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bioRxiv2017

Association of pre-pregnancy body mass index with future offspring metabolic profile: findings from three independent European birth cohorts

BackgroundA high proportion of women start pregnancy overweight/obese. According to the developmental overnutrition hypothesis, this could lead offspring to have metabolic disruption throughout their lives, and, thus perpetuate the obesity epidemic across generations. Concerns about this hypothesis are influencing antenatal care. However, it is unknown whether maternal pregnancy adiposity is associated with long-term risk of adverse metabolic profiles in offspring, and if so, whether this association is causal, via intrauterine mechanisms, or explained by shared familial (genetic, lifestyle, socioeconomic) characteristics. We aimed to determine if associations between maternal body mass index (BMI) with offspring systemic metabolite profile are causal via intrauterine mechanisms or familial factors.\n\nMethods and FindingsWe used one and two-stage individual participant data (IPD) metaanalysis, and a negative-control (paternal BMI) to examine the association between maternal prepregnancy BMI and offspring serum metabolome from three European birth cohorts (offspring age at metabolite assessment 16, 17 and 31 years). Circulating metabolites were quantified by high-throughput nuclear magnetic resonance metabolomics. Results from one-stage IPD meta-analysis (N=5327 to 5377 mother-father-offspring trios) showed that increasing maternal and paternal BMI was associated with an adverse cardio-metabolic profile in offspring. We observed strong positive associations with VLDL-lipoproteins, VLDL-C, VLDL-triglycerides, VLDL-diameter, branched/aromatic amino acids, glycoprotein acetyls, and triglycerides, and strong negative associations with HDL-lipoprotein, HDL-diameter, HDL-C, HDL2-C and HDL3-C (all P<0.003). Stronger magnitudes of associations were present for maternal compared with paternal BMI across these associations, however there was no strong statistical evidence for heterogeneity between them (all bootstrap P >0.003, equivalent to 0.05 after accounting for multiple testing). Results were similar in each individual cohort, and in the two-stage analysis. Offspring BMI showed similar patterns of crosssectional association with metabolic profiles as for parental pre-pregnancy BMI associations, but with greater magnitudes. Adjustment of the parent BMI-offspring metabolite associations for offspring BMI suggested the parental associations were largely due to the association of parental BMI measures with offspring BMI.\n\nConclusionOur findings suggest that maternal BMI-offspring metabolome associations are likely to be largely due to shared genetic or familial lifestyle confounding, rather than intrauterine programming mechanisms. They do not support the introduction of measures to reduce maternal BMI in order to prevent adverse offspring cardio-metabolic health.

epidemiology↗

bioRxiv2017

Depression Linked to Frequent Emergency Department Use in Large 10-year Retrospective Analysis of an Integrated Health Care System

We evaluated general patient features related to depression and frequency of Emergency Department (ED) use in a large integrated health care system. Electronic Health Records of 287,281 adults from a general patient population were studied retrospectively over a 10-year period. Patients with a history of depression were more likely to be seen in the ED and at higher frequency than those without. Frequent ED users were more likely to have a history of depression or psychiatric medication orders than infrequent users. ED visits by depression patients and frequent users have highly correlated complaints and discharge diagnoses with other ED users, often related to pain. Poorly managed depression may be playing a role in frequent ED utilization which may be addressed by universal screening for depression, evaluation of barriers to treatment, and other novel interventions to improve care coordination.

epidemiology↗

bioRxiv2017

Do early life non-cognitive skills matter?A systematic review and meta-analysis of early life effects on academic achievement, psychosocial, language and cognitive, and health outcomes

