Molecular Epidemiology of Escherichia coli isolates from Environmental, Food and Clinical Sources

In the present study diversity of E. coli in the water samples of Cochin estuary were studied for a period of 3 years ranging from January 2010- December 2012. The stations were selected based on the closeness to satellite townships and waste input. Two of the stations (Chitoor and Thevara) were fixed upstream, two in the central part of the estuary namely Bolgatty and Off Marine Science Jetty, and one at the Barmouth. Diversity was assessed in terms of serotypes, phylogenetic groups and genotypes. Two groups of seafood samples such as fish and shellfish collected from the Cochin estuary were used for isolation of E. coli. One hundred clinical E. coli isolates were collected from one public health centre, one hospital and five medical labs in and around Cochin City, Kerala. From our results it was clear that pathogen cycling is occurring through food, water and clinical sources. Pathogen cycling through food is very common and fish and shellfish that harbour these strains might pose potential health risk to consumer. Estuarine environment is a melting pot for various kinds of wastes, both organic and inorganic. Mixing up of waste water from various sources such as domestic, industries, hospitals and sewage released into these water bodies resulting in the co-existence of E. coli from various sources thus offering a conducive environment for horizontal gene transfer. Opportunistic pathogens might acquire genes for drug resistance and virulence turning them to potential pathogens. Prevalence of ExPEC in the Cochin estuary, pose threat to people who use this water for fishing and recreation. Food chain also plays an important role in the transit of virulence genes from the environments to the human. Antibiotic resistant E. coli are widespread in estuarine water, seafood and clinical samples, for reasons well known such as indiscriminate use of antibiotics in animal production systems, aquaculture and human medicine. Since the waste water from these sources entering the estuary provides selection pressure to drug resistant mutants in the environment. It is high time that the authorities concerned should put systems in place for monitoring and enforcement to curb such activities. Microbial contamination can limit people’s enjoyment of coastal waters for contact recreation or shellfish-gathering. E. coli can make people sick if they are present in high levels in water used for contact recreation or shellfish gathering. When feeding, shellfish can filter large volumes of seawater, so any microorganisms present in the water become accumulated and concentrated in the shellfish flesh. If E. coli contaminated shellfish are consumed the impact to human health includes gastroenteritis, urinary tract infections (UTIs), and bacteraemia. In conclusion, the high prevalence of various pathogenic serotypes and phylogenetic groups, multidrug-resistance, and virulence factor genes detected among E. coli isolates from stations close to Cochin city is a matter of concern, since there is a large reservoir of antibiotic resistance genes and virulence traits within the community, and that the resistance genes and plasmid-encoded genes for virulence were easily transferable to other strains. Given the severity of the clinical manifestations of the disease in humans and the inability and/or the potential risks of antibiotic administration for treatment, it appears that the most direct and effective measure towards prevention of STEC and ExPEC infections in humans and ensuring public health may be considered as a priority.

Food scares and trust: A European study

The complex interactions between the determinants of food purchase under risk are explored using the SPARTA model, based on the theory of planned behaviour, and estimated through a combination of multivariate statistical techniques. The application investigates chicken consumption choices in two scenarios: ( a) a 'standard' purchasing situation; and (b) following a hypothetical Salmonella scare. The data are from a nationally representative survey of 2,725 respondents from five European countries: France, Germany, Italy, the Netherlands and the United Kingdom. Results show that the effects and interactions of behavioural determinants vary significantly within Europe. Only in the case of a food scare do risk perceptions and trust come into play. The policy priority should be on building and maintaining trust in food and health authorities and research institutions, while food chain actors could mitigate the consequences of a food scare through public trust. No relationship is found between socio-demographic variables and consumer trust in food safety information.

