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  • Antibiotic Resistance
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  • 1
    In: FEMS Microbiology Ecology, 2016, Vol. 92(11)
    Keywords: Microbiology ; Antibiotic Resistance ; Microbiology ; Antibiotics ; Antibiotic Resistance;
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 2
    Language: English
    In: Applied Microbiology and Biotechnology, 2016, Vol.100(21), pp.9343-9353
    Description: Pig manures are frequently used as fertilizer or co-substrate in biogas plants (BGPs) and typically contain antibiotic residues (ARs), as well as bacteria carrying resistance genes (RGs) and mobile genetic elements (MGEs). A survey of manures from eight pig fattening and six pig breeding farms and digestates from eight BGPs in Lower Saxony, Germany was conducted to evaluate the link between antibiotic usage and ARs to RGs and MGEs present in organic fertilizers. In total, 11 different antibiotics belonging to six substance classes were applied in the farms investigated. Residue analysis revealed concentrations of tetracycline up to 300 mg kg −1 dry weight (DW) in manures and of doxycycline up to 10.1 mg kg −1 DW in digestates indicating incomplete removal during anaerobic digestion. RGs ( sul1 , sul2 , tet (A), tet (M), tet (X), qacE ∆ 1 ) were detected in total community DNA of all samples by PCR-Southern blot hybridization. Broad-host range plasmids (IncP-1, IncQ, IncN, and IncW) and integron integrase genes ( intI1 , intI2 ) were found in most manure samples with IncN and IncW plasmids being more abundant in manure from pig breeding compared to pig fattening farms. IntI1 , IncQ, and IncW plasmids were also detected in all digestates, while IncP-1, IncN, and LowGC plasmids were detected only sporadically. Our findings strongly reinforce the need for further research to identify mitigation strategies to reduce the level of contamination of organic fertilizers with ARs and transferable RGs that are applied to soil and that might influence the mobile resistome of the plant microbiome.
    Keywords: Antibiotic resistance genes ; Mobile genetic elements ; Antibiotics ; Pig husbandry ; Manures ; Digestates
    ISSN: 0175-7598
    E-ISSN: 1432-0614
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  • 3
    Language: English
    In: Science of the Total Environment, 15 April 2018, Vol.621, pp.725-733
    Description: Metal resistance has been associated with antibiotic resistance due to co- or cross-resistance mechanisms. Here, metal contaminated mine soil treated with organic wastes was screened for the presence of mobile genetic elements (MGEs). The occurrence of conjugative IncP-1 and mobilizable IncQ plasmids, as well as of class 1 integrons, was confirmed by PCR and Southern blot hybridization, suggesting that bacteria from these soils have gene-mobilizing capacity with implications for the dissemination of resistance factors. Moreover, exogenous isolation of MGEs from the soil bacterial community was attempted under antibiotic selection pressure by using as recipient. Seventeen putative transconjugants were identified based on increased antibiotic resistance. Metabolic traits and metal resistance of putative transconjugants were investigated, and whole genome sequencing was carried out for two of them. Most putative transconjugants displayed a multi-resistant phenotype for a broad spectrum of antibiotics. They also displayed changes regarding the ability to metabolise different carbon sources, RNA: DNA ratio, growth rate and biofilm formation. Genome sequencing of putative transconjugants failed to detect genes acquired by horizontal gene transfer, but instead revealed a number of nonsense mutations, including in , whose inactivation was linked to the observed resistance to aminoglycosides. Our results confirm that mine soils contain MGEs encoding antibiotic resistance. Moreover, they point out the role of spontaneous mutations in achieving low-level antibiotic resistance in a short time, which was associated with a trade-off in the capability to metabolise specific carbon sources.
    Keywords: Antibiotic Resistance ; Competitive Fitness ; Conjugative Plasmids ; Imipenem ; Integrons ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 4
    In: FEMS Microbiology Letters, 2013, Vol. 348(2), pp.127-132
    Description: LowGC-type plasmids conferring resistance to sulfonamides have been frequently isolated from manure and manured soil. However, knowledge on the dynamics of plasmid-carrying populations in soil and their response to the presence of sulfonamides is scarce. Here, we investigated effects of the sulfonamide resistance conferring plasmid pHHV216 on the fitness of Acinetobacter baylyi BD413 in soil after application of manure with or without the sulfonamide antibiotic sulfadiazine (SDZ). The persistence of A. baylyi BD413 pHHV216 in competition to its plasmid-free variant was followed in soil microcosms. CFU counts showed a decrease in A. baylyi BD413 in manured soils over the experimental period of 32 days by about 0.5 log units. The proportion of the plasmid-carrying populations decreased from 50 to 〈 40% in the absence of SDZ, while the proportion of plasmid-carrying BD413 increased from 50 to about 65% with SDZ added. The data suggest that SDZ introduced via manure into soil was bioaccessible, providing a fitness advantage for the plasmid-carrying population of BD413 in soil, while the plasmid conferred a fitness disadvantage when selective pressure by SDZ was absent. In future, this method may be used as a tool for the assessment of bioavailability of antibiotics in soil.
