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Comprehensive Reviews in Food Science... Jul 2023The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food... (Review)
Review
The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.
Topics: Humans; Food Microbiology; Anti-Bacterial Agents; Drug Resistance, Microbial; Bacteria; Phenotype; Biomarkers
PubMed: 37222539
DOI: 10.1111/1541-4337.13181 -
Current Opinion in Microbiology Aug 2023The increasing prevalence of infections caused by antibiotic-resistant bacteria is a global healthcare crisis. Understanding the spread of resistance is predicated on... (Review)
Review
The increasing prevalence of infections caused by antibiotic-resistant bacteria is a global healthcare crisis. Understanding the spread of resistance is predicated on the surveillance of antibiotic resistance genes within an environment. Bioinformatics and artificial intelligence (AI) methods applied to metagenomic sequencing data offer the capacity to detect known and infer yet-unknown resistance mechanisms, and predict future outbreaks of antibiotic-resistant infections. Machine learning methods, in particular, could revive the waning antibiotic discovery pipeline by helping to predict the molecular structure and function of antibiotic resistance compounds, and optimising their interactions with target proteins. Consequently, AI has the capacity to play a central role in guiding antibiotic stewardship and future clinical decision-making around antibiotic resistance.
Topics: Artificial Intelligence; Bacteria; Drug Resistance, Microbial; Anti-Bacterial Agents
PubMed: 37031568
DOI: 10.1016/j.mib.2023.102305 -
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 -
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 -
Journal of Hazardous Materials Oct 2023Constructed wetlands (CWs) were responsible for the in-depth purification of wastewater, providing an ideal environment for the transport, acquisition, and dissemination...
Constructed wetlands (CWs) were responsible for the in-depth purification of wastewater, providing an ideal environment for the transport, acquisition, and dissemination of antibiotic resistance genes (ARGs). A better understanding of influencing factors and risks of ARGs in CWs was deemed indispensable. In this research, the abundance of ARGs and mobile genetic elements (MGEs) was determined to be higher in summer and spring, ranging from 53.7 to 8.51 × 10 and 30.9-6.02 × 10 copies/mL, respectively. Seasonal variation significantly influenced the abundance of ARGs and MGEs, as well as the co-occurrence patterns among ARGs, MGEs and bacteria. However, the environmental gradients, from the influent (CW01) to the effluent (CW10), did not impose significant effects on the abundance of ARGs and MGEs. Furthermore, the ratios of pathogenic bacteria to ARG hosts and ARG risks index decreased by 50.4% and 88.54% along with the environmental gradients, indicating that CWs could act as barriers to the transfer of ARGs. Partial least squares-path modeling (PLSPM) revealed that temperature was the main driving factor of ARGs, followed by MGEs, stable and differential bacteria. This finding effectively and innovatively explored the driving indicators for the variations and risks of ARGs caused by spatial-temporal variations, providing new insights into the evaluation and control of ARGs in CWs.
Topics: Wetlands; Risk Assessment; Anti-Bacterial Agents; Drug Resistance, Microbial; Seasons
PubMed: 37595473
DOI: 10.1016/j.jhazmat.2023.132314 -
Advances in Experimental Medicine and... 2024The rapid evolution of antibiotic resistance in Clostridioides difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are a...
The rapid evolution of antibiotic resistance in Clostridioides difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are a matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances, and most of the epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways or biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.
Topics: Clostridioides; Clostridioides difficile; Drug Resistance, Microbial; Anti-Bacterial Agents; Biofilms
PubMed: 38175476
DOI: 10.1007/978-3-031-42108-2_9 -
Nature Reviews. Microbiology Oct 2023Antibiotic resistance is currently one of the most important public health problems. The golden age of antibiotic discovery ended decades ago, and new approaches are... (Review)
Review
Antibiotic resistance is currently one of the most important public health problems. The golden age of antibiotic discovery ended decades ago, and new approaches are urgently needed. Therefore, preserving the efficacy of the antibiotics currently in use and developing compounds and strategies that specifically target antibiotic-resistant pathogens is critical. The identification of robust trends of antibiotic resistance evolution and of its associated trade-offs, such as collateral sensitivity or fitness costs, is invaluable for the design of rational evolution-based, ecology-based treatment approaches. In this Review, we discuss these evolutionary trade-offs and how such knowledge can aid in informing combination or alternating antibiotic therapies against bacterial infections. In addition, we discuss how targeting bacterial metabolism can enhance drug activity and impair antibiotic resistance evolution. Finally, we explore how an improved understanding of the original physiological function of antibiotic resistance determinants, which have evolved to reach clinical resistance after a process of historical contingency, may help to tackle antibiotic resistance.
Topics: Humans; Drug Resistance, Microbial; Bacterial Infections; Bacteria; Anti-Bacterial Agents; Biology; Drug Resistance, Bacterial
PubMed: 37208461
DOI: 10.1038/s41579-023-00902-5 -
Comptes Rendus Biologies Mar 2024
Topics: One Health; Drug Resistance, Microbial; Anti-Bacterial Agents
PubMed: 37655922
DOI: 10.5802/crbiol.122 -
Environment International Aug 2023In recent years, the excessive of antibiotics in livestock and poultry husbandry, stemming from extensive industry experience, has resulted in the accumulation of...
In recent years, the excessive of antibiotics in livestock and poultry husbandry, stemming from extensive industry experience, has resulted in the accumulation of residual antibiotics and antibiotic resistance genes (ARGs) in livestock manure. Composting, as a crucial approach for the utilization of manure resources, has the potential to reduce the levels of antibiotics and ARGs in manure, although complete elimination is challenging. Previous studies have primarily focused on the diversity and abundance of ARGs in compost or have solely examined the correlation between ARGs and their carriers, potentially leading to a misjudgment of the actual risk associated with ARGs in compost. To address this gap, this study investigated the transfer potential of ARGs in compost and their co-occurrence with opportunistic pathogenic bacteria by extensively analyzing metagenomic sequencing data of compost worldwide. The results demonstrated that the potential risk of ARGs in compost was significantly lower than in manure, suggesting that composting effectively reduces the risk of ARGs. Further analysis showed that the microbes shifted their life history strategy in manure and compost due to antibiotic pressure and formed metabolic interactions dominated by antibiotic-resistant microbes, increasing ARG dissemination frequency. Therefore, husbandry practice without antibiotic addition was recommended to control ARG evolution, dissemination, and abatement both at the source and throughout processing.
Topics: Animals; Anti-Bacterial Agents; Composting; Genes, Bacterial; Manure; Drug Resistance, Microbial; Risk Assessment
PubMed: 37562342
DOI: 10.1016/j.envint.2023.108126 -
Methods in Molecular Biology (Clifton,... 2024Antibiotic resistance among pathogenic bacteria is one of the most severe global challenges. It is predicted that over ten million lives will be lost annually by 2050.... (Review)
Review
Antibiotic resistance among pathogenic bacteria is one of the most severe global challenges. It is predicted that over ten million lives will be lost annually by 2050. Phage therapy is a promising alternative to antibiotics. However, the ease of development of phage resistance during therapy is a concern. This review focuses on the possible ways to overcome phage resistance in phage therapy.
Topics: Bacteriophages; Phage Therapy; Bacteria; Drug Resistance, Microbial; Anti-Bacterial Agents
PubMed: 37966611
DOI: 10.1007/978-1-0716-3549-0_23