Food crops in a changing climate

Changes in both the mean and the variability of climate, whether naturally forced, or due to human activities, pose a threat to crop production globally. This paper summarizes discussions of this issue at a meeting of the Royal Society in April 2005. Recent advances in understanding the sensitivity of crops to weather, climate and the levels of particular gases in the atmosphere indicate that the impact of these factors on crop yields and quality may be more severe than previously thought. There is increasing information on the importance to crop yields of extremes of temperature and rainfall at key stages of crop development. Agriculture will itself impact on the climate system and a greater understanding of these feedbacks is needed. Complex models are required to perform simulations of climate variability and change, together with predictions of how crops will respond to different climate variables. Variability of climate, such as that associated with El Niño events, has large impacts on crop production. If skilful predictions of the probability of such events occurring can be made a season or more in advance, then agricultural and other societal responses can be made. The development of strategies to adapt to variations in the current climate may also build resilience to changes in future climate. Africa will be the part of the world that is most vulnerable to climate variability and change, but knowledge of how to use climate information and the regional impacts of climate variability and change in Africa is rudimentary. In order to develop appropriate adaptation strategies globally, predictions about changes in the quantity and quality of food crops need to be considered in the context of the entire food chain from production to distribution, access and utilization. Recommendations for future research priorities are given.

Long-chain n-3 PUFA: intakes in the UK and the potential of a chicken meat prototype to increase them

With the wide acceptance of the long-chain (LC) n-3 PUFA EPA and DHA as important nutrients playing a role in the amelioration of certain diseases, efforts to understand factors affecting intakes of these fatty acids along with potential strategies to increase them are vital. Widespread aversion to oil-rich fish, the richest natural source of EPA and DHA, highlights both the highly suboptimal current intakes in males and females across all age-groups and the critical need for an alternative supply of EPA and DHA. Poultry meat is a popular and versatile food eaten in large quantities relative to other meats and is open to increased LC n-3 PUFA content through manipulation of the chicken's diet to modify fatty acid deposition and therefore lipid composition of the edible tissues. It is therefore seen as a favourable prototype food for increasing human dietary supply of LC n-3 PUFA. Enrichment of chicken breast and leg tissue is well established using fish oil or fishmeal, but concerns about sustainability have led to recent consideration of algal biomass as an alternative source of LC n-3 PUFA. Further advances have also been made in the quality of the resulting meat, including achieving acceptable flavour and storage properties as well as understanding the impact of cooking on the retention of fatty acids. Based on these considerations it may be concluded that EPA- and DHA-enriched poultry meat has a very positive potential future in the food chain.

UK Food Standards Agency cis-monounsaturated fatty acid workshop report

The UK Food Standards Agency convened a group of expert scientists to review current research investigating the optimal dietary intake for n-9 cis-monounsaturated fatty acids (MUFA). The aim was to review the mechanisms underlying the reported beneficial effects of MUFA on CHD risk, and to establish priorities for future research. The issue of optimal MUFA intake is contingent upon optimal total fat intake; however, there is no consensus of opinion on what the optimal total fat intake should be. Thus, it was recommended that a large multi-centre study should look at the effects on CHD risk of MUFA replacement of saturated fatty acids in relation to varying total fat intakes; this study should be of sufficient size to take account of genetic variation, sex, physical activity and stage of life factors, as well as being of sufficient duration to account for adaptation to diets. Recommendations for studies investigating the mechanistic effects of MUFA were also made. Methods of manipulating the food chain to increase MUFA at the expense of saturated fatty acids were also discussed.

Identifying antimicrobial resistance genes of human clinical relevance within Salmonella isolated from food animals in Great Britain

To investigate the occurrence of antimicrobial resistance genes of human clinical relevance in Salmonella isolated from livestock in Great Britain. Two hundred and twenty-five Salmonella enterica isolates were characterized using an antimicrobial resistance gene chip and disc diffusion assays. Plasmid profiling, conjugation experiments and identification of Salmonella genomic island 1 (SGI1) were performed for selected isolates. Approximately 43% of Salmonella harboured single or multiple antimicrobial resistance genes with pig isolates showing the highest numbers where 96% of Salmonella Typhimurium harboured one or more resistance genes. Isolates harbouring multiple resistances divided into three groups. Group 1 isolates harboured ampicillin/streptomycin/sulphonamide/tetracycline resistance and similar phenotypes. This group contained isolates from pigs, cattle and poultry that were from several serovars including Typhimurium, 4,[5],12:i:-, Derby, Ohio and Indiana. All Group 2 isolates were from pigs and were Salmonella Typhimurium. They contained a non-sul-type class 1 integron and up to 13 transferrable resistances. All Group 3 isolates harboured a class 1 integron and were isolated from all animal species included in the study. Most isolates were Salmonella Typhimurium and harboured SGI1. Salmonella isolated from livestock was shown to harbour antimicrobial resistance genes although no or little resistance to third-generation cephalosporins or ciprofloxacin, respectively, was detected. The preponderance in pigs of multidrug-resistant Salmonella Typhimurium makes it important to introduce control measures such as improved biosecurity to ensure that they do not pass through the food chain and limit human therapeutic options.