    Keywords: Plasmid ; Sulfadiazine ; Antibiotic Resistance ; Soil ; Antibiotic Selection ; Host Fitness
    ISSN: 0378-1097
    E-ISSN: 1574-6968
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  • 5
    In: FEMS Microbiology Ecology, 2014, Vol. 87(1), pp.78-88
    Description: Difloxacin (DIF) belongs to the class of fluoroquinolone antibiotics that have been intensively used for the treatment of bacterial infections in veterinary and human medicine. The aim of this field study was to compare the effect of manure from DIF-treated pigs and untreated pigs on the bacterial community structure and resistance gene abundance in bulk soil and rhizosphere of maize. A significant effect of DIF manure on the bacterial community composition in bulk soil was revealed by denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA gene fragments amplified from total community DNA. In few samples, quinolone resistance genes qnrB and qnrS1/qnrS2 were detected by PCR and subsequent hybridization, while qnrA was not detected. Quantitative PCR revealed an increased abundance of the integrase gene intI1 of class I integrons and sulfonamide resistance genes sul1 and sul2 in DIF manure-treated bulk soil and rhizosphere, relative to 16S rRNA genes, while traN genes specific for LowGC-type plasmids were increased only in bulk soil. Principal component analysis of DGGE profiles suggested a manure effect in soil until day 28, but samples of days 71 and 140 were found close to untreated soil, indicating resilience of soil community compositions from disturbances by manure. 〈p〉〈fig id="fig0" position="float"〉 〈graphic alt-version="no" position="float" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="fem12191-toc-0001" xlink:type="simple"/〉〈/fig〉 〈/p〉
    Keywords: Difloxacin ; Resistance ; Dgge ; Soil ; Manure ; Rhizosphere
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 6
    In: FEMS Microbiology Ecology, 2016, Vol. 92(2)
    Description: The goal of this study was to determine the fate of antibiotic resistance genes (ARGs) and class 1 integrons following the application of swine and dairy manure to soil. Soil microcosms were amended with either manure from swine fed subtherapeutic levels of antibiotics or manure from dairy cows that were given antibiotics only rarely and strictly for veterinary purposes. Microcosms were monitored for 6 months using quantitative PCR targeting 16S rRNA genes (a measure of bacterial biomass), intI1 , erm (B) , tet (A), tet (W) and tet (X). Swine manure had 10- to 100-fold higher levels of ARGs than the dairy manure, all of which decayed over time after being applied to soil. A modified Collins–Selleck model described the decay of ARGs in the soil microcosms well, particularly the characteristic in which the decay rate declined over time. By the completion of the soil microcosm experiments, ARGs in the dairy manure-amended soils returned to background levels, whereas the ARGs in swine manure remained elevated compared to control microcosms. Our research suggests that the use of subtherapeutic use of antibiotics in animal feed could lead to the accumulation of ARGs in soils to which manure is applied. The application of manure to soil from animals fed subtherapeutic levels of antibiotics can lead to the accumulation of antibiotic resistance genes. Graphical Abstract Figure. The application of manure to soil from animals fed subtherapeutic levels of antibiotics can lead to the accumulation of antibiotic resistance genes.
    Keywords: Antibiotic Resistance ; Dairy ; Manure ; Qpcr ; Subtherapeutic ; Swine
    E-ISSN: 1574-6941
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  • 7
    Language: English
    In: Current Opinion in Microbiology, June 2011, Vol.14(3), pp.236-243
    Description: The usage of antibiotics in animal husbandry has promoted the development and abundance of antibiotic resistance in farm environments. Manure has become a reservoir of resistant bacteria and antibiotic compounds, and its application to agricultural soils is assumed to significantly increase antibiotic resistance genes and selection of resistant bacterial populations in soil. The genome location of resistance genes is likely to shift towards mobile genetic elements such as broad-host-range plasmids, integrons, and transposable elements. Horizontal transfer of these elements to bacteria adapted to soil or other habitats supports their environmental transmission independent of the original host. The human exposure to soil-borne resistance has yet to be determined, but is likely to be severely underestimated.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 8
    In: FEMS Microbiology Ecology, 2015, Vol. 91(6)
    Description: TetX is a flavin-dependent monooxygenase. It has been reported to inactivate all tested tetracyclines. In this study, Escherichia coli overexpressing TetX was added to soil bacterial enrichment cultures along with varying levels of tetracycline and was found to affect community-wide tetracycline resistance levels. Soil microbial communities developed lower levels of tetracycline resistance upon exposure to 25 μg/mL of tetracycline when an E. coli expressing TetX was present (6% of cultivable bacteria were resistant to 40 μg/mL tetracycline). In contrast, in the absence of TetX activity, a similar tetracycline exposure selected for greater levels of resistant bacteria in the soil microbial community (90% of cultivable bacteria were resistant to 40 μg/mL tetracycline). We also describe new metabolites formed after tetracycline transformation by TetX and report the transient generation of redox-active metabolite(s). The results presented here are particularly pertinent in the light of the recent emergence of tet (X) in different bacterial species, including clinical isolates. Overexpression of TetX, a flavin-dependent monooxygenase, affects community-wide tetracycline resistance levels in the soil microbial community. Graphical Abstract Figure. Overexpression of TetX, a flavin-dependent monooxygenase, affects community-wide tetracycline resistance levels in the soil microbial community.
