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Environment International Nov 2023Cyanobacterial harmful algal blooms (cyanoHABs), which are a form of microbial dysbiosis in freshwater environments, are an emerging environmental and public health...
Cyanobacterial harmful algal blooms (cyanoHABs), which are a form of microbial dysbiosis in freshwater environments, are an emerging environmental and public health concern. Additionally, the freshwater environment serves as a reservoir of antibiotic resistance genes (ARGs), which pose a risk of transmission during microbial dysbiosis, such as cyanoHABs. However, the interactions between potential synergistic pollutants, cyanoHABs, and ARGs remain poorly understood. During cyanoHABs, Microcystis and high microcystin levels were dominant in all the nine regions of the river sampled. The resistome, mobilome, and microbiome were interrelated and linked to the physicochemical properties of freshwater. Planktothrix and Pseudanabaena competed with Actinobacteriota and Proteobacteria during cyanoHABs. Forty two ARG carriers were identified, most of which belonged to Actinobacteriota and Proteobacteria. ARG carriers showed a strong correlation with ARGs density, which decreased with the severity of cyanoHAB. Although ARGs decreased due to a reduction of ARG carriers during cyanoHABs, mobile gene elements (MGEs) and virulence factors (VFs) genes increased. We explored the relationship between cyanoHABs and ARGs for potential synergistic interaction. Our findings demonstrated that cyanobacteria compete with freshwater commensal bacteria such as Actinobacteriota and Proteobacteria, which carry ARGs in freshwater, resulting in a reduction of ARGs levels. Moreover, cyanoHABs generate biotic and abiotic stress in the freshwater microbiome, which may lead to an increase in MGEs and VFs. Exploration of the intricate interplays between microbiome, resistome, mobilome, and pathobiome during cyanoHABs not only revealed that the mechanisms underlying the dynamics of microbial dysbiosis but also emphasizes the need to prioritize the prevention of microbial dysbiosis in the risk management of ARGs.
Topics: Humans; Anti-Bacterial Agents; Dysbiosis; Cyanobacteria; Drug Resistance, Microbial; Microcystis; Genes, Bacterial
PubMed: 37897871
DOI: 10.1016/j.envint.2023.108268 -
MicrobiologyOpen Sep 2020The agricultural ecosystem creates a platform for the development and dissemination of antimicrobial resistance, which is promoted by the indiscriminate use of... (Review)
Review
The agricultural ecosystem creates a platform for the development and dissemination of antimicrobial resistance, which is promoted by the indiscriminate use of antibiotics in the veterinary, agricultural, and medical sectors. This results in the selective pressure for the intrinsic and extrinsic development of the antimicrobial resistance phenomenon, especially within the aquaculture-animal-manure-soil-water-plant nexus. The existence of antimicrobial resistance in the environment has been well documented in the literature. However, the possible transmission routes of antimicrobial agents, their resistance genes, and naturally selected antibiotic-resistant bacteria within and between the various niches of the agricultural environment and humans remain poorly understood. This study, therefore, outlines an overview of the discovery and development of commonly used antibiotics; the timeline of resistance development; transmission routes of antimicrobial resistance in the agro-ecosystem; detection methods of environmental antimicrobial resistance determinants; factors involved in the evolution and transmission of antibiotic resistance in the environment and the agro-ecosystem; and possible ways to curtail the menace of antimicrobial resistance.
