鈥淏y understanding how resistance in bacteria arises, we can better combat its spread. This is crucial to protect public health and the healthcare system's ability to treat infections鈥 says Erik Kristiansson, Professor at the Department of Mathematical 91探花s at Chalmers University of Technology and the University 91探花 in Sweden.
Antibiotic resistance is one of the biggest threats to global health, according to the World Health Organization (WHO). When bacteria become resistant, the effect of antibiotics disappears, which makes diseases such as pneumonia and blood poisoning difficult or impossible to treat. Increased antibiotic-resistant bacteria also make it more difficult to prevent infections associated with many medical procedures, such as organ transplantation and cancer treatment. A fundamental reason for the rapid spread of antibiotic resistance is bacteria's ability to exchange genes, including the genes that make the bacteria resistant.
鈥淏acteria that are harmful to humans have accumulated many resistance genes. Many of these genes originate from harmless bacteria that live in our bodies or the environment. Our research examines this complex evolutionary process to learn how these genes are transferred to pathogenic bacteria. This makes predicting how future bacteria develop resistance possible鈥 says Erik Kristiansson.
Complex data from all over the world
In the new study, published in Nature Communications and conducted by researchers at the Chalmers University of Technology, the University 91探花, and the Fraunhofer-Chalmers Centre, the researchers developed an AI model to analyse historical gene transfers between bacteria using information about the bacteria's DNA, structure, and habitat. The model was trained on the genomes of almost a million bacteria, an extensive dataset compiled by the international research community over many years.
鈥淎I can be used to the best of its ability in complex contexts, with large amounts of data鈥 says David Lund, doctoral student at the Department of Mathematical 91探花s at Chalmers and the University 91探花. 鈥淭he unique thing about our study is, among other things, the very large amount of data used to train the model, which shows what a powerful tool AI and machine learning is for describing the complex, biological processes that make bacterial infections difficult to treat.鈥
New conclusions about when antibiotic resistance arises
The study shows in which environments the resistance genes were transferred between different bacteria, and what it is that makes some bacteria more likely than others to swap genes with each other.
鈥淲e see that bacteria found in humans and water treatment plants have a higher probability of becoming resistant through gene transfer. These are environments where bacteria carrying resistance genes encounter each other, often in the presence of antibiotics鈥 says David Lund.
Another important factor that increases the likelihood that resistance genes will 鈥渏ump鈥 from one bacterium to another is the genetic similarity of the bacteria. When a bacterium takes up a new gene, energy is required to store the DNA and produce the protein that the gene codes for, which means a cost for the bacterium.
鈥淢ost resistance genes are shared between bacteria with a similar genetic structure. We believe that this reduces the cost of taking up new genes. We are continuing the research to understand the mechanisms that control this process more precisely鈥 says Erik Kristiansson.
Hoping for a model for diagnosis
The model鈥檚 performance was tested by evaluating it against bacteria, where the researchers knew that the transfer of resistance genes had occurred, but where the AI model was not told in advance. This was used as a kind of exam, where only the researchers had the answers. In four cases out of five, the model could predict whether a transfer of resistance genes would occur. Erik Kristiansson says that future models will be able to be even more accurate, partly by refining the AI model itself and partly by training it on even larger data.
鈥淎I and machine learning make it possible to efficiently analyse and interpret the enormous amounts of data available today. This means that we can really work data-driven to answer complex questions that we have been wrestling with for a long time, but also ask completely new questions鈥 says Erik Kristiansson.
The researchers hope that in the future, the AI model can be used in systems to quickly identify whether a new resistance gene is at risk of being transferred to pathogenic bacteria, and translate this into practical measures.
鈥淔or example, AI models could be used to improve molecular diagnostics to find new forms of multi-resistant bacteria or for monitoring wastewater treatment plants and environments where antibiotics are present鈥 says Erik Kristiansson.