BackgroundSuccess in school and the labour market is due to more than just high intelligence. Associations between traits such as attention, self-regulation, and perseverance in childhood, and later outcomes have been investigated by psychologists, economists, and epidemiologists. Such traits have been loosely referred to as \"non-cognitive\" skills. There has been no attempt to systematically assess the relative importance of non-cognitive skills in early life on later outcomes.\n\nMethodsThe systematic review protocol was registered with the International Prospective Register for Systematic Reviews (PROSPERO, CRD42013006566) in December 2013. We systematically reviewed electronic databases covering psychology, education, health and economics for articles published from database conception until September 2015. Titles and abstracts were screened for eligibility, and from eligible articles data was extracted on study design, sample type and size, age of participants at exposure and outcome, loss to follow up, measurement of exposure and outcome, type of intervention and comparison group, confounding adjustment and results. Where possible we extracted a standardised effect size. We reviewed all studies and rated their evidence quality as better, weak, or poor on the basis of study design and potential for confounding, selection and measurement bias.\n\nResultsWe reviewed 375 studies and provided interpretation of results from 142 (38%) better quality studies comprising randomised controlled trials, quasi-experimental, fixed effects including twin studies, longitudinal and some cross-sectional designs that made reasonable attempts to control confounding. In the academic achievement category outcomes were reported in 78 publications of better quality studies which were consistent with 0.1-0.2 SD effects.\n\nPsychosocial outcomes were reported in 65 better quality studies consistent with effects of 0.3-0.4 SD. For the language and cognitive category there were 42 publications reporting better quality studies consistent with effects of 0.3-0.4 SD. For physical health, results across only eight better quality studies were inconsistent but centred around zero. Analysis of funnel plots consistently showed asymmetric distributions, raising the potential of small study bias which may inflate these observed effects.\n\nConclusionsThe evidence under-pinning the importance of non-cognitive skills for life success is diverse and inconsistent. Nevertheless, there is tentative evidence from published studies that non-cognitive skills associate with modest improvements in academic achievement, psychosocial, and language and cognitive outcomes with effects in the range of 0.2-0.4 SD. The quality of evidence under-pinning this field is generally low with more than a third of studies making little or no attempt to control even the most basic confounding (endogeneity) bias. The evidence could be improved by adequately powering studies, and using procedures and tools that improve the conduct and reporting of RCTs and observational studies. Interventions designed to develop childrens non-cognitive skills could potentially improve opportunities, particularly for disadvantaged children. The inter-disciplinary researchers interested in these skills should take a more rigorous approach to determine which interventions are most effective.

epidemiology↗

bioRxiv2017

Identifying Human Encounters That Shape The Transmission Of Streptococcus Pneumoniae And Other Respiratory Infections

Although patterns of social contacts are believed to be an important determinant of infectious disease transmission, there is little empirical evidence to back this up. Indeed, no previous study has linked individuals risk of respiratory infection with their current pattern of social contacts. We explored whether the frequency of different types of social encounters were associated with current pneumococcal carriage and self-reported acute respiratory symptoms (ARS), though a survey in Uganda in 2014. In total 566 participants were asked about their daily social encounters and about symptoms of ARS in the last two weeks. A nasopharyngeal specimen was also taken from each participant. We found that the frequency of physical (i.e. skin-to-skin), long ([≥]1h) and household contacts - which capture some measure of close (i.e. relatively intimate) contact -, was higher among pneumococcal carriers than non-carriers, and among people with ARS compared to those without, irrespective of their age. With each additional physical encounter the age-adjusted risk of carriage and ARS increased by 6% (95%CI 2-9%) and 9% (1-18%) respectively. In contrast, the number of casual contacts (<5 minutes long) was not associated with either pneumococcal carriage or ARS. A detailed analysis by age of contacts showed that the number of close contacts with young children (<5 years) was particularly higher among older children and adult carriers than non-carriers, while the higher number of contacts among people with ARS was more homogeneous across contacts of all ages. Our findings provide key evidence that the frequency of close interpersonal contact is important for transmission of respiratory infections, but not that of casual contacts. Such results strengthen the evidence for public health measures based upon assumptions of what contacts are important for transmission, and are important to improve disease prevention and control efforts, as well as inform research on infectious disease dynamics.\n\nAuthor summaryAlthough social contacts are an important determinant for the transmission of many infectious diseases it is not clear how the nature and frequency of contacts shape individual infection risk. We explored whether frequency, duration and type of social encounters were associated with someones risk of respiratory infection, using nasopharyngeal carriage (NP) of Streptococcus pneumoniae and acute respiratory symptoms as endpoints. To do so, we conducted a survey in South-West Uganda collecting information on peoples social encounters, respiratory symptoms, and pneumococcal carriage status. Our results show that both pneumococcal carriage and respiratory symptoms are independently associated with a higher number of social encounters, irrespective of a persons age. More specifically, our findings strongly suggest that the frequency of close contacts is important for transmission of respiratory infections, particularly pneumococcal carriage. In contrast, our study showed no association with the frequency of short casual contacts. Those results are essential for both improving disease prevention and control efforts as well as informing research on infectious disease dynamics and transmission models.

