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Sammanfattning

Antimicrobial resistance (AMR) is a major One Health challenge linking human, animal, and environmental health. Livestock production systems play an important role in this context, as they act as reservoirs for antimicrobial resistance genes (ARGs). While antimicrobial use (AMU) is widely recognised as the primary driver of AMR, increasing evidence suggests that AMR dynamics cannot be explained by AMU alone, as environmental and management-related factors may also contribute.

AMR surveillance in livestock relies mainly on phenotypic resistance testing, which captures only a limited fraction of the total resistance reservoir. Shotgun metagenomic sequencing enables comprehensive characterisation of the resistome but has predominantly been applied in high-AMU settings, where strong antibiotic selection may obscure the effects of other drivers. To address this gap, this thesis developed and applied a robust and scalable pipeline for environmental resistome analysis in low-AMU pig farm systems.

The pipeline was optimised by systematically evaluating key methodological steps, including sampling strategy, DNA extraction, sequencing depth and technology, and alternative bioinformatic approaches for assembly and ARG detection. Sock sampling proved to be a practical and standardisable method for farm-level studies, and deep short-read sequencing provided the most sensitive recovery of ARGs in complex farm environments. This workflow was applied in a longitudinal study of ten Swedish farrow-to-finish pig farms followed across a full production cycle.

Despite pronounced temporal shifts in the environmental microbiome, the resistome showed no clear association with AMU, reflecting the low selective pressure in these systems. Resistome diversity and phenotypic resistance in Escherichia coli were not correlated, indicating that genotypic and phenotypic metrics capture complementary dimensions of AMR. Different non-antibiotic factors were associated with these outcomes, highlighting the need to integrate metagenomic and phenotypic approaches when studying AMR in livestock environments within a One Health framework. This work provides a methodological foundation for future large-scale, longitudinal resistome studies.

Nyckelord

One health; pig farm resistome; risk factors; antibiotic; AMR

Publicerad i

Acta Universitatis Agriculturae Sueciae
2026, nummer: 2026:15
Utgivare: Swedish University of Agricultural Sciences

SLU författare

UKÄ forskningsämne

Patobiologi

Publikationens identifierare

  • DOI: https://doi.org/10.54612/a.5h9892gslr
  • ISBN: 978-91-8124-212-6
  • eISBN: 978-91-8124-232-4

Permanent länk till denna sida (URI)

https://res.slu.se/id/publ/145948