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A risk stratification approach for improved interpretation of diagnostic accuracy statistics

Diagnostic accuracy statistics, including predictive values, risk-differences, Youdens index and Area Under the Curve (AUC), assess the promise of novel biomarkers proposed as diagnostic tests. We reinterpret these statistics in light of risk-stratification (how well a biomarker separates those at higher risk from those at lower risk) to better understand their implications for public-health programs. We introduce an intuitively simple statistic, Mean Risk Stratification (MRS): the average change in risk (pre-test vs. post-test) revealed for tested individuals. High MRS implies better risk separation achieved by testing. MRS demonstrates that conventional predictive values can mislead because they do not account for disease prevalence or test-positivity rates. Little risk-stratification is possible for rare diseases, demonstrating a \"high-bar\" to justify population-based screening. Importantly, we demonstrate that the risk-difference, Youdens index, and AUC measure only multiplicative relative gains in risk-stratification: AUC=0.6 achieves only 20% of maximum risk-stratification (AUC=0.9 achieves 80%). However, large relative gains in risk-stratification might not imply large absolute gains if disease is rare or if the test is rarely positive. We illustrate MRS by our experience comparing the performance of cervical cancer screening tests in China vs. the USA. The test with the worst AUC=0.72 in China (visual inspection with ascetic acid) provides twice the risk-stratification of the test with best AUC=0.83 in the USA (human papillomavirus and Pap cotesting) because China has three times more cervical precancer/cancer. MRS could be routinely calculated to better understand the clinical/public-health implications of standard diagnostic accuracy statistics.

Epidemiology

Modeling antimicrobial cycling and mixing: Differences arising from an individual-based versus a population-based perspective

BackgroundIn order to manage bacterial infections in hospitals in the face of antibiotic resistance, the two treatment protocols \"mixing\" and \"cycling\" have received considerable attention both from modelers and clinicians. However, the terms are not used in exactly the same way by both groups.\n\nObjectivesWe aim to investigate a model that comes closer to clinical practice and compare the predictions to the standard model.\n\nMethodsWe set up two deterministic models, implemented as a set of differential equations, for the spread of bacterial infections in a hospital. Following the traditional approach, the first model takes a population-based perspective. The second model, in contrast, takes the drug use of individual patients into account.\n\nResultsThe alternative model can indeed lead to different predictions than the standard model. We provide examples for which in the new model, the opposite strategy maximizes the number of uninfected patients or minimizes the rate of spread of double resistance.\n\nConclusionsWhile the traditional models provide valuable insight, care is needed in the interpretation of results.

epidemiology

A broad sense measure of health and its properties in the HRS

Measuring health is a crucial component of much social research. Two approaches are typical. Health may be measured via either narrowly targeted questions about aspects of disability or chronic conditions. Alternatively, individuals may be asked to self-report their health in some global sense. Both approaches have potential drawbacks. We consider a broad sense measure of health constructed by items from five different batteries related to physical and mental wellbeing. We demonstrate that this measure predicts time until death better than self-reported health, especially for females. Although this measure has promise, we argue that future surveys on health would benefit from the inclusion of additional items focusing on issues salient to younger individuals or other non-disabled respondents.

epidemiology

Statistical and biological uncertainties associated with vaccine efficacy estimates and their implications for dengue vaccine impact projections

Given the limited effectiveness of strategies based solely on vector control to reduce dengue virus (DENV) transmission, it is expected that an effective vaccine could play a pivotal role in reducing the global disease burden of dengue. Of several dengue vaccines under development, Dengvaxia(R) from Sanofi Pasteur recently became the first to become licensed in select countries and to achieve WHO recommendation for use in certain settings, despite the fact that a number of uncertainties about its profile complicate projections of its public health impact. We used a stochastic, agent-based model for DENV transmission to perform simulations of the public health impact of dengue vaccines in light of two key uncertainties: (1) \"statistical uncertainty\" about the numerical value of the vaccines efficacy against disease, and (2) \"biological uncertainty\" about the extent to which its efficacy against disease derives from the amelioration of symptoms, blocking of DENV infection, or some combination thereof. Simulations of a generic dengue vaccine showed that the proportion of disease episodes averted following 20 years of routine vaccination of nine-year olds at 80% coverage was sensitive to both the numerical value of vaccine efficacy and to the extent to which efficacy derives from blocking of DENV infection. Simulations of a vaccine resembling Dengvaxia(R) took into account that vaccine trial results substantially reduced statistical uncertainty but did not address biological uncertainty, resulting in the proportion of disease episodes averted being more sensitive to biological uncertainty than to statistical uncertainty. Taken together, our results indicate limitations associated with the use of symptomatic disease as the primary endpoint of dengue vaccine trials and highlight the importance of considering multiple forms of uncertainty in projections of a vaccines public health impact.

