Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,3 Department of Medicine & Molecular Biology Program, University of Montreal, Montreal, QC, Canada
| | - Santiago Costantino
- 1 Research Center of the Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,2 Department of Ophthalmology, Université de Montréal, Montreal, QC, Canada
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Resistance to Artemisinin Combination Therapies (ACTs): Do Not Forget the Partner Drug! Trop Med Infect Dis 2019; 4:tropicalmed4010026. [PMID: 30717149 PMCID: PMC6473515 DOI: 10.3390/tropicalmed4010026] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 01/30/2023] Open
Abstract
Artemisinin-based combination therapies (ACTs) have become the mainstay for malaria treatment in almost all malaria endemic settings. Artemisinin derivatives are highly potent and fast acting antimalarials; but they have a short half-life and need to be combined with partner drugs with a longer half-life to clear the remaining parasites after a standard 3-day ACT regimen. When introduced, ACTs were highly efficacious and contributed to the steep decrease of malaria over the last decades. However, parasites with decreased susceptibility to artemisinins have emerged in the Greater Mekong Subregion (GMS), followed by ACTs’ failure, due to both decreased susceptibility to artemisinin and partner drug resistance. Therefore, there is an urgent need to strengthen and expand current resistance surveillance systems beyond the GMS to track the emergence or spread of artemisinin resistance. Great attention has been paid to the spread of artemisinin resistance over the last five years, since molecular markers of decreased susceptibility to artemisinin in the GMS have been discovered. However, resistance to partner drugs is critical, as ACTs can still be effective against parasites with decreased susceptibility to artemisinins, when the latter are combined with a highly efficacious partner drug. This review outlines the different mechanisms of resistance and molecular markers associated with resistance to partner drugs for the currently used ACTs. Strategies to improve surveillance and potential solutions to extend the useful therapeutic lifespan of the currently available malaria medicines are proposed.
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Bah SY, Morang'a CM, Kengne-Ouafo JA, Amenga-Etego L, Awandare GA. Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa. Front Genet 2018; 9:575. [PMID: 30538723 PMCID: PMC6277583 DOI: 10.3389/fgene.2018.00575] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023] Open
Abstract
Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.
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Affiliation(s)
- Saikou Y Bah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Vaccine and Immunity Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Collins Misita Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Jonas A Kengne-Ouafo
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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Molecular assays for antimalarial drug resistance surveillance: A target product profile. PLoS One 2018; 13:e0204347. [PMID: 30235327 PMCID: PMC6147503 DOI: 10.1371/journal.pone.0204347] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/05/2018] [Indexed: 11/25/2022] Open
Abstract
Antimalarial drug resistance is a major constraint for malaria control and elimination efforts. Artemisinin-based combination therapy is now the mainstay for malaria treatment. However, delayed parasite clearance following treatment with artemisinin derivatives has now spread in the Greater Mekong Sub region and may emerge or spread to other malaria endemic regions. This spread is of great concern for malaria control programmes, as no alternatives to artemisinin-based combination therapies are expected to be available in the near future. There is a need to strengthen surveillance systems for early detection and response to the antimalarial drug resistance threat. Current surveillance is mainly done through therapeutic efficacy studies; however these studies are complex and both time- and resource-intensive. For multiple common antimalarials, parasite drug resistance has been correlated with specific genetic mutations, and the molecular markers associated with antimalarial drug resistance offer a simple and powerful tool to monitor the emergence and spread of resistant parasites. Different techniques to analyse molecular markers associated with antimalarial drug resistance are available, each with advantages and disadvantages. However, procedures are not adequately harmonized to facilitate comparisons between sites. Here we describe the target product profiles for tests to analyse molecular markers associated with antimalarial drug resistance, discuss how use of current techniques can be standardised, and identify the requirements for an ideal product that would allow malaria endemic countries to provide useful spatial and temporal information on the spread of resistance.
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Boyce RM, Hathaway N, Fulton T, Reyes R, Matte M, Ntaro M, Mulogo E, Waltmann A, Bailey JA, Siedner MJ, Juliano JJ. Reuse of malaria rapid diagnostic tests for amplicon deep sequencing to estimate Plasmodium falciparum transmission intensity in western Uganda. Sci Rep 2018; 8:10159. [PMID: 29977002 PMCID: PMC6033881 DOI: 10.1038/s41598-018-28534-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/25/2018] [Indexed: 01/29/2023] Open
Abstract
Molecular techniques are not routinely employed for malaria surveillance, while cross-sectional, community-based parasite surveys require significant resources. Here, we describe a novel use of malaria rapid diagnostic tests (RDTs) collected at a single facility as source material for sequencing to esimtate malaria transmission intensity across a relatively large catchment area. We extracted Plasmodium falciparum DNA from RDTs, then amplified and sequenced a region of the apical membrane antigen 1 (pfama1) using targeted amplicon deep sequencing. We determined the multiplicity of infection (MOI) for each sample and examined associations with demographic, clinical, and spatial factors. We successfully genotyped 223 of 287 (77.7%) of the samples. We demonstrated an inverse relationship between the MOI and elevation with individuals presenting from the highest elevation villages harboring infections approximately half as complex as those from the lowest (MOI 1.85 vs. 3.51, AOR 0.25, 95% CI 0.09-0.65, p = 0.004). This study demonstrates the feasibility and validity of using routinely-collected RDTs for molecular surveillance of malaria and has real-world utility, especially as the cost of high-throughpout sequencing continues to decline.
