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Peer-reviewedCC BY 4.0PLOS One

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

  • Loide N. Nangolo1
  • Agnetor Kakungu2
  • Sebastian Musundi3
  • Graça K. Kandanda4
  • Samuel Odoyo5
  • Agnes Oclu6
  • Justice Danso7
  • Beverly Egyir
  • Harris Onywera
  • George Githinji
  • Renatus Shilangale
  • Lamech M. Mwapagha
7 affiliations
  1. 1Department of Biology, Chemistry and Physics, Faculty of Health, Natural Resources and Applied Sciences, Namibia University of Science and Technology, Windhoek, Namibia
  2. 2Epidemiology and Demography Department, KEMRI-Wellcome Trust, Kilifi, Kenya
  3. 3Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
  4. 4Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
  5. 5Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
  6. 6Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
  7. 7Central Veterinary Laboratory, Windhoek, Namibia
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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.

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Cite

BibTeXRIS
BibTeX
@article{nangolo2026phenotypic,
  title = {{Phenotypic and genomic characterization of antimicrobial resistance in Escherichia coli and Klebsiella spp. from livestock in Namibia}},
  author = {Loide N. Nangolo and Agnetor Kakungu and Sebastian Musundi and Graça K. Kandanda and Samuel Odoyo and Agnes Oclu and Justice Danso and Beverly Egyir and Harris Onywera and George Githinji and Renatus Shilangale and Lamech M. Mwapagha},
  journal = {PLOS One},
  year = {2026},
  month = oct,
  doi = {10.1371/journal.pone.0359106},
  url = {https://doi.org/10.1371/journal.pone.0359106},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Phenotypic and genomic characterization of antimicrobial resistance in Escherichia coli and Klebsiella spp. from livestock in Namibia
AU  - Loide N. Nangolo
AU  - Agnetor Kakungu
AU  - Sebastian Musundi
AU  - Graça K. Kandanda
AU  - Samuel Odoyo
AU  - Agnes Oclu
AU  - Justice Danso
AU  - Beverly Egyir
AU  - Harris Onywera
AU  - George Githinji
AU  - Renatus Shilangale
AU  - Lamech M. Mwapagha
PY  - 2026
DA  - 2026/10/13
JO  - PLOS One
DO  - 10.1371/journal.pone.0359106
UR  - https://doi.org/10.1371/journal.pone.0359106
AB  - 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.
SN  - 1932-6203
ER  -