New antibiotic resistance found in widespread bacteria

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Newswise — A recent study by Chalmers University of Technology and the University of Gothenburg in Sweden has revealed that the genes responsible for antibiotic resistance in bacteria are more prevalent in our environment than previously thought. Research shows that bacteria in nearly all environments contain these resistance genes, increasing the risk of their spread and exacerbating the problem of bacterial infections that cannot be effectively treated with antibiotics. This highlights the urgent need to tackle antibiotic resistance to prevent the emergence of untreatable bacterial infections.

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Erik Kristiansson, professor in the Department of Mathematical Sciences, underscores the significance of the study findings by saying: ‘We have discovered previously unidentified resistance genes in places that have gone unnoticed until now. These genes could pose a hidden danger to human health. This statement highlights the potential risks associated with the presence of undiscovered antibiotic resistance genes and underscores the need for more research and action to address this threat to human well-being.

The World Health Organization (WHO) recognizes antibiotic resistance as a major global health concern. When bacteria develop resistance to antibiotics, it becomes difficult or even impossible to effectively treat various diseases, including pneumonia, wound infections, tuberculosis and urinary tract infections. According to the United Nations Interagency Coordinating Group on Antimicrobial Resistance (IACG), approximately 700,000 people die each year from infections caused by antibiotic-resistant bacteria. These statistics highlight the serious impact of antibiotic resistance on public health and underscore the urgent need for effective strategies to address this problem.

Looking for resistance genes in new environments

Traditionally, research on antibiotic resistance genes has primarily focused on identifying those genes already present in pathogenic bacteria. However, the recent Swedish study took a different approach, looking at large DNA sequences from various bacteria. The objective was to analyze new variations of resistance genes and determine their prevalence. Researchers studied thousands of bacterial samples obtained from different environments, including the human body, soil and wastewater treatment plants. The study involved analyzing a whopping total of 630 billion DNA sequences. This comprehensive analysis has enabled a broader understanding of the occurrence and distribution of novel forms of resistance genes in different bacterial populations.

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Juan Inda Díaz, the lead author of the paper and a doctoral student in the Department of Mathematical Sciences, explains that processing the large amount of data obtained from the study required considerable effort. The researchers used a methodology called metagenomics, which allowed for the analysis of huge volumes of data. Metagenomics involves the study of genetic material extracted directly from environmental samples, allowing for a comprehensive examination of genetic diversity and functions within microbial communities. This approach proved instrumental in managing and analyzing the large amounts of data generated in the study.

The study revealed that the recently discovered antibiotic resistance genes are widely distributed among bacteria in almost all types of environments. This includes human microbiomes, which refer to the genes of bacteria that reside in and on our bodies. Alarmingly, these resistance genes have also been detected in pathogenic bacteria, which can cause difficult-to-treat infections. The researchers found that the abundance of resistance genes in bacteria in the human and environmental microbiomes was ten times greater than previously known. Furthermore, a staggering 75% of the resistance genes identified in the human microbiome were previously unknown. These findings underscore the magnitude of the antibiotic resistance gene prevalence and underscore the urgent need for global strategies to combat this global health threat.

The researchers underline the need for more knowledge on the problem of antibiotic resistance.

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According to Kristiansson, prior to this study, there was a complete lack of knowledge regarding the presence of these newly discovered resistance genes. Antibiotic resistance is a multifaceted issue and this research demonstrates the need to broaden our understanding of bacterial resistance development and the potential threat posed by these resistance genes in the future. The study underscores the importance of continued research and vigilance in tackling antibiotic resistance to stay ahead of emerging challenges and potential health risks.

Hoping to prevent bacterial outbreaks in healthcare

The research team is actively collaborating with the international EMBARK (Establishing a Monitoring Baseline for Antibiotic Resistance in Key environment) project to incorporate their new data. Led by Johan Bengtsson-Palme, assistant professor in Chalmers University’s Department of Life Sciences, the project focuses on collecting samples from various sources such as wastewater, soil and animals. The goal is to obtain information on the transmission and spread of antibiotic resistance between humans and the environment. By integrating their findings, the team aims to provide valuable insights into the broader understanding of antibiotic resistance dynamics and aid in the development of effective monitoring and control strategies.

Bengtsson-Palme stresses the importance of considering newly discovered forms of resistance genes in risk assessments associated with antibiotic resistance. The techniques developed by the research team offer a means of monitoring these new resistance genes in the environment. By proactively detecting these genes in pathogenic bacteria, there is a greater likelihood of preventing outbreaks in healthcare settings. This proactive approach aims to boost surveillance efforts and improve preparedness to mitigate the spread of antibiotic resistance and associated health risks.

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Read 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 augmented them with a large number of new resistance genes that they had found through an analysis of bacterial DNA. The known and new resistance genes totaled 20,000.

The second database, MGNify, contains large amounts of bacterial DNA from a variety of sources, such as bacteria that live on and in people, in wastewater treatment plants, and from soil and water. These were analyzed to study how common the various resistance genes were in bacterial DNA. The study analyzed a total of 630 billion DNA sequences 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’s not new, but so far it hasn’t 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 genetic set of 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 the laboratory.

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I study Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes was published in the journal Microbiome.

This study was conducted 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.

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