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European Journal of Clinical... Sep 2019The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that... (Review)
Review
The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.
Topics: Actinobacteria; Anti-Bacterial Agents; Drug Resistance, Microbial; Evolution, Molecular; Humans; Phylogeny
PubMed: 31250336
DOI: 10.1007/s10096-019-03580-5 -
Current Opinion in Biotechnology Feb 2023Streams and rivers are widely impacted by human activities ranging from hydrological modifications to point and nonpoint pollution. Among the pollutants that enter lotic... (Review)
Review
Streams and rivers are widely impacted by human activities ranging from hydrological modifications to point and nonpoint pollution. Among the pollutants that enter lotic ecosystems are pharmaceuticals and personal care products, including antibiotics, that may play a role in the occurrence of antibiotic resistance genes (ARGs). Oftentimes, ARGs are detected based on culturing of bacteria or by using quantitative polymerase chain reaction; the limitations of these methods create barriers to our understanding. Use of more exhaustive methods, such as metagenomics, may overcome some of these barriers. The public health and ecological impacts of ARGs may be profound but are largely understudied. Antibiotic resistance is a growing concern for public health.
Topics: Humans; Rivers; Anti-Bacterial Agents; Genes, Bacterial; Ecosystem; Drug Resistance, Microbial
PubMed: 36621219
DOI: 10.1016/j.copbio.2022.102878 -
Methods in Molecular Biology (Clifton,... 2023The construction and screening of metagenomic expression libraries have a great potential to identify novel genes with desired functions. Here, we describe metagenomic...
The construction and screening of metagenomic expression libraries have a great potential to identify novel genes with desired functions. Here, we describe metagenomic library preparation from fecal DNA, screening of libraries for antibiotic resistance genes (ARGs), massively parallel DNA sequencing of the enriched DNA fragments, and a computational pipeline for high-throughput assembly and annotation of functionally selected DNA.
Topics: Metagenomics; Drug Resistance, Microbial; Metagenome; Gene Library; Sequence Analysis, DNA
PubMed: 36445596
DOI: 10.1007/978-1-0716-2855-3_21 -
Proteomics Apr 2022Antibiotic resistance, the ability of a microbial pathogen to evade the effects of antibiotics thereby allowing them to grow under elevated drug concentrations, is an... (Review)
Review
Antibiotic resistance, the ability of a microbial pathogen to evade the effects of antibiotics thereby allowing them to grow under elevated drug concentrations, is an alarming health problem worldwide and has attracted the attention of scientists for decades. On the other hand, the clinical importance of persistence and tolerance as alternative mechanisms for pathogens to survive prolonged lethal antibiotic doses has recently become increasingly appreciated. Persisters and high-tolerance populations are thought to cause the relapse of infectious diseases, and provide opportunities for the pathogens to evolve resistance during the course of antibiotic therapy. Although proteomics and other omics methodology have long been employed to study resistance, its applications in studying persistence and tolerance are still limited. However, due to the growing interest in the topic and recent progress in method developments to study them, there have been some proteomic studies that yield fresh insights into the phenomenon of persistence and tolerance. Combined with the studies on resistance, these collectively guide us to novel molecular targets for the potential drugs for the control of these dangerous pathogens. In this review, we surveyed previous proteomic studies to investigate resistance, persistence, and tolerance mechanisms, and discussed emerging experimental strategies for studying these phenotypes with a combination of adaptive laboratory evolution and high-throughput proteomics.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Bacterial; Drug Resistance, Microbial; Drug Tolerance; Proteomics
PubMed: 35143120
DOI: 10.1002/pmic.202100409 -
Integrative Zoology Nov 2023There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance.... (Review)
Review
There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.
Topics: Animals; Bees; Drug Resistance, Microbial; Bacteria; Anti-Bacterial Agents; Gastrointestinal Microbiome
PubMed: 36892101
DOI: 10.1111/1749-4877.12714 -
GigaScience Jul 2022Screening for antibiotic resistance genes (ARGs) in especially environmental samples with (meta)genomic sequencing is associated with false-positive predictions of...
BACKGROUND
Screening for antibiotic resistance genes (ARGs) in especially environmental samples with (meta)genomic sequencing is associated with false-positive predictions of phenotypic resistance. This stems from the fact that most acquired ARGs require being overexpressed before conferring resistance, which is often caused by decontextualization of putative ARGs by mobile genetic elements (MGEs). Consequent overexpression of ARGs can be caused by strong promoters often present in insertion sequence (IS) elements and integrons and the copy number effect of plasmids, which may contribute to high expression of accessory genes.
RESULTS
Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed, which indicates how mobilized detected ARGs are in bacterial genomes. It is concluded that antibiotic efflux genes are rarely mobilized and even 80% of β-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons.
CONCLUSIONS
In this study, ARGs in all complete bacterial genomes are classified by their association with MGEs, using the proposed ARG-MOB scale. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health. An interactive table of all results is provided for future studies targeting highly mobilized ARGs.
