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Frontiers in Cellular and Infection... 2023
Topics: Drug Resistance, Multiple, Bacterial; Drug Resistance, Bacterial; Gram-Negative Bacteria; Interspersed Repetitive Sequences
PubMed: 37009500
DOI: 10.3389/fcimb.2023.1180510 -
Applied and Environmental Microbiology Jul 2021Spread of biosolids-borne antibiotic resistance is a growing public and environmental health concern. Herein, we conducted incubation experiments involving biosolids,...
Spread of biosolids-borne antibiotic resistance is a growing public and environmental health concern. Herein, we conducted incubation experiments involving biosolids, which are byproducts of sewage treatment processes, and biosolids-amended soil. Quantitative reverse transcription-PCR (RT-qPCR) was employed to assess responses of select antibiotic resistance genes (ARGs) and mobile elements to environmentally relevant concentrations of two biosolids-borne antibiotics, azithromycin (AZ) and ciprofloxacin (CIP). Additionally, we examined sequence distribution of (encoding DNA gyrase; site of action of CIP) to assess potential shifts in genotype. Increasing antibiotic concentrations generally increased the transcriptional activities of (encoding CIP resistance) and and (encoding AZ resistance). The transcriptional activity of , a marker of class 1 integrons, was unaffected by CIP or AZ concentrations, but biosolids amendment increased activity in the soil by 4 to 5 times, which persisted throughout incubation. While the dominant sequences found herein were unrelated to known CIP-resistant genotypes, the increasing CIP concentrations significantly decreased the diversity of genes encoding the DNA gyrase A subunit, suggesting changes in microbial community structures. This study suggests that biosolids harbor transcriptionally active ARGs and mobile elements that could survive and spread in biosolids-amended soils. However, more research is warranted to investigate these trends under field conditions. Although previous studies have indicated that biosolids may be important spreaders of antibiotics and antibiotic resistance genes (ARGs) in environments, the potential activities of ARGs or their responses to environmental parameters have been understudied. This study highlights that certain biosolids-borne antibiotics can induce transcriptional activities of ARGs and mobile genetic elements in biosolids and biosolids-amended soil, even when present at environmentally relevant concentrations. Furthermore, these antibiotics can alter the structure of microbial populations expressing ARGs. Our findings indicate the bioavailability of the antibiotics in biosolids and provide evidence that biosolids can promote the activities and dissemination of ARGs and mobile genes in biosolids and soils that receive contaminated biosolids, thus, underscoring the importance of investigating anthropogenically induced antibiotic resistance in the environment under real-world scenarios.
Topics: Anti-Bacterial Agents; Azithromycin; Bacteria; Bacterial Proteins; Biosolids; Ciprofloxacin; Drug Resistance, Bacterial; Interspersed Repetitive Sequences; Soil; Soil Microbiology; Soil Pollutants
PubMed: 34085858
DOI: 10.1128/AEM.00373-21 -
Research in Microbiology May 2015Approximately 11% the Clostridium difficile genome is made up of mobile genetic elements which have a profound effect on the biology of the organism. This includes... (Review)
Review
Approximately 11% the Clostridium difficile genome is made up of mobile genetic elements which have a profound effect on the biology of the organism. This includes transfer of antibiotic resistance and other factors that allow the organism to survive challenging environments, modulation of toxin gene expression, transfer of the toxin genes themselves and the conversion of non-toxigenic strains to toxin producers. Mobile genetic elements have also been adapted by investigators to probe the biology of the organism and the various ways in which these have been used are reviewed.
Topics: Adaptation, Biological; Bacterial Toxins; Clostridioides difficile; Gene Transfer, Horizontal; Genome, Bacterial; Interspersed Repetitive Sequences
PubMed: 25576774
DOI: 10.1016/j.resmic.2014.12.005 -
FEMS Microbiology Reviews Sep 2011Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance... (Review)
Review
Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.
