Genomic characterization of ESBL-producing Escherichia coli isolates from patients in an orthopaedic ward in Mwanza, Tanzania.
- 1Department of Immunology and Molecular Biology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, P.O. Box 7072, Uganda.
- 2Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, P.O. Box 1464, Tanzania.
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are a major contributor to antimicrobial resistance (AMR) in healthcare settings, yet their genomic diversity and population structure remain poorly characterized in low-resource settings. Orthopaedic wards may facilitate persistence, acquisition, and possible onward spread of resistant organisms due to prolonged hospitalization, frequent antimicrobial exposure, and increased patient vulnerability. This study investigated the genomic characteristics of ESBL-producing E. coli recovered from hospitalized patients in an orthopaedic ward in Mwanza, Tanzania. We performed whole-genome sequencing and comparative genomic analysis of ESBL-confirmed E. coli isolates obtained from stool or rectal swabs of hospitalized patients. Sequence reads were quality controlled and assembled using standard pipelines. Core genome single nucleotide polymorphism (SNP) alignments were generated using Snippy, and recombination was identified and masked using Gubbins prior to phylogenetic reconstruction. Sequence types (STs), phylogroups, predicted serotypes, putative pathotype-associated marker profiles, AMR determinants, plasmid replicons, and virulence-associated genes were identified using established bioinformatics tools and databases. Phylogenetic analysis revealed a polyclonal population structure comprising multiple distinct lineages rather than a single outbreak clone. Several isolates formed low-SNP clusters compatible with recent shared ancestry, possible shared-source exposure, or localized circulation within the ward. The population included internationally recognized sequence types, including ST131, ST1193, ST69, ST617, and ST38. Phylogroup analysis showed a diverse distribution, with phylogroup A most common, followed by B1, B2, D, U/unassigned, C, F, and one cryptic lineage. ESBL production was predominantly associated with blaCTX-M-15, detected in most isolates, alongside additional resistance determinants to aminoglycosides, quinolones, sulfonamides, trimethoprim, and tetracyclines. IncF-family plasmid replicons predominated, with additional IncY plasmids identified. Virulence-associated genes, including fdeC and ybtP/ybtQ, were widely distributed. ESBL-producing E. coli in this orthopaedic ward represent a genomically diverse, multidrug-resistant population dominated by blaCTX-M-15-positive lineages. The coexistence of multiple lineages alongside low-SNP clusters suggests repeated introductions with possible localized circulation; however, genomic similarity alone cannot establish direct transmission. These findings highlight colonized patients as reservoirs of AMR and underscore the need to integrate genomic surveillance into infection prevention and control strategies in resource-constrained healthcare settings.
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BibTeX
@article{mboowa2026genomic,
title = {{Genomic characterization of ESBL-producing Escherichia coli isolates from patients in an orthopaedic ward in Mwanza, Tanzania.}},
author = {Gerald Mboowa and Benson R Kidenya and Ivan Sserwadda and Stephen Kanyerezi and Jeremiah Seni},
journal = {F1000Research},
year = {2026},
month = jun,
doi = {10.12688/f1000research.180294.2},
url = {https://europepmc.org/article/MED/42959011},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genomic characterization of ESBL-producing Escherichia coli isolates from patients in an orthopaedic ward in Mwanza, Tanzania.
AU - Gerald Mboowa
AU - Benson R Kidenya
AU - Ivan Sserwadda
AU - Stephen Kanyerezi
AU - Jeremiah Seni
PY - 2026
DA - 2026/06/25
JO - F1000Research
DO - 10.12688/f1000research.180294.2
UR - https://europepmc.org/article/MED/42959011
AB - Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are a major contributor to antimicrobial resistance (AMR) in healthcare settings, yet their genomic diversity and population structure remain poorly characterized in low-resource settings. Orthopaedic wards may facilitate persistence, acquisition, and possible onward spread of resistant organisms due to prolonged hospitalization, frequent antimicrobial exposure, and increased patient vulnerability. This study investigated the genomic characteristics of ESBL-producing E. coli recovered from hospitalized patients in an orthopaedic ward in Mwanza, Tanzania. We performed whole-genome sequencing and comparative genomic analysis of ESBL-confirmed E. coli isolates obtained from stool or rectal swabs of hospitalized patients. Sequence reads were quality controlled and assembled using standard pipelines. Core genome single nucleotide polymorphism (SNP) alignments were generated using Snippy, and recombination was identified and masked using Gubbins prior to phylogenetic reconstruction. Sequence types (STs), phylogroups, predicted serotypes, putative pathotype-associated marker profiles, AMR determinants, plasmid replicons, and virulence-associated genes were identified using established bioinformatics tools and databases. Phylogenetic analysis revealed a polyclonal population structure comprising multiple distinct lineages rather than a single outbreak clone. Several isolates formed low-SNP clusters compatible with recent shared ancestry, possible shared-source exposure, or localized circulation within the ward. The population included internationally recognized sequence types, including ST131, ST1193, ST69, ST617, and ST38. Phylogroup analysis showed a diverse distribution, with phylogroup A most common, followed by B1, B2, D, U/unassigned, C, F, and one cryptic lineage. ESBL production was predominantly associated with blaCTX-M-15, detected in most isolates, alongside additional resistance determinants to aminoglycosides, quinolones, sulfonamides, trimethoprim, and tetracyclines. IncF-family plasmid replicons predominated, with additional IncY plasmids identified. Virulence-associated genes, including fdeC and ybtP/ybtQ, were widely distributed. ESBL-producing E. coli in this orthopaedic ward represent a genomically diverse, multidrug-resistant population dominated by blaCTX-M-15-positive lineages. The coexistence of multiple lineages alongside low-SNP clusters suggests repeated introductions with possible localized circulation; however, genomic similarity alone cannot establish direct transmission. These findings highlight colonized patients as reservoirs of AMR and underscore the need to integrate genomic surveillance into infection prevention and control strategies in resource-constrained healthcare settings.
SN - 2046-1402
ER -