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Microbiome Jul 2023The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant...
BACKGROUND
The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome.
RESULTS
The human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer.
CONCLUSIONS
Diseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.
Topics: Humans; Gastrointestinal Microbiome; Microbiota; Anti-Bacterial Agents; Drug Resistance, Microbial; Genes, Bacterial
PubMed: 37507809
DOI: 10.1186/s40168-023-01610-1 -
The Journal of Antimicrobial... Nov 2021Clostridioides difficile (CD) is one of the top five urgent antibiotic resistance threats in USA. There is a worldwide increase in MDR of CD, with emergence of novel... (Review)
Review
Clostridioides difficile (CD) is one of the top five urgent antibiotic resistance threats in USA. There is a worldwide increase in MDR of CD, with emergence of novel strains which are often more virulent and MDR. Antibiotic resistance in CD is constantly evolving with acquisition of novel resistance mechanisms, which can be transferred between different species of bacteria and among different CD strains present in the clinical setting, community, and environment. Therefore, understanding the antibiotic resistance mechanisms of CD is important to guide optimal antibiotic stewardship policies and to identify novel therapeutic targets to combat CD as well as other bacteria. Epidemiology of CD is driven by the evolution of antibiotic resistance. Prevalence of different CD strains and their characteristic resistomes show distinct global geographical patterns. Understanding epidemiologically driven and strain-specific characteristics of antibiotic resistance is important for effective epidemiological surveillance of antibiotic resistance and to curb the inter-strain and -species spread of the CD resistome. CD has developed resistance to antibiotics with diverse mechanisms such as drug alteration, modification of the antibiotic target site and extrusion of drugs via efflux pumps. In this review, we summarized the most recent advancements in the understanding of mechanisms of antibiotic resistance in CD and analysed the antibiotic resistance factors present in genomes of a few representative well known, epidemic and MDR CD strains found predominantly in different regions of the world.
Topics: Anti-Bacterial Agents; Clostridioides; Clostridioides difficile; Drug Resistance, Microbial; Microbial Sensitivity Tests
PubMed: 34297842
DOI: 10.1093/jac/dkab231 -
Biochemistry. Biokhimiia Nov 2020This issue of the Biochemistry (Moscow) journal presents reviews and experimental articles on the new strategies for solving the problem of antibiotic resistance and on...
This issue of the Biochemistry (Moscow) journal presents reviews and experimental articles on the new strategies for solving the problem of antibiotic resistance and on the search for novel antimicrobial preparations using the methods of molecular biology, genetics, and nanotechnology. A wide variety of scientific approaches and successful (as a rule) research results give hope for overcoming microbial antibiotic resistance in the fight against infectious diseases.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Humans
PubMed: 33280573
DOI: 10.1134/S0006297920110012 -
Ecotoxicology and Environmental Safety Apr 2023Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can... (Review)
Review
Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.
Topics: Animals; Humans; Bacteria; Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Genes, Bacterial; Anti-Bacterial Agents; Drug Resistance, Microbial; Drug Resistance, Bacterial
PubMed: 36950985
DOI: 10.1016/j.ecoenv.2023.114734 -
Molecular Microbiology Mar 2020The acquisition process of antibiotic resistance in an otherwise susceptible organism is shaped by the ecology of the species. Unlike other relevant human pathogens,... (Review)
Review
The acquisition process of antibiotic resistance in an otherwise susceptible organism is shaped by the ecology of the species. Unlike other relevant human pathogens, Listeria monocytogenes has maintained a high rate of susceptibility to the antibiotics used for decades to treat human and animal infections. However, L. monocytogenes can acquire antibiotic resistance genes from other organisms' plasmids and conjugative transposons. Ecological factors could account for its susceptibility. L. monocytogenes is ubiquitous in nature, most frequently including reservoirs unexposed to antibiotics, including intracellular sanctuaries. L. monocytogenes has a remarkably closed genome, reflecting limited community interactions, small population sizes and high niche specialization. The L. monocytogenes species is divided into variants that are specialized in small specific niches, which reduces the possibility of coexistence with potential donors of antibiotic resistance. Interactions with potential donors are also hampered by interspecies antagonism. However, occasional increases in population sizes (and thus the possibility of acquiring antibiotic resistance) can derive from selection of the species based on intrinsic or acquired resistance to antibiotics, biocides, heavy metals or by a natural tolerance to extreme conditions. High-quality surveillance of the emergence of resistance to the key drugs used in primary therapy is mandatory.
Topics: Animals; Anti-Bacterial Agents; Bacterial Proteins; Drug Resistance, Bacterial; Drug Resistance, Microbial; Humans; Listeria monocytogenes; Microbial Sensitivity Tests; Plasmids
PubMed: 32185838
DOI: 10.1111/mmi.14454 -
Poultry Science Mar 2022Antibiotic resistance is a serious concern for public health. Farm environments are relevant reservoirs of antibiotic resistant bacteria and antibiotic resistance genes...
Antibiotic resistance is a serious concern for public health. Farm environments are relevant reservoirs of antibiotic resistant bacteria and antibiotic resistance genes (ARGs), thus strategies to limit the spread of ARGs from farms to the environment are needed. In this study a broiler farm, where antibiotics have never been used for any purpose, was selected to evaluate if this measure is effective in reducing the ARGs load in farm environment (FE) and in meat processing environment (MPE). Faecal samples from FE and MPE were processed for DNA extraction. Detection and quantification of the 16S rRNA gene and selected ARGs (bla, qnrS, sul2, and tetA) were carried out by PCR and digital droplet PCR (ddPCR), respectively. Generally, the relative abundance of the quantified ARGs in FE was similar or higher than that measured in intensive farms. Furthermore, apart for tetA, no differences in relative abundances of the other ARGs between FE and MPE were determined. These results suggest that the choice to not use antibiotics in broiler farming is not so effective to limit the ARGs spread in MPE and that further sources of ARGs should be considered including the preceding production phase with particular reference to the breeding stage.
