Epidemiology articles within Nature Communications

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  • Article
    | Open Access

    Mendelian randomization (MR) is a method for inferring causal relationships between risk factors and outcomes via associated genetic variants. Here, Burgess et al. develop the contamination mixture method which yields robust MR results in the presence of invalid instrumental variables and groups variants by their effect estimates.

    • Stephen Burgess
    • , Christopher N Foley
    •  & Joanna M. M. Howson

  • Article
    | Open Access

    Spread of antimicrobial-resistant (AR) bacteria is a global concern, but contributing factors remain unclear. Here, authors analyze distribution of AR bacteria in households from three ethnic groups in Tanzania and find that livelihood factors are more strongly associated with AR prevalence than antibiotic use.

    • Murugan Subbiah
    • , Mark A. Caudell
    •  & Douglas R. Call

  • Article
    | Open Access

    Heart failure is a complex syndrome that is associated with many different underlying risk factors. Here, to increase power, the authors jointly analyse cases of heart failure of different aetiologies in a genome-wide association study and identify 11 loci of which ten had not been previously reported.

    • Sonia Shah
    • , Albert Henry
    •  & R. Thomas Lumbers

  • Article
    | Open Access

    Multivariable Mendelian randomization (MR) extends the standard MR framework to consider multiple risk factors in a single model. Here, Zuber et al. propose MR-BMA, a Bayesian variable selection approach to identify the likely causal determinants of a disease from many candidate risk factors as for example high-throughput data sets.

    • Verena Zuber
    • , Johanna Maria Colijn
    •  & Stephen Burgess

  • Article
    | Open Access

    Here, Nelson et al. use amplicon next-generation sequencing of two P. falciparum polymorphic gene regions to investigate the genetic similarity of parasite populations across time and space in a pediatric cohort in Kenya. They identify both micro- and macro-scale structuring of malaria parasites in this high-transmission setting, which could inform future intervention strategies.

    • Cody S. Nelson
    • , Kelsey M. Sumner
    •  & Wendy P. O’Meara

  • Article
    | Open Access

    Relapse, reinfection and recrudescence can all cause recurrent infection after treatment of Plasmodium vivax malaria in endemic areas, but are difficult to distinguish. Here the authors show that they can be differentiated probabilistically and thereby demonstrate the high efficacy of primaquine treatment in preventing relapse.

    • Aimee R. Taylor
    • , James A. Watson
    •  & Nicholas J. White

  • Article
    | Open Access

    Here, the authors investigate the outcome of prevention services scale-up on HIV incidence in a South African large population-based HIV surveillance cohort with over a decade of follow-up and associate a 43% reduction in incidence to earlier male medical circumcision and increased levels of antiretroviral therapy coverage.

    • Alain Vandormael
    • , Adam Akullian
    •  & Frank Tanser

  • Article
    | Open Access

    Cervicovaginal inflammation and human papillomavirus (HPV) are separately associated with increased risk of HIV acquisition. Here the authors longitudinally profile 48 cervicovaginal cytokines and HPV status in a large observational HIV high-risk cohort, and show the same cytokines associate with HPV infection and HIV risk.

    • Lenine J. P. Liebenberg
    • , Lyle R. McKinnon
    •  & Quarraisha Abdool Karim

  • Article
    | Open Access

    From observational studies, alcohol consumption behaviours are known to be correlated in spouses. Here, Howe et al. use partners’ genotypic information in a Mendelian randomization framework and show that a SNP in the ADH1B gene associates with partner’s alcohol consumption, suggesting that alcohol consumption affects mate choice.

    • Laurence J. Howe
    • , Daniel J. Lawson
    •  & Gibran Hemani

  • Article
    | Open Access

    Alterations to the microbiome are now associated with various diseases. Here the authors analyze microbiomes from a large population based cohort and show positive correlations between abundance of Streptococcus spp. and osteoarthritis-related knee pain.

