‘Next-Generation’ surveillance: an epidemiologists’ perspective on the use of molecular information in food safety and animal health decision-making

Advances in the availability and affordability of molecular and genomic data are transforming human health care. Surveillance aimed at supporting and improving food safety and animal health is likely to undergo a similar transformation. We propose a definition of ‘molecular surveillance’ in this context and argue that molecular data are an adjunct to rather than a substitute for sound epidemiological study and surveillance design. Specific considerations with regard to sample collection are raised, as is the importance of the relation between the molecular clock speed of genetic markers and the spatiotemporal scale of the surveillance activity, which can be control- or strategy-focused. Development of standards for study design and assessment of molecular surveillance system attributes is needed, together with development of an interdisciplinary skills base covering both molecular and epidemiological principles

Model applications of decision support systems in meat hygiene programs : a thesis presented in partial fulfilment of the requirements for the degree of Master of Veterinary Science at Massey University

Current systems to ensure safety of meat are to a large degree based on a "procedural" approach which specifies what inspection actions will be taken to protect human health. Both knowledge and disease priorities have changed substantially over recent decades, and moreover the scale of the problems created by any breakdowns in protection has escalated greatly, as food trading and consumption patterns have changed. It is now recognized that meat hygiene needs to focus primarily on ways by which the risk that product will represent a hazard to human health can be effectively reduced, rather than merely ensuring compliance with a defined set of procedures. In addition to human food safety, meat inspection has the potential to contribute information to improve animal health on a national and a local scale. This thesis examines example issues in order to identify possible approaches to the development of decision support systems which assist in protecting meat consumers and improving the health of livestock on farms. The main areas which were explored for this purpose were respiratory disease in lambs and chemical residues in slaughter animals. A literature review of pneumonia and pleurisy in lambs showed that numerous factors have been proposed as predisposing causes for these diseases, but there was surprisingly little valid experimental or observational research evidence to support such statements. A hazard analysis was performed for the micro-organisms which have been isolated from pneumonic lungs. The major commonly detected organisms did not appear to cause a risk to healthy people. However there were a number of micro-organisms which are isolated on occasion from pneumonic and sometimes from healthy sheep lungs that might cause human disease. A case-control study was carried out as an exploratory means to identify risk factors and to generate hypotheses about causal processes. A number of risk factors were initially identified at univariate level. At the second stage the importance of some of these risk factors was quantified in a logistic regression model. Finally a third stage analysis showed the interactions between the factors in a logistic path model, which consisted of three clusters. One cluster included characteristics of the farm and paddocks, one cluster included the yards and practices in the yards, and a third cluster included the types and number of animals on the farm. Two intervention studies were subsequently carried out to evaluate the effect of making various management modifications on the prevalence of pneumonia and pleurisy at slaughter. One intervention study evaluated the time lambs spent in the yards after weaning and the use or oral or injectable drenches. The second intervention study evaluated the use of oral versus injectable drenches and the use of a shower dip versus a wand. The intervention studies showed an effect of time in the yards on pneumonia. There was some association between time in the yards and acute localised pleurisy but none between the other measures tested and respiratory disease. The studies showed clear temporal patterns with regard to pleurisy and pneumonia and enabled comparisons to be made between farms. A study of inspection for pleurisy at slaughterhouses was analysed. The analysis identified the temporal patterns of certain types of pleurisy. Comparisons were made between four participating premises. The sensitivity and specificity of meat inspection for the various types of pleurisy was analysed. The pleurisy data over an eleven year period of the entire country were analysed. Differences were shown between islands and regions. The potential for development of components of a decision support system for pneumonia and pleurisy was illustrated with a number of examples. An important component was to determine how farmers could be assisted in improving the health of their lambs with regard to pleurisy. Ideas to improve farmer involvement were developed. The principles of a decision support system which evaluated the issue of cross-contamination due to handling of product by the inspector were developed. Epidemiological principles of chemical residues in slaughter animals were investigated. A number of statistical quality control tests were applied to known data sets to evaluate what sample sizes would be required to detect changing trends or spatial paterns. Temporal simulations were performed to determine how well clusters in time could be detected. The Moving Average approach was used and it appeared that with the given data set sample sizes well beyond those feasible to achieve would be required. Spatial analyses with a number of different statistics were performed. In this case also, large sample sizes were required for reliable results. It was concluded that use of a risk analysis model to define a risk-reduction strategy targeted to avoid any significant risk to the consumer offered a much more effective tool than a fixed sampling system. This model combines a range of possible risk reduction measures in various mixes, and determines whether or not each of the tested strategies achieves the goal of making it very improbable that a consumer would be exposed to sufficient levels of chemical residues in food to even constitute some minimal public health risk

Preventing Hospital Acquired Infections Through a Workflow-Based Cyber-Physical System

Hospital acquired infections (HAI) are infections acquired within the hospital from healthcare workers, patients or from the environment, but which have no connection to the initial reason for the patient's hospital admission. HAI are a serious world-wide problem, leading to an increase in mortality rates, duration of hospitalisation as well as significant economic burden on hospitals. Although clear preventive guidelines exist, studies show that compliance to them is frequently poor. This paper details the software perspective for an innovative, business process software based cyber-physical system that will be implemented as part of a European Union-funded research project. The system is composed of a network of sensors mounted in different sites around the hospital, a series of wearables used by the healthcare workers and a server side workflow engine. For better understanding, we describe the system through the lens of a single, simple clinical workflow that is responsible for a significant portion of all hospital infections. The goal is that when completed, the system will be configurable in the sense of facilitating the creation and automated monitoring of those clinical workflows that when combined, account for over 90\% of hospital infections.Comment: Proceedings of ENASE 2016, ISBN: 978-989-758-189-

Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis

Background: Infections due to antibiotic-resistant bacteria are threatening modern health care. However, estimating their incidence, complications, and attributable mortality is challenging. We aimed to estimate the burden of infections caused by antibiotic-resistant bacteria of public health concern in countries of the EU and European Economic Area (EEA) in 2015, measured in number of cases, attributable deaths, and disability-adjusted life-years (DALYs). Methods: We estimated the incidence of infections with 16 antibiotic resistance–bacterium combinations from European Antimicrobial Resistance Surveillance Network (EARS-Net) 2015 data that was country-corrected for population coverage. We multiplied the number of bloodstream infections (BSIs) by a conversion factor derived from the European Centre for Disease Prevention and Control point prevalence survey of health-care-associated infections in European acute care hospitals in 2011–12 to estimate the number of non-BSIs. We developed disease outcome models for five types of infection on the basis of systematic reviews of the literature. Findings: From EARS-Net data collected between Jan 1, 2015, and Dec 31, 2015, we estimated 671 689 (95% uncertainty interval [UI] 583 148–763 966) infections with antibiotic-resistant bacteria, of which 63·5% (426 277 of 671 689) were associated with health care. These infections accounted for an estimated 33 110 (28 480–38 430) attributable deaths and 874 541 (768 837–989 068) DALYs. The burden for the EU and EEA was highest in infants (aged <1 year) and people aged 65 years or older, had increased since 2007, and was highest in Italy and Greece. Interpretation: Our results present the health burden of five types of infection with antibiotic-resistant bacteria expressed, for the first time, in DALYs. The estimated burden of infections with antibiotic-resistant bacteria in the EU and EEA is substantial compared with that of other infectious diseases, and has increased since 2007. Our burden estimates provide useful information for public health decision-makers prioritising interventions for infectious diseases

Improving influenza vaccine virus selectionReport of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14–16 June 2010

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90035/1/j.1750-2659.2011.00277.x.pd