Abstract
Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM Bacillus velezensis used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM B. velezensis isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.
Highlights
Enzymes, additives and flavorings produced by microbial fermentation are widely used and indispensable for the food and feed industry
Modified microorganisms (GMM) are frequently employed to increase microbial enzyme production efficiency and/or yield [1]. Their presence is unauthorized in the final products commercialized in the European Union (EU) food and feed chain (EC/2003/1830). Since these Genetically modified microorganisms (GMM) usually carry antimicrobial resistance (AMR) genes used as selection markers, the ingestion of such contaminated products has raised health concerns related to potential AMR horizontal gene transfer to pathogens and other gut microbiota
Using whole-genome sequencing (WGS), this study reports an in-depth genomic characterization and phylogenomic comparison of 10 protease producing genetically modified (GM) B. velezensis strains, carrying a transgenic construct derived from shuttle vector pUB110, that were isolated from four different commercial FE products
Summary
Additives and flavorings produced by microbial fermentation are widely used and indispensable for the food and feed industry. Modified microorganisms (GMM) are frequently employed to increase microbial enzyme production efficiency and/or yield [1]. Their presence is unauthorized in the final products commercialized in the European Union (EU) food and feed chain (EC/2003/1830). Since these GMM usually carry antimicrobial resistance (AMR) genes used as selection markers, the ingestion of such contaminated products has raised health concerns related to potential AMR horizontal gene transfer to pathogens and other gut microbiota. Following a positive signal for at least one of these screening markers, the presence of specific GMM is investigated by targeting their unnatural associations [2,3,4,5,6,7]
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