epidemiology

Signatures of non-neutral processes within the population structure of Streptococcus pneumoniae

Populations of Streptococcus pneumoniae (SP) are typically structured into groups of closely related organisms or lineages, but it is not clear whether they are maintained by selection or neutral processes. Here, we attempt to address this question by applying a machine learning technique to SP whole genomes. Our results indicate that lineages evolved through immune selection on the groEL chaperone protein. The groEL protein is part of the groESL operon and enables a large range of proteins to fold correctly within the physical environment of the nasopharynx, thereby explaining why lineage structure is so stable within SP despite high levels of genetic transfer. SP is also antigenically diverse, exhibiting a variety of distinct capsular serotypes. Associations exist between lineage and capsular serotype but these can be easily perturbed, such as by vaccination. Overall, our analyses indicate that the evolution of SP can be conceptualized as the rearrangement of modular functional units occurring on several different timescales under different pressures: some patterns have locked in early (such as the epistatic interactions between groESL and a constellation of other genes) and preserve the differentiation of lineages, while others (such as the associations between capsular serotype and lineage) remain in continuous flux.

epidemiology

A comprehensive survey of genetic variation in 20,691 subjects from four large cohorts

The Nurses Health Study (NHS), Nurses Health Study II (NHSII), Health Professionals Follow Up Study (HPFS) and the Physicians Health Study (PHS) have collected detailed longitudinal data on multiple exposures and traits for approximately 310,000 study participants over the last 35 years. Over 160,000 study participants across the cohorts have donated a DNA sample and to date, 20,691 subjects have been genotyped as part of genome-wide association studies (GWAS) of twelve primary outcomes. However, these studies utilized six different GWAS arrays making it difficult to conduct analyses of secondary phenotypes or share controls across studies. To allow for secondary analyses of these data, we have created three new datasets merged by platform family and performed imputation using a common reference panel, the 1,000 Genomes Phase I release. Here, we describe the methodology behind the data merging and imputation and present imputation quality statistics and association results from two GWAS of secondary phenotypes (body mass index (BMI) and venous thromboembolism (VTE)).\n\nWe observed the strongest BMI association for the FTO SNP rs55872725 ({beta}=0.45, p=3.48x10-22), and using a significance level of p=0.05, we replicated 19 out of 32 known BMI SNPs. For VTE, we observed the strongest association for the rs2040445 SNP (OR=2.17, 95% CI: 1.79-2.63, p=2.70x10-15), located downstream of F5 and also observed significant associations for the known ABO and F11 regions. This pooled resource can be used to maximize power in GWAS of phenotypes collected across the cohorts and for studying gene-environment interactions as well as rare phenotypes and genotypes.

epidemiology

A structural variant encoding hybrid glycophorins is associated with resistance to severe malaria

Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. Here we analyse whole genome sequence data from worldwide human populations, including 765 new genomes from across sub-Saharan Africa, and identify a diverse array of large copy number variants affecting the host invasion receptor genes GYPA and GYPB. We find that a nearby reported association with severe malaria is explained by a complex structural variant that involves the loss of GYPB and gain of two hybrid genes, each with a GYPB extracellular domain and GYPA intracellular domain. This variant reduces the risk of severe malaria by 40% and has recently risen in frequency in parts of Kenya. We show that the structural variant encodes the Dantu blood group antigen, and therefore a serologically distinct red cell phenotype. These findings demonstrate that structural variation of red blood cell invasion receptors is associated with natural resistance to P. falciparum malaria.

genomics

Pre-Hospital Midazolam for Treatment of Status Epilepticus Before and After the Rapid Anticonvulsant Medication Prior to Arrival Trial (RAMPART): A National Observational Cohort Study

