Antibiotic Resistance Genes Found in Bacteria Everywhere: A New Study
A recent study by Chalmers University of Technology and the University of Gothenburg in Sweden, shows that antibiotic resistance genes in bacteria are much more rampant in our environment than previously anticipated. Bacteria in almost all environments carry resistance genes, risking their spread, and increasing the problem with untreated bacterial infections. This finding underlines the need for understanding antibiotic resistance development in bacteria and of resistance genes, as they pose a threat in the future.
Antibiotic Resistance: A Growing Problem
Antibiotic resistance is consistently becoming a public health problem worldwide. When bacteria develop resistance against antibiotics, it becomes challenging or impossible to treat conditions such as pneumonia, urinary tract infections, TB, and wound infections. According to the United Nations Inter-Agency Coordination Group on Antimicrobial Resistance (IACG), over 700,000 people perish each year due to antibiotic-resistant bacterial infections. Establishing how resistance to antibiotics in bacteria spreads from the environment, domestic animals, and humans is a crucial step for preventing outbreaks in the healthcare sector.
Searching for Antibiotic Resistance Genes in New Environments
While prior research has focused on identifying resistance genes that are already prevalent in pathogenic bacteria, the new Swedish study explored new forms of resistance genes to understand how common they are. The researchers considered vast amounts of DNA sequences from bacteria. They traced the genes in thousands of bacterial samples sourced from different environments, in sewage treatment plants, on people, and in the soil. The study examined over 630 billion DNA sequences in total.
Bacterial Resistance in Almost All Environments
The researchers found that bacterial resistance genes are present almost everywhere, including microbiomes, our environment, and, most alarmingly, pathogenic bacteria. This increases the odds of causing further infections that are difficult to treat. Resistance genes in bacteria in the environment, the ones living on and within people, were found to be ten times more widespread than previously known, and a significant proportion of them were not previously known. Of the resistance genes discovered in bacteria in the human microbiome, 75% of them were not previously known. The findings suggest the existence of an overlooked threat to public health.
The Need for Improved Knowledge and Monitoring of Antibiotic Resistance
The researchers underscore the need for enhanced understanding of antibiotic resistance and call for more knowledge about the problem. According to Erik Kristiansson, a professor in the Department of Mathematical Sciences at the University of Gothenburg, before the study, no one knew the incidence of these new resistance genes. Kristiansson termed drug resistance a complex problem that needs to be understood to mitigate the underlying risks.
Hoping to Prevent Bacterial Outbreaks in Healthcare Sector
The research team is currently integrating new data obtained from the study into the international objective, EMBARK (Establishment of a Monitoring Baseline for Antibiotic Resistance in Key Settings). The project coordinator, Johan Bengtsson-Palme, envisages the initiative will take samples from sewage, animals, and the soil to establish how resistance to antibiotics is disseminated from the environment to humans. By monitoring the presence of new resistance genes in the ecosystem, the team hopes to detect and prevent infections from spreading in the healthcare sector.
Conclusion
Antibiotic resistance is a public health problem that is growing worldwide. The findings of the Swedish study underline the need to explore antibiotic resistance to bacteria’s new forms and to monitor their incidence to improve our understanding of their development. We need a comprehensive approach to understand the process of resistance gene dissemination from environmental bacteria to humans and prevent outbreaks in the healthcare sector. To this end, new monitoring systems could be employed to detect resistance genes in bacteria from a diverse range of environments.
Summary:
A new study by Chalmers University of Technology and the University of Gothenburg in Sweden has underscored that bacteria in almost all environments carry resistance genes, posing a significant threat to public health. The researchers analyzed new forms of resistance genes to establish how prevalent they were and traced genes in thousands of bacterial samples from different environments and bacterial DNA sequences from different sources. The analysis revealed that resistance genes in bacteria in our environment and living on and within humans were ten times more widespread than previously known. The findings suggest an overlooked threat to human health that requires more knowledge about the problem of antibiotic resistance and monitoring to prevent outbreaks in the healthcare sector. The study was carried out by Juan Salvador Inda-Díaz, David Lund, Marcos Parras-Moltó, Anna Johnning, Johan Bengtsson-Palme, and Erik Kristiansson.
