Whole-Genome Sequencing Reveals Temporal Trends in Antibiotic Resistance Genes in Escherichia coli Causing Pediatric Urinary Tract Infections in Central Vietnam

(1) Background: Pediatric urinary tract infections (UTIs) pose significant challenges due to drug-resistant <i>Escherichia coli</i> (<i>E. coli</i>) strains. This study utilizes whole-genome sequencing to analyze temporal trends in antibiotic resistance genes (ARGs) in clinical <i>E. coli</i> isolates from pediatric UTI cases in central Vietnam. (2) Methods: We conducted whole-genome sequencing on 71 <i>E. coli</i> isolates collected from pediatric UTI patients between 2018 and 2020. ARGs were identified, and their prevalence over time was analyzed. Statistical tests were used to correlate ARG presence with antibiotic resistance. (3) Results: Of the 47 <i>E. coli</i> isolates with complete data, 40 distinct ARGs were identified, with a median of 10 resistance genes per isolate. A significant increase in the total number of ARGs per isolate was observed over time, from an average of 8.88 before June 2019 to 11.63 after. Notably, the prevalence of the <i>aadA2</i> gene (aminoglycoside resistance) rose from 0% to 26.7%, and that of the <i>blaNDM-5</i> gene (beta-lactam and carbapenem resistance) increased from 0% to 23.3%. Key correlations include blaEC with cephalosporin resistance, <i>blaNDM-5</i> with carbapenem resistance, and <i>sul2</i> with sulfamethoxazole/trimethoprim resistance. (4) Conclusions: Whole-genome sequencing reveals complex and evolving antibiotic resistance patterns in pediatric <i>E. coli</i> UTIs in central Vietnam, with a marked increase in ARG prevalence over time. Continuous surveillance and targeted treatments are essential to address these trends. Understanding genetic foundations is crucial for effective intervention strategies.