BackgroundImplementation of evidence-based treatment for pre-hospital status epilepticus can improve outcomes. We hypothesized that publication of a pivotal pre-hospital clinical trial (RAMPART), demonstrating superiority of intramuscular midazolam over intravenous lorazepam, altered the national utilization rates of midazolam for pre-hospital treatment of status epilepticus, while upholding its safety and efficacy outside the trial setting.\n\nMethods and FindingsThis is a retrospective, observational cohort study of pre-hospital patient encounters throughout the United States in the National Emergency Medicine Services Information System database, from January 2010 through December 2014. We compared the rates and odds of midazolam use as the first-line treatment for status epilepticus among all adult and pediatric benzodiazepine-treated seizures before and after RAMPART publication (February 2012). Secondary analyses were conducted for rates of airway interventions and rescue therapy, as proxies for safety and efficacy of seizure termination. 156,539 benzodiazepine-treated seizures were identified. Midazolam use increased from 26.1% in January 2010 to 61.7% in December 2014 (difference +35.6%, 95% CI, 32.7%-38.4%). The annual rate of midazolam adoption increased significantly from 5.9% per year to 8.9% per year after the publication of RAMPART (difference +3.0% per year; 95%CI, 1.6%-4.5% per year; adjusted OR 1.24; 95%CI, 1.17-1.32). Overall frequency of rescue therapy and airway interventions changed little after the publication of RAMPART.\n\nConclusionsThese data are consistent with effective, ongoing, but incomplete clinical translation of the RAMPART results. The effects of the trial, however, cannot be isolated. The safety and effectiveness of midazolam for treatment of seizures in prehospital clinical practice appear consistent with trial data, which should encourage continuing increases in utilization.

epidemiology

Non-polio enteroviruses in faeces of children diagnosed with acute flaccid paralysis in Nigeria.

BackgroundThe need to investigate the contribution of non-polio enteroviruses to acute flaccid paralysis (AFP) cannot be over emphasized as we move towards a poliovirus free world. Hence, we aim to identify non-polio enteroviruses recovered from the faeces of children diagnosed with AFP in Nigeria.\n\nMethodsNinety-six isolates, (95 unidentified and one previously confirmed Sabin poliovirus 3) recovered on RD cell culture from the stool of children <15 years old diagnosed with AFP in 2014 were analyzed. All isolates were subjected to RNA extraction, cDNA synthesis and three different PCR reactions (one panenterovirus 5'-UTR and two VP1 amplification assays). VP1 amplicons were then sequenced isolates identified.\n\nResults93.75% (90/96) of the isolates were detected by at least one of the three assays as an enterovirus. Precisely, 79.17% (76/96), 6.25% (6/96), 7.295% (7/96) and 6.25% (6/96) of the isolates were positive for both, positive and negative, negative and positive, as well as negative for both the 5'-UTR and VP1 assays, respectively. In this study, sixty-nine (69) of the 83 VP1 amplicons sequenced were identified as 27 different enterovirus types. The most commonly detected were CV-B3 (10 isolates) and EV-B75 (5 isolates). Specifically, one, twenty-four and two of the enterovirus types identified in this study belong to EV-A, EV-B and EV-C respectively.\n\nDiscussionThis study reports the circulating strains of 27 non-polio enterovirus types in Nigerian children with AFP in 2014 and Nigerian strains of CV-B2, CV-B4, E17, EV-B80, EV-B73, EV-B97, EV-B93, EV-C99 and EV-A120.

epidemiology

Enterovirus A119 in a child with Acute Flaccid Paralysis, Nigeria

The oldest EV-A119 record was in 2008 in a chimpanzee in Cameroon and subsequently in more non-human primates and healthy children. Here we report for the first time the detection of EV-A119 in a child with Acute Flaccid Paralysis, thus suggesting possible association with a clinical condition in humans.

epidemiology

Can you catch Ebola from a stork bite? Inductive reasoning influences on zoonosis risk perception

Emerging zoonoses are a prominent global health threat. Human beliefs are central to drivers of emerging zoonoses, yet little is known about the factors that influence perceived risks of animal contact. We present an inductive account of zoonosis risk perception, suggesting that beliefs about the range of animals that are able to transmit diseases to each other influence zoonosis risk perception. Consistent with our account, in Study 1, we find that participants who endorse higher likelihoods of cross-species disease transmission have stronger intention to report animal bites. In Study 2, using real world descriptions of Ebola virus from the WHO and CDC, we find that communications conveying a broader range of animals as susceptible increase intentions to report animal bites and decrease perceived safety of wild game meat. These results suggest that cognitive factors may be harnessed to modulate zoonosis risk perception and combat emerging infectious diseases.

epidemiology

The Utility of Red Cell Distribution Width as a Parameter for Calculating Indices of Allostatic Load

