ABSTRACT The rising challenge of antibiotic resistance, accelerated by mobile genetic elements carrying antibiotic resistance genes, necessitates effective and environmentally friendly

control strategies. Here we present an approach employing _Shewanella oneidensis_, transformed into an efficient whole-cell DNA scavenger by expressing a highly active nuclease. This

approach aimed at enzymatically eliminating cell-free mobile genetic elements in wastewater treatment plants. The DNA scavenger demonstrated high efficiency and ultrafast degradation with a

model multiple antibiotic resistance plasmid. Experiments across various dosages and hydraulic retention times showed substantial antibiotic resistance gene reduction, even at minimal

scavenging as a new strategy for managing the antibiotic resistance spread. Access through your institution Buy or subscribe This is a preview of subscription content, access via your

institution ACCESS OPTIONS Access through your institution Subscribe to this journal Receive 12 digital issues and online access to articles $119.00 per year only $9.92 per issue Learn more

Buy this article * Purchase on SpringerLink * Instant access to full article PDF Buy now Prices may be subject to local taxes which are calculated during checkout ADDITIONAL ACCESS OPTIONS:

* Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS THE ROLE OF CHEMOTAXIS AND EFFLUX PUMPS ON NITRATE

REDUCTION IN THE TOXIC REGIONS OF A CIPROFLOXACIN CONCENTRATION GRADIENT Article 29 April 2021 ANTIBIOTIC RESISTANCE PROFILE OF NITROGEN-METABOLIZING MICROBES IN ANOXIC‒OXIC PROCESSES FOR

SWINE WASTEWATER TREATMENT Article Open access 20 April 2025 CHLORINE DISINFECTION FACILITATES NATURAL TRANSFORMATION THROUGH ROS-MEDIATED OXIDATIVE STRESS Article Open access 03 May 2021

DATA AVAILABILITY Source data are provided with this paper. REFERENCES * LeGault, K. N. et al. Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts. _Science_

373, eabg2166 (2021). CAS  PubMed  PubMed Central  Google Scholar  * Povolo, V. R. & Ackermann, M. Disseminating antibiotic resistance during treatment. _Science_ 364, 737–738 (2019).

CAS  PubMed  Google Scholar  * Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. _Clin. Microbiol. Rev._ 31,

e00088–00017 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Wang, Y. et al. Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through

bacterial transformation. _ISME J._ 14, 2179–2196 (2020). CAS  PubMed  PubMed Central  Google Scholar  * Nero, T. M. et al. ComM is a hexameric helicase that promotes branch migration during

natural transformation in diverse Gram-negative species. _Nucleic Acids Res._ 46, 6099–6111 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Carvalho, G. et al. Bacterial

transformation buffers environmental fluctuations through the reversible integration of mobile genetic elements. _mBio_ 11, e02443–02419 (2020). CAS  PubMed  PubMed Central  Google Scholar 

* Mendler, K. et al. AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. _Nucleic Acids Res._ 47, 4442–4448 (2019). CAS  PubMed  PubMed Central 

Google Scholar  * Chandrasekaran, S., Venkatesh, B. & Lalithakumari, D. Transfer and expression of a multiple antibiotic resistance plasmid in marine bacteria. _Curr. Microbiol._ 37,

347–351 (1998). CAS  PubMed  Google Scholar  * Jiang, S. C. & Paul, J. H. Gene transfer by transduction in the marine environment. _Appl. Environ. Microbiol._ 64, 2780–2787 (1998). CAS 

PubMed  PubMed Central  Google Scholar  * Hu, B., Khara, P. & Christie, P. J. Structural bases for F plasmid conjugation and F pilus biogenesis in _Escherichia coli_. _Proc. Natl Acad.

Sci. USA_ 116, 14222–14227 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Humphrey, S. et al. Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile

genetic elements. _Nat. Commun._ 12, 6509 (2021). CAS  PubMed  PubMed Central  Google Scholar  * Ju, F. et al. Wastewater treatment plant resistomes are shaped by bacterial composition,

genetic exchange, and upregulated expression in the effluent microbiomes. _ISME J._ 13, 346–360 (2019). PubMed  Google Scholar  * Karkman, A., Do, T. T., Walsh, F. & Virta, M. P. J.

