[Assessment of available and currently applied typing methods including genome-based methods for zoonotic pathogens with a focus on Salmonella enterica]. / Bestandsaufnahme der verfügbaren und aktuell eingesetzten Typisierungsmethoden einschließlich genombasierter Verfahren von Zoonoseerregern am Beispiel von Salmonella enterica.

BACKGROUND: In recent years, whole genome sequencing (WGS) in combination with bioinformatic analyses has become state of the art in evaluating the pathogenicity/resistance potential and relatedness of bacteria. WGS analysis thus represents a central tool in the investigation of the resistance and virulence potential of pathogens, as well as their dissemination via outbreak clusters and transmission chains within the framework of molecular epidemiology. In order to gain an overview of the available genotypic and phenotypic methods used for pathogen typing of Salmonella and Shiga toxin-producing and enterohemorrhagic Escherichia coli (STEC/EHEC) in Germany at state and federal level, along with the availability of WGS-based typing and corresponding analytical methods, a survey of laboratories was conducted. METHODS: An electronic survey of laboratories working for public health protection and consumer health protection was conducted from February to June 2020. RESULTS AND CONCLUSION: The results of the survey showed that many of the participating laboratories provide a wide range of phenotypic and molecular methods. Molecular typing is most commonly used for species identification of Salmonella. In many cases, WGS-based methods have already been established at federal and state institutions or are in the process of being established. The Illumina sequencing technology is the most widely used technology. The survey confirms the importance of molecular biology and whole genome typing technologies for laboratories in the diagnosis of bacterial zoonotic pathogens.

Comparative assessment of DNA-based approaches for the quantification of food allergens.

Governments all over the world have implemented regulatory frameworks concerning food allergen labelling and established or discussed the implementation of thresholds. Therefore, quantitative methods are needed for their surveillance. DNA-based approaches using a matrix-adapted calibration, an internal standard material and a modified standard addition have been developed. In order to enable a comparative assessment of the available quantification methods, experimental framework conditions and uniform performance criteria were defined. For the evaluation of the experimental results using homogenous sample material, the recovery, repeatability and reproducibility were considered along with the limit of detection and the limit of quantification. In addition, muffin dough and muffins spiked with sesame were analysed to assess the suitability of the methods to quantify sesame in model foods. The modified standard addition emerged from the comparative assessment and the analysis of the model foods to be the most appropriate method to quantify traces of allergens in food.