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2. Risk Factors of Streptococcus suis Infection in Vietnam. A Case-Control Study

Author

Nghia, HD, Ho, DT, Tu, LETP, Le, TP, Wolbers, M, Thai, CQ, Cao, QT, Hoang, NV, Nguyen, VM, Nga, TV, Tran, VT, Thao, LETP, Phu, NH, Nguyen, HP, Chau, TT, Tran, TH, Sinh, DX, Dinh, XS, Diep, TS, To, SD, Hang, HT, Hoang, TT, Truong, H, Campbell, J, Chau, NV, Nguyen, VV, Chinh, NT, Nguyen, TC, Dung, NV, Nguyen, VD, Hoa, NT, Ngo, TH, Spratt, BG, Hien, TT, Farrar, J, Schultsz, C, Faculteit der Geneeskunde, AII - Amsterdam institute for Infection and Immunity, and Infectious diseases

Subjects
Bacterial Diseases, Male, Veterinary medicine, Non-Clinical Medicine, Streptococcus suis, Epidemiology, MENINGITIS, Sus scrofa, lcsh:Medicine, Disease, Polymerase Chain Reaction, Foodborne Diseases, Infectious Diseases of the Nervous System, Risk Factors, Zoonoses, lcsh:Science, 0303 health sciences, Multidisciplinary, biology, Zoonotic Diseases, Zoonosis, Middle Aged, Hospitals, 3. Good health, PCR, Infectious Diseases, medicine.anatomical_structure, Veterinary Diseases, Vietnam, Carrier State, Science & Technology - Other Topics, Medicine, Female, Bacterial and Foodborne Illness, Meningitis, Research Article, Adult, medicine.medical_specialty, General Science & Technology, Clinical Research Design, Gastroenterology and Hepatology, CHINA, Infectious Disease Epidemiology, 03 medical and health sciences, Age Distribution, Bacterial Meningitis, Streptococcal Infections, Internal medicine, Throat, MD Multidisciplinary, medicine, Animals, Humans, Biology, 030304 developmental biology, Science & Technology, Health Care Policy, Population Biology, MULTIDISCIPLINARY SCIENCES, 030306 microbiology, business.industry, lcsh:R, Case-control study, biology.organism_classification, medicine.disease, Carriage, Case-Control Studies, Multivariate Analysis, Veterinary Science, lcsh:Q, HONG-KONG, Health Statistics, business
Abstract

BACKGROUND: Streptococcus suis infection, an emerging zoonosis, is an increasing public health problem across South East Asia and the most common cause of acute bacterial meningitis in adults in Vietnam. Little is known of the risk factors underlying the disease. METHODS AND FINDINGS: A case-control study with appropriate hospital and matched community controls for each patient was conducted between May 2006 and June 2009. Potential risk factors were assessed using a standardized questionnaire and investigation of throat and rectal S. suis carriage in cases, controls and their pigs, using real-time PCR and culture of swab samples. We recruited 101 cases of S. suis meningitis, 303 hospital controls and 300 community controls. By multivariate analysis, risk factors identified for S. suis infection as compared to either control group included eating "high risk" dishes, including such dishes as undercooked pig blood and pig intestine (OR(1) = 2.22; 95%CI = [1.15-4.28] and OR(2) = 4.44; 95%CI = [2.15-9.15]), occupations related to pigs (OR(1) = 3.84; 95%CI = [1.32-11.11] and OR(2) = 5.52; 95%CI = [1.49-20.39]), and exposures to pigs or pork in the presence of skin injuries (OR(1) = 7.48; 95%CI = [1.97-28.44] and OR(2) = 15.96; 95%CI = [2.97-85.72]). S. suis specific DNA was detected in rectal and throat swabs of 6 patients and was cultured from 2 rectal samples, but was not detected in such samples of 1522 healthy individuals or patients without S. suis infection. CONCLUSIONS: This case control study, the largest prospective epidemiological assessment of this disease, has identified the most important risk factors associated with S. suis bacterial meningitis to be eating 'high risk' dishes popular in parts of Asia, occupational exposure to pigs and pig products, and preparation of pork in the presence of skin lesions. These risk factors can be addressed in public health campaigns aimed at preventing S. suis infection.

