Community and clinical resistomes and mobilomes: a comparative genomic snapshot of Escherichia coli and Klebsiella pneumoniae
5 affiliations
- 1Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- 2Department of Applied Biology and Biochemistry, National University of Science and Technology, AC939, Ascot, Bulawayo, Zimbabwe
- 3Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- 4Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa
- 5School of Pharmacy, University of Jordan, Amman, Jordan
Abstract
Escherichia coli and Klebsiella pneumoniae are major contributors to antimicrobial resistance (AMR)-related mortality globally. The resistomes, mobilomes, clonalities, and phylogenies of 32 E. coli (15 clinical, 17 community) and 14 K. pneumoniae (6 clinical, 8 community) isolates from KwaZulu-Natal were compared to ascertain similarities and differences between healthcare-related pathogens and community commensals using whole genome sequencing and bioinformatic pipelines. Resistome analysis revealed that blaCTX−M−15 predominated in clinical isolates of both E. coli and K. pneumoniae, whereas blaTEM−1B was more common in community E. coli. Two clinical E. coli harboured blaOXA−181, and one K. pneumoniae carried blaOXA−181 and blaNDM−5; none were detected in community isolates. IncF plasmid replicons were most frequent, and gene cassettes within class 1 integrons, insertion sequences, and transposons contributed to resistome mobilization across both settings. A broad range of sequence types (STs) were detected across both settings, with shared STs limited to ST131, ST10, and ST1193 in E. coli, and ST17 in K. pneumoniae. Phylogeny showed that clinical E. coli clustered with some community isolates, while K. pneumoniae showed limited clustering. The overlap of resistomes, mobilomes, STs and phylogenies suggests genomic relatedness between isolates from both settings, highlighting the importance of AMR surveillance in community settings.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-64511-x.
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BibTeX
@article{mahonisi2026community,
title = {{Community and clinical resistomes and mobilomes: a comparative genomic snapshot of Escherichia coli and Klebsiella pneumoniae}},
author = {Khanyisa Mahonisi and Joshua Mbanga and Arshad Ismail and Sabiha Y. Essack},
journal = {Scientific Reports},
year = {2026},
month = jul,
doi = {10.1038/s41598-026-64511-x},
url = {https://doi.org/10.1038/s41598-026-64511-x},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Community and clinical resistomes and mobilomes: a comparative genomic snapshot of Escherichia coli and Klebsiella pneumoniae
AU - Khanyisa Mahonisi
AU - Joshua Mbanga
AU - Arshad Ismail
AU - Sabiha Y. Essack
PY - 2026
DA - 2026/07/28
JO - Scientific Reports
DO - 10.1038/s41598-026-64511-x
UR - https://doi.org/10.1038/s41598-026-64511-x
AB - Escherichia coli and Klebsiella pneumoniae are major contributors to antimicrobial resistance (AMR)-related mortality globally. The resistomes, mobilomes, clonalities, and phylogenies of 32 E. coli (15 clinical, 17 community) and 14 K. pneumoniae (6 clinical, 8 community) isolates from KwaZulu-Natal were compared to ascertain similarities and differences between healthcare-related pathogens and community commensals using whole genome sequencing and bioinformatic pipelines. Resistome analysis revealed that blaCTX−M−15 predominated in clinical isolates of both E. coli and K. pneumoniae, whereas blaTEM−1B was more common in community E. coli. Two clinical E. coli harboured blaOXA−181, and one K. pneumoniae carried blaOXA−181 and blaNDM−5; none were detected in community isolates. IncF plasmid replicons were most frequent, and gene cassettes within class 1 integrons, insertion sequences, and transposons contributed to resistome mobilization across both settings. A broad range of sequence types (STs) were detected across both settings, with shared STs limited to ST131, ST10, and ST1193 in E. coli, and ST17 in K. pneumoniae. Phylogeny showed that clinical E. coli clustered with some community isolates, while K. pneumoniae showed limited clustering. The overlap of resistomes, mobilomes, STs and phylogenies suggests genomic relatedness between isolates from both settings, highlighting the importance of AMR surveillance in community settings. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-64511-x.
SN - 2045-2322
ER -