The enigmatic etiology of sepsis underscores the vital need for rapid and accurate diagnostic methods. In this context, bacterial whole-genome sequencing (WGS) emerges as a powerful tool at the forefront of clinical microbiology, holding significant promise for enhanced sepsis management. Prompt detection and early initiation of antibiotic therapy are crucial for optimal patient outcomes. This study aimed to evaluate and compare the performance of two bioinformatic pipelines for analysing WGS data from clinical isolates associated with sepsis. The first approach employed an in-house developed pipeline, while the second utilized the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) pipeline. Predicted results from both pipelines were compared to clinically derived data. This study analyzes WGS data generated on Citrobacter isolates collected within a prospective sepsis study at Skaraborg Hospital, Sweden, using the Illumina HiSeq X platform. Phenotypic antimicrobial susceptibility testing (AST) and species identification for these isolates were previously performed using MALDI-TOF MS analysis, adhering to EUCAST guidelines. WGS data analysis commenced with quality control and trimming of FastQ files, followed by de novo assembly and quality assessment of the assembled contigs. Isolates with lower genome coverage were excluded from further analysis to maintain study consistency. Species identification comparing both phenotypic and genotypic methods demonstrated complete agreement between the methods. To evaluate the concordance for antimicrobial resistance (AMR) determination, the predicted genotypic resistance profiles were subsequently compared to the phenotypic AST results generated by the clinical laboratory. WGS revealed widespread beta-lactam resistance in Citrobacter isolates, supported by the identification of diverse resistance genes and plasmids associated with multidrug resistance. Interestingly the study identified the Yersinia pestis plasmid (IncFIIYp) in Citrobacter freundii isolates. The BV-BRC pipeline identified the prevalence of virulence genes encoding functionalities associated with adhesion, iron uptake via siderophores, immune system evasion, secretion system invasion, endotoxin, enterotoxin, and serum resistance. This study identified potentially novel Citrobacter sequence types alongside geographically widespread STs suggesting global circulation of these pathogens and highlighting the necessity for further characterization to elucidate their distribution and virulence.