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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 -
Bioscience Trends Feb 2016Nosocomial infection is a kind of infection, which is spread in various hospital environments, and leads to many serious diseases (e.g. pneumonia, urinary tract... (Review)
Review
Nosocomial infection is a kind of infection, which is spread in various hospital environments, and leads to many serious diseases (e.g. pneumonia, urinary tract infection, gastroenteritis, and puerperal fever), and causes higher mortality than community-acquired infection. Bacteria are predominant among all the nosocomial infection-associated pathogens, thus a large number of antibiotics, such as aminoglycosides, penicillins, cephalosporins, and carbapenems, are adopted in clinical treatment. However, in recent years antibiotic resistance quickly spreads worldwide and causes a critical threat to public health. The predominant bacteria include Methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii. In these bacteria, resistance emerged from antibiotic resistant genes and many of those can be exchanged between bacteria. With technical advances, molecular mechanisms of resistance have been gradually unveiled. In this review, recent advances in knowledge about mechanisms by which (i) bacteria hydrolyze antibiotics (e.g. extended spectrum β-lactamases, (ii) AmpC β-lactamases, carbapenemases), (iii) avoid antibiotic targeting (e.g. mutated vanA and mecA genes), (iv) prevent antibiotic permeation (e.g. porin deficiency), or (v) excrete intracellular antibiotics (e.g. active efflux pump) are summarized.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Cross Infection; Drug Resistance, Microbial; Humans; Hydrolysis; Mutation; beta-Lactamases
PubMed: 26877142
DOI: 10.5582/bst.2016.01020 -
Journal of Exposure Science &... Jan 2020The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built... (Review)
Review
The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Ecology; Gene Transfer, Horizontal; Humans
PubMed: 31591493
DOI: 10.1038/s41370-019-0171-0 -
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 -
Upsala Journal of Medical Sciences May 2014Wild birds have been postulated as sentinels, reservoirs, and potential spreaders of antibiotic resistance. Antibiotic-resistant bacteria have been isolated from a... (Review)
Review
Wild birds have been postulated as sentinels, reservoirs, and potential spreaders of antibiotic resistance. Antibiotic-resistant bacteria have been isolated from a multitude of wild bird species. Several studies strongly indicate transmission of resistant bacteria from human rest products to wild birds. There is evidence suggesting that wild birds can spread resistant bacteria through migration and that resistant bacteria can be transmitted from birds to humans and vice versa. Through further studies of the spatial and temporal distribution of resistant bacteria in wild birds, we can better assess their role and thereby help to mitigate the increasing global problem of antibiotic resistance.
Topics: Animals; Animals, Wild; Birds; Drug Resistance, Microbial
PubMed: 24697355
DOI: 10.3109/03009734.2014.905663 -
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 -
Trends in Microbiology Nov 2017Staphylococcus aureus is a serious human pathogen with remarkable adaptive powers. Antibiotic-resistant clones rapidly emerge mainly by acquisition of... (Review)
Review
Staphylococcus aureus is a serious human pathogen with remarkable adaptive powers. Antibiotic-resistant clones rapidly emerge mainly by acquisition of antibiotic-resistance genes from other S. aureus strains or even from other genera. Transfer is mediated by a diverse complement of mobile genetic elements and occurs primarily by conjugation or bacteriophage transduction, with the latter traditionally being perceived as the primary route. Recent work on conjugation and transduction suggests that transfer by these mechanisms may be more extensive than previously thought, in terms of the range of plasmids that can be transferred by conjugation and the efficiency with which transduction occurs. Here, we review the main routes of antibiotic resistance gene transfer in S. aureus in the context of its biology as a human commensal and a life-threatening pathogen.
Topics: Anti-Bacterial Agents; Conjugation, Genetic; Drug Resistance, Microbial; Humans; Staphylococcal Infections; Staphylococcus Phages; Staphylococcus aureus; Transduction, Genetic
PubMed: 28641931
DOI: 10.1016/j.tim.2017.05.011 -
Poultry Science Dec 2021Livestock farms are generally considered to be the important source of antibiotic resistance genes (ARGs). It is important to explore the spread of ARGs to reduce their...
Livestock farms are generally considered to be the important source of antibiotic resistance genes (ARGs). It is important to explore the spread of ARGs to reduce their harm. This study analyzed 13 resistance genes belonging to 7 types in 68 samples of layer manure including different stages of layer breeding, layer manure fertilizer, and soil from 9 laying hen farms in Guangdong Province. The detection rate of antibiotic resistance genes was extremely high at the layer farm in manure (100%), layer manure fertilizer (100%), and soil (> 95%). The log counts of antibiotic resistance genes in layer manure (3.34-11.83 log copies/g) were significantly higher than those in layer manure fertilizer (3.45-9.80 log copies/g) and soil (0-7.69 log copies/g). In layer manure, ermB was the most abundant antibiotic resistance gene, with a concentration of 3.19 × 10- 6.82 × 10 copies/g. The average abundances of 5 antibiotic resistance genes were above 10 copies/g in the descending order ermB, sul2, tetA, sul1, and strB. The relative abundances of ARGs in layer manure samples from different breeding stages ranked as follows: brooding period (BP), late laying period (LL), growing period (GP), early laying period (EL), and peak laying period (PL). There was no significant correlation between the farm scale and the abundance of antibiotic resistance genes. Moreover, the farther away from the layer farm, the lower the abundance of antibiotic resistance genes in the soil. We also found that compost increases the correlation between antibiotic resistance genes, and the antibiotic resistance genes in soil may be directly derived from layer manure fertilizer instead of manure. Therefore, when applying layer manure fertilizer to cultivated land, the risk of antibiotic resistance genes pollution should be acknowledged, and in-depth research should be conducted on how to remove antibiotic resistance genes from layer manure fertilizer to control the spread of antibiotic resistance genes.
Topics: Animals; Anti-Bacterial Agents; Chickens; Drug Resistance, Microbial; Farms; Female; Genes, Bacterial; Manure; Soil Microbiology
PubMed: 34695626
DOI: 10.1016/j.psj.2021.101485 -
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 -
Upsala Journal of Medical Sciences May 2014The emergence and spread of antibiotic resistance among human pathogens is a relevant problem for human health and one of the few evolution processes amenable to... (Review)
Review
The emergence and spread of antibiotic resistance among human pathogens is a relevant problem for human health and one of the few evolution processes amenable to experimental studies. In the present review, we discuss some basic aspects of antibiotic resistance, including mechanisms of resistance, origin of resistance genes, and bottlenecks that modulate the acquisition and spread of antibiotic resistance among human pathogens. In addition, we analyse several parameters that modulate the evolution landscape of antibiotic resistance. Learning why some resistance mechanisms emerge but do not evolve after a first burst, whereas others can spread over the entire world very rapidly, mimicking a chain reaction, is important for predicting the evolution, and relevance for human health, of a given mechanism of resistance. Because of this, we propose that the emergence and spread of antibiotic resistance can only be understood in a multi-parameter space. Measuring the effect on antibiotic resistance of parameters such as contact rates, transfer rates, integration rates, replication rates, diversification rates, and selection rates, for different genes and organisms, growing under different conditions in distinct ecosystems, will allow for a better prediction of antibiotic resistance and possibilities of focused interventions.
Topics: Anti-Bacterial Agents; Drug Resistance, Microbial; Humans
PubMed: 24678768
DOI: 10.3109/03009734.2014.901444