    • Cindy G. Boer
    • , Djawad Radjabzadeh
    •  & Joyce B. J. van Meurs

  • Article
    | Open Access

    Uterine leiomyomata (UL) or fibroids are neoplasms of the uterine smooth muscle associated with heavy menstrual bleeding and other female reproductive tract morbidity. Here, the authors identify eight previously undescribed genetic loci for UL and further look into genetic overlap with heavy menstrual bleeding and endometriosis.

    • C. S. Gallagher
    • , N. Mäkinen
    •  & C. C. Morton

  • Article
    | Open Access

    Here, the authors study the interplay between the microbiome and faecal and blood metabolome, and how the microbiome interacts in the dialogue between these metabolic compartments, identifying a key role for microbial functions and underscoring their relevance for microbiome therapeutic strategies.

    • Alessia Visconti
    • , Caroline I. Le Roy
    •  & Mario Falchi

  • Article
    | Open Access

    Here, Shah et al. perform a meta-analysis and show that people who live or work in agricultural land in Southeast Asia are on average 1.7 times more likely to be infected with a pathogen than controls, suggesting that agricultural land-use increases infectious disease risk.

    • Hiral A. Shah
    • , Paul Huxley
    •  & Kris A. Murray

  • Comment
    | Open Access

    Forecasting is beginning to be integrated into decision-making processes for infectious disease outbreak response. We discuss how technologies could accelerate the adoption of forecasting among public health practitioners, improve epidemic management, save lives, and reduce the economic impact of outbreaks.

    • Dylan B. George
    • , Wendy Taylor
    •  & Nicholas G. Reich

  • Article
    | Open Access

    Gastric acid inhibitors promote experimental allergy in animals, and have been linked to allergy risk in observational human studies. Here the authors show in a country-wide medical record analysis that allergy development risk is doubled in gastric acid inhibitor users, and is higher in women and in older age.

    • Galateja Jordakieva
    • , Michael Kundi
    •  & Erika Jensen-Jarolim

  • Article
    | Open Access

    Higher educational attainment is positively associated with a number of health outcomes. Here, Sanderson et al. use multivariable Mendelian randomisation analysis to test whether the association of educational attainment with smoking behaviour is direct or indirectly mediated via general cognitive ability.

    • Eleanor Sanderson
    • , George Davey Smith
    •  & Marcus R. Munafò

  • Article
    | Open Access

    Dental caries and periodontitis are among the most common medical conditions. Here, the authors report a GWAS for measures of oral health that reveals 47 risk loci for caries, find genetic correlation with 31 other complex traits and use Mendelian randomization analyses to explore potential causal relationships.

    • Dmitry Shungin
    • , Simon Haworth
    •  & Ingegerd Johansson

  • Article
    | Open Access

    Malaria on Bioko Island has been reduced substantially but many acquire malaria while traveling. Here, the authors use survey data, geostatistical and mathematical modeling to investigate malaria prevalence and mobility patterns and find that in some parts of the island a significant fraction of prevalence is attributable to malaria acquired while traveling.

    • Carlos A. Guerra
    • , Su Yun Kang
    •  & David L. Smith

  • Article
    | Open Access

    Birthweight has been found to associate with later-life health outcomes. Here the authors perform a meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, identifying differentially methylated CpGs in neonatal blood that associate with birthweight.

    • Leanne K. Küpers
    • , Claire Monnereau
    •  & Janine F. Felix

  • Article
    | Open Access

    Protective immunity after influenza virus infection is poorly understood. Here, the authors quantify the dynamics of immunity against influenza A virus infections by fitting individual-level mechanistic models to longitudinal serology, and find that the form and dynamics of protection differ between children and adults.

    • Sylvia Ranjeva
    • , Rahul Subramanian
    •  & Sarah Cobey

  • Article
    | Open Access

    Different from GWAS for susceptibility to disease, GWAS for prognosis or survival may be vulnerable to selection bias. Here, Dudbridge et al present an approach to reduce index event bias in simulated and realistic situations, and apply it to GWAS of survival with idiopathic pulmonary fibrosis and Crohn’s disease prognosis.

