Modelling latent trends from spatio-temporally grouped data using composite link mixed models

Epidemiological data are frequently recorded at coarse spatio-temporal resolutions. The aggregation process is done for several reasons: to protect confidential patients' information, to compare with other datasets at a coarser resolution than the original, or to summarize data in a compact manner. However, we lose detailed patterns that follow the original data, which can be of interest for researchers and public health officials. In this paper we propose the use of the penalized composite link model (Eilers, 2007), together with its mixed model representation, to estimate the underlying trend behind grouped data at a finer spatio-temporal resolution. Also, this model allows the incorporation of fine-scale population into the estimation procedure. We assume the underlying trend is smooth across space and time. The mixed model representation enables the use of sophisticated algorithms such as the SAP algorithm of RodríguezÁlvarez et al. (2015) for fast estimation of the amount of smoothness. We illustrate our proposal with the analysis of data obtained during the largest outbreak of Q fever in the Netherlands.The first and the second authors acknowledge financial support from the Spanish Ministry of Economy and Competitiveness grants MTM2011-28285-C02-02 and MTM2014-52184-P. The third author acknowledges financial support from the Basque Government through the BERC 2014-2017 program and by the Spanish Ministry of Economy and Competitiveness MINECO: BCAM Severo Ochoa excellence accreditation SEV-2013-0323

Co-occurrence of diabetes, myocardial infarction, stroke, and cancer: quantifying age patterns in the Dutch population using health survey data

<p>Abstract</p> <p>Background</p> <p>The high prevalence of chronic diseases in Western countries implies that the presence of multiple chronic diseases within one person is common. Especially at older ages, when the likelihood of having a chronic disease increases, the co-occurrence of distinct diseases will be encountered more frequently. The aim of this study was to estimate the age-specific prevalence of multimorbidity in the general population. In particular, we investigate to what extent specific pairs of diseases cluster within people and how this deviates from what is to be expected under the assumption of the independent occurrence of diseases (i.e., sheer coincidence).</p> <p>Methods</p> <p>We used data from a Dutch health survey to estimate the prevalence of pairs of chronic diseases specified by age. Diseases we focused on were diabetes, myocardial infarction, stroke, and cancer. Multinomial P-splines were fitted to the data to model the relation between age and disease status (single versus two diseases). To assess to what extent co-occurrence cannot be explained by independent occurrence, we estimated observed/expected co-occurrence ratios using predictions of the fitted regression models.</p> <p>Results</p> <p>Prevalence increased with age for all disease pairs. For all disease pairs, prevalence at most ages was much higher than is to be expected on the basis of coincidence. Observed/expected ratios of disease combinations decreased with age.</p> <p>Conclusion</p> <p>Common chronic diseases co-occur in one individual more frequently than is due to chance. In monitoring the occurrence of diseases among the population at large, such multimorbidity is insufficiently taken into account.</p

Infectious reactivation of cytomegalovirus explaining age- and sex-specific patterns of seroprevalence.

Human cytomegalovirus (CMV) is a herpes virus with poorly understood transmission dynamics. Person-to-person transmission is thought to occur primarily through transfer of saliva or urine, but no quantitative estimates are available for the contribution of different infection routes. Using data from a large population-based serological study (n = 5,179), we provide quantitative estimates of key epidemiological parameters, including the transmissibility of primary infection, reactivation, and re-infection. Mixture models are fitted to age- and sex-specific antibody response data from the Netherlands, showing that the data can be described by a model with three distributions of antibody measurements, i.e. uninfected, infected, and infected with increased antibody concentration. Estimates of seroprevalence increase gradually with age, such that at 80 years 73% (95%CrI: 64%-78%) of females and 62% (95%CrI: 55%-68%) of males are infected, while 57% (95%CrI: 47%-67%) of females and 37% (95%CrI: 28%-46%) of males have increased antibody concentration. Merging the statistical analyses with transmission models, we find that models with infectious reactivation (i.e. reactivation that can lead to the virus being transmitted to a novel host) fit the data significantly better than models without infectious reactivation. Estimated reactivation rates increase from low values in children to 2%-4% per year in women older than 50 years. The results advance a hypothesis in which transmission from adults after infectious reactivation is a key driver of transmission. We discuss the implications for control strategies aimed at reducing CMV infection in vulnerable groups