Modelling the bioaccumulation of persistent organic pollutants in agricultural food chains for regulatory exposure assessment

New models for estimating bioaccumulation of persistent organic pollutants in the agricultural food chain were developed using recent improvements to plant uptake and cattle transfer models. One model named AgriSim was based on K OW regressions of bioaccumulation in plants and cattle, while the other was a steady-state mechanistic model, AgriCom. The two developed models and European Union System for the Evaluation of Substances (EUSES), as a benchmark, were applied to four reported food chain (soil/air-grass-cow-milk) scenarios to evaluate the performance of each model simulation against the observed data. The four scenarios considered were as follows: (1) polluted soil and air, (2) polluted soil, (3) highly polluted soil surface and polluted subsurface and (4) polluted soil and air at different mountain elevations. AgriCom reproduced observed milk bioaccumulation well for all four scenarios, as did AgriSim for scenarios 1 and 2, but EUSES only did this for scenario 1. The main causes of the deviation for EUSES and AgriSim were the lack of the soil-air-plant pathway and the ambient air-plant pathway, respectively. Based on the results, it is recommended that soil-air-plant and ambient air-plant pathway should be calculated separately and the K OW regression of transfer factor to milk used in EUSES be avoided. AgriCom satisfied the recommendations that led to the low residual errors between the simulated and the observed bioaccumulation in agricultural food chain for the four scenarios considered. It is therefore recommended that this model should be incorporated into regulatory exposure assessment tools. The model uncertainty of the three models should be noted since the simulated concentration in milk from 5th to 95th percentile of the uncertainty analysis often varied over two orders of magnitude. Using a measured value of soil organic carbon content was effective to reduce this uncertainty by one order of magnitude.

Trophic cul-de-sac, Pyrazus ebeninus, limits trophic transfer through an estuarine detritus-based food web

The importance to food-webs of trophic cul-de-sacs, species that channel energy flow away from higher trophic levels, is seldom considered outside of the pelagic systems in which they were first identified. On intertidal mudflats, inputs of detritus from saltmarshes, macroalgae or microphytobenthos are generally regarded as a major structuring force underpinning food-webs and there has been no consideration of trophic cul-de-sacs to date. A fully orthogonal three-factor experiment manipulating the density of the abundant gastropod, Pyrazus ebeninus, detritus and macrobenthic predators on a Sydney mudflat revealed large deleterious effects of the gastropod, irrespective of detrital loading or the presence of predators. Two months after experimental manipulation, the standing-stock of microphytobenthos in plots with high (44 per m²) densities of P. ebeninus was 20% less than in plots with low (4 per m²) densities. Increasing densities of P. ebeninus from low to high halved the abundance of macroinvertebrates and the average number of species. In contrast, the addition of detritus had differing effects on microphytobenthos (positively affected) and macroinvertebrates (negatively affected). Over the two-months of our experiment, no predatory mortality of P. ebeninus was observed and high densities of P. ebeninus decreased impacts of predators on macroinvertebrate abundances. Given that the dynamics of southeast Australian mudflats are driven more by disturbance than seasonality in predators and their interactions with prey, it is likely that Pyrazus would be similarly resistant to predation and have negative effects on benthic assemblages at other times of the year, outside of our study period. Thus, in reducing microphytobenthos and the abundance and species richness of macrofauna, high abundances of the detritivore P. ebeninus may severely limit the flow of energy up the food chain to commercially-important species. This study therefore suggests that trophic cul-de-sacs are not limited to the eutrophied pelagic systems in which they were first identified, but may exist in other systems as well.