    • Frank Dudbridge
    • , Richard J. Allen
    •  & Riyaz S. Patel

  • Article
    | Open Access

    The genetic underpinnings of alcohol use disorder and consumption are incompletely understood. Here, the authors perform GWAS for Alcohol Use Disorder (AUD) Identification Test-Consumption scores and AUD diagnosis from electronic health records of 274,424 individuals and identify a total of 18 associated loci.

    • Henry R. Kranzler
    • , Hang Zhou
    •  & Joel Gelernter

  • Article
    | Open Access

    Lack of knowledge of individual infection history hinders understanding of immunological interactions among DENV serotypes. Here, the authors introduce a framework to infer the relationship between unobserved infection history and subsequent infection and disease risk, and find complex dependencies.

    • Tim K. Tsang
    • , Samson L. Ghebremariam
    •  & Yang Yang

  • Article
    | Open Access

    In 2014 Guangzhou, China experienced its worse dengue epidemic on record. To determine the reasons for this the authors model historical data under combinations of four time-varying factors and find that past epidemics were limited by one or more unfavourable conditions, but the 2014 epidemic faced none of these restraints.

    • Rachel J. Oidtman
    • , Shengjie Lai
    •  & Hongjie Yu

  • Article
    | Open Access

    Oral ulcerations are sores of the mucous membrane of the mouth and highly prevalent in the population. Here, in a genome-wide association study, the authors identify 97 loci associated with mouth ulcers highlighting genes involved in T cell-mediated immunity and TH1 responses.

    • Tom Dudding
    • , Simon Haworth
    •  & Nicholas J. Timpson

  • Article
    | Open Access

    Estimates of the burden of malaria often don't take wider, indirect effects on overall health into consideration. Here, Uyoga et al. estimate the indirect impact of malaria on children’s health in a case-control study, using the sickle cell trait as a proxy indicator for an effective intervention.

    • Sophie Uyoga
    • , Alex W. Macharia
    •  & Thomas N. Williams

  • Article
    | Open Access

    Here, the authors explore the relationship between socioeconomic position (SEP) across the life course and inflammation in a multi-cohort study and show that educational attainment is most strongly related to inflammation, suggesting that socioeconomic disadvantage in young adulthood is independently associated with later life inflammation.

    • Eloïse Berger
    • , Raphaële Castagné
    •  & Michelle Kelly-Irving

  • Article
    | Open Access

    Sex-stratified medicine is an important and understudied field. Here the authors investigate in a systematic study of the Danish population differences in incidence, risk, and several aspects of diagnoses between sexes and find differences across all areas of disease.

    • David Westergaard
    • , Pope Moseley
    •  & Søren Brunak

  • Article
    | Open Access

    It is unclear whether the sequence and timing of early life neurodevelopment varies across human populations, excluding the effects of disease or malnutrition. Here, the authors show that children of healthy, urban, educated mothers show very similar development across five geographically diverse populations.

    • José Villar
    • , Michelle Fernandes
    •  & Stephen Kennedy

  • Article
    | Open Access

    Similarities in cancers can be studied to interrogate their etiology. Here, the authors use genome-wide association study summary statistics from six cancer types based on 296,215 cases and 301,319 controls of European ancestry, showing that solid tumours arising from different tissues share a degree of common germline genetic basis.

    • Xia Jiang
    • , Hilary K. Finucane
    •  & Sara Lindström

  • Article
    | Open Access

    Population structure can bias the results of genetic and epidemiological analysis. Here, Haworth et al. report that fine-scale structure is detectable in apparently homogeneous samples such as ALSPAC when measured very precisely, and remains detectable in UK Biobank despite conventional approaches to account for it.

    • Simon Haworth
    • , Ruth Mitchell
    •  & Nicholas J. Timpson

  • Article
    | Open Access

    Real-time disease surveillance can aid mitigation of outbreaks. Here, Lu et al. combine an approach using Google search and EHR data with an approach leveraging spatiotemporal synchronicities of influenza activity across states to improve state-level influenza activity estimates in the US.

    • Fred S. Lu
    • , Mohammad W. Hattab
    •  & Mauricio Santillana

  • Article
    | Open Access

    Relevance of indirect protection of household members of vaccinees is unclear. Here, Tsang et al. quantify the direct and indirect protection of vaccination in a randomized controlled trial and show that benefits of individual vaccination remain important even when other household members are vaccinated.

