scholarly journals Core Microbiota Drive the Prevalence of Extracellular Antibiotic Resistome in the Water Compartments

2022 ◽  
Author(s):  
Kai-Feng Yu ◽  
Peng Li ◽  
Yuansheng Huang ◽  
Jun Yang ◽  
Han Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Illumina Miseq ◽  
Shannon Index ◽  
Procrustes Analysis ◽  
Extracellular Dna ◽  
Core Microbiota ◽  
The Core ◽  
Water Compartments

Unlike intracellular chromosome, extracellular DNA (eDNA) may accelerate the spreading of antibiotic resistance genes (ARGs) through natural transformation, but one of the core issues regarding to the taxonomic characterization of eDNA in the complex water environments is largely unknown. Hence, Illumina Miseq sequencing was used to identify the genotype of eDNA from wastewater (WW), river water (RW) and stormwater (SW) runoff. High-throughput qPCR targeting 384 genes was implemented to detect extracellular ARGs (eARGs) and mobile genetic elements (eMGEs). We obtained 2,708,291 high quality sequences from 66 eDNA samples. The SW exhibited the significant higher Shannon Index. Subsequently, we identified 34 core bacteria sources of eDNA widely distributed in the three water compartments. Among which, Pseudomonas, Flavobacterium, Limnohabitans, Burkholderiaceae_unclassified, Methylotenera and Acinetobacter were the most prevalent. A total of 302 eARGs and eMGEs were detected, suggesting that eDNA is an important antibiotic resistance reservoir. Among the 127 shared genes of the three groups, 15 core resistance genes were filtered, including IS6100, sul1 NEW, intI1, ISPps1-pseud, aac3-Via, qacH_351 and ISSm2-Xanthob. The Procrustes analysis and Variance Partitioning Analysis (VPA) demonstrated that core bacteria and MGEs were significantly correlated with eARGs. These results suggested that the occurrence and changes of eARGs in the water compartments may be largely attributed to the core microbiota and eMGEs.

scholarly journals 702. Zinc Blockade of SOS Response Inhibits Horizontal Transfer of Antibiotic Resistance Genes in Enteric Bacteria

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S253-S253
Author(s):  
John Crane ◽  
Mark Sutton ◽  
Muhammad Cheema ◽  
Michael Olyer
Keyword(s):  
Dna Damage ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Horizontal Transfer ◽  
Antibiotic Resistance Genes ◽  
Sos Response ◽  
Enteric Bacteria ◽  
Extracellular Dna ◽  
In Vitro Assays ◽  
E Coli

Abstract Background The SOS response is a conserved response to DNA damage that is found in Gram negative and Gram-positive bacteria. When DNA damage is sustained and severe, activation of error-prone DNA polymerases can induce a higher mutation rate then normally observed, which is called the mutator phenotype or hypermutation. We previously showed that zinc blocked the hypermutation response induced by quinolone antibiotics and mitomycin C in E. coli and Klebsiella pneumoniae (Bunnell BE, Escobar JF, Bair KL, Sutton MD, Crane JK (2017). Zinc blocks SOS-induced antibiotic resistance via inhibition of RecA in Escherichia coli. PLoS ONE 12(5): e0178303. https://doi.org/10.1371/journal.pone.0178303.) In addition to causing copying errors in DNA replication, Beaber et al. showed that induction of the SOS response increased the frequency of horizontal gene transfer into Vibrio cholerae, an organism naturally competent at uptake of extracellular DNA. (Beaber JW, Hochhut B, Waldor MK. 2003. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427:72–74.) Methods. In this study, we tested whether induction of the SOS response could induce transfer of antibiotic resistance from Enterobacter cloacae into E. coli, and whether zinc could inhibit that inter-species transfer of antibiotic resistance. Results. Ciprofloxacin, an inducer of the SOS response, increased the rate of transfer of an extended spectrum β-lactamase (ESBL) gene from Enterobacter into a susceptible E. coli strain. Zinc blocked SOS-induced horizontal transfer of §-lactamase into E. coli. Other divalent metals, such as iron and manganese, failed to inhibit these responses. Conclusion. In vitro assays showed that zinc blocked the ability of RecA to bind to ssDNA, an early step in the SOS response, suggesting the mechanism by which zinc blocks the SOS response. Disclosures All authors: No reported disclosures.