BackgroundAllostatic Load is a construct used to quantify the cumulative burden of exposure to stressors that, over the course of an individuals life, exert a toll on the bodys physiological functions, increasing risks of various chronic ailments and conditions. Studies attempting to quantify allostatic load have used a variety of clinical biomarkers representing primary and secondary mediators. In this study, we demonstrate the value of including red blood cell distribution width (RDW) among the panel of clinical parameters used to calculate allostatic load.\n\nMethodsWe develop a novel formulation of allostatic load using RDW and other standard biomarkers. This index is computed using clinical laboratory data from the NHANES study. The predictive validity of the new index for tertiary outcomes (all-cause mortality and physician-assessed health status) is compared to that of the current formulation using Harrells C index, ROC analysis and regression-based goodness-of-fit measures.\n\nResultsInclusion of RDW as an allostatic load biomarker yields a significantly improved index. It demonstrates a superior ability to predict mortality, health status and biological age than the standard formulation currently in use.\n\nConclusionRDW has shown strong correlations with mortality and a broad spectrum of diseases. A review of the existing literature on allostatic load reveals its underutilization in this area, despite being a standard component of blood count panels. This study is the first to demonstrate its usefulness as a potential allostatic load biomarker.

epidemiology

Exposure to Wood Smoke is Associated with Increased Risk of Asthma and Respiratory Symptoms in a Honduran Population

BackgroundExposure to environmental pollutants has been shown to be associated with asthma, but few studies have evaluated the effect of wood smoke on asthma and disease severity in a developing country, where use of stoves powered by solid fuels is a common practice.\n\nObjectiveIn a population in Olancho, Honduras, we evaluated the association between cooking fuel, stove type and asthma. We also evaluated the effects of these factors on asthma symptoms, lung function, and atopy.\n\nMethodsParticipants with physician-diagnosed asthma (n = 597) and controls without asthma (n = 429) were recruited from the Olancho province in Honduras. Participants were interviewed using a questionnaire and their baseline pulmonary function was measured using spirometry.\n\nResultsThe prevalence of use of wood as a cooking fuel was 66.9% in the study population, of which 42.1% of participants used wood as their only fuel. Use of wood as a cooking fuel was more prevalent among households with lower income, lower maternal education, and less urbanization. The prevalence of use of an open wood stove as the primary cooking stove among participants with asthma was 6.2% higher (95% CI 0.8 - 11.7%, p = .02) than among healthy controls. In a multiple logistic regression model, we identified a significant association between use of an open wood stove and asthma (OR = 1.80, 95% CI = 1.17 - 2.78, p = 0.007), compared to the referent (electric) stove category. Among participants with asthma, we identified a significant association between use of wood as cooking fuel and increased daytime respiratory symptoms (OR = 1.46, CI: 1.01 - 2.58, p = 0.046) and nocturnal symptoms (OR = 2.51, CI: 1.04 - 2.62, p = 0.04), though not with pulmonary function. Among control participants without asthma, use of wood as cooking fuel was associated with atopy (OR = 1.94, CI = 1.14 - 3.33, p = 0.015) and cough (OR = 2.22, CI = 1.09 - 4.88, p = 0.04).\n\nConclusionsUse of an open wood stove for cooking in a developing country appears to be a significant risk factor for asthma and respiratory symptoms. Exposure to wood smoke may play a role in atopic sensitization and respiratory symptoms, leading to the development of obstructive lung disease in susceptible individuals.

epidemiology

The origin and evolution of a pandemic lineage of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae

Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa), whose emergence coincided with domestication of its host. The most recent pandemic has had a deleterious effect on kiwifruit production worldwide. In order to strengthen understanding of population structure, phylogeography and evolutionary dynamics of Psa, we sampled 746 Pseudomonas isolates from cultivated and wild kiwifruit across six provinces in China, of which 87 were Psa. Of 234 Pseudomonas isolated from wild Actinidia spp. none were identified as Psa. Genome sequencing of fifty isolates and the inclusion of an additional thirty from previous studies show that China is the origin of the recently emerged pandemic lineage. However China harbours only a fraction of global Psa diversity, with greatest diversity found in Korea and Japan. Distinct transmission events were responsible for introduction of the pandemic lineage of Psa into New Zealand, Chile and Europe. Two independent transmission events occurred between China and Korea, and two Japanese isolates from 2014 cluster with New Zealand Psa. Despite high similarity at the level of the core genome and negligible impact of within-lineage recombination, there has been substantial gene gain and loss even within the single clade from which the global pandemic arose.\n\nSIGNIFICANCE STATEMENTBleeding canker disease of kiwifruit caused by Pseudomonas syringae pv. actinidiae (Psa) has come to prominence in the last three decades. Emergence has coincided with domestication of the host plant and provides a rare opportunity to understand ecological and genetic factors affecting the evolutionary origins of Psa. Here, based on genomic analysis of an extensive set of strains sampled from China and augmented by isolates from a global sample, we show, contrary to earlier predictions, that China is not the native home of the pathogen, but is nonetheless the source of the recent global pandemic. Our data identify specific transmission events, substantial genetic diversity and point to non-agricultural plants in either Japan or Korea as home to the source population.