Food web structure in a tropical stream ecosystem

This study investigated the structure and properties of a tropical stream food web in a small spatial scale, characterizing its planktonic, epiphytic and benthic compartments. The study was carried out in the Potreirinho Creek, a second-order stream located in the south-east of Brazil. Some attributes of the three subwebs and of the conglomerate food web, composed by the trophic links of the three compartments plus the fish species, were determined. Among compartments, the food webs showed considerable variation in structure. The epiphytic food web was consistently more complex than the planktonic and benthic webs. The values of number of species, number of links and maximum food chain length were significantly higher in the epiphytic compartment than in the other two. Otherwise, the connectance was significantly lower in epiphyton. The significant differences of most food web parameters were determined by the increase in the number of trophic species, represented mainly by basal and intermediate species. High species richness, detritus-based system and high degree of omnivory characterized the stream food web studied. The aquatic macrophytes probably provide a substratum more stable and structurally complex than the sediment. We suggest that the greater species richness and trophic complexity in the epiphytic subweb might be due to the higher degree of habitat complexity supported by macrophyte substrate. Despite differences observed in the structure of the three subwebs, they are highly connected by trophic interactions, mainly by fishes. The high degree of fish omnivory associated with their movements at different spatial scales suggests that these animals have a significant role in the food web dynamic of Potreirinho Creek. This interface between macrophytes and the interconnections resultant from fish foraging, diluted the compartmentalization of the Potreirinho food web.

Data to investigate the role of Pomatoschistus microps in intertidal food webs, sampled off the island of Sylt

Ecological network analysis (ENA) was used to study the effects of Pomatoschistus microps on energy transport through the food web, its impact on other compartments and its possible role as a keystone species in the trophic webs of an Arenicola tidal flat ecosystem and a sparse Zostera noltii bed ecosystem. Three ENA models were constructed: (a) model 1 contains data of the original food web from prior research in the investigated area by Baird et al. (2007), (b) an updated model 2 which included biomass and diet data of P. microps from recent sampling, and (c) model 3 simulating a food web without P. microps. A comparison of energy transport between the different models revealed that more energy is transported from lower trophic levels up the food chain, in the presence of P. microps (models 1 and 2) than in its absence (model 3). Calculations of the keystone index (KSi) revealed the high overall impact (measured as eps_i) of this fish species on food webs. In model 1, P. microps was assigned a low KSi in the Arenicola flat and in the sparse Z. noltii bed. Calculations in model 2 ranked P. microps first for keystoneness and eps_i in both communities, the Arenicola flat and the sparse Z. noltii bed. Taken together, our results give insight into the role of P. microps when considering a whole food web and reveal direct and indirect trophic interactions of this small-sized fish species. These results might illustrate the impact and importance of abundant, widespread species in food webs and facilitate further investigations.

Governance Structure Choices in Supply Chain Management Evidence from Spanish and Chinese Pork Chain Cases

