Abstract
Antibiotic resistance reservoirs within food-producing animals are thought to be a risk to animal and human health. This study describes the minimum natural resistome of pig faeces as the bacteria are under no direct antibiotic selective pressure. The faecal resistome of 257 different genes comprised 56 core and 201 accessory resistance genes. The genes present at the highest relative abundances across all samples were tetW, tetQ, tet44, tet37, tet40, mefA, aadE, ant(9)−1, ermB and cfxA2. This study characterized the baseline resistome, the microbiome composition and the metabolic components described by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in healthy pig faeces, without antibiotic selective pressures. The microbiome hierarchical analysis resulted in a cluster tree with a highly similar pattern to that of the accessory resistome cluster tree. Functional capacity profiling identified genes associated with horizontal gene transfer. We identified a statistically significant positive correlation between the total antibiotic resistome and suggested indicator genes, which agree with using these genes as indicators of the total resistomes. The correlation between total resistome and total microbiome in this study was positive and statistically significant. Therefore, the microbiome composition influenced the resistome composition. This study identified a core and accessory resistome present in a cohort of healthy pigs, in the same conditions without antibiotics. It highlights the presence of antibiotic resistance in the absence of antibiotic selective pressure and the variability between animals even under the same housing, food and living conditions. Antibiotic resistance will remain in the healthy pig gut even when antibiotics are not used. Therefore, the risk of antibiotic resistance transfer from animal faeces to human pathogens or the environment will remain in the absence of antibiotics.
Highlights
The concept to date is that animals, in particular food animals, are potential reservoirs of antimicrobial resistance genes (ARGs) and transfer and survive in the gut microflora and transfer to human or animal pathogens [1]
This study aimed to firstly identify the baseline ARGs, the microbiome composition and the metabolic components described by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in healthy pig faeces, without antibiotic selective pressures
In total 257 ARGs were detected across all pig faecal samples
Summary
The concept to date is that animals, in particular food animals, are potential reservoirs of antimicrobial resistance genes (ARGs) and transfer and survive in the gut microflora and transfer to human or animal pathogens [1]. There is a rich literature on the topic of the presence of specific ARGs, in faecal samples from animals and in environmental reservoirs such as soil or water. Many studies of the animal faecal resistome have focused on the presence of ARGs or antibioticresistant bacteria present in manure [1, 4, 5].
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