Published
2011
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3. Admixture into and within sub-Saharan Africa

Author

Angeliki Kerasidou, J O'Brien, Aaron Vanderwal, Christina Hubbart, Alistair Miles, Catherine L. Moyes, A Nyika, Abier Elzein, J Shelton, Spencer Cca., Anthony Enimil, A Diss, C Hughes, Lucas Amenga-Etego, E Somaskantharajah, Ogobara K. Doumbo, Jacob Almagro Garcia, Valentina D. Mangano, E Drury, Edith Bougama, Angie Green, Busby Gbj., Geraldine M. Clarke, Dominic P. Kwiatkowski, Jiannis Ragoussis, Alphaxard Manjurano, Bronwyn MacInnis, Tobias O. Apinjoh, D Mead, Gareth Maslen, George B.J. Busby, Kirk A. Rockett, Dushyanth Jyothi, C Potter, C Malangone, Muminatou Jallow, I Ragoussis, Ellen M. Leffler, J Rogers, J Stalker, Quang Si Le, J Rodford, D Barnwell, Alieu Mendy, J deVries, Anna E. Jeffreys, Carolyne M. Ndila, E Hilton, Vysaul Nyirongo, The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford [Oxford], The Wellcome Trust Sanger Institute [Cambridge], Medical Research Council Unit The Gambia (MRC), Centre National de Recherche et de Formation sur le Paludisme [Ouagadougou, Burkina Faso] (CNRFP), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Navrongo Health Research Centre [Navrongo, Ghana] (NHRC), Komfo Anokye Teaching Hospital, University of Buéa, KEMRI-Wellcome Trust Research Programme (KWTRP), London School of Hygiene and Tropical Medicine (LSHTM), University of Malawi, University of Bamako [Mali], Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Wellcome Trust, Medical Research Council, Foundation for the National Institutes of Health, Malaria Genomics Epidemiology Network : Vanderwal A, Elzein A, Nyika A, Mendy A, Miles A, Diss A, Kerasidou A, Green A, Jeffreys AE, MacInnis B, Hughes C, Moyes C, Spencer CC, Hubbart C, Malangone C, Potter C, Mead D, Barnwell D, Kwiatkowski DP, Jyothi D, Drury E, Somaskantharajah E, Hilton E, Leffler E, Maslen G, Band G, Busby G, Clarke GM, Ragoussis I, Garcia JA, Rogers J, deVries J, Shelton J, Ragoussis J, Stalker J, Rodford J, O'Brien J, Evans J, Rowlands K, Cook K, Fitzpatrick K, Kivinen K, Small K, Johnson KJ, Rockett KA, Hart L, Manske M, McCreight M, Stevens M, Pirinen M, Hennsman M, Parker M, SanJoaquin M, Seplúveda N, Cook O, Miotto O, Deloukas P, Craik R, Wrigley R, Watson R, Pearson R, Hutton R, Oyola S, Auburn S, Shah S, Le SQ, Molloy S, Bull S, Campino S, Clark TG, Ruano-Rubio V, Cornelius V, Teo YY, Corran P, Silva ND, Risley P, Doyle A, Evans J, Horstmann R, Plowe C, Duffy P, Carucci D, Gottleib M, Tall A, Ly AB, Dolo A, Sakuntabhai A, Puijalon O, Bah A, Camara A, Sadiq A, Khan AA, Jobarteh A, Mendy A, Ebonyi A, Danso B, Taal B, Casals-Pascual C, Conway DJ, Onykwelu E, Sisay-Joof F, Sirugo G, Kanyi H, Njie H, Obu H, Saine H, Sambou I, Abubakar I, Njie J, Fullah J, Jaiteh J, Bojang KA, Jammeh K, Sabally-Ceesay K, Manneh L, Camara L, Yamoah L, Njie M, Njie M, Pinder M, Jallow M, Aiyegbo M, Jasseh M, Keita ML, Saidy-Khan M, Jallow M, Ceesay N, Rasheed O, Ceesay PL, Esangbedo P, Cole-Ceesay R, Olaosebikan R, Correa S, Njie S, Usen S, Dibba Y, Barry A, Djimdé A, Sall AH, Abathina A, Niangaly A, Dembele A, Poudiougou B, Diarra E, Bamba K, Thera MA, Doumbo O, Toure O, Konate S, Sissoko S, Diakite M, Konate AT, Modiano D, Bougouma EC, Bancone G, Ouedraogo IN, Simpore J, Sirima SB, Mangano VD, Troye-Blomberg M, Oduro AR, Hodgson AV, Ghansah A, Nkrumah F, Atuguba F, Koram KA, Amenga-Etego LN, Wilson MD, Ansah NA, Mensah N, Ansah PA, Anyorigiya T, Asoala V, Rogers WO, Akoto AO, Ofori AO, Enimil A, Ansong D, Sambian D, Asafo-Agyei E, Sylverken J, Antwi S, Agbenyega T, Orimadegun AE, Amodu FA, Oni O, Omotade OO, Amodu O, Olaniyan S, Ndi A, Yafi C, Achidi EA, Mbunwe E, Anchang-Kimbi J, Mugri R, Besingi R, Apinjoh TO, Titanji V, Elhassan A, Hussein A, Mohamed H, Elhassan I, Ibrahim M, Kokwaro G, Oluoch T, Macharia A, Ndila CM, Newton C, Opi DH, Kamuya D, Bauni E, Marsh K, Peshu N, Molyneux S, Uyoga S, Williams TN, Marsh V, Manjurano A, Nadjm B, Maxwell C, Drakeley C, Riley E, Mtei F, Mtove G, Wangai H, Reyburn H, Joseph S, Ishengoma D, Lemnge M, Mutabingwa T, Makani J, Cox S, Phiri A, Munthali A, Kachala D, Njiragoma L, Molyneux ME, Moore M, Ntunthama N, Pensulo P, Taylor T, Nyirongo V, Carter R, Fernando D, Karunaweera N, Dewasurendra R, Suriyaphol P, Singhasivanon P, Simmons CP, Thai CQ, Sinh DX, Farrar J, Chuong LV, Phu NH, Hieu NT, Hoang Mai NT, Ngoc Quyen NT, Day N, Dunstan SJ, O'Riordan SE, Hong Chau TT, Hien TT, Allen A, Lin E, Karunajeewa H, Mueller I, Reeder J, Manning L, Laman M, Michon P, Siba P, Allen S, Davis TM., Commission of the European Communities, and Wellcome Trust