    Keywords: Antibiotic Resistance ; 〈Kwd〉〈Italic Toggle="Yes"〉Sphingobacterium〈/Italic〉〈/Kwd〉 ; 〈Kwd〉〈Italic Toggle="Yes"〉Escherichia Coli〈/Italic〉〈/Kwd〉 ; Tetx, Monooxygenase
    E-ISSN: 1574-6941
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  • 9
    Language: English
    In: Reviews in Environmental Science and Bio/Technology, 2018, Vol.17(1), pp.159-185
    Description: Quaternary ammonium compounds (QACs) are surface-active, antimicrobial, high production volume (HPV) chemicals with a broad application in agriculture. This review provides a comprehensive overview of (1) predicted and measured concentrations of QACs in soils including their analysis, (2) sequestration mechanisms in soils based on their physicochemical properties and chemical structure, and (3) implications of concentrations and fate of QACs in soils for the proliferation of antibiotic resistance in the environment. Predicted environmental concentrations (PEC) for QACs that are applied to soils with manure are in the order of 3.5 mg kg −1 . Based on literature data, the median PEC of QAC in sewage sludge amended soils is 25 µg kg −1 . The positively charged QACs are mainly sorbed to clay minerals. We propose that QACs might be sequestered in the interlayer regions of layered silicates in clay-rich soils, reducing their acute toxicity, while increasing their persistence. The release of sequestered QACs from soil can still potentially maintain concentration levels that are sufficient to develop antibiotic resistance in the environment.
    Keywords: Quaternary ammonium compounds ; Quaternary alkylammonium compounds ; Soil ; Environment ; Desinfectant use ; Antibiotic resistance genes ; Biocide susceptibility ; QAC genes ; Class 1 integrons ; Clay minerals ; Montmorillonite ; Interlayer sorption
    ISSN: 1569-1705
    E-ISSN: 1572-9826
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  • 10
    Language: English
    In: Frontiers in microbiology, 2014, Vol.5, pp.765
    Description: Manure is known to contain residues of antibiotics administered to farm animals as well as bacteria carrying antibiotic resistance genes (ARGs). These genes are often located on mobile genetic elements. In biogas plants (BGPs), organic substrates such as manure and plant material are mixed and fermented in order to provide energy, and resulting digestates are used for soil fertilization. The fate of plasmid carrying bacteria from manure during the fermentation process is unknown. The present study focused on transferable antibiotic resistance plasmids from digestates of seven BGPs, using manure as a co-substrate, and their phenotypic and genotypic characterization. Plasmids conferring resistance to either tetracycline or sulfadiazine were captured by means of exogenous plasmid isolation from digestates into Pseudomonas putida KT2442 and Escherichia coli CV601 recipients, at transfer frequencies ranging from 10(-5) to 10(-7). Transconjugants (n = 101) were screened by PCR-Southern blot hybridization and real-time PCR for the presence of IncP-1, IncP-1ε, IncW, IncN, IncP-7, IncP-9, LowGC, and IncQ plasmids. While 61 plasmids remained unassigned, 40 plasmids belonged to the IncP-1ε subgroup. All these IncP-1ε plasmids were shown to harbor the genes tet(A), sul1, qacEΔ1, intI1, and integron gene cassette amplicons of different size. Further analysis of 16 representative IncP-1ε plasmids showed that they conferred six different multiple antibiotic resistance patterns and their diversity seemed to be driven by the gene cassette arrays. IncP-1ε plasmids displaying similar restriction and antibiotic resistance patterns were captured from different BGPs, suggesting that they may be typical of this environment. Our study showed that BGP digestates are a potential source of transferable antibiotic resistance plasmids, and in particular the broad host range IncP-1ε plasmids might contribute to the spread of ARGs when digestates are used as fertilizer.
    Keywords: Incp-1ε Plasmid ; Antibiotic Resistance ; Biogas Plant Digestate ; Class 1 Integrons ; Exogenous Plasmid Isolation
    ISSN: 1664-302X
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