A modelling approach to estimate the incidence of salmonellosis in humans in Portugal

Dissertação de Mestrado Integrado em Medicina VeterináriaEstimates of foodborne illness are relevant for setting food safety priorities and making public health policies. Salmonella spp. is one of the most important pathogens causing foodborne disease. In 2010, despite its progressive decrease in the European Union (EU), the incidence of salmonellosis was still 21.5 cases per 100,000 inhabitants, with a total of 99,020 confirmed cases of human salmonellosis reported by the 31 countries of the EU Member States (MSs). The objectives of this study are to estimate the burden of illness of salmonellosis in Portugal, to account for the domestically acquired, foodborne illness, while identifying data gaps and areas for further research. Estimates of illness due to Salmonella were based on data from 2000-2010 of the Portuguese reported laboratory-based surveillance system, relevant international literature and the Portuguese census population for 2010. The model approach - Burden of Illness (BoI) - defined as the impact of a health problem in an area or population measured by the incidence or number of cases, required accounting for underreporting and underdiagnosis, and estimating the proportion of illness domestically acquired and through foodborne transmission. The uncertainty was accounted with Monte Carlo simulations with 100,000 iterations, generating a mean estimate and 90% credible interval, using the program @Risk 6 (Palisades Corporation). The estimated number of salmonellosis cases is approximately 93 (52,04 –111,23) times higher than the reported from surveillance (239 cases of salmonellosis in 2010). It was estimated that there were 22,201 (11,476 – 35,956) episodes of domestically acquired foodborne Salmonellosis in Portugal for 2010. The multipliers for underreporting and underdiagnosis in Portugal were of 1 and 111.23, respectively. This was the first study to estimate foodborne salmonellosis cases in Portugal.RESUMO - A análise de dados referentes à incidência de doenças de origem alimentar é crucial para a melhoria da segurança alimentar e para a revisão das políticas de Saúde Pública num país. A Salmonella spp. é um dos agentes etiológicos de zoonoses transmitidas por alimentos de maior relevância em todo o mundo. Em 2010, apesar da redução progressiva da sua incidência na União Europeia (EU), ainda se atingem valores de 21,5 casos de salmonelose por 100.000 habitantes nos 31 Estados-Membro (EM) da UE. Este estudo teve por objectivos: calcular a “Carga de Doença” causada por Salmonella spp. em Portugal; estimar os casos de salmonelose domesticamente adquiridos e de origem alimentar; e identificar lacunas no sistema de vigilância existentes, propondo linhas de investigação futuras. Os dados obtidos para calcular a incidência de salmonelose em Portugal, num período de tempo entre 2000 e 2010, foram recolhidos no sistema de vigilância de índole laboratorial; em artigos científicos e no recenseamento da população Portuguesa em 2010. O modelo criado, descrito como o que estima a “Carga da Doença”, caracteriza o impacto de um problema de saúde numa área ou população, através da incidência ou do número de casos observados. Faz ajustamentos para possíveis casos que não são reportados pelo sistema de vigilância e para casos que, apesar de existirem, não foram diagnosticados. Termina por calcular a proporção de casos de salmonelose contraídos por via alimentar e adquiridos domesticamente, incorporando a incerteza que os resultados possam acarretar. A incerteza foi calculada pelo método Monte Carlo, no programa @Risk 6 (Palisade Corporation), com simulações de 100.000 iterações, criando uma média estimativa e intervalos de credibilidade de 90%. O modelo de “Carga de Doença” gerou ocorrências de casos de salmonelose, 93 (52,04 –111,23) vezes superiores aos reportados pelo sistema de vigilância vigente (239 casos de salmonelose em 2010). Em 2010, foram estimados 22,201 (11,476 – 35,956) episódios de salmonelose transmitida por via alimentar e adquirida domesticamente. Os “multiplicadores” obtidos para a “subnotificação” e o “subdiagnóstico” foram, respectivamente, de 1 e 111,23. Este trabalho, pioneiro no cálculo da incidência de casos de salmonelose em Portugal por exposição alimentar, pretende ser um contributo válido e rigoroso para o estudo científico de uma doença, de grande incidência e da maior importância, em saúde pública

Burden of non-communicable disease studies in Europe: a systematic review of data sources and methodological choices.

