A Two-Dimensional Multi-Species Model for Different Listeria Monocytogenes Biofilm Structures and Its Numerical Simulation

[Abstract] In this work we propose a two-dimensional multi-species model to describe the dynamics of biofilms formed by the pathogenic bacteria Listeria monocytogenes. Different Listeria monocytogenes strains produce biofilms with different structures, namely flat, honeycomb and clustered. Previous works showed that glucose impaired uptake and the appearance of damaged or dead cells are critical mechanisms underlying Listeria monocytogenes biofilm dynamics. Here we explicitly propose an extension of the two-dimensional multi-species model proposed by Alpkist and Klapper to account for those mechanisms. The result is a continuous two-dimensional multi-species model with non-linear detachment and mass action nutrient consumption. Moreover, we also propose a set of efficient numerical methods to solve the coupled model and we have developed their computer implementation from scratch in C/C++. Mainly based on finite differences schemes, these numerical techniques include Crank-Nicolson schemes for time discretization, Gibou’s ghost node techniques and level set methods to cope with the free boundary associated to the determination of the time-dependent biofilm domain. To finish with, we compare our simulation results with the dynamics of real biofilms as observed in the laboratory. More precisely, by using model parameters calibrated to experiments, the numerical results clearly illustrate the performance of the proposed model and the numerical methods to reproduce the real dynamics of flat, clustered and honeycomb structures shown by different Listeria monocytogenes strains.ALN and CV acknowledge the funding by MINECO from Spanish Government (Grant MTM2016-76497-R) and by Xunta de Galicia (Grants GRC2014/044 and ED431C2018/033). ALN acknowledges FPU fellowship (FPU13/02191) from the Spanish Government program MECD-FPU. CV and ALN as members of CITIC also akcnowledge the grant ED431G 2019/01, funded by Consellería de Educación, Universidade e Formación Profesional of Xunta de Galicia through FEDER funds with 80%, from FEDER Galicia 2014-2020 Program and 20% from Secretaría Xeral de Universidades. EBC acknowledges funding from Contrato Programa and grant Ref. IN607B 2017/02 from Xunta de Galicia. All grants include FEDER fundsXunta de Galicia; GRC2014/044Xunta de Galicia; ED431C2018/033Xunta de Galicia; ED431G 2019/01Xunta de Galicia; IN607B 2017/0

Overview on the hydrodynamic conditions found in industrial systems and its impact in (bio)fouling formation

Supplementary data to this article can be found online at https://doi.org/10.1016/j.cej.2021.129348.Biofouling is the unwanted accumulation of deposits on surfaces, composed by organic and inorganic particles and (micro)organisms. Its occurrence in industrial equipment is responsible for several drawbacks related to operation and maintenance costs, reduction of process safety and product quality, and putative outbreaks of pathogens. The understanding on the role of operating conditions in biofouling development highlights the hydrodynamic conditions as key parameter. In general, (bio)fouling occurs in a higher extension when laminar flow conditions are used. However, the characteristics and resilience of biofouling are highly dependent on the hydrodynamic conditions under which it is developed, with turbulent conditions being associated to recalcitrant biodeposits. In industrial settings like heat exchangers, fluid distribution networks and stirred tanks, hydrodynamics play a dual function, affecting the process effectiveness while favouring biofouling formation. This review summarizes the hydrodynamics played in conventional industrial settings and provides an overview on the relevance of hydrodynamic conditions in biofouling development as well as in the effectiveness of industrial processes.This work was financially supported by: Base Funding - UIDB/00511/2020 of LEPABE and UIDB/00081/2020 of CIQUP funded by national funds through the FCT/MCTES (PIDDAC); Project Bio cide_for_Biofilm - PTDC/BII-BTI/30219/2017 - POCI-01-0145-FEDER 030219, ABFISH – PTDC/ASP-PES/28397/2017 - POCI-01-0145- FEDER-028397 and ALGAVALOR - POCI-01-0247-FEDER-035234, fun ded by FEDER funds through COMPETE2020 – Programa Operacional Competitividade e Internacionalizaçao ˜ (POCI) and by national funds (PIDDAC) through FCT/MCTES; Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER 000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte; FCT/ SFRH/BD/147276/2019 (Susana Fernandes) and SFRH/BSAB/150379/2019 (Manuel Simoes).info:eu-repo/semantics/publishedVersio

