Effects of antibiotic treatment on antimicrobial resistance in pig microbiomes: a longitudinal study

Abstract

Abstract The United Kingdom has prohibited the prophylactic use of antibiotics in agriculture but they are still critical for disease control. It is thus vital to understand the effects of antibiotic treatment on antimicrobial resistance (AMR) spread. Hi-C metagenomic sequencing can help identify AMR genes in animal microbiomes and assign plasmid-based genes to their bacterial hosts. Leveraging Hi-C, we sequence antibiotically-treated pig microbiomes through time to identify dynamic trends in AMR gene prevalence. Fecal samples were collected at time points prior to and following antibiotic treatment in 6 farms across England when pigs presented with illness. Control samples were collected from 2 of these farms at multiple time points without treatment. Samples were processed using a bioinformatic pipeline that outputs assemblies with information on taxonomic classification and presence/absence of an AMR allele. 115 AMR alleles across 11 antibiotic classes were included. The bacterial species in highest abundance/farm belonged to order Bacteroidales (45.9-53.1%). Tetracycline resistance alleles showed the highest prevalence/farm (28.4-52.8%). No significant association between bacterial species abundance and time point, and AMR allele prevalence and time point was found in all farms (χ2 p>.05). The distribution of the number of AMR alleles/assembly was significantly higher between the first and last time point in 4/6 treated farms and 1/2 control farms (Wilcoxan rank sum p <.01). A higher difference in the proportion of assemblies with greater than 6 AMR alleles between the first and last time point was observed in 1 treated farm (.17 95% CI .013-.21) compared to its control (.03 95% CI .023-.033). Slight acquisition of AMR alleles was observed but we see minimal temporal fluctuations in bacterial species abundance and AMR allele prevalence overall implying that the microbiome is fairly robust to antibiotic treatment. This encourages its responsible use for disease control. Key messages Ensuring that the responsible use of antibiotics does not drastically affect AMR mobilization is key to preserving the efficacy of therapeutics in agriculture. While acquisition of resistance genes over time is seen it cannot conclusively be tied to treatment; Minimal microbiome perturbation post treatment implies that therapeutic antibiotic use is warranted.