epidemiology↗

bioRxiv2017

Heterosubtypic Cross-Reactivity Of HA1 Antibodies To Influenza A, With Emphasis On Nonhuman Subtypes (H5N1, H7N7, H9N2)

Epidemics of influenza A vary greatly in size and age distribution of cases, and this variation i attributed to varying levels of pre-existing immunity. Recent studies have shown that antibody mediated immune responses are more cross-reactive than previously believed, and shape patterns of humoral immunity to influenza A viruses over long periods. Here we quantify antibody responses to the hemagglutinin subunit 1 (HA1) across a range of subtypes using protein microarray analysis of cross-sectional serological surveys carried out in the Netherlanc before and after the A/2009 (H1N1) pandemic. We find significant associations of responses, both within and between subtypes. Interestingly, substantial overall reactivity is observed to HA1 of avian H7N7 and H9N2 viruses. Seroprevalence of H7N7 correlates with antibody titer to A/1968 (H3N2), and is highest in persons born between 1954 and 1969. Seroprevalence of H9N2 is high across all ages, and correlates strongly with A/1957 (H2N2). This correlation is most pronounced in A/2009 (H1N1) infected persons born after 1968 who have never encountered A/1957 (H2N2)-like viruses. We conclude that heterosubtypic antibody crossreactivity, both between human subtypes and between human and nonhuman subtypes, is common in the human population.

epidemiology↗

bioRxiv2017

Validation Of A Novel Molecular Host Response Assay To Diagnose Infection In Hospitalized Patients Admitted To The ICU With Acute Respiratory Failure

PurposeThe discrimination between infectious and non-infectious causes of acute respiratory failure (ARF) in hospitalized patients admitted to the intensive care unit (ICU) is difficult. Using a novel diagnostic test measuring the expression of four RNA biomarkers in blood (SeptiCyte LAB) we aimed to distinguish between infection and inflammation in this setting.\n\nMethodsWe enrolled hospitalized patients with ARF requiring prompt intubation in the ICU from 2011 to 2013. We excluded patients having an established infection diagnosis or an evidently non-infectious reason for intubation. Blood samples were collected upon ICU admission. Test results were categorized into four probability bands (with higher bands indicating a higher probability of infection) and compared with the plausibility of infection as rated by post-hoc assessment using predefined definitions.\n\nResultsOf 467 included patients, 373 (80%) were treated for a suspected infection at admission. Plausibility of infection was classified as ruled-out, undetermined, or confirmed in 41 (11%), 135 (36%), and 197 (53%) of these, respectively. Overall, the pre-test probability of infection was 42%. Test results correlated with the plausibility of infection (Spearmans rho 0.332; p<0.001). After exclusion of undetermined cases, positive predictive values were 29%, 54%, and 76% for probability bands 2, 3, and 4, respectively, whereas the negative predictive value for band 1 was 76%. However, SeptiCyte LAB did not outperform CRP when comparing diagnostic discrimination (AUC 0.731; 95%CI 0.677-0.786 vs. 0.727; 95%CI 0.666-0.788).\n\nConclusionIn a setting of hospitalized patients admitted to the ICU with ARF, the diagnostic value of SeptiCyte LAB seems limited.

epidemiology↗

bioRxiv2017

The role of glycaemic and lipid risk factors in mediating the effect of BMI on coronary heart disease: A two-step, two-sample Mendelian randomization study