Topics: Agriculture; Animals; Anti-Bacterial Agents; Aquaculture; Drug Resistance, Bacterial; Drug Resistance, Microbial; Drug Resistance, Multiple, Bacterial; Ecosystem; Farms; Food Chain; Food Safety; Humans; Livestock; Manure; Public Health; Soil
PubMed: 32710495
DOI: 10.1002/mbo3.1035 -
Trends in Microbiology Aug 2023The nasopharynx is an important microbial reservoir for the emergence and spread of antibiotic-resistant organisms. The nasopharyngeal resistome is an extensive,... (Review)
Review
The nasopharynx is an important microbial reservoir for the emergence and spread of antibiotic-resistant organisms. The nasopharyngeal resistome is an extensive, adaptable reservoir of antibiotic-resistance genes (ARGs) within this niche. Metagenomic sequencing decodes the genetic material of all organisms within a sample using next-generation technologies, permitting unbiased discovery of novel ARGs and associated mobile genetic elements (MGEs). The challenges of sequencing a low-biomass bacterial sample have limited exploration of the nasopharyngeal resistome. Here, we explore the current understanding of the nasopharyngeal resistome, particularly the role of MGEs in propagating antimicrobial resistance (AMR), explore the advantages and limitations of metagenomic sequencing technologies and bioinformatic pipelines for nasopharyngeal resistome analysis, and highlight the key outstanding questions for future research.
Topics: Humans; Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Genes, Bacterial; Nasopharynx; Metagenomics
PubMed: 36967247
DOI: 10.1016/j.tim.2023.02.008 -
Antimicrobial Resistance and Infection... 2019Microbial resistance to classical antibiotics and its rapid progression have raised serious concern in the treatment of infectious diseases. Recently, many studies have... (Review)
Review
Microbial resistance to classical antibiotics and its rapid progression have raised serious concern in the treatment of infectious diseases. Recently, many studies have been directed towards finding promising solutions to overcome these problems. Phytochemicals have exerted potential antibacterial activities against sensitive and resistant pathogens via different mechanisms of action. In this review, we have summarized the main antibiotic resistance mechanisms of bacteria and also discussed how phytochemicals belonging to different chemical classes could reverse the antibiotic resistance. Next to containing direct antimicrobial activities, some of them have exerted in vitro synergistic effects when being combined with conventional antibiotics. Considering these facts, it could be stated that phytochemicals represent a valuable source of bioactive compounds with potent antimicrobial activities.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Outer Membrane; Bacterial Proteins; Drug Resistance, Microbial; Drug Synergism; Gene Expression Regulation, Bacterial; Humans; Phytochemicals
PubMed: 31346459
DOI: 10.1186/s13756-019-0559-6 -
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 -
Eastern Mediterranean Health Journal =... Feb 2021Urinary tract infection is one of the most common infections and its treatment is complicated by the emergence of antibiotic resistance. Resistance patterns of organisms...
BACKGROUND
Urinary tract infection is one of the most common infections and its treatment is complicated by the emergence of antibiotic resistance. Resistance patterns of organisms differ between community-acquired and hospital-associated urinary tract infections.
AIMS
The aim of this study was to determine the most effective antibiotics against uropathogens and if antibiotic resistance differed by setting (inpatient versus outpatient).
METHODS
This 2016-2017 cross-sectional study examined 300 midstream clean-catch urine samples with positive culture (150 outpatient and 150 inpatient samples) for the uropathogens isolated and the resistance of these pathogens to different antibiotics. Samples were obtained from the laboratory of Baharloo hospital, Tehran. The differences in antibiotic resistance between inpatient and outpatient uropathogens were analysed using the chi-squared test.
RESULTS
Escherichia coli (72.0% of the 300 samples) and Klebsiella spp (13.0%) were the most common uropathogens isolated. A greater proportion of inpatient samples showed resistance to ceftriaxone, cefixime, sulfamethoxazole-trimethoprim, ciprofloxacin and nalidixic acid than the outpatient samples (P < 0.05). The most effective antibiotics for Gram-negative uropathogens were imipenem (only 6.0% of these uropathogens overall were antibiotic-resistant), amikacin (6.3%) and nitrofurantoin (10.3%).
CONCLUSIONS
Uropathogen resistant rates in inpatients were higher than outpatient rates. The use of imipenem and amikacin instead of traditional first-line empirical therapy (fluoroquinolone and sulfamethoxazole-trimethoprim) is advised for hospitalized patients with urinary tract infections.