BACKGROUND: Assessment of disability-adjusted life years (DALYs) resulting from non-communicable diseases (NCDs) requires specific calculation methods and input data. The aims of this study were to (i) identify existing NCD burden of disease (BoD) activities in Europe; (ii) collate information on data sources for mortality and morbidity; and (iii) provide an overview of NCD-specific methods for calculating NCD DALYs. METHODS: NCD BoD studies were systematically searched in international electronic literature databases and in grey literature. We included all BoD studies that used the DALY metric to quantify the health impact of one or more NCDs in countries belonging to the European Region. RESULTS: A total of 163 BoD studies were retained: 96 (59%) were single-country or sub-national studies and 67 (41%) considered more than one country. Of the single-country studies, 29 (30%) consisted of secondary analyses using existing Global Burden of Disease (GBD) results. Mortality data were mainly derived (49%) from vital statistics. Morbidity data were frequently (40%) drawn from routine administrative and survey datasets, including disease registries and hospital discharge databases. The majority (60%) of national BoD studies reported mortality corrections. Multimorbidity adjustments were performed in 18% of national BoD studies. CONCLUSION: The number of national NCD BoD assessments across Europe increased over time, driven by an increase in BoD studies that consisted of secondary data analysis of GBD study findings. Ambiguity in reporting the use of NCD-specific BoD methods underlines the need for reporting guidelines of BoD studies to enhance the transparency of NCD BoD estimates across Europe

Burden of disease attributable to risk factors in European countries: a scoping literature review

Objectives: Within the framework of the burden of disease (BoD) approach, disease, and injury burden estimates attributable to risk factors are a useful guide for policy formulation and priority setting in disease prevention. Considering the important differences in methods, and their impact on burden estimates, we conducted a scoping literature review to: (1) map the BoD assessments including risk factors performed across Europe, and (2) identify the methodological choices in comparative risk assessment (CRA) and risk assessment methods. Methods: We searched multiple literature databases, including grey literature websites, and targeted public health agencies' websites. Results: A total of 113 studies were included in the synthesis and further divided into independent BoD assessments (54 studies) and studies linked to the Global Burden of Disease (59 papers). Our results showed that the methods used to perform CRA varied substantially across independent European BoD studies. While there were some methodological choices that were more common than others, we did not observe patterns in terms of country, year, or risk factor. Each methodological choice can affect the comparability of estimates between and within countries and/or risk factors since they might significantly influence the quantification of the attributable burden. From our analysis, we observed that the use of CRA was less common for some types of risk factors and outcomes. These included environmental and occupational risk factors, which are more likely to use bottom-up approaches for health outcomes where disease envelopes may not be available. Conclusions: Our review also highlighted misreporting, the lack of uncertainty analysis, and the under-investigation of causal relationships in BoD studies. Development and use of guidelines for performing and reporting BoD studies will help understand differences, and avoid misinterpretations thus improving comparability among estimates.info:eu-repo/semantics/publishedVersio

Effects of management strategies on animal welfare and productivity under heat stress: a synthesis

Copyright © 2023 Morgado, Lamonaca, Santeramo, Caroprese, Albenzio and Ciliberti. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.Climate change includes different dramatic events, and among them, heat stress exposition is the strongest phenomenon affecting the livestock sector. The effects of heat stress events on animal welfare are complex and the economic impacts for the livestock sector are relevant. Management measures may contribute to improve the resilience to heat stress, but the extent to which they impact on livestock performances and management strategies depend on the magnitude of the stress conditions. Through a pioneering synthesis of existing knowledge from experiments conducted in controlled conditions, we show that management strategies, both adaptation and mitigation measures, halved the negative impacts on the ruminants' performances and welfare induced by heat stress, but the efficacy is low in extreme conditions, which in turn are more and more frequent. These novel findings emphasize the need to deepen research on more effective adaptation and mitigation measures.The authors gratefully acknowledge support from the EU-FORA fellowship programme supported from EFSA and the AXA Research Fund.info:eu-repo/semantics/publishedVersio