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The genes that make bacteria resistant to antibiotics are much more widespread in our environment than previously thought. A new study, from Chalmers University of Technology and the University of Gothenburg in Sweden, shows that bacteria in almost all environments carry resistance genes, risking their spread and exacerbating the problem of untreated bacterial infections. They can be treated with antibiotics.
“We have identified new resistance genes in places where they have not been detected before. These genes may constitute an overlooked threat to human health,” says Erik Kristiansson, Professor in the Department of Mathematical Sciences.
According to the World Health Organization (WHO), antibiotic resistance is one of the greatest threats to global health. When bacteria become resistant to antibiotics, it becomes difficult or impossible to treat diseases such as pneumonia, wound infections, tuberculosis, and urinary tract infections. According to the United Nations Inter-Agency Coordination Group on Antimicrobial Resistance (IACG), 700,000 people die each year from infections caused by antibiotic-resistant bacteria.
Searching for resistance genes in new environments
The genes that make bacteria resistant have been studied for a long time, but traditionally the focus has been on identifying those resistance genes that are already prevalent in pathogenic bacteria. Instead, in the new study from Sweden, the researchers looked at large amounts of DNA sequences from bacteria to analyze new forms of resistance genes to understand how common they are. They have traced the genes in thousands of different bacterial samples from different environments, in and on people, in the soil, and in sewage treatment plants. The study analyzed 630 billion DNA sequences in total.
“Data requires a lot of processing before you can get insights. We have used metagenomics, a methodology that allows us to analyze large amounts of data”, says Juan Inda Díaz, a doctoral student in the Department of Mathematical Sciences, and the main author of the article.
The study showed that novel antibiotic resistance genes are present in bacteria in almost all environments. This also includes our microbiomes, the genes of the bacteria in and on people, and, most alarmingly, pathogenic bacteria, which can lead to further infections that are difficult to treat. The researchers found that resistance genes in bacteria living on and within humans and in the environment were ten times more abundant than previously known. And of the resistance genes found in bacteria in the human microbiome, 75 percent were not previously known.
The researchers underscore the need for more knowledge about the problem of antibiotic resistance.
“Before this study, there was no knowledge about the incidence of these new resistance genes. Antibiotic resistance is a complex problem, and our study shows that we need to improve our understanding of the development of resistance in bacteria and of the resistance genes — that could be a threat in the future,” says Kristiansson.
Hoping to prevent bacterial outbreaks in the healthcare sector
The research team is currently working on integrating the new data into the international EMBARK project (Establishment of a Monitoring Baseline for Antibiotic Resistance in Key Settings). The project is coordinated by Johan Bengtsson-Palme, Assistant Professor in Chalmers’ Department of Life Sciences, and aims to take samples from sources such as sewage, soil and animals to get an idea of how resistance to antibiotics is spreading between humans and the environment.
“It is essential that new forms of resistance genes are taken into account in risk assessments related to antibiotic resistance. Using the techniques we have developed allows us to monitor these new resistance genes in the environment, with the hope that we can detect them in pathogenic bacteria before they can cause outbreaks in a healthcare setting,” says Bengtsson-Palme.
More about the study
The researchers used DNA from two public databases. The first database, ResFinder, contains a couple thousand previously known antibiotic resistance genes in bacteria. The researchers expanded these with a host of new resistance genes that they had found through analysis of bacterial DNA. New and known resistance genes totaled 20,000.
The second database, MGnify, contains large amounts of bacterial DNA from different sources, such as bacteria that live on and in people, in sewage treatment plants, and from soil and water. These were analyzed to investigate how common the various resistance genes were in bacterial DNA. The study analyzed 630 billion DNA sequences in total and the results showed that resistance genes are present in almost all environments. Prior to this study, the incidence of these new resistance genes was not known.
The method used by the researchers is called metagenomics and it is not new, but until now it has not been used to analyze new types of antibiotic resistance genes in such large numbers. Metagenomics is a method of studying the metagenome, which is the complete set of genes from all the different organisms in a given sample or within a given environment. Using the method, it is also possible to study microorganisms that cannot be grown in a laboratory.
This study has been carried out by Juan Salvador Inda-Díaz, David Lund, Marcos Parras-Moltó, Anna Johnning, Johan Bengtsson-Palme and Erik Kristiansson. The researchers work at Chalmers University of Technology, the University of Gothenburg and the Fraunhofer-Chalmers Center in Sweden.
https://www.sciencedaily.com/releases/2023/06/230605181325.htm
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