Free-floating extracellular DNA: Systematic profiling of mobile genetic elements and antibiotic resistance from wastewater

Calderón-Franco, David; Loosdrecht, Mark C.M. van; Abeel, Thomas; Weissbrodt, David G.

doi:10.1016/j.watres.2020.116592

Cited by 87 publications

(57 citation statements)

References 66 publications

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“…In activated sludge, Yuan et al (2019) have identified that the taxa reflected by the iDNA and exDNA fractions are similar, suggesting a correlation between changes in the microbial composition of the activated sludge and in exDNA. Using the same exDNA extraction methodology, we have shown in a previous study that exDNA present in activated sludge mainly originates from decaying microbial populations rather than from transport from the influent (Calderón-Franco et al, 2020).…”

Section: Resultsmentioning

confidence: 99%

Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant

Calderón-Franco

Sarelse

Christou

et al. 2022

Preprint

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In the One Health context, wastewater treatment plants (WWTPs) are central to safeguard water resources. Nonetheless, many questions remain about their effectiveness to prevent the dissemination of antimicrobial resistance (AMR). Most surveillance studies monitor the levels and removal of selected antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in intracellular DNA (iDNA) extracted from WWTP influents and effluents. The role of extracellular free DNA (exDNA) in wastewater is mostly overlooked. In this study, we analyzed the transfer of ARGs and MGEs in a full-scale Nereda® reactor removing nutrients with aerobic granular sludge. We tracked the composition and fate of the iDNA and exDNA pools of influent, sludge, and effluent samples. Metagenomics was used to profile the microbiome, resistome, and mobilome signatures of iDNA and exDNA extracts. Selected ARGs and MGEs were analyzed by qPCR. From 2,840 ARGs identified, the genes arr-3 (2%), tetC (1.6%), sul1 (1.5%), oqxB (1.2%), and aph(3")-Ib (1.2%) were the most abundant among all sampling points and bioaggregates. Pseudomonas, Acinetobacter, Aeromonas, Acidovorax, Rhodoferax, and Streptomyces populations were the main hosts of ARGs in the sludge. In the effluent, 478 resistance determinants were detected, of which 89% from exDNA potentially released by cell lysis during aeration in the reactor. MGEs and multiple ARGs were co-localized on the same extracellular genetic contigs. These can pose a risk for AMR dissemination by transformation into microorganisms of receiving water bodies. Total intracellular ARGs decreased 3-42% as a result of wastewater treatment. However, the ermB and sul1 genes increased by 2 and 1 log gene copies mL-1, respectively, in exDNA from influent to effluent. The exDNA fractions need to be considered in AMR surveillance, risk assessment, and mitigation.

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Section: Resultsmentioning

confidence: 99%

Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant

Calderón-Franco

Sarelse

Christou

et al. 2022

Preprint

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“…However, it must be noted that detection of these organisms via DNA-based PCR does not necessarily indicate the presence of infectious pathogens. Furthermore, it is worth noting that the presence of extracellular DNA in wastewater has been reported ( Yuan et al., 2019 ; Zhang et al., 2019 ; Slipko et al., 2019 ; Calderón-Franco et al., 2021 ). These extracellular DNA could have also contributed to the concentration of the mycobacteria in the treated wastewater.…”

Section: Discussionmentioning

confidence: 99%

Molecular surveillance of tuberculosis-causing mycobacteria in wastewater

Mtetwa

Amoah

Kumari

et al. 2022

Heliyon

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“…Finally, as they have been detected in all tested environmental samples, SXT/R391 ICEs appeared to be widespread and likely ubiquitous. A very recent paper also demonstrate that the elements of this family are likely very abundant in WWTP effluents (Calderón-Franco et al, 2020), even suggesting they would be one of the most abundant ICE family.…”

Section: Abundances Of Sxt/r391 Ices In Aquatic Environmentsmentioning

confidence: 95%

Abundance and environmental host range of the SXT/R391 ICEs in aquatic environmental communities

Roman

Merlin

Baron

et al. 2021

Environmental Pollution

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HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

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Free-floating extracellular DNA: Systematic profiling of mobile genetic elements and antibiotic resistance from wastewater

Cited by 87 publications

References 66 publications

Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant

Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant

Molecular surveillance of tuberculosis-causing mycobacteria in wastewater

Abundance and environmental host range of the SXT/R391 ICEs in aquatic environmental communities

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