HIV with contact-tracing: a case study in Approximate Bayesian Computation

Missing data is a recurrent issue in epidemiology where the infection process may be partially observed. Approximate Bayesian Computation, an alternative to data imputation methods such as Markov Chain Monte Carlo integration, is proposed for making inference in epidemiological models. It is a likelihood-free method that relies exclusively on numerical simulations. ABC consists in computing a distance between simulated and observed summary statistics and weighting the simulations according to this distance. We propose an original extension of ABC to path-valued summary statistics, corresponding to the cumulated number of detections as a function of time. For a standard compartmental model with Suceptible, Infectious and Recovered individuals (SIR), we show that the posterior distributions obtained with ABC and MCMC are similar. In a refined SIR model well-suited to the HIV contact-tracing data in Cuba, we perform a comparison between ABC with full and binned detection times. For the Cuban data, we evaluate the efficiency of the detection system and predict the evolution of the HIV-AIDS disease. In particular, the percentage of undetected infectious individuals is found to be of the order of 40%

Alien Marine Species in the Mediterranean - the 100 ‘Worst Invasives’ and their Impact

A number of marine alien species have been described as invasive or locally invasive in the Mediterranean because of their proliferation, and/or their geographical spread and/or impact on native populations. Based on that information and on the documented impact they have on the biodiversity and socioeconomics of the basin, a preliminary list of the 100 ‘worst’ Invasive Alien Species (IAS) in the Mediterranean has been produced and presented in this work along with details on their impact. Emphasis is given to their impact on socioeconomics (fi sheries/aquaculture, health & sanitation, infrastructure & building), documented for 43 species. Such selection of the ‘worst’ IAS was diffi cult and controversial and is expected to attract much attention and scientifi c criticism since not only can the documentation of the impact of IAS be controversial, but also their inventory can be biased towards the effort and resources devoted to the study of the impact of certain species/taxonomic groups. Thus, while marine plants (phytobenthos and phytoplankton) are fairly well studied, less attention has been paid to the impact of vertebrates and even less to invertebrates. Nevertheless, the list highlights the need for continued research on the issue (monitoring aliens and their impact for an integrated ecosystem based management approach over the entire area). The preliminary list can provide the basis for selecting indicator species within the Mediterranean and thus be the common ground to build cooperation about IAS within countries in the region

Alien Marine Species in the Mediterranean - the 100 ‘Worst Invasives’ and their Impact

A number of marine alien species have been described as invasive or locally invasive in the Mediterranean because of their proliferation, and/or their geographical spread and/or impact on native populations. Based on that information and on the documented impact they have on the biodiversity and socioeconomics of the basin, a preliminary list of the 100 ‘worst’ Invasive Alien Species (IAS) in the Mediterranean has been produced and presented in this work along with details on their impact. Emphasis is given to their impact on socioeconomics (fi sheries/aquaculture, health & sanitation, infrastructure & building), documented for 43 species. Such selection of the ‘worst’ IAS was diffi cult and controversial and is expected to attract much attention and scientifi c criticism since not only can the documentation of the impact of IAS be controversial, but also their inventory can be biased towards the effort and resources devoted to the study of the impact of certain species/taxonomic groups. Thus, while marine plants (phytobenthos and phytoplankton) are fairly well studied, less attention has been paid to the impact of vertebrates and even less to invertebrates. Nevertheless, the list highlights the need for continued research on the issue (monitoring aliens and their impact for an integrated ecosystem based management approach over the entire area). The preliminary list can provide the basis for selecting indicator species within the Mediterranean and thus be the common ground to build cooperation about IAS within countries in the region

Cancer Morbidity Trends and Regional Differences in England - a Bayesian Analysis

Reliable modelling of the dynamics of cancer morbidity risk is important, not least due to its significant impact on healthcare and related policies. We identify morbidity trends and regional differences in England for all-cancer and type-specific incidence between 1981 and 2016. We use Bayesian modelling to estimate cancer morbidity incidence at various age, year, gender, and region levels. Our analysis shows increasing trends in most rates and marked regional variations that also appear to intensify through time in most cases. All-cancer rates have increased significantly, with the highest increase in East, North West and North East. The absolute difference between the rates in the highest- and lowest-incidence region, per 100,000 people, has widened from 39 (95% CI 33-45) to 86 (78-94) for females, and from 94 (85-104) to 116 (105-127) for males. Lung cancer incidence for females has shown the highest increase in Yorkshire and the Humber, while for males it has declined in all regions with the highest decrease in London. The gap between the highest- and lowest-incidence region for females has widened from 47 (42-51) to 94 (88-100). Temporal change in in bowel cancer risk is less manifested, with regional heterogeneity also declining. Prostate cancer incidence has increased with the highest increase in London, and the regional gap has expanded from 33 (30-36) to 76 (69-83). For breast cancer incidence the highest increase has occurred in North East, while the regional variation shows a less discernible increase. The analysis reveals that there are important regional differences in the incidence of all-type and type-specific cancers, and that most of these regional differences become more pronounced over time. A significant increase in regional variation has been demonstrated for most types of cancer examined here, except for bowel cancer where differences have narrowed

Identifying genotype specific elevated-risk areas and associated herd risk factors for bovine tuberculosis spread in British cattle

Bovine tuberculosis (bTB) is a chronic zoonosis with major health and economic impact on the cattle industry. Despite extensive control measures in cattle and culling trials in wildlife, the reasons behind the expansion of areas with high incidence of bTB breakdowns in Great Britain remain unexplained. By balancing the importance of cattle movements and local transmission on the observed pattern of cattle outbreaks, we identify areas at elevated risk of infection from specific Mycobacterium bovis genotypes. We show that elevated-risk areas (ERAs) were historically more extensive than previously understood, and that cattle movements alone are insufficient for ERA spread, suggesting the involvement of other factors. For all genotypes, we find that, while the absolute risk of infection is higher in ERAs compared to areas with intermittent risk, the statistically significant risk factors are remarkably similar in both, suggesting that these risk factors can be used to identify incipient ERAs before this is indicated by elevated incidence alone. Our findings identify research priorities for understanding bTB dynamics, improving surveillance and guiding management to prevent further ERA expansion

Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis)

As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness