Integrating multi-omics to monitor gut microbiome and resistome dynamics in weaned piglets

Abstract

Antimicrobial resistance (AMR) is an emerging global threat, undermining the efficacy of current treatments and calling for sustainable interventions through a ‘One Health’ approach. In the swine industry, the post-weaning period represents a particularly vulnerable stage, and antimicrobials have traditionally been used during this transition to manage infections such as post-weaning diarrhoea, a condition that significantly impacts piglets’ health and productivity. As high-throughput sequencing technologies advance, they offer powerful tools for resistome surveillance, enabling the characterization of antimicrobial resistance genes (ARGs) in various environments. This doctoral thesis focuses on the effect of different post-weaning diarrhoea treatments on the gut microbiome and resistome of piglets with the final aim to develop a monitoring tool for the detection of ARGs in swine production systems. Through the optimization of a bioinformatic pipeline to analyse and integrate shotgun metagenomics and metatranscriptomics data, the construction of a comprehensive collection of 1,396 metagenome-assembled genomes from the pig gut microbiome enabled robust differential gene expression analyses between treatments and sampling times. Altogether, metagenomic and metatranscriptomic resistome profiling identified that half of the ARGs were transcriptionally active and allowed for the generation of an ARG catalogue. This catalogue, including a total of 102 ARGs, comprises most antibiotic classes and has been implemented in a microfluidic platform for the development and validation of a customizable, sensitive, and high-throughput monitoring tool for efficient AMR surveillance from swine faecal samples. Overall, the comprehensive multi-omics approach proposed in this doctoral thesis emerges as a promising tool for the qualitative and quantitative detection of ARGs with the potential to improve AMR monitoring for understanding resistance dynamics and guide responsible antimicrobial interventions in animal production systems.

Date of Award	6 Jun 2025
Original language	English
Supervisor	Maria Ballester Devis (Director), Yuliaxis Ramayo Caldas (Director) & Lourdes Migura Garcia (Director)