Design of experiments for microbiological models

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Hazards and control of risks in artesanal meat products in Portugal

"Salpicão de Vinhais" and "Chouriça de Vinhais" are traditional dry-fermented smoked meat sausages produced in Vinhais, a small region of Trás-os-Montes. The scientific knowledge of this sausage variety is limited. This work aims to collect scientific data that could, partially, fill the gaps in knowledge regarding these products, analyse the data and develop a risk-based study, according to an internationally accepted framework and finally, to explore the effect of hypothetical risk management measures on the safety of consumers, regarding traditional dry fermented meat smoked sausages. Seventy seven samples of ―Salpicão‖ and ―Chouriça de Vinhais‖ were purchased from producers, local markets and retail stores. Their microbiological and physical chemical characteristics were analyzed. The same analyses were performed on the products during the production processes. The raw materials and ingredients were also analyzed. Regarding the pathogenic flora, Staphylococcus aureus, spores of sulphite-reducing clostridia, Escherichia coli 0157:H7, Yersinia spp. and Salmonella spp., were not detected in any of the samples analyzed; Listeria monocytogenes was detected in 14.3% of the samples. The manufacturing process, namely fermentation, ripening/drying and smoking reduced the numbers of pathogen and hygiene indicator microorganisms. According to the Commission Regulation (EC) 2073/2005, 39% of the contaminated samples of ―Salpicão‖ and ―Chouriça de Vinhais‖ were able to support growth of L. monocytogenes. A quantitative microbiological risk assessment using a probabilistic model was developed. Considering the Portuguese population, with data obtained in this work, the calculated risk of listeriosis, for the intermediate age sub-population was 0.1297 cases per year, for the perinatal sub-population, 1.3695 cases per year, and elderly sub-population 0.1995 cases per year. This means that Traditional Dry Fermented Smoked Sausages constitute a low risk for the Intermediate Age and Elderly population (less than 1 case per annum) and an intermediate risk for the Perinatal populations, considering this last group of consumers as adult pregnant women (1-10 cases per annum). The effect of several putative risk management actions such as the adoption of a Performance Objective of 10 CFU/g, 1 CFU/g and 0.04 CFU/g reduced the risk of listeriosis for all sub-groups, at the end of shelf life, by 25.5%, 58.4% and 58.6%, respectively. The effect of bacteriocinogenic strain of Pediococcus acidilactici HA6111-2, previously isolated from ―alheira‖, was studied on both ―Salpicão‖ and ―Chouriça‖, in a challenge test against a cocktail of Listeria innocua, at pilot scale. A reduction of the numbers of Listeria innocua was achieved in all batches, being the biphasic equation the model that gave the better fit. The use of a bacteriocinogenic strain added to the batter reduced the risk of listeriosis for all sub-groups by 26.7%; obtaining a final product with aw below 0.92, supposedly below the growth limits of L. monocytogenes, reduces the risk by 8.6% in all sub-groups of population; the combination of the bacteriocinogenic strain and the limit of aw 0.92 reduces the risk by 41.0%. Traditional dry fermented smoked sausages present low to medium risk to the health of consumers. The use of more restrictive Performance Objectives during processing and/or distribution will result in a further reduction of risk. A more rigorous control of final product water activity and the use of a bacteriocinogenic bioprotective culture during production may contribute significantly to reducing the risk of listeriosis in consumers of these Traditional Dry Fermented Smoked Sausages (TDFSS).O Salpicão de Vinhais e a Chouriça de Vinhais são enchidos fermentados, secos e fumados, produzidos em Vinhais, uma pequena região de Trás-os-Montes. Este trabalho pretende recolher dados científicos que possam preencher, ainda que parcialmente, os lapsos no conhecimento deste tipo de produtos, de acordo com uma abordagem aceite internacionalmente e, finalmente, explorar o efeito potencial que as medidas de gestão de risco podem ter na segurança dos consumidores, relativamente a enchidos tradicionais, fermentados, secos e fumados. Setenta e sete amostras de ―Salpicão‖ e ―Chouriça de Vinhais‖ foram compradas em produtores, mercados locais e hipermercados. As suas características microbiológicas e físico-químicas foram analizadas. As mesmas análises foram realizadas ao produto em curso, em diferentes fases do processo produtivo. As matérias-primas e ingredientes também foram analisadas. Relativamente à flora patogénica, não foram detectados esporos de Staphylococcus aureus, esporos do género Clostridia sulfito-redutores, Escherichia. coli 0157:H7, Yersinia spp. e Salmonella spp; Listeria monocytogenes foi detectada em 14.3% das amostras. O processo de fabrico, nomeadamente fermentação, maturação/secagem e fumagem reduziram o número de patogénicos e microrganismos indicadores de higiene. De acordo com o Regulamento da Comissão (CE) 2073/2005, 39% das amostras de ―Salpicão‖ e ―Chouriça de Vinhais‖ contaminadas eram capazes de permitir o crescimento de L. monocytogenes. Foi desenvolvida uma avaliação quantitativa de risco microbiológico. Considerando a população portuguesa, com os dados obtidos neste trabalho, o risco calculado de listeriose seria de 0.1297 casos por ano para a população de idade intermédia, 1.3695 casos por ano para a sub-população perinatal, e 0.1995 casos por ano para a sub-população sénior. Isto significa que Enchidos Tradicionais Secos, Fermentados e Fumados constituem um alimento de baixo risco para para a população de idade intermédia e população sénior (menos de 1 caso por ano) e são um alimento de risco intermédio para a população perinatal, ou seja, mulheres grávidas adultas (entre 1 a 10 casos por ano). A adopção de um Objectivo de ―Performance‖ de atingir 10 UFC/g, 1 UFC/g e 0,04 UFC/g no produto final reduziram o risco de listeriose para todos os sub-grupos da população, em 25.5%, 58.4% e 58.6%, respectivamente. O efeito da estirpe bacteriocinogénica de Pediococcus acidilactici HA6111-2, previamente isolada em alheira, foi estudada tanto no Salpicão como na Chourila de Vinhais, num ―challence test‖ contra um cocktail de Listeria innocua, à escala piloto. Foi observado, em todos os lotes, uma redução dos números de Listeria innocua, abaixo do limite de detecção (1.5 log UFC/g), A equação bifásica foi que forneceu o melhor ajuste da redução dos números de Listeria innocua, devido ao da estirpe bacteriocinogénica de Pediococcus acidilactici HA6111-2. A aplicação de uma estirpe bacteriocinogénica à adoba reduziu o risco de listeriose, em todos os sub-grupos populacionais em 26.7%; obter um produto final com aw inferior a 0.92 reduziu o risco de listeriose, em todos os sub-grupos populacionais em 8.6%; a combinação destes dois factores reduziu o risco de listeriose, em todos os sub-grupos populacionais em 41.0%. Os Enchidos Tradicionais Secos, Fermentados e Fumados apresentam um risco baixo ou médio para a saúde dos consumidores. A aplicação de Objectivos de ―Performance‖ durante o processamento e/ou distribuição resulta numa redução do risco. Um controlo mais rigoroso da actividade de água do produto final e o uso de uma cultura bioprotectiva bacteriocinogenica durante a produção, podem contribuir para reduzir significativamente o risco de listeriose nos consumidores deste tipo de produto tradicional

