Assessment of seasonal variations in antibiotic resistance genes and microbial communities in sewage treatment plants for public health monitoring

Abhishek Keer; Yukti Oza; Dattatray Mongad; Dinesh Ramakrishnan; Dhiraj Dhotre; Abdelfattah Ahmed; Alimuddin Zumla; Yogesh Shouche; Avinash Sharma

doi:10.1016/j.envpol.2025.126367

Assessment of seasonal variations in antibiotic resistance genes and microbial communities in sewage treatment plants for public health monitoring

Environ Pollut. 2025 Jun 15:375:126367. doi: 10.1016/j.envpol.2025.126367. Epub 2025 May 2.

Authors

Abhishek Keer¹, Yukti Oza¹, Dattatray Mongad¹, Dinesh Ramakrishnan², Dhiraj Dhotre¹, Abdelfattah Ahmed², Alimuddin Zumla³, Yogesh Shouche¹, Avinash Sharma⁴

Affiliations

¹ BRIC- National Centre for Cell Science, Pune, 411007, India.
² Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469, Potsdam, Germany.
³ Department of Infection, Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, Gower Street, London, WC1E 6BT, UK.
⁴ BRIC- National Centre for Cell Science, Pune, 411007, India. Electronic address: avinash@nccs.res.in.

PMID: 40320120
DOI: 10.1016/j.envpol.2025.126367

Abstract

The spread of antimicrobial resistance (AMR) around the globe, especially in the urban cities with high population, is a major concern. Therefore, the current study aims at identifying antibiotic resistant bacteria, microbial community compositions and the quantification of antimicrobial resistant genes from six sewage treatment plants (STPs) across Pune city in Maharashtra, India. A total of 106 isolates obtained were tested against six antibiotics in which the highest resistance was observed against trimethoprim (24.53 %). The qPCR assays of seven antibiotic resistance genes revealed abundance of bla_imp-1 and mecA genes in the summer and monsoon seasons followed by bla_NDM-1 gene in the summer and winter seasons. The alpha diversity indices depicted highest microbial diversity of inlet samples during winter, followed by inlet samples during the summer and monsoon seasons. Comparative analysis revealed Bifidobacterium (51 %), Pseudomonas (28.7 %) and Zoogloea (17.6 %) as the most abundant genera in the inlet samples during the summer, monsoon and winter seasons respectively while Acinetobacter (31 %) and Flavobacterium (23 % in winter and 18.2 % in summer) dominated the outlet samples. The co-network analysis revealed positive and negative interactions in the winter and monsoon but only positive interactions in the summer season. Venn diagrams showed higher abundance of ASVs in the outlet samples than the inlet. The top genera correlated exactly opposite with the pH compared to BOD and COD. PICRUSt2-based functional prediction revealed a higher abundance of methicillin resistance, β-lactamase resistance and multidrug resistance genes in inlet samples while chloramphenicol resistance was found higher in outlet samples. Further, we observed that potential pathogens causing infectious disease such as pertussis, shigellosis and tuberculosis were present in all three seasons.

Keywords: 16S rRNA gene sequencing; Antibiotic resistance; Seasonal variation; Sewage treatment plants; qPCR.

MeSH terms

Anti-Bacterial Agents
Bacteria / genetics
Drug Resistance, Bacterial* / genetics
Drug Resistance, Microbial* / genetics
Environmental Monitoring*
Genes, Bacterial
India
Microbiota
Public Health
Seasons
Sewage* / microbiology

Substances

Sewage
Anti-Bacterial Agents