BackgroundThe extent to which effects of BMI on coronary heart disease (CHD) are mediated by gylcaemic and lipid risk factors is unclear.\n\nMethodsWe used two-sample Mendelian randomization to determine the causal effect of: (i) BMI on CHD (60,801 cases; 123, 504 controls), type 2 diabetes (T2DM; 34,840 cases; 114,981 controls), fasting glucose (n=46,186), insulin (n=38,238), HbA1c (n=46,368), LDL-cholesterol (LDL-C), HDL-cholesterol (HDL-C) and triglycerides (n=188,577); (ii) glycaemic and lipids traits on CHD; and (iii) extent to which these traits mediated any effect of BMI on CHD.\n\nFindingsOne standard deviation (SD) increase in BMI (~ 4.5kg/m2) increased CHD (odds ratio=1.45 (95% confidence interval (CI): 1.27, 1.66)) and T2DM (1.96 (1.35, 2.83)), and levels of fasting glucose (0.07mmol/l (95%CI 0.03, 0.11)), HbA1c (0.05% (95%CI 0.01, 0.08)), fasting insulin (0.18log pmol/l (95%CI 0.14, 0.22)) and triglycerides (0.20 SD (95%CI 0.14, 0.26)), and lowered levels of HDL-C (-0.23 SD (95%CI -0.32, -0.15)). BMI was not causally related to LDL-C. After accounting for potential pleiotropy, triglycerides, HbA1c and T2DM were causally related to CHD. The BMI-CHD effect reduced from 1.45 to 1.16 (95%CI 0.99, 1.36) and to 1.36 (95%CI 1.19, 1.57) with genetic adjustment for triglycerides or HbA1c respectively, and to 1.09 (95%CI 0.94, 1.27) with adjustment for both.\n\nInterpretationIncreased triglyceride levels and poor glycaemic control appear to mediate much of the effect of BMI on CHD.\n\nFundingEuropean Research Council (669545), European Union (733206), China Medical Board (CMB_2015/16), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico and UK Medical Research Council (MC_UU_12013/5).

epidemiology↗

bioRxiv2017

Sex-associated autosomal DNA methylation differences are wide-spread and stablethroughout childhood

Almost all species show sexual discordance in many traits and diseases. DNA methylation is known to contribute to these differences through well-established mechanisms including X-inactivation in females, imprinting and parent-of-origin effects. Here we investigate sex discordance in DNA methylation throughout childhood in a sample of 700 individuals from the Avon Longitudinal Study of Parents and Children. We show that autosomal sex-discordant methylation is widespread, affecting approximately 12,000 CpG sites at any given age, and stable; at least 8,500 sites are consistently different across all time points and a large proportion discordant in both the fetal and adult brain cortices. Just over 1,000 methylation differences change from birth to late adolescence, 90% of these between birth and around age seven. Sexually discordant CpG sites are enriched in genomic loci containing androgen but not estrogen targets and in genes involved in tissue development but not housekeeping functions. A methylation-derived sex score capturing the variance was calculated at each time point and found to be highly correlated between time points. This score is nominally associated with sex hormone levels in childhood as well as some phenotypes previously linked to sex hormone levels. These findings suggest that sex-discordant autosomal DNA methylation is widespread throughout the genome, likely due to the first androgen exposures in utero. It is then stably maintained from birth to late adolescence. Methylation variation at sex-discordant sites within the sexes, as summarized by the methylation sex score, likely reflects in utero androgen exposure which is relevant to human health.\n\nSignificance StatementAlthough we know that sex hormones are critical for establishing sexual discordance, less is known about how this discordance is achieved and maintained. Here we present evidence for widespread differences in DNA methylation between male and female children. We show that most of these differences are established prenatally, likely due to the first androgen exposures in utero, and then stably maintained throughout childhood, despite extreme fluctuations in the levels of these very same hormones. Our results support a role for DNA methylation as a means for recording and maintaining the effects of exposure to sex hormones and thus to better understand sexual variation and how it is driven by the prenatal environment.

epidemiology↗

bioRxiv2017

Assessing The Efficiency Of Catch-Up Campaigns For Introduction Of Pneumococcal Conjugate Vaccine; A Modelling Study Based On Data From Kilifi, Kenya

