title: A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains.
abstract: Malaria is a major public health problem that is actively being addressed in a global eradication campaign. Increased population mobility through international air travel has elevated the risk of re-introducing parasites to elimination areas and dispersing drug-resistant parasites to new regions. A simple genetic marker that quickly and accurately identifies the geographic origin of infections would be a valuable public health tool for locating the source of imported outbreaks. Here we analyse the mitochondrion and apicoplast genomes of 711 Plasmodium falciparum isolates from 14 countries, and find evidence that they are non-recombining and co-inherited. The high degree of linkage produces a panel of relatively few single-nucleotide polymorphisms (SNPs) that is geographically informative. We design a 23-SNP barcode that is highly predictive (~92%) and easily adapted to aid case management in the field and survey parasite migration worldwide.
authors.affiliation: Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Mark D
authors.initials: MD
authors.lastname: Preston
authors.affiliation: Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
authors.forename: Susana
authors.initials: S
authors.lastname: Campino
authors.affiliation: Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Samuel A
authors.initials: SA
authors.lastname: Assefa
authors.affiliation: 1] Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA [2] International Center for Medical Research and Training, Carerra 125, Cali, Colombia.
authors.forename: Diego F
authors.initials: DF
authors.lastname: Echeverry
authors.affiliation: 1] College of Medicine, University of Malawi, Blantyre 3, Malawi [2] Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre 30096 BT3, Malawi [3] Malaria Capacity Development Consortium, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK.
authors.forename: Harold
authors.initials: H
authors.lastname: Ocholla
authors.affiliation: Medical Research Council Laboratories (UK), Fajara PO Box 273, The Gambia.
authors.forename: Alfred
authors.initials: A
authors.lastname: Amambua-Ngwa
authors.affiliation: Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Lindsay B
authors.initials: LB
authors.lastname: Stewart
authors.affiliation: 1] Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK [2] Medical Research Council Laboratories (UK), Fajara PO Box 273, The Gambia.
authors.forename: David J
authors.initials: DJ
authors.lastname: Conway
authors.affiliation: 1] KEMRI-Wellcome Trust Research Programme, Kilifi 80108, Kenya [2] Department of Parasitology, Institute of Tropical Medicine, University of Tübingen, Tübingen 72074, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Borrmann
authors.affiliation: Department of Rural Health, Faculty of Health Sciences, Divine Word University, Madang PO Box 483, Papua New Guinea.
authors.forename: Pascal
authors.initials: P
authors.lastname: Michon
authors.affiliation: Institut de Recherche en Sciences de la Sant, Bobo-Dioulasso BP 545, Burkina Faso.
authors.forename: Issaka
authors.initials: I
authors.lastname: Zongo
authors.affiliation: Institut de Recherche en Sciences de la Sant, Bobo-Dioulasso BP 545, Burkina Faso.
authors.forename: Jean-Bosco
authors.initials: JB
authors.lastname: Ouédraogo
authors.affiliation: 1] Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK [2] Malaria Research and Training Centre, Faculty of Medicine, Pharmacy and Dentistry, University of Bamako, Bamako BP1805, Mali.
authors.forename: Abdoulaye A
authors.initials: AA
authors.lastname: Djimde
authors.affiliation: Malaria Research and Training Centre, Faculty of Medicine, Pharmacy and Dentistry, University of Bamako, Bamako BP1805, Mali.
authors.forename: Ogobara K
authors.initials: OK
authors.lastname: Doumbo
authors.affiliation: 1] Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DS, UK [2] Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand.
authors.forename: Francois
authors.initials: F
authors.lastname: Nosten
authors.affiliation: Pathogen Genomics Laboratory, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
authors.affiliation: Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Teun
authors.initials: T
authors.lastname: Bousema
authors.affiliation: Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Drakeley
authors.affiliation: Malaria Pathogenesis and Human Immunity Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Rick M
authors.initials: RM
authors.lastname: Fairhurst
authors.affiliation: Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Colin J
authors.initials: CJ
authors.lastname: Sutherland
authors.affiliation: Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Cally
authors.initials: C
authors.lastname: Roper
authors.affiliation: Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
authors.forename: Taane G
authors.initials: TG
authors.lastname: Clark
mesh_terms: D018503:Genome, Protozoan; D005843:Geography; D006801:Humans; D016778:Malaria, Falciparum / Q000469:parasitology*; D010802:Phylogeny; D010963:Plasmodium falciparum / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D020641:Polymorphism, Single Nucleotide