Antibiotic-resistance genes in waste water. _Trends Microbiol._ 26, 220–228 (2018). CAS  PubMed  Google Scholar  * Zhang, Y. et al. Cell-free DNA: A neglected source for antibiotic

resistance genes spreading from WWTPs. _Environ. Sci. Technol._ 52, 248–257 (2018). CAS  PubMed  Google Scholar  * He, H. et al. Degradation and deactivation of bacterial antibiotic

resistance genes during exposure to free chlorine, monochloramine, chlorine dioxide, ozone, ultraviolet light, and hydroxyl radical. _Environ. Sci. Technol._ 53, 2013–2026 (2019). CAS 

PubMed  Google Scholar  * Chang, P. H., Juhrend, B., Olson, T. M., Marrs, C. F. & Wigginton, K. R. Degradation of extracellular antibiotic resistance genes with UV254 treatment.

_Environ. Sci. Technol._ 51, 6185–6192 (2017). CAS  PubMed  Google Scholar  * Zhang, Z. et al. Effects of UV disinfection on phenotypes and genotypes of antibiotic-resistant bacteria in

secondary effluent from a municipal wastewater treatment plant. _Water Res._ 157, 546–554 (2019). CAS  PubMed  Google Scholar  * Zhang, Y., Gu, A. Z., He, M., Li, D. & Chen, J.

Subinhibitory concentrations of disinfectants promote the horizontal transfer of multidrug resistance genes within and across genera. _Environ. Sci. Technol._ 51, 570–580 (2017). CAS  PubMed

  Google Scholar  * Dunlop, P. S. M., Ciavola, M., Rizzo, L., McDowell, D. A. & Byrne, J. A. Effect of photocatalysis on the transfer of antibiotic resistance genes in urban wastewater.

_Catal. Today_ 240, 55–60 (2015). CAS  Google Scholar  * Heidelberg, J. F. et al. Genome sequence of the dissimilatory metal ion-reducing bacterium _Shewanella oneidensis_. _Nat.

Biotechnol._ 20, 1118–1123 (2002). CAS  PubMed  Google Scholar  * Fredrickson, J. K. et al. Towards environmental systems biology of _Shewanella_. _Nat. Rev. Microbiol._ 6, 592–603 (2008).

CAS  PubMed  Google Scholar  * Fan, G., Graham, A. J., Kolli, J., Lynd, N. A. & Keitz, B. K. Aerobic radical polymerization mediated by microbial metabolism. _Nat. Chem._ 12, 638–646

(2020). CAS  PubMed  PubMed Central  Google Scholar  * Lawrence, J. M. et al. Synthetic biology and bioelectrochemical tools for electrogenetic system engineering. _Sci. Adv._ 8, eabm5091

(2022). CAS  PubMed  PubMed Central  Google Scholar  * Xiong, Z. et al. A wireless and battery-free wound infection sensor based on DNA hydrogel. _Sci. Adv._ 7, eabj1617–eabj1617 (2021). CAS

  PubMed  PubMed Central  Google Scholar  * Baslé, A. et al. Crystal structure of NucB, a biofilm-degrading endonuclease. _Nucleic Acids Res._ 46, 473–484 (2017). PubMed Central  Google

Scholar  * Hirose, A., Kouzuma, A. & Watanabe, K. Towards development of electrogenetics using electrochemically active bacteria. _Biotechnol. Adv._ 37, 107351 (2019). CAS  PubMed 

Google Scholar  * Hau, H. H. & Gralnick, J. A. Ecology and biotechnology of the genus _Shewanella_. _Annu. Rev. Microbiol._ 61, 237–258 (2007). CAS  PubMed  Google Scholar  * Fan, Y. Y.

et al. Rapid and highly efficient genomic engineering with a novel iEditing device for programming versatile extracellular electron transfer of electroactive bacteria. _Environ. Microbiol._