BackgroundThe World Health Organisation recommends the use of catch-up campaigns as part of the introduction of pneumococcal conjugate vaccines (PCVs) to accelerate herd protection and hence PCV impact. The value of a catch-up campaign is a trade-off between the costs of vaccinating additional age groups and the benefit of additional direct and indirect protection. There is a paucity of observational data, particularly from low-middle income countries to quantify the optimal breadth of such catch-up campaigns.\n\nMethodsIn Kilifi, Kenya PCV10 was introduced in 2011 using the 3-dose EPI infant schedule and a catch-up campaign in children <5 years old. We fitted a transmission dynamic model to detailed local data including nasopharyngeal carriage and invasive pneumococcal disease (IPD) to infer the marginal impact of the PCV catch-up campaign over hypothetical routine cohort vaccination in that setting, and to estimate the likely impact of alternative campaigns and their dose-efficiency.\n\nResultsWe estimated that, within 10 years of introduction, the catch-up campaign among <5y olds prevents an additional 65 (48 to 84) IPD cases, compared to PCV cohort introduction alone. Vaccination without any catch-up campaign prevented 155 (121 to 193) IPD cases and used 1321 (1058 to 1698) PCV doses per IPD case prevented. In the years after implementation, the PCV programme gradually accrues herd protection and hence its dose-efficiency increases: 10 years after the start of cohort vaccination alone the programme used 910 (732 to 1184) doses per IPD case averted. We estimated that a two-dose catch-up among <1y olds uses an additional 910 (732 to 1184) doses per additional IPD case averted. Furthermore, by extending a single dose catch-up campaign to children 1 to <2y old and subsequently to 2 to <5y olds the campaign uses an additional 412 (296 to 606) and 543 (403 to 763) doses per additional IPD case averted. These results were not sensitive to vaccine coverage, serotype competition, the duration of vaccine protection or the relative protection of infants.\n\nConclusionsWe find that catch-up campaigns are a highly dose-efficient way to accelerate population protection against pneumococcal disease.

epidemiology↗

bioRxiv2017

Diagnostic Prediction Tools For Bacteraemia Caused By 3rd Generation Cephalosporin-Resistant Enterobacteriaceae In Suspected Bacterial Infections: A Nested Case-Control Study

ObjectivesCurrent guidelines for empirical antibiotic treatment poorly predict the presence of 3rd generation cephalosporin resistant Enterobacteriaceae (3GC-R EB) as a cause of infection, thereby increasing unnecessary carbapenem use. We aimed to develop diagnostic scoring systems to better predict the presence of 3GC-R EB as a cause of bacteraemia.\n\nMethodsA retrospective nested case-control study was performed that included patients [≥]18 years in whom blood cultures were obtained and intravenous antibiotics were initiated. Each patient with 3GC-R EB bacteraemia was matched to four control infection episodes within the same hospital, based on blood culture date and onset location (community or hospital). Starting from 32 described clinical risk factors at infection onset, selection strategies were used to derive scoring systems for the probability of community- and hospital-onset 3GC-R EB bacteraemia.\n\nResults3GC-R EB bacteraemia occurred in 90 of 22,506 (0.4%) community-onset and in 82 of 8,110 (1.0%) hospital-onset infections, and these cases were matched to 360 community-onset and 328 hospital-onset control episodes, respectively. The derived community-onset and hospital-onset scoring system consisted of 6 and 9 predictors, respectively, with c-statistics of 0.807 (95% confidence interval 0.756-0.855) and 0.842 (0.794-0.887). With selected score cutoffs, the models identified 3GC-R EB bacteraemia with equal sensitivity as existing guidelines, but reduced the proportion of patients classified as at risk for 3GC-R EB bacteraemia (i.e. eligible for empiric carbapenem therapy) with 40% in patients with community-onset and 49% in patients with hospital-onset infection.\n\nConclusionsThese prediction rules for 3GC-R EB bacteraemia may reduce unnecessary empiric carbapenem use.

epidemiology↗

bioRxiv2017

Physical Activity Phenotyping With Activity Bigrams, And Their Association With BMI

