<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Florence E Buytaers</style></author><author><style face="normal" font="default" size="100%">Marie-Alice Fraiture</style></author><author><style face="normal" font="default" size="100%">Bas Berbers</style></author><author><style face="normal" font="default" size="100%">Els Vandermassen</style></author><author><style face="normal" font="default" size="100%">Stefan Hoffman</style></author><author><style face="normal" font="default" size="100%">N. Papazova</style></author><author><style face="normal" font="default" size="100%">Kevin Vanneste</style></author><author><style face="normal" font="default" size="100%">Marchal, Kathleen</style></author><author><style face="normal" font="default" size="100%">Nancy Roosens</style></author><author><style face="normal" font="default" size="100%">Sigrid C.J. De Keersmaecker</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products</style></title><secondary-title><style face="normal" font="default" size="100%">Food Chemistry: Molecular Sciences</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">AMR</style></keyword><keyword><style  face="normal" font="default" size="100%">genetically modified microorganism</style></keyword><keyword><style  face="normal" font="default" size="100%">identification</style></keyword><keyword><style  face="normal" font="default" size="100%">long and short read sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">microbial fermentation products</style></keyword><keyword><style  face="normal" font="default" size="100%">shotgun metagenomics</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">Jan-07-2021</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The presence of a genetically modified microorganism (GMM) or its DNA, often harboring antimicrobial resis- tance (AMR) genes, in microbial fermentation products on the market is prohibited by European regulations. GMMs are currently screened for through qPCR assays targeting AMR genes and vectors, and then confirmed by targeting known specific GM constructs/events. However, when the GMM was not previously characterized and an isolate cannot be obtained, its presence cannot be proven. We present a metagenomics approach cap- able of delivering the proof of presence of a GMM in a microbial fermentation product, with characterization based on the detection of AMR genes and vectors, species and unnatural associations in the GMM genome. In our proof‐of‐concept study, this approach was performed on a case with a previously isolated and sequenced GMM, an unresolved case for which no isolate was obtained, and a non‐GMM‐contaminated sample, all repre- sentative for the possible scenarios to occur in routine setting. Both short and long read sequencing were used. This workflow paves the way for a strategy to detect and characterize unknown GMMs by enforcement laboratories.&lt;br&gt;
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