By Xiangyu Deng, Henk C. den Bakker, Rene S. Hendriksen
This publication offers a well timed and thorough image into the rising and quickly evolving zone of utilized genomics of foodborne pathogens. pushed via the drastic improve of complete genome shot gun sequencing (WGS) applied sciences, genomics functions have gotten more and more priceless or even crucial in learning, surveying and controlling foodborne microbial pathogens. The sizeable possibilities introduced through this pattern are usually at odds with the shortcoming of bioinformatics knowledge between foodstuff defense and public healthiness pros, considering the fact that such services isn't a part of a standard nutrition microbiology curriculum and talent set. additional complicating the problem is the big and ever evolving physique of bioinformatics instruments which could obfuscate beginners to this zone. even if reports, tutorials and books will not be in brief offer within the fields of bioinformatics and genomics, earlier there has now not been a entire and customised resource of data designed for and available to microbiologists attracted to employing state of the art genomics in foodstuff protection and public well-being study. This booklet fills this void with a well-selected selection of subject matters, case reports, and bioinformatics instruments contributed via specialists on the leading edge of foodborne pathogen genomics research.
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Additional info for Applied Genomics of Foodborne Pathogens
This will in time ensure or enable harmonization and standardization of whole genome sequencing and data analysis, with the final aim to produce comparable data for the GMI initiative, and thereby consistent data for the GMI database. Therefore, the laboratory analysis work performed for this type of proficiency testing should be done employing the methods routinely used in the individual laboratories. The proficiency testing performed in this area has consisted of two wet-lab and one dry-lab components targeting Salmonella, E.
GMI in 2014 performed a pilot proficiency test with a limited number of laboratories to test the developed IT system and corresponding protocol. eu) and the USFDA GenomeTrakr and Microbiologics®. org). 55 laboratories, from all continents, signed up for the test. g. ). This will in time ensure or enable harmonization and standardization of whole genome sequencing and data analysis, with the final aim to produce comparable data for the GMI initiative, and thereby consistent data for the GMI database.
Coli received through the WCNYSDOH PulseNet laboratory are sequenced. In addition, sequencing is performed on sample requested by the US CDC for Salmonella and E. coli O157. Samples are extracted and DNA sequenced in real-time and are multiplexed with other samples. For samples that pass quality metrics, a biosample accession number is requested from NCBI. Once the metadata associated with the biosample accession at NCBI is confirmed, the Biosample # is uploaded to the PulseNet national database by the Wadsworth PulseNet laboratory.
Applied Genomics of Foodborne Pathogens by Xiangyu Deng, Henk C. den Bakker, Rene S. Hendriksen