BackgroundAnalysis of physical activity usually focuses on a small number of summary statistics derived from accelerometer recordings: average counts per minute, and the proportion of time spent in moderate-vigorous physical activity or in sedentary behaviour. We show how bigrams, a concept from the field of text mining, can be used to describe how a persons activity levels change across (brief) time points. These variables can, for instance, differentiate between two people with the same time in moderate activity, where one person often stays in moderate activity from one moment to the next and the other does not.\n\nMethodsWe use data on 4810 participants of the Avon Longitudinal Study of Parents and Children (ALSPAC). We generate a profile of bigram frequencies for each participant and test the association of each frequency with body mass index (BMI), as an exemplar.\n\nResultsWe found several associations between changes in bigram frequencies and BMI. For instance, a 1 standard deviation decrease in the number of adjacent minutes in sedentary then moderate activity (or vice versa), with a corresponding increase in the number of adjacent minutes in moderate then vigorous activity (or vice versa), was associated with a 2.36 kg/m2 lower BMI [95% CI: -3.47, -1.26], after accounting for the time spent at sedentary, low, moderate and vigorous activity.\n\nConclusionsActivity bigrams are novel variables that capture how a persons activity changes from one moment to the next. These variables can be used to investigate how sequential activity patterns associate with other traits.\n\nKey MessagesO_LIEpidemiologists typically use only a small number of variables to analyse the association of physical activity with other traits, such as the average counts per minute and the proportion of time spent in moderate-vigorous physical activity or being sedentary.\nC_LIO_LIWe demonstrate how activity bigrams can be used as a set of interpretable variables describing how a persons activity levels change from one moment to the next.\nC_LIO_LITesting the association of activity bigrams with exposures or outcomes can help us gain further understanding of how physical activity is associated with other traits; with further research they might provide evidence for more refined public health advice.\nC_LI

epidemiology↗

bioRxiv2017

DNA Methylation As A Marker For Prenatal Smoke Exposure In Adults

Prenatal cigarette smoke is an environmental stressor that has a profound effect on DNA methylation in the exposed offspring. We have previously shown that some of these effects persist throughout childhood and into adolescence. Of interest is whether these signals persist into adulthood.\n\nWe conducted an analysis to investigate associations between reported maternal smoking in pregnancy and DNA methylation in peripheral blood of women in the Avon Longitudinal Study of Parents and Children (ALSPAC) (n=754; mean age 30 years). We observed associations at 15 CpG sites in 11 gene regions, MYO1G, FRMD4A, CYP1A1, CNTNAP2, ARL4C, AHRR, TIFAB, MDM4, AX748264, DRD1, FTO (FDR < 5%). All but two of these CpG sites have previously been identified in relation to prenatal smoke exposure in the offspring at birth and the majority showed persistent hypermethylation among the offspring of smokers.\n\nWe confirmed that most of these associations were not driven by own smoking and that they were still present 18 years later (N = 656; mean age 48 years). In addition, we replicated findings of a persistent methylation signal related to prenatal smoke exposure in peripheral blood among men in the ALSPAC cohort (N = 230; mean age 53 years). For both participant groups, there was a strong signal of association above that expected by chance at CpG sites previously associated with prenatal smoke exposure in newborns (Wilcoxon rank sum p-value < 2.2 x 10-4). Furthermore, we found that a prenatal smoking score, derived by combining methylation values at these CpG sites, could predict whether the mothers of the ALSPAC women smoked during pregnancy with an AUC 0.69 (95% 0.67, 0.73).

epidemiology↗

bioRxiv2017

Predicting The Impact Of Pneumococcal Conjugate Vaccine Programme Options In Vietnam: A Dynamic Transmission Model

