Year: 2026
Type: article
Abstract: Background Antimicrobial resistance (AMR) is a major One Health challenge facilitated by the persistence and dissemination of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) across interconnected human, animal, and environmental compartments. Despite growing recognition of environmental reservoirs in AMR ecology, integrated resistome and mobilome studies across One Health interfaces remain limited in Africa. This study applied shotgun metagenomic sequencing to culture-derived pools of multidrug-resistant (MDR) E. coli to characterize resistome composition and mobilome signatures across human, animal, and environmental sources in uMgungundlovu District, South Africa Methods A total of 539 MDR E. coli isolates recovered from human, food-animal, wastewater, and other environmental sources were grouped into 20 source-specific pools. ARGs, plasmid-associated sequences, and MGE-associated sequences were annotated against the Comprehensive Antibiotic Resistance Database, ACLAME, and MetaStorm MGE database, respectively. Analyses included alpha diversity, Bray–Curtis dissimilarity, clustering, ordination, and permutational multivariate analysis of variance (PERMANOVA); MetaCompare prioritized pools using ARG–MGE–pathogen co-occurrence patterns. Results Across the 20 pools, 247 distinct ARGs were detected, of which 86 (35%) occurred in at least one pool from each of the three sectors. Antibiotic inactivation and target protection were the most highly represented resistance mechanisms. ARG richness, Shannon diversity, and Simpson diversity did not differ significantly among sectors. Hierarchical clustering and ordination demonstrated substantial cross-sector overlap and within-sector heterogeneity. Nevertheless, PERMANOVA identified a significant but modest association between source sector and resistome composition (pseudo-F = 1.585, R 2 = 0.157, p = 0.022), with no significant evidence of unequal multivariate dispersion ( F 2 , 17 = 2.498, p = 0.086). Of 1,012 plasmid-associated features, 713 (70%) occurred in at least one pool from each sector, while 232 of 975 MG E-associated features (24%) were shared. Exploratory random forest classification did not significantly outperform classification under permuted source labels ( p = 0.053). Conclusion These findings reveal modest sector-associated resistome structuring alongside substantial cross-sector overlap in ARG, plasmid-associated, and MGE-associated signatures. Although the pooled data do not establish direct transmission, active mobility, or physical ARG–MGE linkage, they identify shared resistome patterns and source groups that warrant targeted, isolate-resolved and linkage-aware investigation within integrated One Health surveillance.
Source: Frontiers in Bioinformatics
Language: English
Subfield: Microbiology (medical)
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $3,077
Awards: G5769975648, G6229225067
OpenAlex ID: W7223138206