Led by two internationally recognized researchers, Bálint Kintses and Csaba Pál, researchers from the National Laboratory of Biotechnology operating at the ELKH Biological Research Centre (BRC) in Szeged have developed a new functional metagenomic testing method called DEEPMINE (Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics). The procedure makes possible to more realistically model the likelihood of resistance in clinically relevant pathogens to new antibiotics than current widely used methods. With DEEPMINE, the expected effectiveness of antibiotic candidates can be projected, providing valuable assistance in finding the most promising research directions even in the early stages of development. The scientific work was carried out in collaboration with researchers from Budapest, Pécs and Israel, and a paper presenting the results , which have proven to be of great interest internationally, was published in the prestigious journal Nature Microbiology.
The novelty value of the procedure developed under the leadership of the Szeged-based researchers comes from two important features. Firstly, unlike traditional laboratory methods that test various antimicrobial agents on model bacteria, this method tests clinical pathogens that are relevant in practice. Secondly, it models the key mechanism of real-life resistance development, called horizontal gene transfer, more accurately. The combination of these two approaches is a unique strategy worldwide. The results suggest that this could be an effective tool for pharmaceutical developers to predict the potential resistance risk in new antibiotics that will be released to the market in the future, enabling more effective competition with the currently multi-drug resistant pathogens.
A global public health problem
Antibiotic resistance is a major global public health problem, with increasing numbers of bacteria in clinical practice becoming resistant to all available antibiotics. Annually, antibiotic resistance is responsible for approximately 700,000 deaths worldwide. The problem's significance is highlighted by the fact that the World Health Organization (WHO) has designated it as a top priority to promote the fight against multi-drug resistant pathogens. Pessimistic estimates suggest that antibiotic resistance may become one of the leading causes of death by 2050 if no effective new antibacterial agents are introduced into therapy soon.
Antibiotic research and development are supported at the government level in many countries, but the huge costs of such endeavors stand in stark contrast to the unpredictable effectiveness time frame, which can be as short as just a few years. Thus, there is an urgent need for methods that can predict the potential resistance risk already in the drug development phase. This would allow for the shaping of new developments to ensure the longest possible clinical effectiveness period. However, in addition to the current efficacy and safety of the drug candidate, many other factors must be considered. The interaction between the bacterium and the drug it is exposed to does not occur in an isolated environment, but many other interactions also influence the development of resistance. One important factor in real-life settings is the exposure of resistance genes to the environment, such as the soil and other bacteria in the hospital environment, which plays a crucial role in bacterial resistance to various antibiotics. Through the mechanism of horizontal gene transfer, these genes can be incorporated into pathogenic microorganisms from the environment, giving them new traits. Therefore, it is crucial for drug developers to model this mechanism as well, but currently, this approach is not part of routine exploratory tests, probably due to the vast number of potential resistance genes and the difficulty of incorporating foreign genetic material. The methods used in the pharmaceutical industry today mainly focus on de novo mutations that occur in the bacteria, ignoring the effect of horizontal gene transfer.
Not trivial, but not impossible
Researchers have now tried to find a solution to this problem. The method developed in Szeged models the above process in a new approach that better resembles the real clinical environment, in which pathogens adapt to antibiotics, says Bálint Kintses, who, along with colleagues, has been working for many years on advancing techniques for defeating antibiotic resistance. The researchers isolated resistance genes from microorganisms found in environmental samples, including wastewater and soil samples collected widely, to build a DNA library, which they introduced into several clinically relevant pathogens, including Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, and Shigella sonnei species, using a genome engineering approach with the help of a modified bacteriophage. They then examined which expressed resistance genes made the given bacterial species resistant to clinically applied and currently under development antibacterial agents. The actual appearance of resistance is significantly influenced by the genetic characteristics of individual bacteria, as not every resistance gene is compatible with any genetic environment. In the experiment, therefore, pathogenic bacteria carrying resistance genes only became truly resistant to a drug or drug candidate if a given resistance gene could become functional in the given bacterium.
The risk is greater than one would think
This finding is of particular importance from the point of view of pharmaceutical research, because even though a large number of resistance genes were already known up to now, there was no evidence that most of them are functionally compatible with the genetic background of multi-drug resistant pathogens relevant to clinical care. And if these genes are not species-specific, they can easily be transferred between species, which makes them highly mobilizable and thus able to neutralize the effects of future new antibiotics, even in the short term.
The research results indicate that the resistance potential of bacteria posing serious therapeutic challenges to clinical patient care is much greater than we think. About 60-70 percent of the resistance genes present in the environment are capable of being expressed in each of the pathogens tested, rendering them resistant to even the drugs under development that represent the hope of the future. There are also species-specific resistance genes that can only develop actual resistance in specific bacterial species. This finding is of paramount importance for drug research because although a large number of resistance genes have already been known, there has been no evidence that most of these are functionally compatible with the genetic background of clinically relevant, multiply drug-resistant pathogens. And if these genes are not species-specific, they can easily be transferred between species, making them easily mobilizable and thus able to quickly render future new antibiotics ineffective.
Where do we stand in the arms race against bacteria?
Based on the above, the question arises as to whether there is any hope of ever overcoming antibiotic resistance in pathogens, or whether it is inevitable that we will succumb to a banal infection, as we did before the discovery of penicillin.
The wider the range of drugs to which a particular pathogen has already become resistant, the greater the likelihood that it will quickly become resistant to a new drug with a similar mechanism of action. However, according to researchers, if the drug development process were deliberately directed from the early stages, for example, through their new method, to bypass the most significant resistance mechanisms, this would undoubtedly increase the success rate of drug development and give hope for the effective treatment of the most dreaded clinical infections in the long term. The importance of developing methods that take resistance evolution into account has been emphasized by experts for years. The ideal situation would be for research groups working on this issue to bring about a paradigm shift in antibiotic development. The new functional metagenomic approach developed by the researchers of BRC would clearly benefit the industry if implemented.