Contributions to mathematical modelling and numerical simulation of biofilms

Programa Oficial de Doutoramento en Métodos Matemáticos e Simulación Numérica en Enxeñaría e Ciencias Aplicadas. 551V01[Abstract]The main goal of this PhD work is the development and numerical resolution of mathematical models that simulate the dynamics of bacterial biofilm systems, paying special attention to those biofilms formed by the Listeria monocytogenes, a pathogen of special relevance in food safety. A biofihn is a layer of microorganisms attached to a surface and protected by a matrix of exopolysaccharides. Biofilm structures difficult the removal of microorganisms, thus the study of the type of structures formed throughout a biofilm life cycle is key to design elimination techniques. In the present work, we develop different models that simulate the dynamics of biofilms formed by different strains of L. monocytogenes. We start with a 1D model that can be used to describe the formation of flat biofilms. Afterwards, we apply the acquired knowledge to develop a 2D model capable of describing more complex structures. All this models are solved with efficient numerical methods and robust numerical techniques, such as the Level Set method, that guarantees the good behaviour of the obtained solutions. Finally, the numerical results are compared with the experimental measurements obtained in the Instituto de Investigaciones Marinas, CSIC (Vigo, Spain), and the Micalis Institute, INRA (Massy, France).[Resumen]El objetivo fundamental de esta tesis consiste en el desarrollo y resolución numérica de modelos matemáticos que reproduzcan la dinámica de biopelículas, en especial, aquellas formadas por Listeria monocytogenes, un patógeno especialmente relevante en la seguridad alimentaria. Una biopelícula es una capa de microorganismos adheridos a una superficie y protegidos por una matriz de expolisacáridos. La estructura de las biopelículas hace difícil la eliminación de los microorganismos, de ahí que sea fillldamental estudiar el tipo de estructuras que se forman durante la vida de una biopelícula para poder diseñar nuevas técnicas de eliminación. En el presente trabajo, desarrollamos modelos que simulan la dinámica de biopelículas de diferentes cepas de L. monocytogenes. Comenzamos estableciendo un modelo 1D capaz de describir la formación de biopelículas planas para, posteriormente, aplicar los conocimientos adquiridos al desarrollo de un modelo 2D capaz de describir estructuras más complejas. Estos modelos se resuelven con métodos numéricos eficientes y técnicas numéricas robustas, como el método Level Set, que garantizan el buen comportamiento de las soluciones. Finalmente, los resultados obtenidos son comparados con las imágenes de microscopía procedentes de experimentos realizados en el Instituto de Investigaciones Marinas, CSIC (Vigo, España) yen el Micalis Institute, INRA (Massy, Francia).[Resumo ] O obxectivo fundamental desta tese é o desenvolvemento e resolución numérica de modelos matemáticos que reproduzan a dinámica de biopelículas, en especial, aquelas formadas por Lisieria monocytogenes, un patóxeno de especial relevancia na seguridade alimentaria. Unha biopelícula é unha capa de microorganismos adheridos a unha superficie e protexidos por unha matriz de expolisacáridos. A estructura das biopelículas fai difícil a eliminación dos microorganismos, de aí que sexa fundamental estudar o tipo de estructuras que se forman ao longo da vida dunha biopelícula para poder deseñar novas técnicas de eliminación. No presente traballo, desenvolvemos modelos que simulan a evolución de diferentes cepas de L. monocytogenes. Comezamos establecendo un modelo 1D capaz de describir a dinámica de cepas chás para, posteriormente, aplicar os coñecementos adquiridos ao desenvolvemento dun modelo 2D capaz de describir estruturas máis complexas. Todos estes modelos resólvense con métodos numéricos eficientes e técnicas numéricas robustas, como o método Level Set, que garanten o bo comportamento das solucións. Finalnlente, os resultados obtidos compáranse coas imáxes de microscopía obtidas en experimentos realizados no Instituto de Investigacions Mariñas, CSIC (Vigo, España) e no Micalis Institute, INRA (Massy, Francia)