Front Propagation in Random Media

This PhD thesis deals with the problem of the propagation of fronts under random circumstances. A statistical model to represent the motion of fronts when are evolving in a media characterized by microscopical randomness is discussed and expanded, in order to cope with three distinct applications: wild-land fire simulation, turbulent premixed combustion, biofilm modeling. In the studied formalism, the position of the average front is computed by making use of a sharp-front evolution method, such as the level set method. The microscopical spread of particles which takes place around the average front is given by the probability density function linked to the underlying diffusive process, that is supposedly known in advance. The adopted statistical front propagation framework allowed a deeper understanding of any studied field of application. The application of this model introduced eventually parameters whose impact on the physical observables of the front spread have been studied with Uncertainty Quantification and Sensitivity Analysis tools. In particular, metamodels for the front propagation system have been constructed in a non intrusive way, by making use of generalized Polynomial Chaos expansions and Gaussian Processes.The Thesis received funding from Basque Government through the BERC 2014-2017 program. It was also funded by the Spanish Ministry of Economy and Competitiveness MINECO via the BCAM Severo Ochoa SEV-2013-0323 accreditation. The PhD is fundend by La Caixa Foundation through the PhD grant “La Caixa 2014”. Funding from “Programma Operativo Nazionale Ricerca e Innovazione” (PONRI 2014-2020) , “Innotavive PhDs with Industrial Characterization” is kindly acknowledged for a research visit at the department of Mathematics and Applications “Renato Caccioppoli” of University “Federico II” of Naples

