Metagenomic exploration of antibiotic resistome in treated wastewater effluents and their receiving water

Raza, Shahbaz; Jo, Hyejun; Kim, Jungman; Shin, Hanseob; Hur, Hor‐Gil; Unno, Tatsuya

doi:10.1016/j.scitotenv.2020.142755

Cited by 39 publications

(11 citation statements)

References 52 publications

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“… 2020 ; Raza et al . 2021 ). However, it is currently troublesome to compare the outcomes of various metagenomics studies due to complex data analysis and to the lack of standardized methods and protocols between different platforms.…”

Section: Metagenomics To Address Environmental Amr Detectionmentioning

confidence: 99%

Knowledge gaps in the assessment of antimicrobial resistance in surface waters

Niegowska

Sanseverino

Navarro

et al. 2021

FEMS Microbiology Ecology

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The spread of antibiotic resistance in the water environment has been widely described. However, still many knowledge gaps exist regarding the selection pressure from antibiotics, heavy metals and other substances present in surface waters as a result of anthropogenic activities, as well as the extent and impact of this phenomenon on aquatic organisms and humans. In particular, the relationship between environmental concentrations of antibiotics and the acquisition of ARGs by antibiotic-sensitive bacteria as well as the impact of heavy metals and other selective agents on antimicrobial resistance (AMR) need to be defined. Currently, established safety values are based on the effects of antibiotic toxicity neglecting the question of AMR spread. In turn, risk assessment of antibiotics in waterbodies remains a complex question implicating multiple variables and unknowns reinforced by the lack of harmonized protocols and official guidelines. In the present review, we discussed current state-of-the-art and the knowledge gaps related to pressure exerted by antibiotics and heavy metals on aquatic environments and their relationship to the spread of AMR. Along with this latter, we reflected on i) the risk assessment in surface waters, ii) selective pressures contributing to its transfer and propagation, and iii) the advantages of metagenomics in investigating AMR. Furthermore, the role of microplastics in co-selection for metal and antibiotic resistance, together with the need for more studies in freshwater are highlighted.

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Section: Metagenomics To Address Environmental Amr Detectionmentioning

confidence: 99%

Knowledge gaps in the assessment of antimicrobial resistance in surface waters

Niegowska

Sanseverino

Navarro

et al. 2021

FEMS Microbiology Ecology

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“…4 b). According to Nguyen et al (2021) and Raza et al (2021) , ARGs conferring resistance to sulfonamides and tetracyclines are frequently detected in MWWTPE regardless of predominant bacteria taxa, season, and location. Gene sul1 usually prevails in MWW worldwide due to high sequence conservation and transfer among different species ( Wei et al, 2018 ).…”

Section: Resultsmentioning

confidence: 99%

Metagenomic analysis of MWWTP effluent treated via solar photo-Fenton at neutral pH: Effects upon microbial community, priority pathogens, and antibiotic resistance genes

Vilela

Neto

Starling

et al. 2021

Science of The Total Environment

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The effectiveness of advanced technologies on eliminating antibiotic resistant bacteria (ARB) and resistance genes (ARGs) from wastewaters have been recently investigated. Solar photo-Fenton has been proven effective in combating ARB and ARGs from Municipal Wastewater Treatment Plant effluent (MWWTPE). However, most of these studies have relied solely on cultivable methods to assess ARB removal. This is the first study to investigate the effect of solar photo-Fenton upon ARB and ARGs in MWWTPE by high throughput metagenomic analysis (16S rDNA sequencing and Whole Genome Sequencing). Treatment efficiency upon priority pathogens and resistome profile were also investigated. Solar photo-Fenton (30 mg L −1 of Fe 2+ intermittent additions and 50 mg L −1 of H 2 O 2 ) reached 76–86% removal of main phyla present in MWWTPE. An increase in Proteobacteria abundance was observed after solar photo-Fenton and controls in which H 2 O 2 was present as an oxidant (Fenton, H 2 O 2 only, solar/H 2 O 2 ). Hence, tolerance mechanisms presented by this group should be further assessed. Solar photo-Fenton achieved complete removal of high priority Staphylococcus and Enterococcus , as well as Klebsiella pneumoniae and Pseudomonas aeruginosa . Substantial reduction of intrinsically multi-drug resistant bacteria was detected. Solar photo-Fenton removed nearly 60% of ARGs associated with sulfonamides, macrolides, and tetracyclines, and complete removal of ARGs related to β-lactams and fluoroquinolones. These results indicate the potential of using solar-enhanced photo-Fenton to limit the spread of antimicrobial resistance, especially in developing tropical countries.

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“…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 . The genes of int I1 and sul1 have been considered as indicators for anthropological activities 60, 61 , which is corresponding to our sampling sites significantly influenced by human beings. It is no surprising that int I1 is one of the most prevalent MGEs.…”

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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Metagenomic exploration of antibiotic resistome in treated wastewater effluents and their receiving water

Cited by 39 publications

References 52 publications

Knowledge gaps in the assessment of antimicrobial resistance in surface waters

Knowledge gaps in the assessment of antimicrobial resistance in surface waters

Metagenomic analysis of MWWTP effluent treated via solar photo-Fenton at neutral pH: Effects upon microbial community, priority pathogens, and antibiotic resistance genes

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

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