scholarly journals Antibiotic resistance genes and mobile genetic elements removal from treated wastewater by sewage-sludge biochar and iron-oxide coated sand

2020 ◽  
Author(s):  
David Calderón-Franco ◽  
Apoorva Seeram ◽  
Gertjan Medema ◽  
Mark C. M. van Loosdrecht ◽  
David G. Weissbrodt
Keyword(s):  
Antibiotic Resistance ◽  
Iron Oxide ◽  
Sewage Sludge ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Environmental Dna ◽  
Extracellular Dna ◽  
Treated Wastewater ◽  
Dna Adsorption ◽  
Coated Sand

AbstractDisinfection of treated wastewater in wastewater treatment plants (WWTPs) is used to minimize emission of coliforms, pathogens, and antibiotic resistant bacteria (ARB) in the environment. However, the fate of free-floating extracellular DNA (eDNA) that do carry antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) is overlooked. Water technologies are central to urban and industrial ecology for sanitation and resource recovery. Biochar produced by pyrolysis of sewage sludge and iron-oxide-coated sands recovered as by-product of drinking water treatment were tested as adsorbents to remove ARGs and MGEs from WWTP effluent. DNA adsorption properties and materials applicability were studied in batch and up-flow column systems at bench scale. Breakthrough curves were measured with ultrapure water and treated wastewater at initial DNA concentrations of 0.1-0.5 mg mL-1 and flow rates of 0.1-0.5 mL min-1. Batch tests with treated wastewater indicated that the adsorption profiles of biochar and iron-oxide coated sand followed a Freundlich isotherm, suggesting a multilayer adsorption of nucleic acids. Sewage-sludge biochar exhibited higher DNA adsorption capacity (1 mg g-1) and longer saturation breakthrough times (4 to 10 times) than iron-oxide coated sand (0.2 mg g-1). The removal of a set of representative ARGs and MGEs was measured by qPCR comparing the inlet and outlet of the plug-flow column fed with treated wastewater. ARGs and MGEs present as free-floating eDNA were adsorbed by sewage-sludge biochar at 85% and iron-oxide coated sand at 54%. From the environmental DNA consisting of the free-floating extracellular DNA plus the intracellular DNA of the cells present in the effluent water, 97% (sewage-sludge biochar) and 66% (iron-oxide coated sand) of the tested genes present were removed. Sewage-sludge biochar displayed interesting properties to minimize the spread of antimicrobial resistances to the aquatic environment while strengthening the role of WWTPs as resource recovery factories.Graphical abstractHighlightsSewage-sludge biochar and iron oxide coated sands were tested to adsorb DNA and cells.Biochar removed 97% of genes tested from environmental DNA of unfiltered effluent.85% of ARGs and MGEs of free-floating extracellular DNA were retained by biochar.Biochar is a WWTP by-product that can be re-used for public health sanitation.

scholarly journals Antibiotic Resistance Genes in Different Animal Manure and their Derived Organic Fertilizer

2020 ◽  
Author(s):  
Yan Xu ◽  
Houyu Li ◽  
Rongguang Shi ◽  
Jiapei Lv ◽  
Bihan Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Bacterial Resistance ◽  
Organic Fertilizer ◽  
Poultry Manure ◽  
Antibiotic Resistance Genes ◽  
Animal Manure ◽  
Procrustes Analysis ◽  
Organic Fertilizers

Abstract Background: The prevalence of antibiotic resistance genes (ARGs) in animal manure poses threats to the environmental safety. Organic fertilizers fermented by livestock and poultry manure are directly applied to farmland, which would cause the potential outbreak of bacterial resistance in agricultural environment. This study investigated the composition of ARGs in different animal manure and their derived organic fertilizers. Results: Results showed that the abundance of several ARGs, such as sul 2, Tet B-01, Tet G-01 and Tet M-01 in organic fertilizer samples was 12%~96% lower than in animal manure. However, there was an increasing of Tet K and erm C abundance from animal manure to the organic fertilizers. No correlation between ARGs and environmental factors such as pH, TN, antibiotics was observed by Redundancy analysis (RDA). Procrustes analysis revealed the significant correlation between bacterial community structures and the ARGs abundance (r=0.799, p<0.01). Non-metric multidimensional scaling (NMDS) analysis suggested that microorganisms in organic fertilizer may be derived from animal manure. Additional, pathogenic bacteria (especially Actinomadura ) would proliferate rather than decrease from manure to organic fertilizer. Conclusion: Overall, this research suggests that the composting treatment of manure could effectively reduce these ARGs and pathogens,even cause partial ARGs and pathogens proliferation. It also shows that the microorganism might significantly influence ARGs profiles in composting.

scholarly journals Evolution of Antibiotic Resistance and the Relationship between the Antibiotic Resistance Genes and Microbial Compositions under Long-Term Exposure to Tetracycline and Sulfamethoxazole

2019 ◽  
Vol 16 (23) ◽  
pp. 4681 ◽  
Author(s):  
Bingbing Du ◽  
Qingxiang Yang ◽  
Ruifei Wang ◽  
Ruimin Wang ◽  
Qiang Wang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
The Core ◽  
Aerobic Wastewater Treatment ◽  
The Relationship ◽  
Bacterial Groups ◽  
Wastewater Treatment Systems

The removal of antibiotics and widespread of antibiotic resistance genes (ARGs) have received continuous attention due to the possible threats to environment. However, little information is available on the evolution of antibiotic resistance and the relationship between ARGs and microbial communities under long-term exposure to sub-inhibitory concentrations of antibiotics. In our study, two laboratory-scale anoxic-aerobic wastewater treatment systems were established and operated for 420 days to investigate the evolution of antibiotic resistance under exposure of 5 mg·L−1 tetracycline (TC) or 5 mg·L−1 TC and 1 mg·L−1 sulfamethoxazole (SMX). The average removal rates of TC and SMX were about 59% and 72%, respectively. The abundance of the main ARGs responsible for resistance to TC and SMX increased obviously after antibiotics addition, especially when TC and SMX in combination (increased 3.20-fold). The tetC and sul1 genes were the predominant genes in the development of TC and SMX resistance, in which gene sul1 had the highest abundance among all the detected ARGs. Network analysis revealed that under antibiotic pressure, the core bacterial groups carrying multiple ARGs formed and concentrated in about 20 genera such as Dechloromonas, Candidatus Accumulibacter, Aeromonas, Rubrivivax, in which intI1 played important roles in transferring various ARGs except sul3.

scholarly journals A Mechanism of Unidirectional Transformation, Leading to Antibiotic Resistance, Occurs within Nasopharyngeal Pneumococcal Biofilm Consortia

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
Santiago M. Lattar ◽  
Xueqing Wu ◽  
Jennifer Brophy ◽  
Fuminori Sakai ◽  
Keith P. Klugman ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Extracellular Dna ◽  
Antibiotic Resistant ◽  
Content Type ◽  
Serotype Replacement ◽  
Genes Encoding ◽  
Receptor Cross Talk ◽  
Or Genes

ABSTRACT Streptococcus pneumoniae acquires genes for resistance to antibiotics such as streptomycin (Str) or trimethoprim (Tmp) by recombination via transformation of DNA released by other pneumococci and closely related species. Using naturally transformable pneumococci, including strain D39 serotype 2 (S2) and TIGR4 (S4), we studied whether pneumococcal nasopharyngeal transformation was symmetrical, asymmetrical, or unidirectional. Incubation of S2 Tet and S4 Str in a bioreactor simulating the human nasopharynx led to the generation of Spn Tet/Str recombinants. Double-resistant pneumococci emerged soon after 4 h postinoculation at a recombination frequency (rF) of 2.5 × 10 −4 while peaking after 8 h at a rF of 1.1 × 10 −3 . Acquisition of antibiotic resistance genes by transformation was confirmed by treatment with DNase I. A high-throughput serotyping method demonstrated that all double-resistant pneumococci belonged to one serotype lineage (S2 Tet/Str ) and therefore that unidirectional transformation had occurred. Neither heterolysis nor availability of DNA for transformation was a factor for unidirectional transformation given that the density of each strain and extracellular DNA (eDNA) released from both strains were similar. Unidirectional transformation occurred regardless of the antibiotic-resistant gene carried by donors or acquired by recipients and regardless of whether competence-stimulating peptide-receptor cross talk was allowed. Moreover, unidirectional transformation occurred when two donor strains (e.g., S4 Str and S19F Tmp ) were incubated together, leading to S19F Str/Tmp but at a rF 3 orders of magnitude lower (4.9 × 10 −6 ). We finally demonstrated that the mechanism leading to unidirectional transformation was due to inhibition of transformation of the donor by the recipient. IMPORTANCE Pneumococcal transformation in the human nasopharynx may lead to the acquisition of antibiotic resistance genes or genes encoding new capsular variants. Antibiotics and vaccines are currently putting pressure on a number of strains, leading to an increase in antibiotic resistance and serotype replacement. These pneumococcal strains are also acquiring virulence traits from vaccine types via transformation. In this study, we recapitulated multiple-strain colonization with strains carrying a resistance marker and selected for those acquiring resistance to two or three antibiotics, such as would occur in the human nasopharynx. Strains acquiring dual and triple resistance originated from one progenitor, demonstrating that transformation was unidirectional. Unidirectional transformation was the result of inhibition of transformation of donor strains. Unidirectional transformation has implications for the understanding of acquisition patterns of resistance determinants or capsule-switching events.

scholarly journals Method for Determining the Profile of Antibiotic Resistance Genes in the Vibrio cholera Strains by RT-PCR

2021 ◽  
pp. 79-86
Author(s):  
A. S. Gladkikh ◽  
I. S. Fedotova ◽  
L. V. Mironova
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
Experimental Studies ◽  
Antibiotic Resistance Genes ◽  
Illumina Miseq ◽  
Test System ◽  
Diffusion Method ◽  
Disk Diffusion Method ◽  
Integrase Gene

The aim of the work was to design and carry out experimental studies of a set of reagents to identify the spectrum of genes that determine the resistance of the Vibrio cholerae strains to antibacterial drugs.Materials and methods. V. cholerae strains isolated from humans and environmental objects during epidemiological complications and the cholera-free period were included in the study. Sensitivity to antimicrobial drugs was evaluated by the disk diffusion method. Whole genome sequencing was performed on an Illumina MiSeq. The profile of resistance genes was determined based on a comparison with the ResFinder database. The temperature regime, the composition of the reaction mixtures, and the reaction parameters were optimized; the specificity, sensitivity and reproducibility of the constructed prototype test system were measured.Results and discussion. The spectrum of antibiotic resistance and the profile of resistance genes were determined for the studied strains. To develop multiplex PCR, we selected the most common in the V. cholerae populations genes, which are responsible for resistance to tetracycline (tetA), streptomycin (strA), florfenicol/ chloramphenicol (floR) and trimethoprim/sulfamethoxazole (two variants of the dihydrofolate reductase gene: dfrA1 and dhfR), as well as SXT element integrase gene (int). In the reaction, markers were specifically detected in accordance with the genomic resistance profile, which correlates with the phenotypic manifestation of resistance determined by the disco-diffusion method. The sensitivity of the developed panel of primers and probes for V. cholerae strains was 103 –104 CFU/ml. Therefore, taking into account the specificity, rapidity and simplicity of the reaction, the developed system of primers and probes can be successfully applied for a preliminary assessment of the resistance of the V. cholerae strains to antimicrobial agents. 

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