title: Population genetic analyses of Helicobacter pylori isolates from Gambian adults and children.
abstract: The gastric pathogen Helicobacter pylori is one of the most genetically diverse of bacterial species. Much of its diversity stems from frequent mutation and recombination, preferential transmission within families and local communities, and selection during persistent gastric mucosal infection. MLST of seven housekeeping genes had identified multiple distinct H. pylori populations, including three from Africa: hpNEAfrica, hpAfrica1 and hpAfrica2, which consists of three subpopulations (hspWAfrica, hspCAfrica and hspSAfrica). Most detailed H. pylori population analyses have used strains from non-African countries, despite Africa's high importance in the emergence and evolution of humans and their pathogens. Our concatenated sequences from seven H. pylori housekeeping genes from 44 Gambian patients (MLST) identified 42 distinct sequence types (or haplotypes), and no clustering with age or disease. STRUCTURE analysis of the sequence data indicated that Gambian H. pylori strains belong to the hspWAfrica subpopulation of hpAfrica1, in accord with Gambia's West African location. Despite Gambia's history of invasion and colonisation by Europeans and North Africans during the last millennium, no traces of Ancestral Europe1 (AE1) population carried by those people were found. Instead, admixture of 17% from Ancestral Europe2 (AE2) was detected in Gambian strains; this population predominates in Nilo-Saharan speakers of North-East Africa, and might have been derived from admixture of hpNEAfrica strains these people carried when they migrated across the Sahara during the Holocene humid period 6,000-9,000 years ago. Alternatively, shared AE2 ancestry might have resulted from shared ancestral polymorphisms already present in the common ancestor of sister populations hpAfrica1 and hpNEAfrica.
authors.affiliation: Vaccinology, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Ousman
authors.initials: O
authors.lastname: Secka
authors.affiliation: Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Vienna, Austria.
authors.forename: Yoshan
authors.initials: Y
authors.lastname: Moodley
authors.affiliation: Vaccinology, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Martin
authors.initials: M
authors.lastname: Antonio
authors.affiliation: Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Medicine, University of California San Diego, La Jolla, California, United States of America.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Berg
authors.affiliation: Clinical Services Department, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Mary
authors.initials: M
authors.lastname: Tapgun
authors.affiliation: Clinical Services Department, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Robert
authors.initials: R
authors.lastname: Walton
authors.affiliation: Vaccinology, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Archibald
authors.initials: A
authors.lastname: Worwui
authors.affiliation: Clinical Services Department, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Vivat
authors.initials: V
authors.lastname: Thomas
authors.affiliation: Clinical Services Department, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Tumani
authors.initials: T
authors.lastname: Corrah
authors.affiliation: Department of Paediatric Gastroenterology Great North Children's Hospital, Royal Victoria Infirmary, Newcastle upon Tyne, Tyne and Wear, United Kingdom.
authors.forename: Julian E
authors.initials: JE
authors.lastname: Thomas
authors.affiliation: Bacterial Diseases Programme, Medical Research Council Unit, Fajara, The Gambia.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Adegbola
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D005075:Biological Evolution; D002648:Child; D002675:Child, Preschool; D005260:Female; D005714:Gambia; D005753:Gastric Mucosa / Q000382:microbiology; D005798:Genes, Bacterial; D020043:Genes, Essential; D014644:Genetic Variation; D006239:Haplotypes; D016481:Helicobacter Infections / Q000208:ethnology / Q000382:microbiology; D016480:Helicobacter pylori / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008875:Middle Aged; D058885:Multilocus Sequence Typing; D055815:Young Adult