Abstract
Group antimicrobial administration is used to control disease in livestock, but we have little insight into how this impacts antimicrobial resistance (AMR) gene dynamics. Here, a longitudinal study was carried out during a single production cycle on a commercial pig unit with high historic and current antimicrobial usage. Quantitative PCR, 16S rRNA gene metabarcoding and shotgun metagenomic sequencing were used to track faecal AMR gene abundance and diversity and microbiome alpha diversity. Shotgun metagenomic sequencing identified 144 AMR genes in total, with higher AMR gene diversity present in young pigs compared to dry sows. Irrespective of in-feed antibiotic treatment or changes in microbiome diversity, mean AMR gene copy number was consistently high, with some AMR genes present at copy numbers comparable to the bacterial 16S rRNA gene. In conclusion, AMR gene prevalence and abundance were not influenced by antibiotic use, either during the production cycle or following whole-herd medication. The high levels of certain genes indicate they are widely disseminated throughout the microbial population, potentially aiding stability. Despite the high and relatively stable levels of resistance genes against the main antimicrobials used, these compounds continue to control production limiting diseases on this unit.
Highlights
Group antimicrobial administration is used to control disease in livestock, but we have little insight into how this impacts antimicrobial resistance (AMR) gene dynamics
In the dry sow accommodation, high levels of AMR genes were detected in the absence of group antimicrobial administration
Previous work has demonstrated high baseline levels of specific AMR genes[36] and phenotypic resistance in Escherichia coli isolates[37,38] in unmedicated pigs, our initial expectation was that AMR gene abundances would markedly increase in response to antimicrobial administration as a result of selective pressure being exerted on specific genes[39]
Summary
Group antimicrobial administration is used to control disease in livestock, but we have little insight into how this impacts antimicrobial resistance (AMR) gene dynamics. Quantitative PCR, 16S rRNA gene metabarcoding and shotgun metagenomic sequencing were used to track faecal AMR gene abundance and diversity and microbiome alpha diversity. Shotgun metagenomic sequencing identified 144 AMR genes in total, with higher AMR gene diversity present in young pigs compared to dry sows. Molecular studies have revealed a higher richness and diversity of AMR genes in pigs administered oxytetracycline in-feed[19], with farm origin being associated with AMR gene abundances in faeces at slaughter using both quantitative PCR20 and metagenomic[21] datasets. Faecal samples were taken from dry sows during and after a partial depopulation event which involved antibiotic administration to every pig on the farm to assess if this practice impacted on AMR gene abundance. Microbiome alpha diversity, AMR gene abundance and AMR gene diversity were measured by 16S rRNA gene metabarcoding, quantitative PCR (qPCR) and shotgun metagenomic sequencing, respectively
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