Biology subjects

Sonkar, V.

Publications and source records attributed to Sonkar, V..

3 recordsLinked to original sources

bioRxiv2026

Contig-Resolved Genetic Context of Antimicrobial Resistome in Sediments of Two Contrasting Wastewater-Impacted Rivers

River sediments harbor diverse antimicrobial resistance (AMR) determinants; however, gene abundance alone provides limited insight into their genomic context, mobility potential, and associated bacterial hosts. This study employed an assembly- and read-mapping metagenomic framework to surface-sediment metagenomes (40.78 Gb clean data) from two contrasting wastewater-impacted Indian rivers, Adyar (Chennai) and Musi (Hyderabad), retaining sample-, contig- and open reading frame level provenance. ARG-carrying contigs (ACCs; n = 2,402) were annotated for mobile genetic elements (MGEs), biocide/metal resistance genes (BMRGs), virulence factor genes (VFGs), nitrogen-cycling genes (NCycGs), and putative host taxonomy. The resistomes exhibited substantial diversity (264 ARG subtypes) and spatial heterogeneity, with subtype richness in the Adyar (up to 171 subtypes) than in the Musi, where richness progressively declined downstream. Rank IV determinants dominated ARG abundance (77.82%), whereas Rank I determinants accounted for only 9.89%. MGEs were detected on just 3.12% (75/2,402) of ACCs, predominantly comprising plasmid-like contigs and proximal ARG-MGE associations. Co-occurrence with BMRGs was observed on 386 ACCs, whereas VFGs were uncommon (26 ACCs) and primarily represented dual-annotated efflux and envelope-integrity determinants rather than independent virulence loci. NCyc annotations were sparse (12 ACCs), with no evidence of complete nitrification or denitrification pathways. Taxonomic classification resolved 217 ACCs to the species level, with no matches to curated human pathogenic bacteria. Only two Acinetobacter-assigned ACCs exhibited both genus-level pathogenicity and mobility evidence. These findings highlight the importance of integrating mobility and host-taxonomic information to distinguish baseline environmental resistance from potential priorities for AMR surveillance.

genomics↗

bioRxiv2026

Rapid Antimicrobial Resistance Decline Coupled with Microbial Community Shifts in Sewage Polluted River Mesocosms

Antimicrobial resistance poses a global health threat, yet the fate of antimicrobial resistance genes (ARGs) and microbial communities from wastewaters in receiving rivers is rarely quantified. This study investigated the degradation kinetics of ARGs in sewage-polluted river water mesocosms and under sulfamethoxazole and copper stress, separately and in combination. Seven clinically relevant ARGs (blaCTX-M, blaNDM, qnrS, sul2, tetW, ermF, and aph(3'')-Ib), a mobile genetic element marker (intI1) and bacterial marker genes (uidA, 16S rDNA) were quantified by qPCR. Bacterial community changes were monitored using 16S rDNA amplicon sequencing. All target genes decayed with approximately first-order kinetics in all conditions, with qnrS (half-life: 8.0 h) and blaCTX-M (8.4 h) declining most rapidly and intI1 (32.5 h) and sul2 (46.5 h) declining most slowly. Ordination showed that ARG composition shifted primarily over time rather than by antibiotic/metal treatment. Bacterial communities shifted from initially Campylobacterota dominated ([≥] 90%) to Pseudomonadota, Bacillota, and Actinomycetota dominated communities over 168 h. Quantitative microbiome profiling showed a 95% reduction in ASV richness. PICRUSt2 analysis suggested progressive enrichment of aerobic and several metabolic pathways, as the mesocosms transitioned from highly polluted anoxic conditions to oxygenated conditions. Shifts in microbial community composition were coupled with changes in the resistome as identified by Procrustes analyses (r = 0.841, p = 0.001) and other analyses. Together, results show that river self-purification can rapidly reduce ARG loads, at least in warmer climates. This study provides approximate kinetic parameters for mathematical models to predict the fate of ARGs in rivers.

microbiology↗

bioRxiv2024

Field monitoring and hydraulic modelling quantify untreated wastewater as dominant source of AMR in a small river running through a big city

Quantifying sources of antimicrobial resistance (AMR) in rivers receiving various waste streams is essential for targeting mitigation strategies yet rarely performed. This study combined field monitoring with hydraulic modelling and mass balance calculations to attribute sources of AMR in the Musi River running through Hyderabad, India, a city renowned for pharmaceutical manufacturing. We quantified antibiotic resistance genes (ARGs), resistant bacteria (ARBs), and physicochemical parameters in water and sediment samples in the dry and wet season. Absolute ARG and ARB abundances spiked in the city, declining again downstream. Changes were more gradual in the wet season. Pollution levels were significantly different between upstream, city and downstream stretches and seasons. Hydraulic modelling revealed that 60-80% or 20-40% of the river water in the city derived from untreated sewage during the dry or wet seasons, respectively. This established municipal waste, not pharmaceutical sources, as the dominant driver of AMR in the Musi. Linear discriminant analysis identified dissolved oxygen and total nitrogen as reliable proxies for distinguishing AMR-polluted from less-polluted sites. The Musi, with insufficient wastewater treatment and limited dilution of point-source loadings, is typical for many urban rivers in resource-limited countries highlighting the urgent need for improved wastewater management to reduce AMR exposures.

microbiology↗