The author participated in the 6 th EU Framework Project ―Q-pork Chains (FP6-036245-2)‖ from 2007 to 2009. With understanding of work reports from China and other countries, it is found that compared with other countries, China has great problems in pork quality and safety. By comparing the pork chain management between China and Spain, It is found that the difference in governance structure is one of the main differences in pork chain management between Spain and China. In China, spot-market relationship still dominates governance structure of pork chain, especially between the numerous house-hold pig holders and the great number of small slaughters. While in Spain, chain agents commonly apply cooperatives or integrations to cooperate. It also has been proven by recent studies, that in quality management at the chain level that supply chain integration has a direct effect on quality management practices (Han, 2010). Therefore, the author started to investigate the governance structure choices in supply chain management. And it has been set as the first research objective, which is to explain the governance structure choices process and the influencing factors in supply chain management, analyzing the pork chains cases in Spain and in China. During the further investigation, the author noticed the international trade of pork between Spain and China is not smooth since the signature of bi-lateral agreement on pork trade in 2007. Thus, another objective of the research is to find and solve the problems exist in the international pork chain between Spain and China. For the first objective, to explain the governance structure choices in supply chain management, the thesis conducts research in three main sections. 10 First of all, the thesis gives a literature overview in chapter two on Supply Chain Management (SCM), agri-food chain management and pork chain management. It concludes that SCM is a systems approach to view the supply chains as a whole, and to manage the total flow of goods inventory from the supplier to the ultimate customer. It includes the bi-directional flow of products (materials and services) and information, and the associated managerial and operational activities. And it also is a customer focus to create unique and individual source of customer value with an appropriate use of resources, leading to customer satisfaction and building competitive chain advantages. Agri-food chain management and pork chain management are applications of SCM in agri-food sector and pork sector respectively. Then, the research gives a comparative study in chapter three in the pork chain and pork chain management between Spain and China. Many differences are found, while the main difference is governance structure in pork chain management. Furthermore, the author gives an empirical study on governance structure choice in chapter five. It is concluded that governance structure of supply chain consists of a collection of rules/institutions/constraints structuring the transactions between the various stakeholders. Based on the overview on literatures closely related with governance structure, such as transaction cost economics, transaction value analysis and resource-based view theories, seven hypotheses are proposed, which are: Hypothesis 1: Transaction cost has positive relationship with governance structure choice Hypothesis 2: Uncertainty has positive relationship with transaction cost; higher uncertainty exerts high transaction cost Hypothesis 3: The relationship between asset specificity and transaction cost is positive Hypothesis 4: Collaboration advantages and governance structure choice have positive relationship11 Hypothesis 5: Willingness to collaborate has positive relationship with collaboration advantages Hypothesis 6: Capability to collaborate has positive relationship with collaboration advantages Hypothesis 7: Uncertainty has negative effect on collaboration advantages It is noted that as transaction cost value is negative, the transaction cost mentioned in the hypotheses is its absolute value. To test the seven hypotheses, Structural Equation Model (SEM) is applied and data collected from 350 pork slaughtering and processing companies in Jiangsu, Shandong and Henan Provinces in China is used. Based on the empirical SEM model and its results, the seven hypotheses are proved. The author generates several conclusions accordingly. It is found that the governance structure choice of the chain not only depends on transaction cost, it also depends on collaboration advantages. Exchange partners establish more stable and more intense relationship to reduce transaction cost and to maximize collaboration advantages. ―Collaboration advantages‖ in this thesis is defined as the joint value achieved through transaction (mutual activities) of agents in supply chains. This value forms as improvements, mainly in mutual logistics systems, cash response, information exchange, technological improvements and innovative improvements and quality management improvements, etc. Governance structure choice is jointly decided by transaction cost and collaboration advantages. Chain agents take different governance structures to coordinate in order to decrease their transaction cost and to increase their collaboration advantages. In China´s pork chain case, spot market relationship dominates the governance structure among the numerous backyard pig farmer and small family slaughterhouse 12 as they are connected by acquaintance relationship and the transaction cost in turn is low. Their relationship is reliable as they know each other in the neighborhood; as a result, spot market relationship is suitable for their exchange. However, the transaction between large-scale slaughtering and processing industries and small-scale pig producers is becoming difficult. The information hold back behavior and hold-up behavior of small-scale pig producers increase transaction cost between them and large-scale slaughtering and processing industries. Thus, through the more intense and stable relationship between processing industries and pig producers, processing industries reduce the transaction cost and improve the collaboration advantages with their chain partners, in which quality and safety collaboration advantages be increased, meaning that processing industries are able to provide consumers products with better quality and higher safety. It is also drawn that transaction cost is influenced mainly by uncertainty and asset specificity, which is in line with new institutional economics theories developed by Williamson O. E. In China´s pork chain case, behavioral uncertainty is created by the hold-up behaviors of great numbers of small pig producers, while big slaughtering and processing industries having strong asset specificity. On the other hand, ―collaboration advantages‖ is influenced by chain agents´ willingness to collaborate and chain agents´ capabilities to cooperate. With the fast growth of big scale slaughtering and processing industries, they are more willing to know and make effort to cooperate with their chain members, and they are more capable to create joint value together with other chain agents. Therefore, they are now the main chain agents who drive more intense and stable governance structure in China‘s pork chain. For the other objective, to find and solve the problems in the international pork chain between Spain and China, the research gives an analysis in chapter four on the 13 international pork chain. This study gives explanations why the international trade of pork between Spain and China is not sufficient from the chain perspective. It is found that the first obstacle is the high quality and safety requirement set by Chinese government. It makes the Spanish companies difficult to get authorities to export. Other aspects, such as Spanish pork is not competitive in price compared with other countries such as Denmark, United States, Canada, etc., Chinese consumers do not have sufficient information on Spanish pork products, are also important reasons that Spain does not export great quantity of pork products to China. It is concluded that China´s government has too much concern on the quality and safety requirements to Spanish pork products, which makes trade difficult to complete. The two countries need to establish a more stable and intense trade relationship. They also should make the information exchange sufficient and efficient and try to break trade barriers. Spanish companies should consider proper price strategies to win the Chinese pork market

