Antimicrobial resistance determinants in silage

Abstract

Animal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. However, resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer's body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have? For this purpose, we have analyzed bioinformatically 52 freely available deep sequenced silage samples from shotgun metagenome next-generation sequencing. A total of 16 perfect matched ARGs occurred 54 times in the samples. More than half of these ARGs are mobile because they can be linked to integrative mobile genetic elements, prophages or plasmids. Our results point to a neglected but substantial ARG source in the food chain.

Figure 1

Silage core bacteriome. Relative abundances of genera that achieved more than 1% of the bacterial hits in any of the samples. The elements of the PRJNA495415 dataset were taken on days 0, 7, 14 and 28 were classified into groups A, B, C and D, respectively. All items from BioProject PRJNA764355 are assigned to group E.

Figure 2

Identifed antimicrobial resistance genes (ARGs) by samples. Perfect ARG matches were plotted by samples. The data of the PRJNA495415 taken on days 0, 7, 14 and 28 were classified in groups A, B, C and D, respectively. All samples from BioProject PRJNA764355 were assigned to group E.

Figure 3

Mobile antimicrobial resistance gene frequency by bacteria of origin. The size of the dots indicates the occurrence frequency of the ARGs flanked by iMGE, positioned in a plasmid or a phage.