epidemiology

Mathematical models of SIR disease spread with combined non-sexual and sexual transmission routes

The emergence of diseases such as Zika and Ebola has highlighted the need to understand the role of sexual transmission in the spread of diseases with a primarily non-sexual transmission route. In this paper we develop a number of low-dimensional models which are appropriate for a range of assumptions for how a disease will spread if it has sexual transmission through a sexual contact network combined with some other transmission mechanism, such as direct contact or vectors. The equations derived provide exact predictions for the dynamics of the corresponding simulations in the large population limit.

epidemiology

Modeling disease spread in populations with birth, death, and concurrency

The existence of sexual partnerships that overlap in time (concurrent relationships) is believed by some to be a significant contributing factor to the spread of HIV, although this is controversial. We derive an analytic model which allows us to investigate and compare disease spread in populations with and without concurrency. We can identify regions of parameter space in which its impact is negligible, and other regions in which it plays a major role. We also see that the impact of concurrency on the initial growth phase can be much larger than its impact on the equilibrium size. We see that the effect of concurrency saturates, which leads to the perhaps surprising conclusion that interventions targeting concurrency may be most effective in populations with low to moderate levels of concurrency.\n\nAuthor SummaryWe consider the spread of an infectious disease through a population modeled by a dynamic network with demographic turnover. We develop a stochastic model of the disease and derive governing equations that exactly predict the large population (deterministic) limit of the stochastic model. We use this to investigate the role of concurrency and find that interventions targeting concurrency may be most effective in populations with lower levels of concurrency.\n\nOur model is not intended to be an accurate representation of any single population. Rather it is intended to give general insights for intervention design and to provide a framework which can be further specialized to particular populations.\n\nThis model is the first model to allow for analytic investigation of the impact of concurrent partnerships in a population exhibiting demographic turnover. Thus it will be useful for investigating the \"concurrency hypothesis.\"

epidemiology

A location-specific spreadsheet for estimating Zika risk and timing for Zika vector surveillance, using U.S. military facilities as an example

Local Zika virus transmission in the United States involving one or both of the known vector species, Aedes aegypti and Ae. albopictus, is of major concern. To assist efforts to anticipate the risks of transmission, we developed an Excel spreadsheet tool that uses vector and virus temperature thresholds, remotely sensed maximum temperature, and habitat suitability from models to answer the questions: \"is Zika transmission likely here?\" and \"when should we conduct vector surveillance?\". An example spreadsheet, updated regularly and freely available, uses near real-time and forecast temperature data to generate guidance, based on a novel four level Zika risk code, for 733 U.S. military facilities in the 50 states, the District of Columbia, and the territories of Guam and Puerto Rico.

epidemiology

Structure of general-population antibody titer distributions to influenza A virus

Seroepidemiological studies aim to understand population-level exposure and immunity to infectious diseases. Results from serological assays are normally presented as binary outcomes describing the presence or absence of pathogen-specific antibody, despite the fact that many assays measure continuous quantities. A populations natural distribution of antibody titers to an endemic infectious disease may in fact include information on multiple serological states - e.g. naivete, recent infection, non-recent infection - depending on the disease in question and the acquisition and waning patterns of host immunity. In this study, we investigate a collection of 20,152 general-population serum samples from southern Vietnam collected between 2009 and 2013 from which we report antibody titers to the influenza virus HA1 protein using a continuous titer measurement from a protein microarray assay. We describe the distributions of antibody titers to subtypes 2009 H1N1 and H3N2. Using a model selection approach to fit mixture distributions, we show that 2009 H1N1 antibody titers fall into four titer subgroups and that H3N2 titers fall into three subgroups. For H1N1, our interpretation is that the two highest-titer subgroups correspond to recent infection and historical infection, which is consistent with 2009 pandemic attack rates. For H3N2, observations censored at the highest titer dilutions make similar interpretations difficult to validate.

epidemiology