23, 1238–1255 (2021). CAS  PubMed  Google Scholar  * Trémillon, N. et al. Production and purification of staphylococcal nuclease in _Lactococcus lactis_ using a new expression-secretion

system and a pH-regulated mini-reactor. _Microb. Cell Fact._ 9, 37 (2010). PubMed  PubMed Central  Google Scholar  * Jordt, H. et al. Coevolution of host–plasmid pairs facilitates the

emergence of novel multidrug resistance. _Nat. Ecol. Evol._ 4, 863–869 (2020). PubMed  PubMed Central  Google Scholar  * Che, Y. et al. Conjugative plasmids interact with insertion sequences

to shape the horizontal transfer of antimicrobial resistance genes. _Proc. Natl Acad. Sci. USA_ 118, e2008731118 (2021). CAS  PubMed  PubMed Central  Google Scholar  * Harding, C. M.,

Hennon, S. W. & Feldman, M. F. Uncovering the mechanisms of _Acinetobacter baumannii_ virulence. _Nat. Rev. Microbiol._ 16, 91–102 (2018). CAS  PubMed  Google Scholar  * Meng, F. et al.

Characterization of the size-fractionated biomacromolecules: tracking their role and fate in a membrane bioreactor. _Water Res._ 45, 4661–4671 (2011). CAS  PubMed  Google Scholar  * Grady,

C. L., Daigger, G. T., Love, N. G. & Filipe, C. D. _Biological Wastewater Treatment_ (CRC Press, 2011). * Davis, M. L. & Masten, S. J. _Principles Of Environmental Engineering_

(McGraw Hill, 2013). * Deng, Y. & Zhao, R. Advanced oxidation processes (AOPs) in wastewater treatment. _Curr. Pollut. Rep._ 1, 167–176 (2015). CAS  Google Scholar  * Suresh, C., Ameta,

R. A. _Advanced Oxidation Processes For Wastewater Treatment: Emerging Green Chemical Technology_ (Academic Press, 2018). * Rasouly, A. & Nudler, E. Reactive oxygen species as the long

arm of bactericidal antibiotics. _Proc. Natl Acad. Sci. USA_ 116, 9696–9698 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Paulus, G. K. et al. The impact of on-site hospital

wastewater treatment on the downstream communal wastewater system in terms of antibiotics and antibiotic resistance genes. _Int. J. Hyg. Environ. Health_ 222, 635–644 (2019). CAS  PubMed 

Google Scholar  * Wang, Z. et al. Effect of humic substances on the anaerobic digestion of secondary sludge in wastewater treatment plants: A review. _Environ. Chem. Lett._ 21, 3023–3040

(2023). CAS  Google Scholar  * Nybroe, O., Jørgensen, P. E. & Henze, M. Enzyme activities in waste water and activated sludge. _Water Res._ 26, 579–584 (1992). CAS  Google Scholar  *

Senturk, M. _Enzyme Inhibitors and Activators_ (IntechOpen, 2017). * Leveson-Gower, R. B., Mayer, C. & Roelfes, G. The importance of catalytic promiscuity for enzyme design and

evolution. _Nat. Rev. Chem._ 3, 687–705 (2019). CAS  Google Scholar  * Datta, S., Christena, L. R. & Rajaram, Y. R. S. Enzyme immobilization: an overview on techniques and support

materials. _3 Biotech_ 3, 1–9 (2013). PubMed  Google Scholar  * Chen, G., Huang, S., Ma, X., He, R. & Ouyang, G. Encapsulating and stabilizing enzymes using hydrogen-bonded organic

frameworks. _Nat. Protoc._ 18, 2032–2050 (2023). CAS  PubMed  Google Scholar  * Ding, N. et al. Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription

factor-based biosensor. _Nucleic Acids Res._ 48, 10602–10613 (2020). CAS  PubMed  PubMed Central  Google Scholar  * Mordaka, P. M. & Heap, J. T. Stringency of synthetic promoter

sequences in _Clostridium_ revealed and circumvented by tuning promoter library mutation rates. _ACS Synth. Biol._ 7, 672–681 (2018). CAS  PubMed  Google Scholar  * Calderón-Franco, D., van

Loosdrecht, M. C. M., Abeel, T. & Weissbrodt, D. G. Free-floating extracellular DNA: systematic profiling of mobile genetic elements and antibiotic resistance from wastewater. _Water