Topics: Animals; Anti-Bacterial Agents; Drug Resistance, Bacterial; Gene Transfer, Horizontal; Genes, Bacterial; Gram-Negative Bacteria; Humans; Interspersed Repetitive Sequences; Recombination, Genetic; Selection, Genetic
PubMed: 21517914
DOI: 10.1111/j.1574-6976.2011.00273.x -
Microbiology Spectrum Jan 2018Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been...
Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms. Herein I discuss the potential functions that the genes that are dubbed virulence or antibiotic resistance genes may have in their original hosts in nonclinical, natural ecosystems. In addition, I discuss the potential bottlenecks modulating the transfer of virulence and antibiotic resistance determinants and the consequences in terms of speciation of acquiring one or another of both categories of genes. Finally, I propose that exaptation, a process by which a change of function is achieved by a change of habitat and not by changes in the element with the new functionality, is the basis of the evolution of virulence determinants and of antibiotic resistance genes.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Infections; Drug Resistance, Multiple, Bacterial; Evolution, Molecular; Gene Transfer, Horizontal; Genetic Speciation; Genome, Bacterial; Interspersed Repetitive Sequences; Virulence
PubMed: 29350130
DOI: 10.1128/microbiolspec.MTBP-0006-2016 -
International Journal of Antimicrobial... May 2023Pseudomonas aeruginosa (P. aeruginosa) are ubiquitous opportunistic pathogens that combine intrinsic and acquired multidrug resistance phenotypes. Due to different types...
OBJECTIVES
Pseudomonas aeruginosa (P. aeruginosa) are ubiquitous opportunistic pathogens that combine intrinsic and acquired multidrug resistance phenotypes. Due to different types of acquired genes, carbapenem resistance has been expanding in this species. This study hypothesised that the spread of carbapenem resistance among P. aeruginosa is influenced by phylogenomic features, being distinct for different genes.
METHODS
To test this hypothesis, the genomes of P. aeruginosa harbouring bla or bla genes were compared. The bla gene was selected because, although frequent, it is almost restricted to this species and bla gene due to its wide interspecies distribution. A group of genomes harbouring the genes bla (n = 116) or bla (n = 27), available in GenBank, was characterised based on core phylogenomic analysis, functional categories in the accessory genome and mobile genetic elements flanking the selected genes.
RESULTS
Most bla gene hosts belonged to multilocus sequence types (ST) ST111 (n = 32 of 116) and ST233 (n = 27 of 116) and were reported in Europe (n = 75 of 116). The bla gene hosts were distributed by different STs (ST38, ST773, ST235, ST357 and ST654), frequently from Asia (n = 11 of 27). Significant differences in the prevalence of functional protein/enzyme annotations per number of accessory genomes were observed between bla+ and bla+. The bla gene was frequently inserted in the Tn402-like and Tn21 transposons family and rarely in IS6100, while bla gene was preferentially flanked by ISAba125 and ble genes or associated with IS91 insertion sequence.
CONCLUSION
The hypothesis that carbapenem resistance gene acquisition is not random among phylogenomic lineages was confirmed, suggesting the importance of phylogeny in the dissemination of antibiotic resistance genes.
Topics: Pseudomonas aeruginosa; beta-Lactamases; Drug Resistance, Bacterial; Phylogeny; Genome, Bacterial; DNA Transposable Elements; Interspersed Repetitive Sequences; Carbapenems
PubMed: 36924802
DOI: 10.1016/j.ijantimicag.2023.106788 -
PloS One 2020Antibiotic resistant bacteria (ARB) and their genes (ARGs) have become recognised as significant emerging environmental pollutants. ARB and ARGs in sewage sludge can be...