Topics: Animals; Anti-Bacterial Agents; Chickens; Drug Resistance, Microbial; Farms; Genes, Bacterial; RNA, Ribosomal, 16S
PubMed: 35091251
DOI: 10.1016/j.psj.2021.101675 -
ELife Jun 2020Surveillance strategies based on whole genome sequencing could help with the early identification and detection of new forms of drug-resistant gonorrhoea.
Surveillance strategies based on whole genome sequencing could help with the early identification and detection of new forms of drug-resistant gonorrhoea.
Topics: Anti-Bacterial Agents; Drug Resistance, Microbial; Genomics; Gonorrhea; Humans; Neisseria gonorrhoeae
PubMed: 32602460
DOI: 10.7554/eLife.59379 -
International Journal of Environmental... May 2023The role of microplastics (MPs) in the spread of antibiotic resistance genes (ARGs) is increasingly attracting global research attention due to their unique ecological... (Review)
Review
The role of microplastics (MPs) in the spread of antibiotic resistance genes (ARGs) is increasingly attracting global research attention due to their unique ecological and environmental effects. The ubiquitous use of plastics and their release into the environment by anthropic/industrial activities are the main sources for MP contamination, especially of water bodies. Because of their physical and chemical characteristics, MPs represent an ideal substrate for microbial colonization and formation of biofilm, where horizontal gene transfer is facilitated. In addition, the widespread and often injudicious use of antibiotics in various human activities leads to their release into the environment, mainly through wastewater. For these reasons, wastewater treatment plants, in particular hospital plants, are considered hotspots for the selection of ARGs and their diffusion in the environment. As a result, the interaction of MPs with drug-resistant bacteria and ARGs make them vectors for the transport and spread of ARGs and harmful microorganisms. Microplastic-associated antimicrobial resistance is an emerging threat to the environment and consequently for human health. More studies are required to better understand the interaction of these pollutants with the environment as well as to identify effective management systems to reduce the related risk.
Topics: Humans; Microplastics; Wastewater; Plastics; Genes, Bacterial; Drug Resistance, Microbial; Anti-Bacterial Agents; Hospitals
PubMed: 37239594
DOI: 10.3390/ijerph20105868 -
Journal of Microbiology and... Jan 2021Bacterial biofilm is a community of bacteria that are embedded and structured in a self-secreted extracellular matrix. An important clinical-related characteristic of... (Review)
Review
Bacterial biofilm is a community of bacteria that are embedded and structured in a self-secreted extracellular matrix. An important clinical-related characteristic of bacterial biofilms is that they are much more resistant to antimicrobial agents than the planktonic cells (up to 1,000 times), which is one of the main causes of antibiotic resistance in clinics. Therefore, infections caused by biofilms are notoriously difficult to eradicate, such as lung infection caused by in cystic fibrosis patients. Understanding the resistance mechanisms of biofilms will provide direct insights into how we overcome such resistance. In this review, we summarize the characteristics of biofilms and chronic infections associated with bacterial biofilms. We examine the current understanding and research progress on the major mechanisms of antibiotic resistance in biofilms, including quorum sensing. We also discuss the potential strategies that may overcome biofilm-related antibiotic resistance, focusing on targeting biofilm EPSs, blocking quorum sensing signaling, and using recombinant phages.
Topics: Anti-Bacterial Agents; Bacteria; Bacteriophages; Biofilms; Cystic Fibrosis; Drug Resistance, Bacterial; Drug Resistance, Microbial; Humans; Pseudomonas Infections; Pseudomonas aeruginosa; Quorum Sensing
PubMed: 33323672
DOI: 10.4014/jmb.2010.10021 -
Proceedings. Biological Sciences Oct 2022Bacteriocins, toxic peptides involved in the competition between bacterial strains, are extremely diverse. Previous work on bacteriocin dynamics has highlighted the role...
Bacteriocins, toxic peptides involved in the competition between bacterial strains, are extremely diverse. Previous work on bacteriocin dynamics has highlighted the role of non-transitive 'rock-paper-scissors' competition in maintaining the coexistence of different bacteriocin profiles. The focus to date has primarily been on bacteriocin interactions at the within-host scale (i.e. within a single bacterial population). Yet in species such as , with relatively short periods of colonization and limited within-host diversity, ecological outcomes are also shaped by processes at the epidemiological (between-host) scale. Here, we first investigate bacteriocin dynamics and diversity in epidemiological models. We find that in these models, bacteriocin diversity is more readily maintained than in within-host models, and with more possible combinations of coexisting bacteriocin profiles. Indeed, maintenance of diversity in epidemiological models does not require rock-paper-scissors dynamics; it can also occur through a competition-colonization trade-off. Second, we investigate the link between bacteriocin diversity and diversity at antibiotic resistance loci. Previous work has proposed that bacterial duration of colonization modulates the fitness of antibiotic resistance. Due to their inhibitory effects, bacteriocins are a plausible candidate for playing a role in the duration of colonization episodes. We extend the epidemiological model of bacteriocin dynamics to incorporate an antibiotic resistance locus and demonstrate that bacteriocin diversity can indeed maintain the coexistence of antibiotic-sensitive and -resistant strains.
Topics: Anti-Bacterial Agents; Bacteria; Bacteriocins; Drug Resistance, Microbial; Streptococcus pneumoniae
PubMed: 36196547
DOI: 10.1098/rspb.2022.1197