Epidemiological analysis of antimicrobial resistance in the food chain in the metagenomics era: from antimicrobial resistant pathogens to the faecal resistome of humans and livestock

Chapter 1 directly extracted from environmental samples (e.g. faecal samples) without the need for cloning into an expression vector and subsequent selective media screening. The resulting sequence reads are subsequently processed by e.g. assembly or read classification as further described in paragraph 1.3.