Pilot market surveillance of GMM contaminations in alpha-amylase food enzyme products: A detection strategy strengthened by a newly developed qPCR method targeting a GM Bacillus licheniformis producing alpha-amylase

Marie-Alice Fraiture; Andrea Gobbo; Chloé Guillitte; Ugo Marchesi; Daniela Verginelli; Joke De Greve; Jolien D'aes; Kevin Vanneste; Nina Papazova; Nancy H C Roosens

doi:10.1016/j.fochms.2023.100186

Pilot market surveillance of GMM contaminations in alpha-amylase food enzyme products: A detection strategy strengthened by a newly developed qPCR method targeting a GM Bacillus licheniformis producing alpha-amylase

Food Chem (Oxf). 2023 Dec 6:8:100186. doi: 10.1016/j.fochms.2023.100186. eCollection 2024 Jul 30.

Affiliations

¹ Sciensano, Transversal Activities in Applied Genomics (TAG), rue Juliette Wytsman 14, 1050 Brussels, Belgium.
² Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M.Aleandri", Unità Operativa Semplice a valenza Direzionale - Ricerca e controllo degli organismi geneticamente modificati, via Appia Nuova 1411, 00178 Roma, Italia.

Abstract

Using high-throughput metagenomics on commercial microbial fermentation products, DNA from a new unauthorized genetically modified microorganism (GMM), namely the GM B. licheniformis strain producing alpha-amylase (GMM alpha-amylase2), was recently discovered and characterized. On this basis, a new qPCR method targeting an unnatural association of sequences specific to the GMM alpha-amylase2 strain was designed and developed in this study, allowing to strengthen the current GMM detection strategy. The performance of the newly developed qPCR method was assessed for its specificity and sensitivity to comply with the minimum performance requirements established by the European Network of GMO Laboratories for GMO analysis. Moreover, the transferability of the in house validated qPCR method was demonstrated. Finally, its applicability was confirmed by a pilot market surveillance of GMM contaminations conducted for the first time on 40 alpha-amylase food enzyme products labelled as containing alpha-amylase. This pilot market surveillance allowed also to highlight numerous contaminations with GMM alpha-amylase2, including frequent cross-contaminations with other GMM strains previously characterized. In addition, the presence of full-length AMR genes, raising health concerns, was also reported.

Keywords: Alpha-amylase; Antimicrobial resistance genes; Food and feed safety and traceability; Genetically modified bacteria; Surveillance; qPCR detection.