Discussing State-of-the-Art Spatial Visualization Techniques Applicable for the Epidemiological Surveillance Data on the Example of Campylobacter spp. in Raw Chicken Meat.

Within the European activities for the 'Monitoring and Collection of Information on Zoonoses', annually EFSA publishes a European report, including information related to the prevalence of Campylobacter spp. in Germany. Spatial epidemiology becomes here a fundamental tool for the generation of these reports, including the representation of prevalence as an essential element. Until now, choropleth maps are the default visualization technique applied in epidemiological monitoring and surveillance reports made by EFSA and German authorities. However, due to its limitations, it seems to be reasonable to explore alternative chart type. Four maps including choropleth, cartogram, graduated symbols and dot-density maps were created to visualize real-world sample data on the prevalence of Campylobacter spp. in raw chicken meat samples in Germany in 2011. In addition, adjacent and coincident maps were created to visualize also the associated uncertainty. As an outcome, we found that there is not a single data visualization technique that encompasses all the necessary features to visualize prevalence data alone or prevalence data together with their associated uncertainty. All the visualization techniques contemplated in this study demonstrated to have both advantages and disadvantages. To determine which visualization technique should be used for future reports, we recommend to create a dialogue between end-users and epidemiologists on the basis of sample data and charts. The final decision should also consider the knowledge and experience of end-users as well as the specific objective to be achieved with the charts.

A strategy to establish Food Safety Model Repositories.

Transferring the knowledge of predictive microbiology into real world food manufacturing applications is still a major challenge for the whole food safety modelling community. To facilitate this process, a strategy for creating open, community driven and web-based predictive microbial model repositories is proposed. These collaborative model resources could significantly improve the transfer of knowledge from research into commercial and governmental applications and also increase efficiency, transparency and usability of predictive models. To demonstrate the feasibility, predictive models of Salmonella in beef previously published in the scientific literature were re-implemented using an open source software tool called PMM-Lab. The models were made publicly available in a Food Safety Model Repository within the OpenML for Predictive Modelling in Food community project. Three different approaches were used to create new models in the model repositories: (1) all information relevant for model re-implementation is available in a scientific publication, (2) model parameters can be imported from tabular parameter collections and (3) models have to be generated from experimental data or primary model parameters. All three approaches were demonstrated in the paper. The sample Food Safety Model Repository is available via: http://sourceforge.net/projects/microbialmodelingexchange/files/models and the PMM-Lab software can be downloaded from http://sourceforge.net/projects/pmmlab/. This work also illustrates that a standardized information exchange format for predictive microbial models, as the key component of this strategy, could be established by adoption of resources from the Systems Biology domain.

Emerging antimicrobial resistance in commensal Escherichia coli with public health relevance.

In 2009, 1462 Escherichia coli isolates were collected in a systematic resistance monitoring approach from primary production, slaughterhouses and at retail and evaluated on the basis of epidemiological cut-off values. Besides resistance to antimicrobial classes that have been extensively used for a long time (e.g. sulphonamides and tetracyclines), resistance to (fluoro)quinolones and third-generation cephalosporins was observed. While in the poultry production chain the majority (60%) of isolates from laying hens was susceptible to all antimicrobials tested, most isolates from broilers, chicken meat and turkey meat showed resistance to at least one (85-93%) but frequently even to several antimicrobial classes (73-84%). In the cattle and pig production chain, the share of isolates showing resistance to at least one antimicrobial was lowest (16%) in dairy cows, whereas resistance to at least one antimicrobial ranged between 43% and 73% in veal calves, veal and pork. Resistance rates to ciprofloxacin and nalidixic acid in isolates from broilers were 41.1% and 43.1%, respectively. Likewise, high resistance rates to (fluoro)quinolones were observed in isolates from chicken meat and turkey meat. In contrast, ciprofloxacin resistance was less frequent in E. coli isolates from the cattle and pig production chain with highest rate in veal calves (13.3%). Highest resistance rates to cephalosporins were observed in broilers and chicken meat, with 5.9% and 6.2% of the isolates showing resistance. In dairy cattle and veal, no isolates with cephalosporin resistance were detected, whereas 3.3% of the isolates from veal calves showed resistance to ceftazidime. Resistance to (fluoro)quinolones and cephalosporins in E. coli isolates is of special concern because they are critically important antimicrobials in human antimicrobial therapy. The emergence of this resistance warrants increased monitoring. Together with continuous monitoring of antimicrobial usage, management strategies should be regularly assessed and adapted.