Population-Based Estimate of Melioidosis, Kenya.
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ABSTRACT:
SUBMITTER: Muthumbi EM
PROVIDER: S-EPMC6478202 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Recombination is a fundamental evolutionary force. Therefore the population recombination rate ? plays an important role in the analysis of population genetic data; however, it is notoriously difficult to estimate. This difficulty applies both to the accuracy of commonly used estimates and to the computational efforts required to obtain them. Some particularly popular methods are based on approximations to the likelihood. They require considerably less computational efforts than the full-likelihood method with not much less accuracy. Nevertheless, the computation of these approximate estimates can still be very time consuming, in particular when the sample size is large. Although auxiliary quantities for composite likelihood estimates can be computed in advance and stored in tables, these tables need to be recomputed if either the sample size or the mutation rate ? changes. Here we introduce a new method based on regression combined with boosting as a model selection technique. For large samples, it requires much less computational effort than other approximate methods, while providing similar levels of accuracy. Notably, for a sample of hundreds or thousands of individuals, the estimate of ? using regression can be obtained on a single personal computer within a couple of minutes while other methods may need a couple of days or months (or even years). When the sample size is smaller (n ? 50), our new method remains computational efficient but produces biased estimates. We expect the new estimates to be helpful when analyzing large samples and/or many loci with possibly different mutation rates.
| S-EPMC3664856 | biostudies-literature
Project description:Background & aimsAccurate HCV incidence estimates are critical for monitoring progress towards HCV elimination goals, including an 80% reduction in HCV incidence by 2030. Moreover, incidence estimates can help guide prevention and treatment programming, particularly in the context of the US opioid epidemic.MethodsAn inexpensive, Genedia-based HCV IgG antibody avidity assay was evaluated as a platform to estimate cross-sectional, population-level primary HCV incidence using 1,840 HCV antibody and RNA-positive samples from 875 individuals enrolled in 5 cohort studies in the US and India. Using samples collected <2 years following HCV seroconversion, the mean duration of recent infection (MDRI) was calculated by fitting a maximum likelihood binomial regression model to the probability of appearing recent. Among samples collected ≥2 years post-HCV seroconversion, an individual-level false recent ratio (FRR) was calculated by estimating the probability of appearing recent using an exact binomial test. Factors associated with falsely appearing recent among samples collected ≥2 years post seroconversion were determined by Poisson regression with generalized estimating equations and robust variance estimators.ResultsAn avidity index cut-off of <40% resulted in an MDRI of 113 days (95% CI 84-146), and FRRs of 0.4% (95% CI 0.0-1.2), 4.6% (95% CI 2.2-8.3), and 9.5% (95% CI 3.6-19.6) among individuals who were HIV-uninfected, HIV-infected, and HIV-infected with a CD4 count <200/μl, respectively. No variation was seen between HCV genotypes 1 and 3. In hypothetical scenarios of high-risk settings, a sample size of <1,000 individuals could reliably estimate primary HCV incidence.ConclusionsThis cross-sectional approach can estimate primary HCV incidence for the most common genotypes. This tool can serve as a valuable resource for program and policy planners seeking to monitor and reduce HCV burden.Lay summaryDetermining the rate of new hepatitis C virus (HCV) infections in a population is critical to monitoring progress toward HCV elimination and to appropriately guide control efforts. However, since HCV infections are most often initially asymptomatic, it is difficult to estimate the rate of new HCV infections without following HCV-uninfected people over time and repeatedly testing them for HCV infection. Here, we present a novel, resource-efficient method to estimate the rate of new HCV infections in a population using data from a single timepoint.
| S-EPMC7458132 | biostudies-literature
Project description:Sarcopenia and muscle weakness are responsible for considerable health care expenditure but little is known about these costs in the UK. To address this, we estimated the excess economic burden for individuals with muscle weakness regarding the provision of health and social care among 442 men and women (aged 71-80 years) who participated in the Hertfordshire Cohort Study (UK). Muscle weakness, characterised by low grip strength, was defined according to the Foundation for the National Institutes of Health criteria (men < 26 kg, women < 16 kg). Costs associated with primary care consultations and visits, outpatient and inpatient secondary care, medications, and formal (paid) as well as informal care for each participant were calculated. Mean total costs per person and their corresponding components were compared between groups with and without muscle weakness. Prevalence of muscle weakness in the sample was 11%. Mean total annual costs for participants with muscle weakness were £4592 (CI £2962-£6221), with informal care, inpatient secondary care and primary care accounting for the majority of total costs (38%, 23% and 19%, respectively). For participants without muscle weakness, total annual costs were £1885 (CI £1542-£2228) and their three highest cost categories were informal care (26%), primary care (23%) and formal care (20%). Total excess costs associated with muscle weakness were £2707 per person per year, with informal care costs accounting for 46% of this difference. This results in an estimated annual excess cost in the UK of £2.5 billion.
