Influence of bacterial morphotype on urine culture and molecular epidemiological differences in Escherichia coli harboring bacterial morphotype-induced urinary tract infections

Bacteria that adhere to epithelial cells, form intracellular bacterial communities (IBCs), or transition to filamentous forms are referred to as morphotype-positive bacteria. Escherichia coli (E. coli) with this morphotype plays a critical role in urinary tract infections (UTIs), yet its impact on urine culture outcomes and molecular epidemiological characteristics remains unclear. In this retrospective study, we assessed the effect of bacterial morphotype on urine culture results and investigated the molecular differences between E. coli strains with and without this morphotype, using PCR and whole genome sequencing (WGS). We observed that E. coli with the morphotype-positive phenotype frequently appeared in urine sediments, leading to fewer colony-forming units (CFUs) in culture and contributing to false-negative results. However, vortexing the urine samples significantly increased CFUs, improving culture sensitivity. Additionally, E. coli with the positive morphotype carried more adhesion-related virulence genes (VGs), with the majority belonging to phylogenetic group B2. Whole genome sequencing further revealed a broader array of virulence genes in these strains. Our findings demonstrate that vortexing is an effective method to enhance urine culture positivity by releasing intracellular bacteria, and that morphotype-positive E. coli harbors a diverse set of virulence factors, indicating their potential high pathogenicity. These results highlight the importance of detecting bacterial morphotypes in urine samples for accurate UTI diagnosis and emphasize the need for increased attention to these highly virulent strains. Uropathogenic Escherichia coli (UPEC) is widely acknowledged as the primary pathogen responsible for urinary tract infections (UTIs). Following adherence to the epithelium, UPEC undergoes periodic morphological changes, such as filamentation, which not only contribute to immune evasion but also lead to false-negative results. This study focuses on three transient stages of UPEC morphological changes: adherence to the epithelium, formation of intracellular bacterial communities (IBCs), and the presence of filamentous UPEC. Any one of these characteristics is acceptable to classify UPEC strains as morphotype-positive UPEC. This study reported the prevalence of UPEC with the bacterial morphotype and established a direct relationship between urine culture and bacterial morphotype. The molecular epidemiological distinctions were both revealed. These findings provide further evidence of the necessary for bacterial morphotype detection, and greater attention should be given to E. coli harboring this bacterial morphotype.