Burden of disease attributable to risk factors in European countries: a scoping literature review

Abstract Objectives Within the framework of the burden of disease (BoD) approach, disease and injury burden estimates attributable to risk factors are a useful guide for policy formulation and priority setting in disease prevention. Considering the important differences in methods, and their impact on burden estimates, we conducted a scoping literature review to: (1) map the BoD assessments including risk factors performed across Europe; and (2) identify the methodological choices in comparative risk assessment (CRA) and risk assessment methods. Methods We searched multiple literature databases, including grey literature websites and targeted public health agencies websites. Results A total of 113 studies were included in the synthesis and further divided into independent BoD assessments (54 studies) and studies linked to the Global Burden of Disease (59 papers). Our results showed that the methods used to perform CRA varied substantially across independent European BoD studies. While there were some methodological choices that were more common than others, we did not observe patterns in terms of country, year or risk factor. Each methodological choice can affect the comparability of estimates between and within countries and/or risk factors, since they might significantly influence the quantification of the attributable burden. From our analysis we observed that the use of CRA was less common for some types of risk factors and outcomes. These included environmental and occupational risk factors, which are more likely to use bottom-up approaches for health outcomes where disease envelopes may not be available. Conclusions Our review also highlighted misreporting, the lack of uncertainty analysis and the under-investigation of causal relationships in BoD studies. Development and use of guidelines for performing and reporting BoD studies will help understand differences, avoid misinterpretations thus improving comparability among estimates. Registration The study protocol has been registered on PROSPERO, CRD42020177477 (available at: https://www.crd.york.ac.uk/PROSPERO/ )

Methodological considerations in injury burden of disease studies across Europe: a systematic literature review

Background: Calculating the disease burden due to injury is complex, as it requires many methodological choices. Until now, an overview of the methodological design choices that have been made in the burden of disease (BoD) studies in injury populations is not available. The aim of this systematic literature review was to identify existing injury BoD studies undertaken across Europe and to comprehensively review the methodological design choices and assumption parameters that have been made to calculate years of life lost (YLL) and years lived with disability (YLD) in these studies. Methods: We searched EMBASE, MEDLINE, Cochrane Central, Google Scholar, Web of Science, and the grey literature supplemented by hand-searching, for BoD studies. We included injury BoD studies that quantified the BoD expressed in YLL, YLD, and disability-adjusted life years (DALY) in countries within the European Region between early 1990 and mid-2021. Results: We retrieved 2,914 results of which 48 performed an injury-specific BoD assessment. Single-country independent and Global Burden of Disease (GBD)-linked injury BoD studies were performed in 11 European countries. Approximately 79% of injury BoD studies reported the BoD by external cause-of-injury. Most independent studies used the incidence-based approach to calculate YLDs. About half of the injury disease burden studies applied disability weights (DWs) developed by the GBD study. Almost all independent injury studies have determined YLL using national life tables. Conclusions: Considerable methodological variation across independent injury BoD assessments was observed; differences were mainly apparent in the design choices and assumption parameters towards injury YLD calculations, implementation of DWs, and the choice of a life table for YLL calculations. The development and use of guidelines for performing and reporting of injury BoD studies are crucial to enhance transparency and comparability of injury BoD estimates across Europe and beyond.info:eu-repo/semantics/publishedVersio

Methodological considerations in injury burden of disease studies across Europe: a systematic literature review.