Topics: Anti-Bacterial Agents; DNA Transposable Elements; Drug Resistance, Microbial; Genes, Bacterial; Humans; Phylogeny
PubMed: 35906888
DOI: 10.1093/gigascience/giac072 -
Nature Ecology & Evolution Apr 2021Tackling antibiotic resistance necessitates deep understanding of how resource competition within and between species modulates the fitness of resistant microbes. Recent... (Review)
Review
Tackling antibiotic resistance necessitates deep understanding of how resource competition within and between species modulates the fitness of resistant microbes. Recent advances in ecological coexistence theory offer a powerful framework to probe the mechanisms regulating intra- and interspecific competition, but the significance of this body of theory to the problem of antibiotic resistance has been largely overlooked. In this Perspective, we draw on emerging ecological theory to illustrate how changes in resource niche overlap can be equally important as changes in competitive ability for understanding costs of resistance and the persistence of resistant pathogens in microbial communities. We then show how different temporal patterns of resource and antibiotic supply, alongside trade-offs in competitive ability at high and low resource concentrations, can have diametrically opposing consequences for the coexistence and exclusion of resistant and susceptible strains. These insights highlight numerous opportunities for innovative experimental and theoretical research into the ecological dimensions of antibiotic resistance.
Topics: Bacteria; Biological Evolution; Drug Resistance, Microbial
PubMed: 33526890
DOI: 10.1038/s41559-020-01385-w -
The Science of the Total Environment Jan 2022Antibiotic resistance comprising of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) is an emerging problem causing global human health risks.... (Review)
Review
Antibiotic resistance comprising of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) is an emerging problem causing global human health risks. Several reviews exist on antibiotic resistance in various environmental compartments excluding the air-borne resistome. An increasing body of recent evidence exists on the air-borne resistome comprising of antibiotic resistance in air-borne bioaerosols from various environmental compartments. However, a comprehensive review on the sources, dissemination, behavior, fate, and human exposure and health risks of the air-borne resistome is still lacking. Therefore, the current review uses the source-pathway-receptor-impact-mitigation framework to investigate the air-borne resistome. The nature and sources of antibiotic resistance in the air-borne resistome are discussed. The dissemination pathways, and environmental and anthropogenic drivers accounting for the transfer of antibiotic resistance from sources to the receptors are highlighted. The human exposure and health risks posed by air-borne resistome are presented. A health risk assessment and mitigation strategy is discussed. Finally, future research directions including key knowledge gaps are summarized.
Topics: Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Anti-Bacterial Agents; Drug Resistance, Microbial; Genes, Bacterial; Humans
PubMed: 34798728
DOI: 10.1016/j.scitotenv.2021.150154 -
Environment International May 2020Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health... (Review)
Review
Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health challenge. While traditionally associated with pathogens in clinical environments, it is becoming increasingly clear that non-clinical environments may also be reservoirs of ARGs. The recent improvements in rapid and affordable next generation sequencing technologies along with sophisticated bioinformatics platforms has the potential to revolutionize diagnostic microbiology and microbial surveillance. Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. However, different platforms may significantly vary and therefore, it is crucial to choose the tools that are most suitable for the specific analysis being conducted. This review provides a detailed account of available bioinformatics platforms for identification and characterization of ARGs and associated genetic elements within single bacterial isolates and complex environmental samples. It focuses primarily on currently available ARG databases, employing a comprehensive benchmarking pipeline to identify ARGs in four bacterial genomes (Aeromonas salmonicida, Bacillus cereus, Burkholderia sp. and Escherichia coli) and three shotgun metagenomes (human gut, poultry litter and soil) providing insight into which databases should be used for different analytical scenarios.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Genes, Bacterial; Genome, Bacterial; Humans; Metagenome
PubMed: 32234679
DOI: 10.1016/j.envint.2020.105667 -
Methods in Molecular Biology (Clifton,... 2021Antibiotics are antimicrobial agents primarily produced by certain bacteria and fungi. These drugs are some of the biological weapons used by the producers to survive in... (Review)
Review
Antibiotics are antimicrobial agents primarily produced by certain bacteria and fungi. These drugs are some of the biological weapons used by the producers to survive in their dense and multispecies communities where the resources could be scarce. Thus, the microorganisms, as antibiotic producers, also have the skills to avoid the antibiotic affect from immemorial time. However, the antibiotic resistance is a current global health threat because of the overuse, abuse, or use of antibiotics. Nowadays, resistance to all the antibiotic classes has emerged, which results in 700,000 annual deaths due to the drug-resistant diseases, and forecasts are dramatic for the coming years. This chapter reviews the evolution of the antibiotics discovery, the worldwide antibiotics resistances threat, their economical and clinical impact, as well as how the academia and the enterprises are facing the need of new antibiotics discovery or antimicrobial therapies implementation.
Topics: Animals; Anti-Bacterial Agents; Drug Resistance, Microbial; Humans
PubMed: 33977439
DOI: 10.1007/978-1-0716-1358-0_1