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Functional Metagenomics
Published in Vineet Kumar, Vinod Kumar Garg, Sunil Kumar, Jayanta Kumar Biswas, Omics for Environmental Engineering and Microbiology Systems, 2023
Kripa Pancholi, Anupama Shrivastav
Mobile genetic elements allow the mobility of DNA, and when the mobility of DNA chunks is intracellular, they are called transposons. Transposons are DNA sequences that move from one location to another location in the genome. Such a transposable DNA sequence is called transposons. This intracellular mobility is gained through transformation or transduction. The transposons are able to transpose the genome, but are not able to undergo conjugational transfer. Perhaps, transposons of the conjugative elements can be transferred to a whole new host with the help of transformation and this transposable element can be trapped through different methods (Partridge et al. 2018). The vector selected here should have the target site of transposons in a bunch of strains. The activation of the silent gene and the inactivation of the lethal gene results in a change of phenotype that helps in the detection of transposition, and after the transposition, the vector having this element is isolated. DNA sequencing and functional analysis along with transposons trapping allow the isolation of new mobile functional elements having antibiotic resistance genes. This method is used in metagenomics by forming libraries in host or vector. And later, it is transformed to an appropriate host through transposons vector along with screening to deactivate the target.
Antibiotic Resistance of Staphylococcus Aureus: a Review
Published in Megh R Goyal, Sustainable Biological Systems for Agriculture, 2018
Divya Lakshminarayanan, Jessen George, Suriyanarayanan Sarvajayakesavalu
The antibiotics basically target cell wall synthesis, protein synthesis; the selection pressure applied by the antibiotics that used in clinical and agricultural settings has promoted the evolution and spread of genes that confer resistance.1 Development of antibiotic resistance is conferred by mutation and selection by medical antibiotics, resistance can occur in organism by the acquisition of a novel antibiotic resistance gene by horizontal gene transfer (HGT) has a relevant role in emergence, through conjugation, transformation, or transduction through various mobile genetic elements like plasmids, transposons, integrons and so forth.13, 29 Internal mechanisms include mutational modification of gene targets, over expression of various efflux pumps; whereas acquired resistance involves enzymatic inactivation of the drug and bypassing of the target. Practices like application of sewage sludge and manure may introduce complex mixtures of bacteria containing drug resistance genes, veterinary and medical antibiotics, and other chemicals to land, where interactions may occur with indigenous soil bacteria.29
Silver as an Antimicrobial Agent: The Resistance Issue
Published in Huiliang Cao, Silver Nanoparticles for Antibacterial Devices, 2017
Kristel Mijnendonckx, Rob Van Houdt
Silver resistance determinants are widely found among environmental and clinically relevant bacteria. Next to chemical detoxification, for instance, by precipitation in the periplasm via reduction to elemental silver or the formation of Ag2S crystals, bacterial silver resistance mechanisms result from active efflux systems. Efflux pumps are either P-type ATPases, which pump Ag+ from the cell cytoplasm to the periplasm, or three-polypeptide membrane potential-dependent cation/proton antiporters (HME-RND family), which pump Ag+ from the periplasm to the exterior of the cell. These resistance mechanisms are often harboured by mobile genetic elements, facilitating their spread. This is of concern because the extensive use of silver-based products will increase the release of silver in the environment, putatively inducing the dissemination of silver resistance (and thereby cross-resistance to antibiotics). Future studies need to pinpoint the precise mechanisms of Ag+ and Ag NPs toxicity and resistance. Detailed, comprehensive knowledge can improve and direct the many applications of silver (e.g. antimicrobial, bioremediation, nanomaterials) and will allow assessing the risks associated with human health and ecosystems more accurately.
Recommendations for the use of metagenomics for routine monitoring of antibiotic resistance in wastewater and impacted aquatic environments
Published in Critical Reviews in Environmental Science and Technology, 2023
Benjamin C. Davis, Connor Brown, Suraj Gupta, Jeannette Calarco, Krista Liguori, Erin Milligan, Valerie J. Harwood, Amy Pruden, Ishi Keenum
Next-generation sequencing (NGS) is a powerful and promising tool for monitoring of aquatic environments (Garner et al., 2021a). Shotgun metagenomics applies NGS for the sequencing of DNA extracted across microbial populations inhabiting the sampled environment. The resulting metagenome (i.e., the collection of NGS reads captured from a sample) can be analyzed to characterize the resistome (i.e., the collective ARGs carried across a microbial community). The most common approach is to align the metagenome against publicly-available databases to compare metagenome-derived sequences to those of functionally verified ARGs, which currently number in the thousands (Alcock et al., 2020). The number and types of ARGs can then be compared across samples of interest. Detected ARGs can be classified and ranked by various means; this includes the antibiotics to which they encode resistance, the mechanism of resistance, and their degree of clinical relevance (i.e., extent to which they are found to interfere with treatment of human infections). The genetic context of various ARGs can further be explored to determine more information about the ARG of interest (chromosomally-bound or inter/intra-cellularly mobile), what kinds of mobile genetic elements (MGEs, e.g., plasmids, integrons, transposons) they are carried on, or whether they occur in known human pathogens or the commensal environmental flora. Metagenomics is also being utilized to mine putative and/or uncharacterized ARGs from public repositories to expand our knowledge of the known, emerging, and latent resistome (Arango-Argoty et al., 2018; Berglund et al., 2019).
Taxonomic, metabolic traits and species description of aromatic compound degrading Indian soil bacterium Pseudomonas bharatica CSV86T
Published in Journal of Environmental Science and Health, Part A, 2023
Balaram Mohapatra, Prashant S. Phale
With persistence nature, aromatics has exerted selection pressure on the microbial communities to adapt and evolve efficient metabolic processes to detoxify or use them as the sole source of carbon and energy.[8] Such evolution is aided by genetic exchange and recombination mediated through mobile genetic elements referred as horizontal gene transfer (HGT). Both culture-based and metagenomic studies have indicated that members of Pseudomonas are most abundant (constituting up to 50%) at various impacted sites in the ecosystem. Such ubiquity is reflected by opportunistic and nutritional versatility of Pseudomonas with faster growth, ability to counter/resist oxidative stress and larger genome sizes with plasticity. Hence it is considered to be a model organism for microbial ecology and pollutant biodegradation studies.[8–10]
An invisible workforce in soil: The neglected role of soil biofilms in conjugative transfer of antibiotic resistance genes
Published in Critical Reviews in Environmental Science and Technology, 2022
Shan Wu, Yichao Wu, Bin Cao, Qiaoyun Huang, Peng Cai
Microbes acquire and spread antibiotic resistance by genetic mutation and horizontal transfer of ARGs (Andersson & Hughes, 2014). The horizontal transfer of ARGs is the principle driving force for the development and accumulation of antibiotic resistance in the environment (Zhang et al., 2017). There are three major pathways of horizontal gene transfer: (1) conjugation, the transfer of mobile genetic elements such as plasmids, integrons, transposons, and insertion sequence, etc. from donor cells to recipient cells through direct physical contact, (2) transformation, the uptake of naked DNA by competent cells, and (3) transduction, the bacteriophage-mediated transfer of genetic information. Of these, conjugation is the primary mode of horizontal gene transfer in the environment (Thomas & Nielsen, 2005; Wang et al., 2015).