Discovery of Novel Antibiotic Resistance Determinants in Forest and Grassland Soil Metagenomes

Willms, Inka M.; Kamran, Aysha; Aßmann, Nils Frederik; Krone, Denis; Bolz, Simon Henning; Fiedler, Fabian; Nacke, Heiko

doi:10.3389/fmicb.2019.00460

Cited by 29 publications

(22 citation statements)

References 48 publications

(61 reference statements)

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“…Furthermore, a transposase gene, ISPme1, was also identified upstream of BlaCM1, indicating that the antibiotic resistant gene might be mobile. Novel sulfonamide resistance genes AEW9_dhps01, SEW2_dhps01, and SEW5_dhps01, and AEG2_DHPS01 were also detected in forest and grassland soils from Germany, which were relatively unexposed to human intervention (Willms et al, 2019). The study also identified major facilitator superfamily (MFS) efflux pump mediated tetracycline resistance.…”

Section: Discoveries In Novel Antibiotics Resistant Genes Through Expmentioning

confidence: 80%

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

et al. 2020

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A multitude of factors, such as drug misuse, lack of strong regulatory measures, improper sewage disposal, and low-quality medicine and medications, have been attributed to the emergence of drug resistant microbes. The emergence and outbreaks of multidrug resistance to last-line antibiotics has become quite common. This is further fueled by the slow rate of drug development and the lack of effective resistome surveillance systems. In this review, we provide insights into the recent advances made in computational approaches for the surveillance of antibiotic resistomes, as well as experimental formulation of combinatorial drugs. We explore the multiple roles of antibiotics in nature and the current status of combinatorial and adjuvant-based antibiotic treatments with nanoparticles, phytochemical, and other non-antibiotics based on synergetic effects. Furthermore, advancements in machine learning algorithms could also be applied to combat the spread of antibiotic resistance. Development of resistance to new antibiotics is quite rapid. Hence, we review the recent literature on discoveries of novel antibiotic resistant genes though shotgun and expression-based metagenomics. To decelerate the spread of antibiotic resistant genes, surveillance of the resistome is of utmost importance. Therefore, we discuss integrative applications of whole-genome sequencing and metagenomics together with machine learning models as a means for state-of-the-art surveillance of the antibiotic resistome. We further explore the interactions and negative effects between antibiotics and microbiomes upon drug administration.

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Section: Discoveries In Novel Antibiotics Resistant Genes Through Expmentioning

confidence: 80%

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

et al. 2020

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“…The metagenomic libraries AEW1, AEW5, SEG8 and SEW5, used for function-based screening, were reported previously [ 26 , 27 ], whereas library AEW4 was constructed in this study as described by Nacke et al [ 26 ]. Names of the metagenomic libraries refer to the designation of soil samples from which the libraries were derived.…”

Section: Methodsmentioning

confidence: 99%

“…Names of the metagenomic libraries refer to the designation of soil samples from which the libraries were derived. The samples AEW1, AEW4 and AEW5 represent spruce (AEW1) and beech (AEW4 and AEW5) forest soil collected within the German Biodiversity Exploratory Schwäbische Alb, whereas the samples SEG8 and SEW5 represent grassland (non-fertilized pasture) and beech forest soil, respectively, collected within the German Biodiversity Exploratory Schorfheide-Chorin [ 26 , 27 , 53 ]. All samples were derived from A horizons (topsoil) and metagenomic libraries were constructed using the plasmid pCR-XL-TOPO (Thermo Fisher Scientific, Braunschweig, Germany).…”

Section: Methodsmentioning

confidence: 99%

Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics

et al. 2021

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Antibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge about their diversity, mobility and encoded resistance spectra gained increasing public attention. This knowledge offers opportunities with respect to improved risk prediction and development of strategies to tackle antibiotic resistance, and might help to direct the design of novel antibiotics, before further resistances reach hospital settings or the animal sector. Here, metagenomic libraries, which comprise genes of cultivated microorganisms, but, importantly, also those carried by the uncultured microbial majority, were screened for novel ARGs from forest and grassland soils. We detected three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes. These ARGs were derived from phylogenetically diverse soil bacteria and predicted to encode antibiotic inactivation, antibiotic efflux, or alternative variants of target enzymes. Moreover, deduced gene products show a minimum identity of ~21% to reference database entries and confer high-level resistance. This highlights the vast potential of functional metagenomics for the discovery of novel ARGs from soil ecosystems.

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“…Surprisingly, even remote environments or the sponge microbiota may host AMR genes or plasmids [ 84 , 96 ], and novel antibiotic resistance determinants have been also discovered in forest and grassland soil metagenomes [ 97 ], thus hosting diverse and novel resistance genes that may be harnessed by phylogenetically distinct bacteria and may act as a reservoir of functional resistance genes [ 98 ]. The occurrence of MDR bacteria in wildlife is clearly influenced by many and different factors that have not yet been fully understood [ 99 , 100 ].…”

Section: Amr In the Environmentmentioning

confidence: 99%

Country Income Is Only One of the Tiles: The Global Journey of Antimicrobial Resistance among Humans, Animals, and Environment

et al. 2020

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Antimicrobial resistance (AMR) is one of the most complex global health challenges today: decades of overuse and misuse in human medicine, animal health, agriculture, and dispersion into the environment have produced the dire consequence of infections to become progressively untreatable. Infection control and prevention (IPC) procedures, the reduction of overuse, and the misuse of antimicrobials in human and veterinary medicine are the cornerstones required to prevent the spreading of resistant bacteria. Purified drinking water and strongly improved sanitation even in remote areas would prevent the pollution from inadequate treatment of industrial, residential, and farm waste, as all these situations are expanding the resistome in the environment. The One Health concept addresses the interconnected relationships between human, animal, and environmental health as a whole: several countries and international agencies have now included a One Health Approach within their action plans to address AMR. Improved antimicrobial usage, coupled with regulation and policy, as well as integrated surveillance, infection control and prevention, along with antimicrobial stewardship, sanitation, and animal husbandry should all be integrated parts of any new action plan targeted to tackle AMR on the Earth. Since AMR is found in bacteria from humans, animals, and in the environment, we briefly summarize herein the current concepts of One Health as a global challenge to enable the continued use of antibiotics.

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Discovery of Novel Antibiotic Resistance Determinants in Forest and Grassland Soil Metagenomes

Cited by 29 publications

References 48 publications

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics

Country Income Is Only One of the Tiles: The Global Journey of Antimicrobial Resistance among Humans, Animals, and Environment

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