Collaborative nowcasting of COVID-19 hospitalization incidences in Germany

Real-time surveillance is a crucial element in the response to infectious disease outbreaks. However, the interpretation of incidence data is often hampered by delays occurring at various stages of data gathering and reporting. As a result, recent values are biased downward, which obscures current trends. Statistical nowcasting techniques can be employed to correct these biases, allowing for accurate characterization of recent developments and thus enhancing situational awareness. In this paper, we present a preregistered real-time assessment of eight nowcasting approaches, applied by independent research teams to German 7-day hospitalization incidences during the COVID-19 pandemic. This indicator played an important role in the management of the outbreak in Germany and was linked to levels of non-pharmaceutical interventions via certain thresholds. Due to its definition, in which hospitalization counts are aggregated by the date of case report rather than admission, German hospitalization incidences are particularly affected by delays and can take several weeks or months to fully stabilize. For this study, all methods were applied from 22 November 2021 to 29 April 2022, with probabilistic nowcasts produced each day for the current and 28 preceding days. Nowcasts at the national, state, and age-group levels were collected in the form of quantiles in a public repository and displayed in a dashboard. Moreover, a mean and a median ensemble nowcast were generated. We find that overall, the compared methods were able to remove a large part of the biases introduced by delays. Most participating teams underestimated the importance of very long delays, though, resulting in nowcasts with a slight downward bias. The accompanying prediction intervals were also too narrow for almost all methods. Averaged over all nowcast horizons, the best performance was achieved by a model using case incidences as a covariate and taking into account longer delays than the other approaches. For the most recent days, which are often considered the most relevant in practice, a mean ensemble of the submitted nowcasts performed best. We conclude by providing some lessons learned on the definition of nowcasting targets and practical challenges

Circulation of pertussis and poor protection against diphtheria among middle-aged adults in 18 European countries

Reported incidence of pertussis in the European Union (EU) and the European Economic Area (EEA) varies and may not reflect the real situation, while vaccine-induced protection against diphtheria and tetanus seems sufficient. We aimed to determine the seroprevalence of DTP antibodies in EU/EEA countries within the age groups of 40-49 and 50-59 years. Eighteen countries collected around 500 samples between 2015 and 2018 (N = 10,302) which were analysed for IgG-DTP specific antibodies. The proportion of sera with pertussis toxin antibody levels ≥100 IU/mL, indicative of recent exposure to pertussis was comparable for 13/18 countries, ranging between 2.7-5.8%. For diphtheria the proportion of sera lacking the protective level (</p

Tracing the Origin of Food-borne Disease Outbreaks:A Network Model Approach

Background: Food-borne disease outbreaks constitute a large health burden on society. One of the challenges when investigating such outbreaks is to trace the origin of the outbreak. In this study, we consider a network model to determine the spatial origin of the contaminated food product that caused the outbreak. Methods: The network model we use replaces the classic geographic distance of a network by an effective distance so that two nodes connected by a long-range link may be more strongly connected than their geographic distance would suggest. Furthermore, the effective distance transforms complex spatial patterns into regular topological patterns, creating a means for easier identification of the origin of the spreading phenomenon. Because detailed information on food distribution is generally not available, the model uses the gravity model from economics: the flow of goods from one node to another increases with population size and decreases with the geographical distance between them. Results: This effective distance network approach has been shown to perform well in a large Escherichia coli O104:H4 outbreak in Germany in 2011. In this article, we apply the same method to various food-borne disease outbreaks in the Netherlands. We found the effective distance network approach to fail in certain scenarios. Conclusions: Great care should be taken as to whether the underlying network model correctly captures the spreading mechanism of the outbreak in terms of spatial scale and single or multiple source outbreak.</p

Graph-Based Spatial Segmentation of Health-Related Areal Data

Smoothing is often used to improve the readability and interpretability of noisy areal data. However there are many instances where the underlying quantity is discontinuous. In this case, specific methods are needed to estimate the piecewise constant spatial process. A well-known approach in this setting is to perform segmentation of the signal using the adjacency graph, as does the graph-based fused lasso. But this method does not scale well to large graphs. This article introduces a new method for piecewise-constant spatial estimation that (i) is fast to compute on large graphs and (ii) yields sparser models than the fused lasso (for the same amount of regularization), giving estimates that are easier to interpret. We illustrate our method on simulated data and apply it to real data on overweight prevalence in the Netherlands. Healthy and unhealthy zones are identified which cannot be explained by demographic of socio-economic characteristics. We find that our method is capable of identifying such zones and can assist policy makers with their health-improving strategies. The implementation of our method in R is publicly available at github.com/goepp/graphseg