Res._ 189, 116592 (2021). PubMed  Google Scholar  * Almagro Armenteros, J. J. et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. _Nat. Biotechnol._ 37,

420–423 (2019). CAS  PubMed  Google Scholar  Download references ACKNOWLEDGEMENTS H.-Q.Y. and Q.T.’s team members were financially supported by the National Natural Science Foundation of

China (22322610, 22176184, 51821006 and 52192684), the National Key Research and Development Program of China (2018YFA0901301 and 2019YFA0905503), the Program for Changjiang Scholars and

Innovative Research Team in University from the Ministry of Education of China, and the USTC Research Funds of the Double First-Class Initiative (YD2400002005). S.H. was supported by the

National Institute of Environmental Health Sciences Superfund Basic Research Program of the USA (NIH-2P42ES004911-27A1-Project4). AUTHOR INFORMATION Author notes * These authors contributed

equally: Yang Li, Syed A. Hashsham. AUTHORS AND AFFILIATIONS * School of Life Sciences, University of Science and Technology of China, Hefei, China Yang Li & Hong Sun * Department of

Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA Syed A. Hashsham * CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science

and Engineering, University of Science and Technology of China, Hefei, China Fei-Fei Chen, Qiang Tang & Han-Qing Yu * Center for Microbial Ecology, Michigan State University, East

Lansing, MI, USA James M. Tiedje Authors * Yang Li View author publications You can also search for this author inPubMed Google Scholar * Syed A. Hashsham View author publications You can

also search for this author inPubMed Google Scholar * Fei-Fei Chen View author publications You can also search for this author inPubMed Google Scholar * Hong Sun View author publications

You can also search for this author inPubMed Google Scholar * Qiang Tang View author publications You can also search for this author inPubMed Google Scholar * Han-Qing Yu View author

publications You can also search for this author inPubMed Google Scholar * James M. Tiedje View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS

Q.T. devised the concept. Y.L., S.A.H., F.-F.C. and H.S. performed the DNA scavenger construction and evaluation tests, and analysed the results. Q.T. and Y.L. wrote the manuscript. Q.T.,

H.-Q.Y. and J.M.T. revised the manuscript. CORRESPONDING AUTHORS Correspondence to Qiang Tang, Han-Qing Yu or James M. Tiedje. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no

competing interests. PEER REVIEW PEER REVIEW INFORMATION _Nature Water_ thanks Feng Ju and Benno Ter Kuile for their contribution to the peer review of this work. ADDITIONAL INFORMATION

PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION

Supplementary Methods, Figs. 1–17, Tables 1–4 and References. SUPPLEMENTARY DATA 1 Statistical source data for Supplementary Figs. 7–12, 14, 15 and 17. SUPPLEMENTARY DATA 2 Source data for

Supplementary Figs. 2–5 and 13. SOURCE DATA SOURCE DATA FIG. 2 Statistical source data. SOURCE DATA FIG. 3 Statistical source data. SOURCE DATA FIG. 3 Full-length, unprocessed gels or blots.

SOURCE DATA FIG. 4 Statistical source data. SOURCE DATA FIG. 5 Statistical source data. SOURCE DATA FIG. 5 Full-length, unprocessed gels or blots. SOURCE DATA FIG. 6 Statistical source

data. SOURCE DATA FIG. 6 Full-length, unprocessed gels or blots. SOURCE DATA FIG. 7 Statistical source data. RIGHTS AND PERMISSIONS Springer Nature or its licensor (e.g. a society or other

partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this

article is solely governed by the terms of such publishing agreement and applicable law. Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Li, Y., Hashsham, S.A., Chen, FF. _et

al._ Engineered DNA scavenger for mitigating antibiotic resistance proliferation in wastewater treatment. _Nat Water_ 2, 758–769 (2024). https://doi.org/10.1038/s44221-024-00289-4 Download

citation * Received: 05 January 2024 * Accepted: 15 July 2024 * Published: 19 August 2024 * Issue Date: August 2024 * DOI: https://doi.org/10.1038/s44221-024-00289-4 SHARE THIS ARTICLE

Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy to clipboard Provided

by the Springer Nature SharedIt content-sharing initiative