Genomic evidence of clinically relevant antimicrobial resistance genes and mobile plasmids in wastewater-associated environmental bacteria
TL;DR
This study provides genome-level baseline evidence that wastewater-associated, non-clinical Gram-negative bacteria in Namibia harbor clinically relevant AMR determinants, reinforcing the value of wastewater-based genomic surveillance for understanding environmental AMR dissemination, and emphasizing the public health implications of wastewater reuse.
Abstract
Wastewater treatment plants (WWTPs) are increasingly recognized as environmental reservoirs for antimicrobial resistance (AMR), yet genome-level data on non-clinical Gram-negative bacteria in wastewater remain scarce in many low- and middle-income settings. This study characterized the resistome, plasmid content, and genetic diversity of environmentally associated Gram-negative bacteria recovered from wastewater systems to elucidate their contribution to environmental AMR persistence. Influent and effluent samples (n = 30) were collected from three wastewater treatment plants. Sixteen Gram-negative isolates were recovered and identified using the VITEK system and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Antimicrobial susceptibility testing was performed phenotypically, followed by whole-genome sequencing and bioinformatic analyses to identify antimicrobial resistance genes (ARGs), plasmid replicons, virulence-associated genes, and sequence types.The isolates comprised of Enterobacter cloacae (n = 5), Raoultella planticola (n = 3), Raoultella ornithinolytica (n = 3), Citrobacter freundii (n = 3), and Aeromonas spp . (n = 2). Multidrug resistance was observed phenotypically across influent and effluent samples. Genomic analysis identified clinically relevant ARGs, including bla ACT , bla CTX-M-15 , bla CMY , qnr variants, fosA , aadA , sul1 , and tet genes, frequently associated with IncF, IncQ, IncL/M, and Col-type plasmids and virulent determinants including yersiniabactin and enterobactin . Resistance and plasmid profiles persisted in effluent-derived isolates, suggesting environmental persistence and potential transmission.This study provides genome-level baseline evidence that wastewater-associated, non-clinical Gram-negative bacteria in Namibia harbor clinically relevant AMR determinants, reinforcing the value of wastewater-based genomic surveillance for understanding environmental AMR dissemination, and emphasizing the public health implications of wastewater reuse.