BackgroundCatch-up campaigns (CCs) at the introduction of the pneumococcal conjugate vaccines (PCVs) may accelerate the impact of PCVs. However, limited vaccine supplies may delay vaccine introduction if additional doses are needed for such campaigns. We studied the relative impact of introducing PCV13 with and without catch-up campaign, and the implications of potential introduction delays.\n\nMethodsWe used a dynamic transmission model applied to the population of Nha Trang in Sout central Vietnam. Four strategies were considered: routine vaccination (RV) only, and RV alongside catch-up campaigns among <1y olds (CC1), <2y olds (CC2) and <5y olds (CC5). The model was parameterised with local data on human social contact rates, and was fitted to local carriage data. Post-PCV predictions were based on best estimates of parameters governing post-PCV dynamics, including serotype competition, vaccine efficacy and duration of protection.\n\nResultsOur model predicts elimination of vaccine-type (VT) carriage across all age groups within 10 years of introduction in all scenarios with near-complete replacement by non-VT. Most of the benefit of CCs is predicted to occur within the first 3 years after introduction, with the highest impact in the first year, when IPD incidence is predicted to be 11% (95%CrI 9 - 14%) lower than RV with CC1, 25% (21 - 30 %) lower with CC2 and 38% (32 - 46%) lower with CC5.\n\nHowever, CCs would only prevent more cases of IPD insofar such campaigns do not delay introduction by more than 31 (95%CrI 30 - 32) weeks with CC1, 58 (53 - 63) weeks with CC2 and 89 (78 - 101) weeks for CC5.\n\nConclusionCCs are predicted to offer a substantial additional reduction in pneumococcal disease burden over RV alone, if their implementation does not result in much introduction delay. Those findings are important to help guide vaccine introduction in countries that have not yet introduced PCV, particularly in Asia.

epidemiology↗

bioRxiv2017

Characteristics Of Human Encounters And Social Mixing Patterns Relevant To Infectious Diseases Spread By Close Contact: A Survey In Southwest Uganda

Quantification of human interactions relevant to infectious disease transmission through social contact is central to predict disease dynamics, yet data from low-resource settings remain scarce. We undertook a social contact survey in rural Uganda, whereby participants were asked to recall details about the frequency, type, and socio-demographic characteristics of any conversational encounter that lasted for [≥]5 minutes (henceforth defined as contacts) during the previous day. An estimate of the number of casual contacts (i.e. <5 minutes) was also obtained. A total of 568 individuals were included. On average participants reported having routine contact with 7.2 individuals (range 1-25). Children aged 5-14 years had the highest frequency of contacts and the elderly ([≥]65 years) the fewest (P<0.001). A strong age-assortative pattern was seen, particularly outside the household and increasingly so for contacts occurring further away from home. Adults aged 25-64 years tended to travel more and further than others, and males travelled more frequently than females. Our study provides detailed information on contact patterns and their spatial characteristics in an African setting. It therefore fills an important knowledge gap that will help more accurately predict transmission dynamics and the impact of control strategies in such areas.

epidemiology↗

bioRxiv2017

Impact of rapid susceptibility testing and antibiotic selection strategy on the emergence and spread of antibiotic resistance in gonorrhea

BackgroundIncreasing antibiotic resistance limits treatment options for gonorrhea. We examined the extent to which a hypothetical point-of-care (POC) test reporting antibiotic susceptibility profiles could slow the spread of resistance.\n\nMethodsWe developed a deterministic compartmental model describing gonorrhea transmission in a single-sex population with three antibiotics available to treat infections. Probabilities of resistance emergence on treatment and fitness costs associated with resistance were based on characteristics of ciprofloxacin, azithromycin, and ceftriaxone. We evaluated time to 1% and 5% prevalence of resistant strains among all isolates with: (1) empiric treatment (azithromycin plus ceftriaxone), and treatment guided by POC tests determining susceptibility to (2) ciprofloxacin only and (3) all three antibiotics.\n\nFindingsBased on current gonococcal susceptibility patterns in the United States, the model indicated that continued empiric dual antibiotic treatment without POC testing resulted in >5% of isolates being resistant to both azithromycin and ceftriaxone within 15 years. When either POC test was used in 10% of identified cases, this was delayed by 5 years. The three antibiotic POC test delayed the time to reach 1% prevalence of triply-resistant strains by 6 years, while the ciprofloxacin-only test resulted in no delay. Results were less sensitive to assumptions about fitness costs and test characteristics with increasing test uptake. The main limitation of this study is that we made simplifying assumptions to describe gonorrhea transmission and the emergence and spread of resistance in the population.\n\nConclusionsRapid diagnostics that report antibiotic susceptibility have the potential to extend the usefulness of existing antibiotics for treatment of gonorrhea. Monitoring resistance patterns will be critical with the introduction of such tests.

epidemiology↗

bioRxiv2017

A mathematical model for Dengue and Chikungunya inMexico.