| S-EPMC6330088 | biostudies-literature
Project description:A melioidosis case cluster of 10 blood culture-positive patients occurred in eastern Sri Lanka after an extreme weather event. Four infections were caused by Burkholderia pseudomallei isolates of sequence type 594. Whole-genome analysis showed that the isolates were genetically diverse and the case cluster was nonclonal.
| S-EPMC8545001 | biostudies-literature
Project description:IntroductionInfluenza disease burden and economic impact data are needed to assess the potential value of interventions. Such information is limited from resource-limited settings. We therefore studied the cost of influenza in Peru.MethodsWe used data collected during June 2009-December 2010 from laboratory-confirmed influenza cases identified through a household cohort in Peru. We determined the self-reported direct and indirect costs of self-treatment, outpatient care, emergency ward care, and hospitalizations through standardized questionnaires. We recorded costs accrued 15-day from illness onset. Direct costs represented medication, consultation, diagnostic fees, and health-related expenses such as transportation and phone calls. Indirect costs represented lost productivity during days of illness by both cases and caregivers. We estimated the annual economic cost and the impact of a case of influenza on a household.ResultsThere were 1321 confirmed influenza cases, of which 47% sought health care. Participants with confirmed influenza illness paid a median of $13 [interquartile range (IQR) 5-26] for self-treatment, $19 (IQR 9-34) for ambulatory non-medical attended illness, $29 (IQR 14-51) for ambulatory medical attended illness, and $171 (IQR 113-258) for hospitalizations. Overall, the projected national cost of an influenza illness was $83-$85 millions. Costs per influenza illness represented 14% of the monthly household income of the lowest income quartile (compared to 3% of the highest quartile).ConclusionInfluenza virus infection causes an important economic burden, particularly among the poorest families and those hospitalized. Prevention strategies such as annual influenza vaccination program targeting SAGE population at risk could reduce the overall economic impact of seasonal influenza.
| S-EPMC4910177 | biostudies-literature
Project description:Chronic hepatitis B infection (CHB) is a significant problem worldwide with around 300 million people infected. Ambitious goals have been set towards its elimination as a public health threat by 2030. However, accurate seroprevalence estimates in many countries are lacking or fail to provide representative population estimates, particularly in the WHO African Region (AFRO). This means the full extent of HBV infection is not well described, leading to a lack of investment in diagnostics, treatment and disease prevention. Clinical trials in the WHO AFRO region have been increasing over time and many test for infectious diseases including hepatitis B virus (HBV) to determine baseline eligibility for participants, however these screening data are not reported. Here we review data from six clinical trials completed at the KEMRI-Wellcome Trust Research Programme between 2016 and 2023 that screened for HBV using hepatitis B surface antigen (HBsAg) as part of the trial exclusion criteria. 1727 people had HBsAg results available, of which 60 tested positive. We generated a crude period HBV prevalence estimate of 3.5% (95% CI 2.6-4.5%), and after standardisation for sex and age to account for the population structure of the Kilifi Health Demographics Surveillance System (KHDSS), the prevalence estimate increased to 5.0% (95% CI 3.4-6.6%). The underrepresentation of women in these trials was striking with 1263/1641 (77%) of participants being male. Alanine aminotransferase (ALT) was significantly higher in the HBsAg positive group but was not outside the normal range. We argue that routine collation and publishing of data from clinical trials could increase precision and geographical representation of global HBV prevalence estimates, enabling evidence-based provision of clinical care pathways and public health interventions to support progress towards global elimination targets. We do acknowledge when using clinical trials data for seroprevalence estimates, that local population structure data is necessary to allow standardisation of results, and the point of care tests used here are limited in sensitivity and specificity.
