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Antibiotic resistomes of healthy pig faecal metagenomes

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 comprise...

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Autores principales: Joyce, Aoife, McCarthy, Charley G. P., Murphy, Sinead, Walsh, Fiona
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562245/
https://www.ncbi.nlm.nih.gov/pubmed/31091181
http://dx.doi.org/10.1099/mgen.0.000272
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author Joyce, Aoife
McCarthy, Charley G. P.
Murphy, Sinead
Walsh, Fiona
author_facet Joyce, Aoife
McCarthy, Charley G. P.
Murphy, Sinead
Walsh, Fiona
author_sort Joyce, Aoife
collection PubMed
description 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.
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spelling pubmed-65622452019-06-21 Antibiotic resistomes of healthy pig faecal metagenomes Joyce, Aoife McCarthy, Charley G. P. Murphy, Sinead Walsh, Fiona Microb Genom Research Article 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. Microbiology Society 2019-05-15 /pmc/articles/PMC6562245/ /pubmed/31091181 http://dx.doi.org/10.1099/mgen.0.000272 Text en © 2019 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Joyce, Aoife
McCarthy, Charley G. P.
Murphy, Sinead
Walsh, Fiona
Antibiotic resistomes of healthy pig faecal metagenomes
title Antibiotic resistomes of healthy pig faecal metagenomes
title_full Antibiotic resistomes of healthy pig faecal metagenomes
title_fullStr Antibiotic resistomes of healthy pig faecal metagenomes
title_full_unstemmed Antibiotic resistomes of healthy pig faecal metagenomes
title_short Antibiotic resistomes of healthy pig faecal metagenomes
title_sort antibiotic resistomes of healthy pig faecal metagenomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562245/
https://www.ncbi.nlm.nih.gov/pubmed/31091181
http://dx.doi.org/10.1099/mgen.0.000272
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