Genomic characterization of virulence and disinfectant resistant determinants in multidrug-resistant Escherichia coli and Klebsiella pneumoniae from urban wastewater treatment plants in Windhoek, Namibia

Abstract

Aim This cross-sectional study characterized virulence factors, disinfectant resistance genes, and antimicrobial resistance determinants in multidrug-resistant Escherichia coli and Klebsiella pneumoniae from four urban wastewater treatment plants (WWTPs) in Windhoek, Namibia.Materials and methods Twenty-three isolates were identified using biochemical tests and MALDI-TOF, followed by antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS). Bioinformatic analyses assessed antimicrobial resistance genes (ARGs), virulence factors (VFs), disinfectant resistance genes (DRGs), sequence types, phylogenetic relationships, and co-occurrence with plasmid-associated sequences.Results High phenotypic resistance was observed to ampicillin (70%) and amoxicillin and cefuroxime (≥50%). WGS identified clinically important lineages, including E. coli ST410 and K. pneumoniae ST70, ST20, and ST219. Isolates harbored extended-spectrum β-lactamase genes, notably blaCTX-M-15, plasmid-mediated quinolone resistance determinants, and virulence genes associated with iron acquisition (yersiniabactin), adhesion, and capsule biosynthesis. Disinfectant resistance genes, including qacE, were also detected, with several resistance and virulence determinants co-occurring with plasmid-associated sequences. Phylogenetic analysis revealed close genetic relatedness among isolates from treated effluent, indicating persistence of clinically relevant lineages within wastewater systems.Conclusion Wastewater-based genomic surveillance provides an effective approach for characterizing AMR, virulence, and disinfectant resistance, supporting genome-informed surveillance and wastewater management in water-scarce settings.