BACKGROUND Calculating the disease burden due to injury is complex, as it requires many methodological choices. Until now, an overview of the methodological design choices that have been made in burden of disease (BoD) studies in injury populations is not available. The aim of this systematic literature review was to identify existing injury BoD studies undertaken across Europe and to comprehensively review the methodological design choices and assumption parameters that have been made to calculate years of life lost (YLL) and years lived with disability (YLD) in these studies. METHODS We searched EMBASE, MEDLINE, Cochrane Central, Google Scholar, and Web of Science, and the grey literature supplemented by handsearching, for BoD studies. We included injury BoD studies that quantified the BoD expressed in YLL, YLD, and disability-adjusted life years (DALY) in countries within the European Region between early-1990 and mid-2021. RESULTS We retrieved 2,914 results of which 48 performed an injury-specific BoD assessment. Single-country independent and Global Burden of Disease (GBD)-linked injury BoD studies were performed in 11 European countries. Approximately 79% of injury BoD studies reported the BoD by external cause-of-injury. Most independent studies used the incidence-based approach to calculate YLDs. About half of the injury disease burden studies applied disability weights (DWs) developed by the GBD study. Almost all independent injury studies have determined YLL using national life tables. CONCLUSIONS Considerable methodological variation across independent injury BoD assessments was observed; differences were mainly apparent in the design choices and assumption parameters towards injury YLD calculations, implementation of DWs, and the choice of life table for YLL calculations. Development and use of guidelines for performing and reporting of injury BoD studies is crucial to enhance transparency and comparability of injury BoD estimates across Europe and beyond

Burden of non-communicable disease studies in Europe : a systematic review of data sources and methodological choices

Background Assessment of disability-adjusted life years (DALYs) resulting from non-communicable diseases (NCDs) requires specific calculation methods and input data. The aims of this study were to (i) identify existing NCD burden of disease (BoD) activities in Europe; (ii) collate information on data sources for mortality and morbidity; and (iii) provide an overview of NCD-specific methods for calculating NCD DALYs. Methods NCD BoD studies were systematically searched in international electronic literature databases and in grey literature. We included all BoD studies that used the DALY metric to quantify the health impact of one or more NCDs in countries belonging to the European Region. Results A total of 163 BoD studies were retained: 96 (59%) were single-country or sub-national studies and 67 (41%) considered more than one country. Of the single-country studies, 29 (30%) consisted of secondary analyses using existing Global Burden of Disease (GBD) results. Mortality data were mainly derived (49%) from vital statistics. Morbidity data were frequently (40%) drawn from routine administrative and survey datasets, including disease registries and hospital discharge databases. The majority (60%) of national BoD studies reported mortality corrections. Multimorbidity adjustments were performed in 18% of national BoD studies. Conclusion The number of national NCD BoD assessments across Europe increased over time, driven by an increase in BoD studies that consisted of secondary data analysis of GBD study findings. Ambiguity in reporting the use of NCD-specific BoD methods underlines the need for reporting guidelines of BoD studies to enhance the transparency of NCD BoD estimates across Europe

Burden of disease attributable to risk factors in European countries: a scoping literature review

Abstract Objectives Within the framework of the burden of disease (BoD) approach, disease and injury burden estimates attributable to risk factors are a useful guide for policy formulation and priority setting in disease prevention. Considering the important differences in methods, and their impact on burden estimates, we conducted a scoping literature review to: (1) map the BoD assessments including risk factors performed across Europe; and (2) identify the methodological choices in comparative risk assessment (CRA) and risk assessment methods. Methods We searched multiple literature databases, including grey literature websites and targeted public health agencies websites. Results A total of 113 studies were included in the synthesis and further divided into independent BoD assessments (54 studies) and studies linked to the Global Burden of Disease (59 papers). Our results showed that the methods used to perform CRA varied substantially across independent European BoD studies. While there were some methodological choices that were more common than others, we did not observe patterns in terms of country, year or risk factor. Each methodological choice can affect the comparability of estimates between and within countries and/or risk factors, since they might significantly influence the quantification of the attributable burden. From our analysis we observed that the use of CRA was less common for some types of risk factors and outcomes. These included environmental and occupational risk factors, which are more likely to use bottom-up approaches for health outcomes where disease envelopes may not be available. Conclusions Our review also highlighted misreporting, the lack of uncertainty analysis and the under-investigation of causal relationships in BoD studies. Development and use of guidelines for performing and reporting BoD studies will help understand differences, avoid misinterpretations thus improving comparability among estimates. Registration The study protocol has been registered on PROSPERO, CRD42020177477 (available at: https://www.crd.york.ac.uk/PROSPERO/ )

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved