Extracellular DNA (eDNA): Neglected and Potential Sources of Antibiotic Resistant Genes (ARGs) in the Aquatic Environments

Sivalingam, Periyasamy; Poté, John; Prabakar, K.

doi:10.3390/pathogens9110874

Cited by 45 publications

(22 citation statements)

References 86 publications

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“…2b ) can be widely distributed, and eMGEs potentially play an important role in the proliferation of ARGs. As to the fact that the aminoglycoside resistance genes have been detected in intercellular samples from typical environmental compartments 31 , it is no surprising that these genes were commonly found in the extracellular fractions 58 . In addition, the core genes resistant to aminoglycoside, such as aadA2-1, aadA5 and aadA17 , are generally encoded by plasmids, transposons and integrons, which may facilitate their disseminations through HGT 59 .…”

Section: Discussionmentioning

confidence: 99%

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

Yu¹,

Li²,

Huang³

et al. 2022

Preprint

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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.

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Section: Discussionmentioning

confidence: 99%

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

Yu¹,

Li²,

Huang³

et al. 2022

Preprint

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“…Microbial eDNA is ubiquitous and can be found everywhere where microbial life is present. It is released by the process of cell death and lysis and may be secreted by living cells, but is not enclosed in living cells, may not remain with the cells from which it originated, and may persist for some time before it is finally degraded [ 1 ]. eDNA is involved in microbial survival, often contributes to the structure of biofilms as a matrix component [ 2 , 3 , 4 , 5 , 6 , 7 , 8 ], and acts to preserve a dynamic pool of genes via horizontal gene transfer (HGT) within the biofilm community.…”

Section: Introductionmentioning

confidence: 99%

eDNA Inactivation and Biofilm Inhibition by the PolymericBiocide Polyhexamethylene Guanidine Hydrochloride (PHMG-Cl)

Moshynets

Baranovskyi

Iungin

et al. 2022

IJMS

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The choice of effective biocides used for routine hospital practice should consider the role of disinfectants in the maintenance and development of local resistome and how they might affect antibiotic resistance gene transfer within the hospital microbial population. Currently, there is little understanding of how different biocides contribute to eDNA release that may contribute to gene transfer and subsequent environmental retention. Here, we investigated how different biocides affect the release of eDNA from mature biofilms of two opportunistic model strains Pseudomonas aeruginosa ATCC 27853 (PA) and Staphylococcus aureus ATCC 25923 (SA) and contribute to the hospital resistome in the form of surface and water contaminants and dust particles. The effect of four groups of biocides, alcohols, hydrogen peroxide, quaternary ammonium compounds, and the polymeric biocide polyhexamethylene guanidine hydrochloride (PHMG-Cl), was evaluated using PA and SA biofilms. Most biocides, except for PHMG-Cl and 70% ethanol, caused substantial eDNA release, and PHMG-Cl was found to block biofilm development when used at concentrations of 0.5% and 0.1%. This might be associated with the formation of DNA–PHMG-Cl complexes as PHMG-Cl is predicted to bind to AT base pairs by molecular docking assays. PHMG-Cl was found to bind high-molecular DNA and plasmid DNA and continued to inactivate DNA on surfaces even after 4 weeks. PHMG-Cl also effectively inactivated biofilm-associated antibiotic resistance gene eDNA released by a pan-drug-resistant Klebsiella strain, which demonstrates the potential of a polymeric biocide as a new surface-active agent to combat the spread of antibiotic resistance in hospital settings.

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“…Freshwater resources are a precious commodity and essential to human life and have been declared a human right by the United Nations General Assembly in Resolution 64/292 (Ki-moon and General 2010; Daily et al 2012). However, the spread and dissemination of ARB and ARGs in the fresh water environment have become a global health concern and considered to be an emerging environmental pollutant (Sivalingam et al 2020;Devarajan et al 2016;Sanderson et al 2016). Several factors other than antibiotics influence the spread and dissemination of ARGs in the environment (Devarajan et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Occurrence of toxic metals and their selective pressure for antibiotic-resistant clinically relevant bacteria and antibiotic-resistant genes in river receiving systems under tropical conditions

Salah

Laffite

Sivalingam³

et al. 2021

Environ Sci Pollut Res

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The co-occurrence of heavy metals, antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) from hospital effluents spreading into the river receiving systems and evaluating associated risks are topics of scientific interest and still under-studied in developing countries under tropical conditions. To understand the selectors of the ARGs, we examined the occurrence of heavy metals (Cr, Co, Ni, Cu, Cd, Pb and Zn), associated ARB (β-lactam-resistant Escherichia coli, β-lactam-resistant Enterobacteriaceae, and carbapenem-resistant Enterobacteriaceae) and ARGs (blaOXA, blaCTX-M, blaIMP, blaTEM) in water and sediments from two sub-urban rivers receiving urban and hospital effluent waters in the Democratic Republic of the Congo (DRC). High abundances of ARB and ARGs were observed in all sediment samples. All the metal contents correlated negatively with grain size (− 0.94 ≤ r ≤ − 0.54, p < 0.05) except for Ni and positively with organic matter content and total copies of 16 s rRNA (0.42 ≤ r ≤ 0.79, p < 0.05), except for Ni and Zn. The metals had a significant positive correlation with the faecal indicator Enterococcus except for Ni and Cd (0.43 ≤ r ≤ 0.67, p < 0.05). Carbapenem-resistant Enterobacteriaceae correlated negatively with Zn (r = − 0.44, p < 0.05) and positively with all the rest of toxic metals (0.58 ≤ r ≤ 1.0, p < 0.05). These results suggested that some metals had a great influence on the persistence of ARB and ARGs in sediments. Overall, this study strongly recommends the managing urban wastewater to preserve water resources used for human and agricultural purposes. Additionally, we recommend the utilizing biological indicators (faecal indicator bacteria, ARB, ARGs) when investigating urban wastewater pollutions.

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Extracellular DNA (eDNA): Neglected and Potential Sources of Antibiotic Resistant Genes (ARGs) in the Aquatic Environments

Cited by 45 publications

References 86 publications

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

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

eDNA Inactivation and Biofilm Inhibition by the PolymericBiocide Polyhexamethylene Guanidine Hydrochloride (PHMG-Cl)

Occurrence of toxic metals and their selective pressure for antibiotic-resistant clinically relevant bacteria and antibiotic-resistant genes in river receiving systems under tropical conditions

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