Subjects
0301 basic medicine, Population genetics, Gene flow, 0302 clinical medicine, MESH: Genetic Variation, Biology (General), African Continental Ancestry Group, media_common, Genetics, 0303 health sciences, education.field_of_study, Human migration, General Neuroscience, 030305 genetics & heredity, General Medicine, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Geography, Genomics and Evolutionary Biology, MESH: Human Migration, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Medicine, admixture, gene-flow, Research Article, Gene Flow, QH301-705.5, Science, media_common.quotation_subject, Human Migration, Population, Black People, Genomics, Biology, africa, chromosome painting, evolutionary biology, genomics, human, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Genetic variation, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, MESH: Africa South of the Sahara, Allele, education, Africa South of the Sahara, MESH: Gene Flow, MESH: Genome, Human, 030304 developmental biology, Genetic diversity, MESH: Humans, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], General Immunology and Microbiology, business.industry, Genome, Human, Haplotype, Genetic Variation, MESH: Haplotypes, 030104 developmental biology, Genetic epidemiology, Haplotypes, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Agriculture, Evolutionary biology, Africa, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: African Continental Ancestry Group, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, 030217 neurology & neurosurgery, Demography, Diversity (politics)
Abstract

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology. DOI: http://dx.doi.org/10.7554/eLife.15266.001, eLife digest Our genomes contain a record of historical events. This is because when groups of people are separated for generations, the DNA sequence in the two groups’ genomes will change in different ways. Looking at the differences in the genomes of people from the same population can help researchers to understand and reconstruct the historical interactions that brought their ancestors together. The mixing of two populations that were previously separate is known as admixture. Africa as a continent has few written records of its history. This means that it is somewhat unknown which important movements of people in the past generated the populations found in modern-day Africa. Busby et al. have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations. As has been shown in other regions of the world, the new analysis showed that all African populations are the result of historical admixture events. However, Busby et al. could characterize these events to unprecedented level of detail. For example, multiple ethnic groups from The Gambia and Mali all show signs of sharing the same set of ancestors from West Africa, Europe and Asia who mixed around 2000 years ago. Evidence of a migration of people from Central West Africa, known as the Bantu expansion, could also be detected, and was shown to carry genes to the south and east. An important next step will be to now look at the consequences of the observed gene-flow, and ask if it has contributed to spreading beneficial, or detrimental, mutations around Africa. DOI: http://dx.doi.org/10.7554/eLife.15266.002

Published
2016
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