Genomic insights into cefotaxime-susceptible and cefotaxime-resistant Escherichia coli from urinary and bloodstream infections in the Czech Republic, with detailed characterization of ST404

Purpose Extraintestinal pathogenic Escherichia coli is a major cause of urinary tract infections (UTI), which may progress to bloodstream infections (BSI). While multidrug-resistant lineages represent a well-recognized clinical threat, antibiotic-susceptible lineages remain underexplored. We aimed to compare cefotaxime-susceptible (CTX-S; n = 359) and cefotaxime-resistant (CTX-R; n = 267) E. coli isolates from UTI and BSI in Czechia to assess their genome and phylogenetic context. Additionally, we investigated the global population structure of sequence type (ST) 404. Methods Totally, 626 isolates were randomly collected from nine hospitals in 2022–2023 and tested for antibiotic susceptibility. Whole-genome sequencing was performed to analyse mobile genetic elements (MGEs), antibiotic resistance (ARGs) and virulence-associated genes (VAGs), and phylogenetic backgrounds in UTI and BSI isolates. Results No significant differences were observed between BSI and UTI isolates. CTX-R lineages (predominantly ST131 and ST38) carried more ARGs while CTX-S isolates displayed greater ST diversity and less ARGs. ST404 frequently harbored various MGEs, particularly IncX1 plasmids and Tn 7 /Tn 3 -linked integrons; over 67% isolates contained pUTI89-like plasmids. Conclusion CTX-S and CTX-R lineages exhibit distinct genomic profiles, underscoring the importance of continued surveillance of both susceptible and resistant lineages. ST404 represents a lineage characterized by a high burden of diverse MGEs and potential epidemiological relevance.