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

Abstract

<ns3:p> Background Extended-spectrum β-lactamase (ESBL)-producing <ns3:italic>Escherichia coli</ns3:italic> 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 and transmission due to prolonged hospitalization, frequent antimicrobial exposure, and increased patient vulnerability. This study investigated the genomic characteristics of ESBL-producing <ns3:italic>E. coli</ns3:italic> recovered from hospitalized patients in an orthopaedic ward in Mwanza, Tanzania. Methods We performed whole-genome sequencing and comparative genomic analysis of ESBL-confirmed <ns3:italic>E. coli</ns3:italic> 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), 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 tight phylogenetic clusters within the ward, consistent with local circulation of closely related strains. The population included internationally recognized sequence types, including ST131, ST1193, ST69, ST617, and ST38. ESBL production was predominantly associated with <ns3:italic>bla</ns3:italic> <ns3:sub>CTX-M-15</ns3:sub> , 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 <ns3:italic>fdeC</ns3:italic> and <ns3:italic>ybtP/ybtQ</ns3:italic> , were widely distributed. Conclusions ESBL-producing <ns3:italic>E. coli</ns3:italic> in this orthopaedic ward represent a genomically diverse, multidrug-resistant population dominated by <ns3:italic>bla</ns3:italic> <ns3:sub>CTX-M-15</ns3:sub> -positive lineages. The coexistence of multiple lineages alongside closely related clusters suggests ongoing circulation of high-risk clones. 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. </ns3:p>