Phylogeny, Antimicrobial Susceptibility Profile and Biosafety Implications of Novel Uropathogenic Bacterial Sequence Types Isolated from Catheter-Associated Urinary Tract Infections

Background Antimicrobial resistance (AMR) is a serious global health problem driven by antibiotic overuse and misuse in various parts, contributing to the emergence of resistant microorganisms. Catheter-associated urinary tract infections (CAUTIs) represent a predominant cause of healthcare-associated infections and are progressively complicated by antimicrobial resistance (AMR). In resource constrained settings like Basra, Iraq, the lack of region-specific genomic evidence exacerbates the risk of disseminating multidrug-resistant pathogens, posing significant biosecurity concerns. Objective This is the first study set in Basra city to establish the molecular and phylogenetic baseline for uropathogens in this region to enhance biosafety protocols and clinical outcomes. Methods A multicenter cross-sectional study was conducted on 140 catheterized ICU patients across five teaching hospitals in Basra, Iraq. Bacterial characterization was accomplished using standard microbiological methods and confirmed via 16S rRNA sequencing. Phylogeny was mapped using IQ-TREE and antimicrobial susceptibility testing was conducted using the VITEK 2 system according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Statistical associations were assessed using Chi square, Odds Ratio (OR), multivariate logistic regression analysis, One- Way ANOVA and Fisher’s exact tests. Results Significant bacteriuria was confirmed in 49.28% of cases. Klebsiella pneumoniae (21.7%) and Escherichia coli (18.8%) were the leading pathogens. Twelve novel sequence types (IQB001–IQB0012) were recognized and registered in GenBank. Statistical analysis revealed a “Symptom-Culture Gap,” where clinical symptoms were insufficient to anticipate infection (P >0.05), while strong association was observed between prolonged catheterization (>7 days) and infection risk. Alarmingly, phenotypic resistance profiling of the 12 novel sequence types revealed that resistance to carbapenems reached 80%, while cephalosporin resistance approached 100%, with tigecycline retaining the highest activity (60% susceptibility). Conclusion The emergence of novel, multidrug-resistant (MDR) sequence types in Basra’s ICUs emphasizes an urgent need for improved biosecurity surveillance. These findings provide a molecular blueprint for tracking the distribution of resistant genotypes. Employing genomic-based biosafety measures is crucial to mitigate the risk of regional outbreaks and to preserve the efficiency of last-resort antibiotics.