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Affiliation(s)
- Ross M Boyce
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.
| | - Nick Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Travis Fulton
- Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA
| | - Raquel Reyes
- Division of General Medicine & Clinical Epidemiology, University of North Carolina at Chapel Hill, 5039 Old Clinic Building, CB 7110, Chapel Hill, 27599, USA
| | - Michael Matte
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Moses Ntaro
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Edgar Mulogo
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Andreea Waltmann
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Mark J Siedner
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, 125 Nashua Street, Suite 722, Boston, 02114, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.,Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA.,Curriculum in Genetics and Microbiology, University of North Carolina at Chapel Hill, 321 South Columbia Street, Chapel Hill, NC, 27516, USA
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47
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Next-Generation Sequencing and Bioinformatics Protocol for Malaria Drug Resistance Marker Surveillance. Antimicrob Agents Chemother 2018; 62:AAC.02474-17. [PMID: 29439965 DOI: 10.1128/aac.02474-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
The recent advances in next-generation sequencing technologies provide a new and effective way of tracking malaria drug-resistant parasites. To take advantage of this technology, an end-to-end Illumina targeted amplicon deep sequencing (TADS) and bioinformatics pipeline for molecular surveillance of drug resistance in P. falciparum, called malaria resistance surveillance (MaRS), was developed. TADS relies on PCR enriching genomic regions, specifically target genes of interest, prior to deep sequencing. MaRS enables researchers to simultaneously collect data on allele frequencies of multiple full-length P. falciparum drug resistance genes (crt, mdr1, k13, dhfr, dhps, and the cytochrome b gene), as well as the mitochondrial genome. Information is captured at the individual patient level for both known and potential new single nucleotide polymorphisms associated with drug resistance. The MaRS pipeline was validated using 245 imported malaria cases that were reported to the Centers for Disease Control and Prevention (CDC). The chloroquine resistance crt CVIET genotype (mutations underlined) was observed in 42% of samples, the highly pyrimethamine-resistant dhpsIRN triple mutant in 92% of samples, and the sulfadoxine resistance dhps mutation SGEAA in 26% of samples. The mdr1 NFSND genotype was found in 40% of samples. With the exception of two cases imported from Cambodia, no artemisinin resistance k13 alleles were identified, and 99% of patients carried parasites susceptible to atovaquone-proguanil. Our goal is to implement MaRS at the CDC for routine surveillance of imported malaria cases in the United States and to aid in the adoption of this system at participating state public health laboratories, as well as by global partners.
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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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Prosser C, Meyer W, Ellis J, Lee R. Evolutionary ARMS Race: Antimalarial Resistance Molecular Surveillance. Trends Parasitol 2018; 34:322-334. [PMID: 29396203 DOI: 10.1016/j.pt.2018.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 01/13/2023]
Abstract
Molecular surveillance of antimalarial drug resistance markers has become an important part of resistance detection and containment. In the current climate of multidrug resistance, including resistance to the global front-line drug artemisinin, there is a consensus to upscale molecular surveillance. The most salient limitation to current surveillance efforts is that skill and infrastructure requirements preclude many regions. This includes sub-Saharan Africa, where Plasmodium falciparum is responsible for most of the global malaria disease burden. New molecular and data technologies have emerged with an emphasis on accessibility. These may allow surveillance to be conducted in broad settings where it is most needed, including at the primary healthcare level in endemic countries, and extending to the village health worker.
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Affiliation(s)
- Christiane Prosser
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia; Westmead Institute for Medical Research, Westmead, NSW, Australia.
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia; Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - John Ellis
- School of Life Sciences, University of Technology Sydney, NSW, Australia
| | - Rogan Lee
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW, Australia
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Abstract
Together, malaria and the neglected tropical diseases (NTDs) kill more than 800,000 people annually, while creating long-term disability in millions more. International support for mass drug administration, bed nets, and other preventive measures has resulted in huge public health gains, while support for translational research is leading to the development of some new neglected disease drugs, diagnostics, and vaccines. However, funding for basic science research has not kept up, such that we are missing opportunities to create a more innovative pipeline of control tools for parasitic and related diseases. There is an urgent need to expand basic science approaches for neglected diseases, especially in the areas of systems biology and immunology; ecology, evolution, and mathematical biology; functional and comparative OMICs; gene editing; expanded use of model organisms; and a new single-cell combinatorial indexing RNA sequencing approach. The world’s poor deserve access to innovation for neglected diseases. It should be considered a fundamental human right.
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Affiliation(s)
- Peter J. Hotez
- Texas Children’s Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Biology, Baylor University, Waco, Texas, United States of America
- * E-mail:
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