Population regulation in snowshoe hare and Canadian lynx: Asymmetric food web configurations between hare and lynx

The snowshoe hare and the Canadian lynx in the boreal forests of North America show 9- to 11-year density cycles. These are generally assumed to be linked to each other because lynx are specialist predators on hares. Based on time series data for hare and lynx, we show that the dominant dimensional structure of the hare series appears to be three whereas that of the lynx is two. The three-dimensional structure of the hare time series is hypothesized to be due to a three-trophic level model in which the hare may be seen as simultaneously regulated from below and above. The plant species in the hare diet appear compensatory to one another, and the predator species may, likewise, be seen as an internally compensatory guild. The lynx time series are, in contrast, consistent with a model of donor control in which their populations are regulated from below by prey availability. Thus our analysis suggests that the classic view of a symmetric hare–lynx interaction is too simplistic. Specifically, we argue that the classic food chain structure is inappropriate: the hare is influenced by many predators other than the lynx, and the lynx is primarily influenced by the snowshoe hare.

Comparison of aquatic food chains using nitrogen isotopes.

Recent studies have shown the utility of delta(15)N to model trophic structure and contaminant bioaccumulation in aquatic food webs. However, cross-system comparisons in delta(15)N can be complicated by differences in delta(15)N at the base of the food chain. Such baseline variation in delta(15)N is difficult to resolve using plankton because of the large temporal variability in the delta(15)N of small organisms that have fast nitrogen turnover. Comparisons using large primary consumers, which have stable tissue isotopic signatures because of their slower nitrogen turnover, show that delta(15)N increases markedly with the human population density in the lake watershed. This shift in delta(15)N likely reflects the high delta(15)N of human sewage. Correcting for this baseline variation in delta(15)N, we report that, contrary to expectations based on previous food-web analysis, the food chains leading up to fish varied by about only one trophic level among the 40 lakes studied. Our results also suggest that the delta(15)N signatures of nitrogen at the base of the food chain will provide a useful tool in the assessment of anthropogenic nutrient inputs.

Presence of microplastics and nanoplastics in food, with particular focus on seafood

Acknowledgements: The Panel wishes to thank the members of the Working Group on the presence of microplastics and nanoplastics in food, with particular focus on seafood: Francesco Cubadda, Christer Hogstrand, Peter Hollman, Hendrik Van Loveren, Anne-Katrine Lundebye and Annette Petersen for the preparatory work on this statement, the hearing expert: Stephanie Wright and EFSA staff member: Karen Mackay for the support provided to this statement.

Sustainability practices and indicators in food retail logistics:findings from an exploratory study

The aim of this paper is to provide an overview and an analysis of recent developments and changes in the implementation of sustainability practices by food retailers. It also aims to explore whether the sustainability measurement criteria and indicators identified in the literature can be applied in practice. A literature review identified the current trends, developments and the proposed sustainability objectives, criteria and indicators. Via case study research, we collected empirical data from four retailers. This involved both qualitative and quantitative data drawn from questionnaires and in-depth interviews with logistics directors from four retailers' distribution centres. The empirical data collected from the interviews indicate similarities in some of the characteristics of distribution centres, as well as differences. However, it was difficult to make cross-company comparisons due to the absence of benchmarks or assessments of the relative importance of each sustainability criterion and indicator. This research focused only on two sustainability objectives. Further research on other sustainability objectives is therefore required. Lessons learnt from the four case studies can be taken into consideration when developing future sustainability performance rating scales. The paper provides an in-depth analysis of sustainability in the food chain, with emphasis on food retailing. Its value lies in presenting an attempt to test in practice how a number of sustainability objectives, criteria and indicators are applied in logistics-related processes, identifying the gaps and reporting the potential difficulties.