DOI: 10.12688/f1000research.180294.2 ISSN: 2046-1402

Genomic characterization of ESBL-producing Escherichia coli isolates from patients in an orthopaedic ward in Mwanza, Tanzania

Gerald Mboowa, Benson R Kidenya, Ivan Sserwadda, Stephen Kanyerezi, Jeremiah Seni
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Background 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. Methods 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. Results 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 bla CTX-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. Conclusions ESBL-producing E. coli in this orthopaedic ward represent a genomically diverse, multidrug-resistant population dominated by bla CTX-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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