| S-EPMC10783622 | biostudies-literature
Project description:BackgroundFollowing the contested national elections in 2007, violence occurred throughout Kenya. The objective of this study was to assess the prevalence, characteristics, and health consequences of the 2007-2008 election-related violence.MethodsA cross-sectional, national, population-based cluster survey of 956 Kenyan adults aged ≥ 18 years was conducted in Kenya in September 2011 utilizing a two-stage 90 x 10 cluster sample design and structured interviews and questionnaires. Prevalence of all forms of violence surrounding the 2007 election period, symptoms of major depressive disorder (MDD) and posttraumatic stress disorder (PTSD), and morbidity related to sexual and physical violence were assessed.ResultsOf 956 households surveyed, 916 households participated (response rate 95.8%). Compared to pre-election, election-related sexual violence incidents/1000 persons/year increased over 60-fold (39.1-2370.1; p < .001) with a concurrent 37-fold increase in opportunistic sexual violence (5.2-183.1; p < .001). Physical and other human rights violations increased 80-fold (25.0-1987.1; p < .001) compared to pre-election. Overall, 50% of households reported at least one physical or sexual violation. Households reporting violence were more likely to report violence among female household members (66.6% vs. 58.1%; p = .04) or among the Luhya ethnic group (17.0% vs. 13.8%; p = 0.03). The most common perpetrators of election-related sexual violence were reported to be affiliated with government or political groups (1670.5 incidents/1000 persons per year); the Kalenjin ethnic group for physical violations (54.6%). Over thirty percent of respondents met MDD and PTSD symptom criteria; however, symptoms of MDD (females, 63.3%; males, 36.7%; p = .01) and suicidal ideation (females, 68.5%; males, 31.5%; p = .04) were more common among females. Substance abuse was more common among males (males, 71.2%; females, 28.8%; p < .001).ConclusionOn a national level in Kenya, politically-motivated and opportunistic sexual and physical violations were commonly reported among sampled adults with associated health and mental health outcomes.
| S-EPMC3932993 | biostudies-literature
Project description:The HOXB13 missense mutation G84E (rs138213197) is associated with increased risk of prostate cancer, but the current estimate of increased risk has a wide confidence interval (width of 95% confidence interval (CI) >200-fold) so the point estimate of 20-fold increased risk could be misleading. Population-based family studies can be more informative for estimating risks for rare variants, therefore, we screened for mutations in an Australian population-based series of early-onset prostate cancer cases (probands). We found that 19 of 1,384 (1.4%) probands carried the missense mutation, and of these, six (32%) had a family history of prostate cancer. We tested the 22 relatives of carriers diagnosed from 1998 to 2008 for whom we had a DNA sample, and found seven more carriers and one obligate carrier. The age-specific incidence for carriers was estimated to be, on average, 16.4 (95% CI 2.5-107.2) times that for the population over the time frame when the relatives were at risk prior to baseline. We then estimated the age and birth year- specific cumulative risk of prostate cancer (penetrance) for carriers. For example, the penetrance for an unaffected male carrier born in 1950 was 19% (95% CI 5-46%) at age 60 years, 44% (95% CI 18-74%) at age 70 years and 60% (95% CI 30-85%) at age 80 years. Our study has provided a population-based estimate of the average risk of prostate cancer for HOXB13 missense mutation G84E carriers that can be used to guide clinical practice and research. This study has also shown that the majority of hereditary prostate cancers due to the HOXB13 missense mutation are 'sporadic' in the sense that unselected cases with the missense mutation do not typically report having a family history of prostate cancer.
| S-EPMC3574137 | biostudies-literature
Project description:BackgroundEpidemiological studies of incidence play an essential role in quantifying disease burden, resource planning, and informing public health policies. A variety of measures for estimating cancer incidence have been used. Appropriate reporting of incidence calculations is essential to enable clear interpretation. This review uses colorectal cancer (CRC) as an exemplar to summarize and describe variation in commonly employed incidence measures and evaluate the quality of reporting incidence methods.MethodsWe searched four databases for CRC incidence studies published between January 2010 and May 2020. Two independent reviewers screened all titles and abstracts. Eligible studies were population-based cancer registry studies evaluating CRC incidence. We extracted data on study characteristics and author-defined criteria for assessing the quality of reporting incidence. We used descriptive statistics to summarize the information.ResultsThis review retrieved 165 relevant articles. The age-standardized incidence rate (ASR) (80%) was the most commonly reported incidence measure, and the 2000 U.S. standard population the most commonly used reference population (39%). Slightly more than half (54%) of the studies reported CRC incidence stratified by anatomical site. The quality of reporting incidence methods was suboptimal. Of all included studies: 45 (27%) failed to report the classification system used to define CRC; 63 (38%) did not report CRC codes; and only 20 (12%) documented excluding certain CRC cases from the numerator. Concerning the denominator estimation: 61% of studies failed to state the source of population data; 24 (15%) indicated census years; 10 (6%) reported the method used to estimate yearly population counts; and only 5 (3%) explicitly explained the population size estimation procedure to calculate the overall average incidence rate. Thirty-three (20%) studies reported the confidence interval for incidence, and only 7 (4%) documented methods for dealing with missing data.ConclusionThis review identified variations in incidence calculation and inadequate reporting of methods. We outlined recommendations to optimize incidence estimation and reporting practices. There is a need to establish clear guidelines for incidence reporting to facilitate assessment of the validity and interpretation of reported incidence.
| S-EPMC9118801 | biostudies-literature
Project description:One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is "how many individuals do I need to sample from each population?" This question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5-100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise F(ST) values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.
| S-EPMC3440332 | biostudies-literature