    • Tim K. Tsang
    • , Vicky J. Fang
    •  & Simon Cauchemez

  • Article
    | Open Access

    While human lifespan is only moderately heritable, “getting old” runs in families. Here, van den Berg et al. study mortality data from three-generation cohorts to define a threshold for longevity and find that individuals have an increasing survival advantage with each additional relative in the top 10% survivors of their birth cohort.

    • Niels van den Berg
    • , Mar Rodríguez-Girondo
    •  & P. Eline Slagboom

  • Article
    | Open Access

    Robust surveillance methods are needed for trachoma control and recrudescence monitoring, but existing methods have limitations. Here, Pinsent et al. analyse data from nine trachoma-endemic populations and provide operational thresholds for interpretation of serological data in low transmission and post-elimination settings.

    • Amy Pinsent
    • , Anthony W. Solomon
    •  & Michael. T. White

  • Article
    | Open Access

    Nutritional experience can have phenotypic consequences in subsequent generations, as is evident from studies in animals and plants. Here, Vågerö et al. find in a large three-generation cohort that access to food in the paternal grandfather associates with all-cause and cancer mortality in male grandchildren.

    • Denny Vågerö
    • , Pia R. Pinger
    •  & Gerard J. van den Berg

  • Article
    | Open Access

    Studying the genetic underpinnings of physical activity and sleep duration can be confounded by self-reporting. Here, Doherty et al. use data from 91,105 UK Biobank participants, whose activity had been monitored for a week by a wearable device, for genome-wide association analysis and identify 14 loci.

    • Aiden Doherty
    • , Karl Smith-Byrne
    •  & Cecilia M. Lindgren

  • Article
    | Open Access

    Typhoid fever is caused by the bacterium Salmonella Typhi. Here, Park et al. analyse the genomes of 249 S. Typhi isolates from 11 sub-Saharan African countries, identifying genes and plasmids associated with antibiotic resistance and showing that multi-drug resistance is highly pervasive in sub-Saharan Africa.

    • Se Eun Park
    • , Duy Thanh Pham
    •  & Stephen Baker

  • Article
    | Open Access

    Treatment-seeking for fever is widely used to estimate treatment of childhood infections, but cross-country comparisons are problematic. Here, the authors estimate the probability of seeking treatment for fever at public facilities across 29 countries by quantifying person-level latent variables.

    • Victor A. Alegana
    • , Joseph Maina
    •  & Andrew J. Tatem

  • Article
    | Open Access

    The decision when to stop an intervention is a critical component of parasite elimination programmes, but reliance on surveillance data alone can be inaccurate. Here, Michael et al. combine parasite transmission model predictions with disease survey data to more reliably determine when interventions can be stopped.

    • Edwin Michael
    • , Morgan E. Smith
    •  & Frank O. Richards

  • Article
    | Open Access

    The basis for associations between lung cancer and major histocompatibility complex genes is not completely understood. Here the authors further consider genetic variation within the MHC region in lung cancer patients and identify independent associations within HLA genes that explain MHC lung cancer associations in Europeans and Asian populations.

    • Aida Ferreiro-Iglesias
    • , Corina Lesseur
    •  & Paul Brennan

  • Article
    | Open Access

    There is increasing urgency to understand the spatiotemporal dynamics of dengue in non-endemic regions. Here, the authors reconstruct likely dengue transmission chains in the city of Porto Alegre based on geo-located cases only, and find that most transmission events occur over short-distances.

    • Giorgio Guzzetta
    • , Cecilia A. Marques-Toledo
    •  & Stefano Merler

  • Article
    | Open Access

    Plasmodium vivax incidence in Malaysia has declined markedly over the last decade, despite evidence of chloroquine resistance. Here, Auburn et al. compare population structure of P. vivax in Malaysia to regions with intermediate and high transmission and identify genetic regions under putative selection.

    • Sarah Auburn
    • , Ernest D. Benavente
    •  & Ric N. Price

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