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Genome-based surveillance of transmissible colistin and carbapenem resistances of Gram-negative bacteria (GÜCCI)

Project

Food and consumer protection

This project contributes to the research aim 'Food and consumer protection'. Which funding institutions are active for this aim? What are the sub-aims? Take a look:
Food and consumer protection


Project code: BfR-BIOS-08-1339-105
Contract period: 01.01.2019 - 30.12.2021
Purpose of research: Experimental development

The project focuses on the main topic pathogens with special resistances. The main objectives are (i) the assessment of complex scenarios with the focus on horizontal resistance transfer via plasmids, incorporating the results of modern sequence-based typing techniques; (ii) deriving universal standards and essential requirements for valid data analysis, (iii) identification of facilitating factors and impediments to timely implementation of these; (iv) the development of strategies for the combination of clinical epidemiological information with genome data and (v) knowledge transfer to the qualified professional community. In a cross-sectoral approach, two selected antibiotic resistances with very high public health relevance are processed. On the one hand, it is about gaining scientific knowledge with immediate public health relevance, specifically, a better assessment of the potential risk (i) mcr-mediated colistin resistance in isolates of animals and food and their importance for human-pathogenic isolates and (ii) carbapenemase-producing enterobacterales in animals and food as a potential reservoir of resistance development in human isolates. On the other hand, the project implements the urgently needed implementation of a core technology for genome-based pathogen and resistance surveillance in leading public health and veterinary public health institutions and the epidemiologically adequate evaluation and evaluation. BfR part of the project: BfR is involved in all work packages of the project. To achieve the goal of providing and validating a suitable extraction / sequencing / evaluation method for identifying plasmid sequence information in whole genome data within routine examinations, the following tasks are planned: • Selection of the isolates / genome sequences to be characterized taking into account the bioinformatic and epidemiological questions to be answered • Inventory of existing tools for NGS and SMS evaluation taking into account various issues in close cooperation with the teams of the corresponding project partners • Comparative study and evaluation of the suitability of different methods for separating plasmid sequence information from WGS data • Experimental study and comparative evaluation of extraction techniques to optimize the sequencing results for their suitability for specific enrichment of plasmid sequence information • Compilation of the available epidemiological information on the selected isolates • Preparation of the technical concept for the evaluation of the chosen questions

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Subjects

Framework programme

BMEL Frameworkprogramme 2008

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