An emulation-based approach for interrogating reactive transport models

We present a new approach to understand the interactions among different chemical and biological processes modelled in environmental reactive transport models (RTMs) and explore how the parameterisation of these processes influences the results of multi-component RTMs. We utilize a previously published RTM consisting of 20 primary species, 20 secondary complexes, 17 mineral reactions and 2 biologically-mediated reactions which describes bio-stimulation using sediment from a contaminated aquifer. We choose a subset of the input parameters to vary over a range of values. The result is the construction of a new dataset that describes the model behaviour over a range of environmental conditions. Using this dataset to train a statistical model creates an emulator of the underlying RTM. This is a condensed representation of the original RTM that facilitates rapid exploration of a broad range of environmental conditions and sensitivities. As an illustration of this approach, we use the emulator to explore how varying the boundary conditions in the RTM describing the aquifer impacts the rates and volumes of mineral precipitation. A key result of this work is the recognition of an unanticipated dependency of pyrite precipitation on pCO2 in the injection fluid due to the stoichiometry of the microbially-mediated sulphate reduction reaction. This complex relationship was made apparent by the emulator, while the underlying RTM was not specifically constructed to create such a feedback. We argue that this emulation approach to sensitivity analysis for RTMs may be useful in discovering such new coupled sensitives in geochemical systems and for designing experiments to optimise environmental remediation. Finally, we demonstrate that this approach can maximise specific mineral precipitation or dissolution reactions by using the emulator to find local maxima, which can be widely applied in environmental systems.</p

Front propagation in random media.

244 p.This PhD thesis deals with the problem of the propagation of fronts under random circumstances. Astatistical model to represent the motion of fronts when are evolving in a media characterized bymicroscopical randomness is discussed and expanded, in order to cope with three distinctapplications: wild-land fire simulation, turbulent premixed combustion, biofilm modeling. In thestudied formalism, the position of the average front is computed by making use of a sharp-frontevolution method, such as the level set method. The microscopical spread of particles which takesplace around the average front is given by the probability density function linked to the underlyingdiffusive process, that is supposedly known in advance. The adopted statistical front propagationframework allowed a deeper understanding of any studied field of application. The application ofthis model introduced eventually parameters whose impact on the physical observables of the frontspread have been studied with Uncertainty Quantification and Sensitivity Analysis tools. Inparticular, metamodels for the front propagation system have been constructed in a non intrusiveway, by making use of generalized Polynomial Chaos expansions and Gaussian Processes.bcam:basque center for applied mathematic

Supply Chain Optimization and Economic Analysis of Using Industrial Spent Microbial Biomass (SMB) in Agriculture

This thesis uses a mixed integer program to minimize the transport and storage cost of delivering spent microbial biomass (SMB), a bio-coproduct resulting from the production of 1,3-propanediol, to farm fields as a soil amendment and fertilizer substitute. The case study examines focuses on a bioprocessing facility and corn production in East Tennessee. The results indicate on-farm storage of SMB minimizes transport and storage costs of the material. A one percent decrease in the moisture content of SMB results in less than five percent decrease in the total transport and storage costs. Future research should investigate farmers\u27 willingness to adopt the practice, cost sharing design, and to apply SMB to other crop production

Parameters uncertainties and error propagation in modified atmosphere packaging modelling

IATE Axe 5 : Application intégrée de la connaissance, de l’information et des technologies permettant d’accroître la qualité et la sécurité des aliments Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699International audienceMathematical models are instrumental tools to predict gas (O2 and CO2) evolution in headspaces of Modified Atmosphere Packaging (MAP). Such models simplify the package design steps as they allow engineers to estimate the optimal values of packaging permeability for maintaining the quality and safety of the packed food. However, these models typically require specifying several input parameter values (such as maximal respiration rates) that are obtained from experimental data and are characterized by high uncertainties due to biological variation. Although treating and modelling this uncertainty is essential to ensure the robustness of designed MAPs, this subject has seldom been considered in the literature. In this work, we describe an optimisation system based on a MAP mathematical model that determines optimal permeabilities of packaging, given certain food parameters. To integrate uncertainties in the model while keeping the optimisation computational burden relatively low, we propose to use an approach based on interval analysis rather than the more classical probabilistic approach. The approach has two advantages: it makes a minimal amount of unverified assumption concerning uncertainties, and it requires only a few evaluations of the model. The results of these uncertainty studies are optimal values of permeabilities described by fuzzy sets. This approach was conducted on three case studies: chicory, mushrooms and blueberry. Sensitivity analysis on input parameters in the model MAP was also performed in order to point out that parameter influences are dependent on the considered fruit or vegetable. A comparison of the interval analysis methodology with the probabilistic one (known as Monte Carlo) was then performed and discussed

Life Cycle Environmental Impacts for Anaerobic Treatment of Domestic Wastewater

The electricity requirement for aeration in conventional activated sludge treatment of domestic wastewater contributes to high costs and greenhouse gas emissions. Anaerobic treatment, on the other hand, requires no aeration and produces methane that can be converted to electricity and heat. However, the effluent from anaerobic treatment contains dissolved methane¿a potent greenhouse gas¿that would ultimately be released to the atmosphere. Therefore, there is a need to assess the life cycle environmental and economic impacts of anaerobic and aerobic treatment technologies to understand the long-term sustainability of these wastewater treatment options