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Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India
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  • Published: 29 December 2025

Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India

  • Deepjyoti Paul1,
  • Daizee Talukdar1,
  • Ramani Shyam Kapuganti1,
  • Vaishali Gupta1,
  • Lekshmi Narendrakumar1,
  • Pradipta Jana1,
  • Pawan Kumar1,
  • Jyoti Singh1,
  • Shalini Kumari1,
  • Chandana Basak1,
  • Kajal Kamboj1,
  • Susmita Bakshi1,
  • Shruti Lal1,
  • Subhash Tanwar1,
  • Roshan Kumar1,
  • Prabhakar Babele1,
  • Manish Bajpai1,
  • Yashwant Kumar1,
  • Ankur Mutreja  ORCID: orcid.org/0000-0002-1118-80752,
  • Sukhendu Mandal3,
  • Nitya Wadhwa  ORCID: orcid.org/0000-0002-9435-18421,
  • Sanjay K. Banerjee4 &
  • …
  • Bhabatosh Das  ORCID: orcid.org/0000-0002-2447-53801 

Nature Communications , Article number:  (2025) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Antimicrobial resistance
  • Genetics research
  • Mobile elements

Abstract

The emergence and spread of antimicrobial resistance (AMR) in clinically important bacterial pathogens has severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiotics in microbially dense environments. In this study, we use sewage samples (n = 381) collected from six Indian states between June and December 2023 to assess the concentration of eleven antibiotics, microbial diversity, and ARG richness. We find antibiotics from seven drug classes and detect over 2000 bacterial amplicon sequence variants (ASVs). Metagenomic (n = 220) and isolated genome sequences (n = 305) of aerobic and anaerobic bacterial species identify 82 ARGs associated with 80 mobile genetic elements (MGEs). These MGEs are predominantly present in multidrug-resistant (MDR) bacterial pathogens. Comparative core genome analysis of MDR bacterial isolates (n = 7166) shows strong genetic similarity between sewage-derived strains and clinical pathogens. Our results highlight sewage as a significant reservoir for ARGs, where genetic exchanges occur and facilitate the evolution and spread of AMR pathogens in both community and healthcare settings. Additionally, the dipstick-based assay developed for ARGs detection can be used for sewage surveillance in low-resource settings for better understanding of resistance prevalence.

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Data availability

All genomic datasets, including 16S metagenomic, shotgun metagenomic, and whole-genome sequencing (WGS) data generated in this study have been deposited in the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/), under BioProject ID PRJEB81436. All previously published genome sequence data used in the study are available in the NCBI database, with accession details provided in Supplementary Dataset 9b-j. The study also utilized publicly available databases, including CARD, KEGG, and NCBI, along with bioinformatics tools such as DADA2, Kraken2, and ABRicate among others.

Code availability

All codes used for data analysis and data generation have been deposited in a publicly accessible GitHub repository (https://github.com/daizee-gwh/urban-sewage-AMR-metagenomics).

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Acknowledgements

We extend our sincere gratitude to Prof. Ganesan Karthikeyan and Prof. Pramod K Garg for their generous support to complete this study. Authors also acknowledge Prof. Sudhansu Vrati, Prof. Arindam Maitra, and Dr. Onkar Nath Tiwari for their support to the execution of this research. This study was funded by the Department of Biotechnology, Government of India, under the surveillance project titled “Genomic Surveillance for SARS-CoV-2 in India: Indian SARS-CoV-2 Genomics Consortium (INSACOG)- Phase II: Sewage Surveillance” (Ref. RAD/22017/19/2022-KGD-DBT, dated 29/12/2022); Expansion of INSACOG- Wastewater Surveillance of SARS-CoV-2, Emerging Pathogens and AMR through Genomics-Based Methods (Ref No: GCI-13012/2/2025-GCl), as well as the Translational Research Program (TRP) (No. BT/PR30159/MED/15/188/2018).

Author information

Authors and Affiliations

  1. Microbial Research Centre, BRIC-Translational Health Science and Technology Institute (THSTI), Faridabad, India

    Deepjyoti Paul, Daizee Talukdar, Ramani Shyam Kapuganti, Vaishali Gupta, Lekshmi Narendrakumar, Pradipta Jana, Pawan Kumar, Jyoti Singh, Shalini Kumari, Chandana Basak, Kajal Kamboj, Susmita Bakshi, Shruti Lal, Subhash Tanwar, Roshan Kumar, Prabhakar Babele, Manish Bajpai, Yashwant Kumar, Nitya Wadhwa & Bhabatosh Das

  2. Cambridge Institute for Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK

    Ankur Mutreja

  3. Department of Microbiology, University of Calcutta, College Street, Kolkata, India

    Sukhendu Mandal

  4. Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER-Guwahati), Changsari, Guwahati, Assam, India

    Sanjay K. Banerjee

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  1. Deepjyoti Paul
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Contributions

B.D. conceptualized and designed the research. D.P., D.T., R.S.K., V.G., L.N., P.J., P.K., J.S., S.K., C.B., K.K., S.B., S.L., S.T., R.K., P.B., M.B., and Y.K. performed experiments. S.M., D.P., and S.K.B. contributed to the investigation and sample collection. B.D., D.P., and A.M. contributed to the development of dipstick-based detection of ARGs. D.P., D.T., K.R.S., N.W., and B.D. contributed to formal analysis, validation and writing the original draft. All the authors approved the final version of the manuscript.

Corresponding author

Correspondence to Bhabatosh Das.

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Paul, D., Talukdar, D., Kapuganti, R.S. et al. Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India. Nat Commun (2025). https://doi.org/10.1038/s41467-025-68034-3

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  • Received: 02 March 2025

  • Accepted: 15 December 2025

  • Published: 29 December 2025

  • DOI: https://doi.org/10.1038/s41467-025-68034-3

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