Topics: Anti-Bacterial Agents; Cross-Sectional Studies; Drug Resistance, Bacterial; Drug Resistance, Microbial; Humans; Inpatients; Iran; Microbial Sensitivity Tests; Outpatients
PubMed: 33665796
DOI: 10.26719/emhj.20.085 -
The Journal of Antibiotics Jul 2020The scarcity of novel antibiotic compounds in a time of increasing resistance rates has begun to ring alarm bells at the highest echelons of government. Large new... (Review)
Review
The scarcity of novel antibiotic compounds in a time of increasing resistance rates has begun to ring alarm bells at the highest echelons of government. Large new financial incentives to accelerate antibiotic research and development, such as market entry rewards (MERs), are being considered. However, there is little focus on how to sustain the efficacy of new, promising antibiotics reaching the market. Currently, inappropriate use of antibiotics is commonplace, which has accelerated resistance development. In an attempt to halt this trend, antibiotic stewardship policies are being implemented in many resource-rich settings. Unfortunately, this has not yet had an impact on the amount of antibiotics being prescribed globally. One important hurdle is misalignment of incentives. While governments and health services are incentivized to promote prudent use of this common good, pharmaceutical companies are incentivized to increase volume of sales to maximize profits. This problem must be addressed or else the major efforts going into developing new antibiotics will be in vain. In this paper we outline an approach to realign the incentives of pharmaceutical companies with wider antibiotic conservation efforts by making a staged bonus a component of an MER for antibiotic developers when resistance to their drug remains low over time. This bonus could address the lack of stewardship focus in any innovation-geared incentive.
Topics: Animals; Anti-Bacterial Agents; Drug Industry; Drug Resistance, Microbial; Humans
PubMed: 32203126
DOI: 10.1038/s41429-020-0300-y -
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 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Dec 2020The discovery of antibiotics is a big revolution in human history, and its clinical application has saved countless lives. However, with the widespread and abuse of... (Review)
Review
The discovery of antibiotics is a big revolution in human history, and its clinical application has saved countless lives. However, with the widespread and abuse of antibiotics, many pathogens have developed resistance, and even "Super Bacteria" resistance to multiple drugs have evolved. In the arms race between humans and pathogens, humans are about to face a situation where no medicine is available. Research on microbial antibiotic resistance genes, resistance mechanisms, and the spread of resistance has attracted the attention of many scientific researchers, and various antibiotic resistance gene databases and analysis tools have emerged. In this review, we collect the current databases that focus on antibiotics resistance genes, and discuss these databases in terms of database types, data characteristics, antibiotics resistance gene prediction models and the types of analyzable sequences. In addition, a few gene databases of anti-metal ions and anti-biocides are also involved. It is believed that this summary will provide a reference for how to select and use antibiotic resistance gene databases.
Topics: Anti-Bacterial Agents; Bacterial Infections; Drug Resistance, Bacterial; Drug Resistance, Microbial; Humans; Metals
PubMed: 33398956
DOI: 10.13345/j.cjb.200375 -
BMC Biology Sep 2017Antibiotic natural products are ancient and so is resistance. Consequently, environmental bacteria harbor numerous and varied antibiotic resistance elements.... (Review)
Review
Antibiotic natural products are ancient and so is resistance. Consequently, environmental bacteria harbor numerous and varied antibiotic resistance elements. Nevertheless, despite long histories of antibiotic production and exposure, environmental bacteria are not resistant to all known antibiotics. This means that there are barriers to the acquisition of a complete resistance armamentarium. The sources, distribution, and movement of resistance mechanisms in different microbes and bacterial populations are mosaic features that act as barriers to slow this movement, thus moderating the emergence of bacterial pan-resistance. This is highly relevant to understanding the emergence of resistance in pathogenic bacteria that can inform better antibiotic management practices and influence new drug discovery.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial
PubMed: 28915805
DOI: 10.1186/s12915-017-0423-1