Application of genomics and metagenomics to improve food safety based on an enhanced characterisation of antimicrobial resistance

Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes

“…The increasing burden of AMR is not limited to healthcare systems but spreads also in food-producing environments. Considering this, untargeted techniques are needed for surveillance and rapid detection of resistant food-borne pathogens from a One Health perspective ( Torres et al, 2021 ; Pennone et al, 2022 ; Pillay et al, 2022 ). Shotgun metagenomics, i.e., untargeted sequencing of all DNA material present in a sample, is a valuable tool to profile the composition of microbial communities for the identification of potential pathogens and AMR genes, as shown with short read-sequencing (Illumina) ( Bengtsson-Palme, 2017 ; Oniciuc et al, 2018 ; Pillay et al, 2022 ).…”

“…Moreover, with this technique, the selection and dissemination of AMR in microbiomes of food-producing animals and their environments can be better studied using, for instance, fecal samples as a proxy, to track horizontal gene transfer between commensal and pathogenic bacteria ( Bengtsson-Palme, 2017 ; Torres et al, 2021 ). Long-read sequencing (Oxford Nanopore Technologies, ONT) can also be used for pathogen and AMR detection by shotgun metagenomics ( Pennone et al, 2022 ; Pillay et al, 2022 ). Oxford Nanopore technology is portable, generating sequencing results in real-time and making on-site use possible, without the need to send samples to centralized sequencing laboratories using big laboratory equipment ( Leggett and Clark, 2017 ).…”

Detection of Acquired Antibiotic Resistance Genes in Domestic Pig (Sus scrofa) and Common Carp (Cyprinus carpio) Intestinal Samples by Metagenomics Analyses in Hungary

“…Among the 25 countries that have reported to the European Surveillance of Veterinary Antimicrobial Consumption (ESVAC) every year since 2011, the overall sales of antimicrobials decreased by 43.2% during 2011–2020. As a result, when assessed per kg biomass, the antimicrobial consumption in the EU was overall lower in food-producing animals than in humans between 2016 and 2018 [ 4 , 7 , 8 ].…”

“…These surveillance approaches may be further facilitated by applying next-generation sequencing (NGS) techniques that have revolutionized the analysis of complex bacterial communities as well through metagenomic analyses [ 25 , 26 ]. Metagenomic methods can overcome the limitations of culture-based approaches as the entire repertoire of resistance genes (the resistome) can be assessed in a sample without culturing single isolates of pre-selected species, which may cause a loss of relevant information [ 7 ]. Metagenomics may also contribute to the identification and characterization of non-culturable, difficult-to-culture, or slow growing microorganisms and be used for the tracking of genetic determinants of AMR or virulence [ 27 , 28 ].…”

“…Metagenomics may also contribute to the identification and characterization of non-culturable, difficult-to-culture, or slow growing microorganisms and be used for the tracking of genetic determinants of AMR or virulence [ 27 , 28 ]. Since shotgun metagenomic sequencing facilitates the detection of a wider range of ARGs in complex bacterial communities compared to conventional PCR-based approaches, it may contribute to the tracing of ARGs between different habitats and environments and to identifying potential routes of dissemination [ 7 , 25 , 26 ]. Although the de novo assembly of NGS reads into metagenomic contigs may result in the loss of some low abundance data, their assembly into contigs allows for a more accurate detection and identification of ARGs and potentially the exploration of their immediate genetic environment [ 26 , 29 ].…”