11th International Conference on Predictive Modelling in Food: book of abstracts

It is our great pleasure to welcome you in Bragança, Portugal, for the 11th International Conference of Predictive Modelling in Food (ICPMF11). Since 1992, ten ICPMF editions have taken place, providing a forum for the exchange of ideas, identification of research needs and novel approaches for the advancement of predictive modelling towards ensuring safety and quality of foods. Bragança is a typically-Portuguese old town (Romanic origin dates back to the 10th century), located by the Natural Park of Montesinho – one of the wildest forest zones of Europe – and the Douro Valley – the third oldest protected wine region in the world; and surrounded by traditional villages of a distinctive rustic beauty. Bragança houses several traditional industries producing a myriad of local foods, such as cheese, fermented meats, wine, chestnuts and honey, which provide substantial economic sustainability to the region. ICPMF11 reunites food researchers, stakeholders, risk assessors and users of predictive models to present recent developments and trends in modelling approaches for food quality, safety and sustainability. We succeeded to gather a significant number of delegates from over the world to participate in a comprehensive scientific programme that includes keynote lectures, oral communications and posters, allocated in sessions focusing on: . Advances in predictive microbiology modelling . Predictive modelling in innovative food processing and preservation technologies . Advances in microbial dynamics and interactions . Advances in software and database tools . Meta-analysis protocols and applications . Advances in risk assessment methods and integration of omics techniques . Advances in predictive modelling in food quality and safety . Predictive mycology . Individual cell and whole-cell modelling Apart from those, ICPMF11 features for the first time a special session dedicated to “Innovative approaches for ensuring safety of traditional foods” and the Round Table: “Assuring the Safety of Traditional Foods: A Scientific Contribution to Protecting our Cultural Heritage”. We, as food researchers based in a Mediterranean mountain region, are aware that the production of traditional foods plays a key role in the development of rural regions, since the agricultural commodities used as raw materials are generally produced locally, allowing and stimulating local commercialisation, thus contributing to a sustainable environment, and employment in rural populations. It was inspiring for us to have received many submissions from both developed and developing countries on the valorisation of traditional foods through the application of up-to-date modelling research. Besides that, one morning workshop and three afternoon tutorials were programmed during the day before the scientific programme. The workshop “How to benefit from the Risk Assessment Modelling and Knowledge Integration Platform (RAKIP)” was organised by Matthias Filter. The parallel tutorials “Towards an integrated predictive software map: Practical examples of use of predictive microbiology software tools for food safety and quality”; “Advanced methods in predictive microbiology” and “Topics in quantitative microbial risk assessment using R” were organised by Fernando Pérez-Rodríguez, Pablo Fernández, Alberto Garre and Mariem Ellouze; by Lihan Huang, Cheng-An Hwang and Vasco Cadavez; and by Patrick Njage and Ana Sofia Ribeiro Duarte, respectively. We thank these organisers for their proposals. Abstracts, reviewed by the ICPMF11 Scientific Committee, are published in the present Book of Abstracts while peer-reviewed original research articles will be invited to be published in ICPMF11 Special Issues in the International Journal of Food Microbiology and Microbial Risk Analysis. To stimulate the participation of postgraduate students and young researchers, two kinds of awards were arranged: the Young Researcher Best Oral Presentation prizes, sponsored by Elsevier; and the Developing Scientist Best Poster prizes, sponsored by the International Committee on Food Microbiology and Hygiene (ICFMH) of the International Union of Microbiological Societies (IUMS). For the first time, this ICPMF edition gives out two awards for the Senior Researcher Best Oral Presentation, sponsored by the open-access journal Foods – MDPI. In addition to the scientific programme, we prepared an exciting social programme for delegates to appreciate the rich culture, gastronomy and traditions of Bragança, w includes welcome reception, live music, tasting of regional food and a gala dinner in the Castle of Bragança. We look forward to lively discussions, and hope that this meeting will give you the opportunity to strengthen friendship and cooperation, and build new contacts for future research endeavours.info:eu-repo/semantics/publishedVersio

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

Dynamic Optimal Control for Multi-chemotherapy Treatment of Dual Listeriosis Infection in Human and Animal Population

Following the rising cases of high hospitalization versa-vise incessant fatality rates and the close affinity of listeriosis with HIV/AIDS infection, which often emanates from food-borne pathogens associated with listeria monocytogenes infection, this present paper seek and formulated as penultimate model, an 8-Dimensional classical mathematical Equations which directly accounted for the biological interplay of dual listeriosis virions with dual set of population (human and animals). The model was studied under multiple chemotherapies (trimethoprim-sulphamethoxazole with a combination of penicillin or ampicillin and/or gentamicin). Using ODE’s, the positivity and boundedness of system solutions was investigated with model presented as an optimal control problem. In the analysis that follows, the study explored classical Pontryagin’s Maximum Principle with which the model optimality control system as well as existence and uniqueness of the control system were established. In correlating the derived model with clinical implications, numerical validity of the model was conducted. Results indicated that under cogent and adherent to specify multiple chemotherapies, maximal recovery of both human and animal infected population was tremendously achieved with consequent rapid decline to near zero infection growth. The study therefore suggests further articulation of more chemotherapies and early application at onset of infection for a visible elimination of listeriosis infection

The emergence of biofilms:Computational and experimental studies

The response of biofilms to any external stimuli is a cumulative response aggregated from individual bacteria residing within the biofilm. The organizational complexity of biofilm can be studied effectively by understanding bacterial interactions at cell level. The overall aim of the thesis is to explore the complex evolutionary behaviour of bacterial biofilms. This thesis is divided into three major studies based on the type of perturbation analysed in the study. The first study analyses the physics behind the development of mushroom-shaped structures from the influence of nutrient cues in biofilms. Glazier-Graner-Hogeweg model is used to simulate the cell characteristics. From the study, it is observed that chemotaxis of bacterial cells towards nutrient source is one of the major precursors for formation of mushroom-shaped structures. The objective of the second study is to analyse the impact of environmental conditions on the inter-biofilm quorum sensing (QS) signalling. Using a hybrid convection-diffusion-reaction model, the simulations predict the diffusivity of QS molecules, the spatiotemporal variations of QS signal concentrations and the competition outcome between QS and quorum quenching mutant bacterial communities. The mechanical effects associated with the fluid-biofilm interaction is addressed in the third study. A novel fluid-structure interaction model based on fluid dynamics and structural energy minimization is developed in the study. Model simulations are used to analyse the detachment and surface effects of the fluid stresses on the biofilm. In addition to the mechanistic models described, a separate study is carried out to estimate the computational efficiency of the biofilm simulation models