Whole-Genome Sequencing, Annotation and Phenotypic Taxonomic Confirmation of a Multidrug-Resistant Escherichia coli Strain Isolated from the Blood of a Sepsis Patient

Sepsis (blood stream infection) caused by multidrug-resistant (MDR) bacteria, particularly Escherichia coli , represents a significant global health threat due to high morbidity, mortality, and limited treatment options. E. coli , a major causative agent of bloodstream infections, has evolved highly virulent and MDR strains, which contribute to the increasing burden of antimicrobial resistance (AMR), complicating clinical management and reducing the efficacy of conventional antibiotic therapies. In this study, we characterised the genomic and phenotypic drug resistance mechanism of E. coli 266631E isolated from a sepsis patient, highlighting the negative implications of MDR E. coli in sepsis. Antimicrobial susceptibility testing and minimum inhibitory concentration analysis revealed resistance to multiple antibiotics, including amoxicillin, cefotaxime, ciprofloxacin, gentamicin, and tobramycin. Whole genome sequencing identified a broad array of AMR genes encoding resistance to various antibiotic classes, such as macrolides, fluoroquinolones, aminoglycosides, carbapenems, and cephalosporins. Notably, the CTX-M-15 gene, a key extended-spectrum β-lactamase determinant, was found in both the bacterial chromosome and an IncF-type plasmid, emphasizing the potential for horizontal gene transfer and rapid dissemination of resistance. Confirming the taxonomy of the novel and unidentified bacterial strain through querying its 16S rRNA sequence and genome in recognised bacterial taxonomic databases presented a challenge. The isolate showed genetic similarity to E. coli, E. fergusonii , and Shigella species despite their phenotypic differences and variations in their pathogenic traits. However, a simple phenotypic laboratory procedure, based on the biochemical and cultural differences among these bacteria in Coliform ChromoSelect Agar, confirmed the isolate as E. coli . This study underscores the critical importance of integrating phenotypic methods with genomic tools for the accurate identification of clinically significant bacteria. It also highlights the need for both phenotypic and genetic surveillance of key MDR variants in healthcare settings to enable timely, precise diagnosis and targeted treatment of life-threatening infections such as sepsis.