We present a model that incorporates two co-circulating viral diseases, Dengue and Chikungunya, where we allow secondary infections from either of the two diseases. We only consider one vector population, Ae. aegypti since in the Mexican region where we set our scenarios, only this species has been reported to transmit both viruses. We estimate the basic reproduction number and perform numerical simulations for different scenarios where we may observe coexistence of Dengue and Chikungunya; we also compare the results of the model with Dengue and Chikungunya data from Mexico 2015 and we obtain a good model fit. To complete our findings we perform a sensitivity analysis, and calculate the partial rank correlation coefficients (PRCCs) to determine the parameter values influence on the reproduction numbers and predict fate of the diseases.\n\nWe show that R0 for each one of the viruses is highly sensitive to the mosquito biting rate and the transmission rates for both diseases with positive influence and the average lifespan of mosquito along with the human recovery rate with negative influence on both diseases. Our results are consistent with those of previous authors.

epidemiology↗

bioRxiv2017

Role of inter-related population-level host traits in determining pathogen richness and zoonotic risk

Zoonotic diseases are an increasingly important source of human infectious diseases, and host pathogen richness of reservoir host species is a critical driver of spill-over risk. Population-level traits of hosts such as population size, host density and geographic range size have all been shown to be important determinants of host pathogen richness. However, empirically identifying the independent influences of these traits has proven difficult as many of these traits directly depend on each other. Here we develop a mechanistic, metapopulation, susceptible-infected-recovered model to identify the independent influences of these population-level traits on the ability of a newly evolved pathogen to invade and persist in host populations in the presence of an endemic pathogen. We use bats as a case study as they are highly social and an important source of zoonotic disease. We show that larger populations and group sizes had a greater influence on the chances of pathogen invasion and persistence than increased host density or the number of groups. As anthropogenic change affects these traits to different extents, this increased understanding of how traits independently determine pathogen richness will aid in predicting future zoonotic spill-over risk.

epidemiology↗

bioRxiv2017

Antibiotic Resistance Detection Is Essential For Gonorrhoea Point-Of-Care Testing: A Mathematical Modelling Study

Antibiotic resistance is threatening to make gonorrhoea untreatable. Point-of-care (POC) tests that detect resistance promise individually tailored treatment, but might lead to more treatment and higher levels of resistance. We investigate the impact of POC tests on antibiotic-resistant gonorrhoea. We used data about the prevalence and incidence of gonorrhoea in men who have sex with men (MSM) and heterosexual men and women (HMW) to calibrate a mathematical gonorrhoea transmission model. With this model, we simulated four clinical pathways for the diagnosis and treatment of gonorrhoea: POC test with (POC + R) and without (POC - R) resistance detection, culture, and nucleic acid amplification tests (NAATs). We calculated the proportion of resistant infections, cases averted after 5 years, and compared how fast resistant infections spread in the populations. The proportion of resistant infections after 30 years is lowest for POC + R (median MSM: 0.18%, HMW: 0.12%), and increases for culture (MSM: 1.19%, HWM: 0.13%), NAAT (MSM: 100%, HMW: 99.27%), and POC - R (MSM: 100%, HMW: 99.73%). NAAT leads to 36 366 (median MSM) and 1 228 (median HMW) observed cases after 5 years. When compared with NAAT, POC + R results in most cases averted after 5 years (median MSM: 3 353, HMW: 118 per 100 000 persons). POC tests that detect resistance with intermediate sensitivity slow down resistance spread more than NAAT. POC tests with very high sensitivity for the detection of resistance are needed to slow down resistance spread more than using culture. POC with high sensitivity to detect antibiotic resistance can keep gonorrhoea treatable longer than culture or NAAT. POC tests without reliable resistance detection should not be introduced because they can accelerate the spread of antibiotic-resistant gonorrhoea.

epidemiology↗