Valeriia Ladyhina defends thesis on antimicrobial resistance dynamics in Swedish pig farms

The UAC congratulates Valeriia Ladyhina on the successful defense of her PhD thesis: "Dynamics of antimicrobial resistance in the livestock environment." The thesis was defended at the Swedish University of Agricultural Sciences (SLU) on 27 March 2026, making Valeriia the fourth PhD student from UAC's second cohort to complete her doctoral studies.

Studying resistance directly on the farms

Antimicrobial resistance is a so-called One Health challenge. It does not stay within the walls of hospitals or clinics. It develops and spreads across humans, animals, and the environment, and livestock production can be one of the major contributors. Around 73% of all antibiotics produced globally are used in food-producing animals, making farms a critical but still incompletely understood piece of the AMR puzzle.

Valeriia's research focused on pig farms in Sweden, one of the countries with the lowest antibiotic use in livestock in Europe. That low-use context is particularly interesting, as most previous resistome studies have been conducted in high-use settings, where strong antibiotic pressure dominates the picture and can mask the effect of other factors. By working in Sweden, Valeriia could look for what else drives resistance when antibiotics are largely out of the equation.

Four studies from methodology to application

Phenotypic resistance in Swedish pig farms. Using two indicator bacteria, Escherichia coli and Enterococcus faecium, Valeriia described the baseline patterns of antimicrobial resistance across farms as a starting point and reference for the rest of the work.

Building a reproducible pipeline for resistome research. Before studying resistance at scale, Valeriia systematically tested every step of the analytical process: how to collect samples, how to transport and store them, which DNA extraction kit to use, how deep to sequence, and which bioinformatic tools to apply. A key finding was that sock sampling, which involves walking through pig pens with fabric boots, is a practical, non-invasive, and standardisable method for capturing the farm-level resistome. Deep short-read sequencing with Illumina proved superior to long-read alternatives for this type of complex environmental sample.

Longitudinal resistome dynamics. Applying the validated pipeline, Valeriia followed ten Swedish farrow-to-finish pig farms across a full production cycle, which is approximately six months. Despite clear shifts in the microbiome over time, the resistome showed no clear association with antibiotic use. Other factors were at play, and they varied by antibiotic class. Some resistance genes increased with age while others decreased. The analysis resulted in a complex picture over the cycle.

Risk factors for resistance. Combining resistome data with detailed farm management information such as floor material, herd mixing strategies, pest presence, visitor patterns, temperature and humidity, Valeriia used statistical modelling to identify which factors were associated with resistance outcomes, both for resistome diversity and phenotypic resistance. Resistome diversity and phenotypic resistance in E. coli were not correlated with each other, confirming that genotypic and phenotypic methods capture different and complementary dimensions of AMR and different outcomes drove each outcome.

Applying this research in Sweden and beyond

Valeriia's work makes two contributions that go beyond the Swedish context. First, it provides a validated, scalable methodology that other research groups can now use for large-scale, longitudinal resistome studies, something the field has lacked until now. Second, it demonstrates that in low-use settings, antibiotic use alone does not explain resistance dynamics. Farm management, animal husbandry practices, and environmental conditions all play a role. Addressing AMR in livestock will require understanding and acting on that complexity.

We warmly congratulate Valeriia on a rigorous and practically grounded body of work. Her thesis is a strong contribution to One Health AMR research and to the work UAC's second cohort has produced.