NAuRA: Genomic Tool to Identify Staphylococcal Enterotoxins in Staphylococcus aureus Strains Responsible for FoodBorne Outbreaks.

Autor:	Merda D; French Agency for Food, Environmental and Occupational Health & Safety (ANSES), University of Paris-Est, Maisons-Alfort, France., Felten A; French Agency for Food, Environmental and Occupational Health & Safety (ANSES), University of Paris-Est, Maisons-Alfort, France., Vingadassalon N; French Agency for Food, Environmental and Occupational Health & Safety (ANSES), University of Paris-Est, Maisons-Alfort, France., Denayer S; Scientific Service of FoodBorne Pathogens, Sciensano, Brussels, Belgium., Titouche Y; Laboratory of Analytical Biochemistry and Biotechnology, University of Mouloud Mammeri, Tizi Ouzou, Algeria., Decastelli L; National Reference Laboratory for Coagulase-Positive Including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy., Hickey B; Department of Agriculture, Food and the Marine, Kildare, Ireland., Kourtis C; State General Laboratory, Food Microbiology Laboratory, Nicosia, Cyprus., Daskalov H; National Center of Food Safety, NDRVI, BFSA, Sofia, Bulgaria., Mistou MY; French Agency for Food, Environmental and Occupational Health & Safety (ANSES), University of Paris-Est, Maisons-Alfort, France., Hennekinne JA; French Agency for Food, Environmental and Occupational Health & Safety (ANSES), University of Paris-Est, Maisons-Alfort, France.
Jazyk:	angličtina
Zdroj:	Frontiers in microbiology [Front Microbiol] 2020 Jun 30; Vol. 11, pp. 1483. Date of Electronic Publication: 2020 Jun 30 (Print Publication: 2020).
DOI:	10.3389/fmicb.2020.01483
Abstrakt:	Food contamination by staphylococcal enterotoxins (SEs) is responsible for many food poisoning outbreaks (FPOs) each year, and they represent the third leading cause of FPOs in Europe. SEs constitute a protein family with 27 proteins. However, enzyme immunoassays can only detect directly in food the five classical SEs (SEA-SEE). Thus, molecular characterization methods of strains found in food are now used for FPO investigations. Here, we describe the development and implementation of a genomic analysis tool called NAuRA (Nice automatic Research of alleles) that can detect the presence of 27 SEs genes in just one analysis- and create a database of allelic data and protein variants for harmonizing analyses. This tool uses genome assembly data and the 27 protein sequences of SEs. To include the different divergence levels between SE-coding genes, parameters of coverage and identity were generated from 10,000 simulations and a dataset of 244 assembled genomes from strains responsible for outbreaks in Europe as well as the RefSeq reference database. Based on phylogenetic inference performed using maximum-likelihood on the core genomes of the strains in this collection, we demonstrated that strains responsible for FPOs are distributed throughout the phylogenetic tree. Moreover, 71 toxin profiles were obtained using the NAuRA pipeline and these profiles do not follow the evolutionary history of strains. This study presents a pioneering method to investigate strains isolated from food at the genomic level and to analyze the diversity of all 27 SE-coding genes together. (Copyright © 2020 Merda, Felten, Vingadassalon, Denayer, Titouche, Decastelli, Hickey, Kourtis, Daskalov, Mistou and Hennekinne.)
Databáze:	MEDLINE
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