About this Research Topic
Antimicrobial resistance (AMR) presents an ever-evolving challenge, imposing a significant health and economic burden on communities worldwide. Shockingly, it claims the lives of at least 1.27 million people globally.
Traditionally, AMR studies have been confined to culture-dependent methods geared towards clinically significant bacterial pathogens. In the past two decades, however, it has become clear that AMR problem involves a much broader range of bacteria in many different ecological compartments, including human and veterinary medicine, wildlife, agriculture and even pristine environments.
Besides, there is an active horizontal exchange of AMR genes among different ecological niches, which resulted in the proposal of One Health approach to study AMR. The main problem in studying AMR in the environmental microbiota lies in our present inability to cultivate the majority of microbial diversity.
With the development of high-throughput and automated sequencing technologies, the metagenomic approach offers an excellent opportunity for a more comprehensive access to microbial diversity, including AMR and mobile genetic elements (MGEs) involved in AMR dissemination. Thus, the metagenomic approach offers great opportunities for our understanding of occurrence, diversity and dynamics of AMR and MGEs within and among a variety of ecological compartments, including clinical, communal, agricultural, and environmental settings.
Antimicrobials and AMR are the products of long-term evolution and evolved as integral parts in many microbial ecosystems as signalling and regulatory networks. Thus, they play an important role in keeping the homeostasis of microbial communities. The discovery and extensive use of antimicrobials in clinical and veterinary practice, agriculture, aquaculture and horticulture affected the delicate balance of natural antimicrobial production in many ecosystems and introduced a strong evolutionary pressure of antimicrobials.
The response of the microbial world to this selection resulted in the mobilisation and dissemination of AMR genes to many other ecosystems, where they were not present previously. The extent of AMR dissemination is still to be evaluated and the metagenomic approach could be helpful, especially with MGEs that are mainly responsible for this process.
The main aim of this research topic is focused on the studies that use metagenomics to investigate the occurrence, diversity and dynamics of AMR and the corresponding MGEs in various microbial ecosystems. Despite its advantages, the metagenomic approach has its challenges, particularly in terms of methodology, integration into the processes of routine diagnostics and the standardization of procedures. These issues must be addressed to ensure the validity of comparisons across different studies. Hence, this research topic also emphasizes methodological aspects, including advances in bioinformatics and quality assurance aspects, aimed at refining state-of-the-art approaches for AMR elucidation through metagenomics.
The topic editors eagerly invite contributions, including research articles, reviews, mini reviews, methods and other article formats accepted in this specialty that focus on the following areas:
1. Metagenomic assessment of AMR and MGEs in clinical settings, encompassing patients and hospital environments.
2. Metagenomic assessment of AMR and MGEs in animals including farms, domestic and wild animals, and their environments.
3. Metagenomic assessment of AMR and MGEs in agriculture, food and food products.
4. Metagenomic assessment of AMR and MGEs in the environment, spanning from pristine to contaminated environments, such as soil and aquatic ecosystems.
5. Developments in methodologies, especially bioinformatics, that allow better detection and description of AMR and MGE genes. Generation of comprehensive and carefully curated AMR and MGEs databases, updates of existing databases with data obtained through metagenomic analysis.
Traditionally, AMR studies have been confined to culture-dependent methods geared towards clinically significant bacterial pathogens. In the past two decades, however, it has become clear that AMR problem involves a much broader range of bacteria in many different ecological compartments, including human and veterinary medicine, wildlife, agriculture and even pristine environments.
Besides, there is an active horizontal exchange of AMR genes among different ecological niches, which resulted in the proposal of One Health approach to study AMR. The main problem in studying AMR in the environmental microbiota lies in our present inability to cultivate the majority of microbial diversity.
With the development of high-throughput and automated sequencing technologies, the metagenomic approach offers an excellent opportunity for a more comprehensive access to microbial diversity, including AMR and mobile genetic elements (MGEs) involved in AMR dissemination. Thus, the metagenomic approach offers great opportunities for our understanding of occurrence, diversity and dynamics of AMR and MGEs within and among a variety of ecological compartments, including clinical, communal, agricultural, and environmental settings.
Antimicrobials and AMR are the products of long-term evolution and evolved as integral parts in many microbial ecosystems as signalling and regulatory networks. Thus, they play an important role in keeping the homeostasis of microbial communities. The discovery and extensive use of antimicrobials in clinical and veterinary practice, agriculture, aquaculture and horticulture affected the delicate balance of natural antimicrobial production in many ecosystems and introduced a strong evolutionary pressure of antimicrobials.
The response of the microbial world to this selection resulted in the mobilisation and dissemination of AMR genes to many other ecosystems, where they were not present previously. The extent of AMR dissemination is still to be evaluated and the metagenomic approach could be helpful, especially with MGEs that are mainly responsible for this process.
The main aim of this research topic is focused on the studies that use metagenomics to investigate the occurrence, diversity and dynamics of AMR and the corresponding MGEs in various microbial ecosystems. Despite its advantages, the metagenomic approach has its challenges, particularly in terms of methodology, integration into the processes of routine diagnostics and the standardization of procedures. These issues must be addressed to ensure the validity of comparisons across different studies. Hence, this research topic also emphasizes methodological aspects, including advances in bioinformatics and quality assurance aspects, aimed at refining state-of-the-art approaches for AMR elucidation through metagenomics.
The topic editors eagerly invite contributions, including research articles, reviews, mini reviews, methods and other article formats accepted in this specialty that focus on the following areas:
1. Metagenomic assessment of AMR and MGEs in clinical settings, encompassing patients and hospital environments.
2. Metagenomic assessment of AMR and MGEs in animals including farms, domestic and wild animals, and their environments.
3. Metagenomic assessment of AMR and MGEs in agriculture, food and food products.
4. Metagenomic assessment of AMR and MGEs in the environment, spanning from pristine to contaminated environments, such as soil and aquatic ecosystems.
5. Developments in methodologies, especially bioinformatics, that allow better detection and description of AMR and MGE genes. Generation of comprehensive and carefully curated AMR and MGEs databases, updates of existing databases with data obtained through metagenomic analysis.
Keywords: metagenomics, antimicrobial resistance, bioinformatics, environmental antimicrobial resistance, diagnostics, clinical antimicrobial resistance, one health, resistance genes
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