Antibiotic resistant bacteria (ARB) and their genes (ARGs) have become recognised as significant emerging environmental pollutants. ARB and ARGs in sewage sludge can be transmitted back to humans via the food chain when sludge is recycled to agricultural land, making sludge treatment key to control the release of ARB and ARGs to the environment. This study investigated the fate of antibiotic resistant Escherichia coli and a large set of antibiotic resistance genes (ARGs) during full scale anaerobic digestion (AD) of sewage sludge at two U.K. wastewater treatment plants and evaluated the impact of thermal hydrolysis (TH) pre-treatment on their abundance and diversity. Absolute abundance of 13 ARGs and the Class I integron gene intI1 was calculated using single gene quantitative (q) PCR. High through-put qPCR analysis was also used to determine the relative abundance of 370 ARGs and mobile genetic elements (MGEs). Results revealed that TH reduced the absolute abundance of all ARGs tested and intI1 by 10-12,000 fold. After subsequent AD, a rebound effect was seen in many ARGs. The fate of ARGs during AD without pre-treatment was variable. Relative abundance of most ARGs and MGEs decreased or fluctuated, with the exception of macrolide resistance genes, which were enriched at both plants, and tetracyline and glycopeptide resistance genes which were enriched in the plant employing TH. Diversity of ARGs and MGEs decreased in both plants during sludge treatment. Principal coordinates analysis revealed that ARGs are clearly distinguished according to treatment step, whereas MGEs in digested sludge cluster according to site. This study provides a comprehensive within-digestor analysis of the fate of ARGs, MGEs and antibiotic resistant E. coli and highlights the effectiveness of AD, particularly when TH is used as a pre-treatment, at reducing the abundance of most ARGs and MGEs in sludgeand preventing their release into the environment.
Topics: Anaerobiosis; Anti-Bacterial Agents; Drug Resistance, Bacterial; Escherichia coli; Genes, Bacterial; Genes, MHC Class I; Humans; Hydrolysis; Integrons; Interspersed Repetitive Sequences; Macrolides; Sewage; Wastewater
PubMed: 33259486
DOI: 10.1371/journal.pone.0237283 -
FEMS Microbiology Reviews Sep 2011Antibiotic resistance in Gram-negative bacteria is often due to the acquisition of resistance genes from a shared pool. In multiresistant isolates these genes, together... (Review)
Review
Antibiotic resistance in Gram-negative bacteria is often due to the acquisition of resistance genes from a shared pool. In multiresistant isolates these genes, together with associated mobile elements, may be found in complex conglomerations on plasmids or on the chromosome. Analysis of available sequences reveals that these multiresistance regions (MRR) are modular, mosaic structures composed of different combinations of components from a limited set arranged in a limited number of ways. Components common to different MRR provide targets for homologous recombination, allowing these regions to evolve by combinatorial evolution, but our understanding of this process is far from complete. Advances in technology are leading to increasing amounts of sequence data, but currently available automated annotation methods usually focus on identifying ORFs and predicting protein function by homology. In MRR, where the genes are often well characterized, the challenge is to identify precisely which genes are present and to define the boundaries of complete and fragmented mobile elements. This review aims to summarize the types of mobile elements involved in multiresistance in Gram-negative bacteria and their associations with particular resistance genes, to describe common components of MRR and to illustrate methods for detailed analysis of these regions.
Topics: Anti-Bacterial Agents; Drug Resistance, Multiple, Bacterial; Gene Order; Gene Transfer, Horizontal; Genes, Bacterial; Gram-Negative Bacteria; Interspersed Repetitive Sequences; Recombination, Genetic
PubMed: 21564142
DOI: 10.1111/j.1574-6976.2011.00277.x -
Clinical Microbiology and Infection :... May 2016
Topics: Anti-Bacterial Agents; Bacterial Infections; Colistin; Drug Resistance, Bacterial; Gene Transfer, Horizontal; Humans; Interspersed Repetitive Sequences; Plasmids
PubMed: 27021419
DOI: 10.1016/j.cmi.2016.03.009 -
Current Opinion in Genetics &... Dec 2015Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of... (Review)
Review
Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C=5.7Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as 'junk' DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression.
Topics: DNA, Plant; Evolution, Molecular; Gene Expression Regulation, Plant; Genetic Variation; Genome Size; Genome, Plant; Interspersed Repetitive Sequences; Magnoliopsida; Phylogeny
PubMed: 26605684
DOI: 10.1016/j.gde.2015.10.006