Phenotypic and genomic characterization of antimicrobial resistance in Escherichia coli and Klebsiella spp. from livestock in Namibia

Abstract

Objectives Antimicrobial resistance (AMR) is a growing concern within the One Health framework. This study characterized AMR in Escherichia coli and Klebsiella spp. isolated from livestock fecal samples across commercial and communal farms in Namibia. Methods About 140 fecal samples were collected from cattle, sheep, and chickens on farms in Namibia. Isolates were identified using the VITEK® 2 system and MALDI-ToF mass spectrometry. Antimicrobial susceptibility testing was performed using the Kirby–Bauer disc diffusion method against nine antibiotics. Genomic DNA was extracted and subjected to whole-genome sequencing (WGS) using Illumina NextSeq 2000 platform. Results AMR genes were identified using ResFinder and Abricate, plasmid-associated replicons using plasmid analysis tools, and virulence-associated genes using VirulenceFinder. Phenotypic analyses showed resistance to β-lactams, tetracyclines, aminoglycosides, and fluoroquinolones among the tested isolates. WGS identified diverse resistance determinants and sequence types, including E. coli ST101 and ST1431, K. oxytoca ST2, and K. pneumoniae ST22. Multiple plasmid replicons were detected; however, their presence alone does not establish that individual resistance genes were plasmid-borne or that horizontal gene transfer occurred. Conclusions This study provides the first genomic evidence of livestock-associated AMR in Namibia, identifying resistance determinants and multidrug-resistant E. coli and Klebsiella spp. in the sampled livestock population. The findings provide baseline genomic data for AMR surveillance and support strengthened antimicrobial stewardship and One Health monitoring. The concurrent detection of chromosomal resistance-associated mutations and diverse plasmid replicons illustrates the complexity of resistance mechanisms, although the present short-read data do not establish the direct physical linkage of individual ARGs to plasmids. These findings highlight the need for coordinated surveillance across animal, human, and environmental health sectors in Namibia.