Valeriia Ladyhina
Who are you? Could you give a short presentation of yourself and your research area?
My name is Valeriia Ladyhina, and I recently completed my PhD in Biomedical Sciences, which was the part of Uppsala Antibiotic Center. During my previous education, I studied human and animal physiology, innovative medicine, and bioinformatics, which all came together in my PhD project.
My research focuses on antimicrobial resistance, or AMR. This is when bacteria become resistant to antibiotics, making infections harder to treat and it is one of the biggest global health challenges today. In my project, I studied how antimicrobial resistance develops and behaves in pig farm environments. We wanted to understand what is happening with resistant bacteria in these environments, how resistance changes over time as pigs grow, how antibiotic treatments influence this process and is there anything else that also might affect the resistance that we can use to reduce the problem of AMR.
My project consisted of two main parts. The first part was to develop a method (or protocol) to study antimicrobial resistance using metagenomics, which is a technique that allows us to sequence DNA from all bacteria in an environment – not just the ones we can grow in the lab. This type of research includes several important steps, such as sampling, sample transportation, DNA extraction, sequencing, and bioinformatic analysis. There are many different ways to perform each of these steps, and the choices we make can strongly affect the final results. Because of this, we tested different approaches to find the most reliable way to capture as complete a picture as possible of both the bacterial community (which can include thousands of different species) and the collection of all resistance genes.
The second part of my project focused on testing our develped protocol and understanding what drives antimicrobial resistance in real farm environments. We already know that using antibiotics can lead to the development of resistant bacteria. However, an important part of my research was to look beyond that. I wanted to understand whether other factors, such as the environment or farm management, could also play a role. To do this, we worked with 10 Swedish pig farms, where animals are generally healthy and receive very few antibiotic treatments. This allowed us to study resistance in a system with low antibiotic pressure and better explore other possible influences. For example, we looked at factors such as:
Metals like zinc and copper, which are sometimes used in animal feed and may also influence bacterial resistance
Floor materials, such as concrete or straw, which can affect how bacteria survive and spread in the environment
We also studied the relationship between the bacterial community (microbiome) in pig farm and the collection of all antibiotic resistance genes in those bacteria (resistome). As pigs grow, their diet changes – from milk to solid feed – which also changes their microbiome. We wanted to see if these changes could explain changes in resistance. Interestingly, we found that while both the microbiome and resistome change over time, they do not always follow the same patterns.
In this project, we were not able to clearly prove that these non-antibiotic factors directly control resistance due to small number of the studied farms. However, we showed that antimicrobial resistance is a complex process influenced by many interacting factors, not just antibiotic use. Overall, my research highlights that to better understand and control antibiotic resistance, we need to study the whole system – including animals, their environment, and management practices – and continue exploring these connections in future research.
How does your research align with the One Health? (please refer to relevant aspects of the connections between human health, animal health, plant health and ecosystem health)
In my work, I study antimicrobial resistance in pig farm environments, which is directly related to animal health. Healthy animals usually need fewer antibiotics, which helps reduce the risk of resistant bacteria appearing. At the same time, it is quite surprising that around 73% of all antibiotics used globally are actually used in animals, mainly in livestock production. This shows how important it is to study antibiotic resistance not only in humans, but also in animals. However, resistant bacteria don’t stay only in animals. They can spread into the environment, for example through manure, dust, contact with other animals or water on farms. This connects to ecosystem health, because resistance genes can persist in the environment and be taken up by other bacteria.
This environmental spread can also affect plant health, since manure is often used as fertilizer. Resistant bacteria and their genes can enter the soil and interact with plant-associated microbes. Finally, there is a clear link to human health. Resistant bacteria from farms can reach humans through food, direct contact with animals (especially for farmers), or through the environment, making infections harder to treat.
An important part of my research shows that antimicrobial resistance is not only driven by antibiotic use, but also by environmental and management factors. This means that solving the problem requires a whole-system approach, not just focusing on one area. Overall, my work supports the One Health idea by showing that to control antimicrobial resistance, we need to consider the connections between animals, humans, and the environment together, rather than studying them separately.
What are your plans after your PhD?
At the moment, my future plans are not fully decided, but I am very motivated to continue working in science. I would like to stay in research and further deepen my understanding of antimicrobial resistance.
One direction I find particularly interesting is studying how resistance genes actually become active. In my PhD, I looked at which resistance genes are present, but an important next step is to understand when and why these genes are “turned on.” This can be studied using transcriptomics, which looks at which genes are actively being used by bacteria at a given time. I am also interested in linking this to phenotypic resistance, which is the real-world ability of bacteria to survive antibiotic treatment. By combining these different levels – what genes are present, which are active, and how bacteria behave – we can better understand how resistance actually works.
In addition, I would like to explore more practical solutions. For example, it could be interesting to study whether changes in feeding practices could influence bacterial communities and help reduce resistance on farms. Finally, I would like to work on larger-scale studies, including not just a small number of farms, but potentially hundreds. This would give stronger data and help identify which factors – beyond antibiotic use – really influence resistance. The long-term goal would be to provide useful, science-based recommendations to farmers to help reduce antimicrobial resistance in livestock and support the One Health approach.
Links to Uppsala Antibiotic Center:
https://www.uu.se/en/centre/uppsala-antibiotic-center/news/archive/2026-03-31-valeriia-ladyhina-defends-thesis-on-antimicrobial-resistance-dynamics-in-swedish-pig-farms
https://www.uu.se/en/centre/uppsala-antibiotic-center/communication/the-amr-studio/episode-59
https://www.uu.se/en/centre/uppsala-antibiotic-center/research/veterinary--environmental-sciences/amr-dynamics-in-livestock
Link to youtube with recorded webinar on the topic https://youtu.be/QnUnvPvz5q4?si=3kqHTqvDx1RhuAPG