Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 18 4 2026 08 04 544 552 Conny Tjampakasari Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia Fithriyah Sjatha Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia Andi Yasmon Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia Agus Syahrurachman Department of Microbiology, School of Medicine and Health Sciences, Universitas Katolik Indonesia Atma Jaya, Jakarta, Indonesia Nadia Guntari Departement of Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia 2025 05 02 2026 07 08 Background and Objectives: Escherichia coli is the leading cause of urinary tract infections (UTIs) and has shown increasing resistance to trimethoprim–sulfamethoxazole (TMP-SMX). Resistance to TMP-SMX is commonly associated with the acquisition of resistance genes such as dfr and sul, often mediated by horizontal gene transfer. This study aimed to characterize the presence of dfr (dfrA1, dfrA5, dfrA7/17) and sul (sul1 and sul2) genes and to describe sequence variations in selected E. coli isolates. Materials and Methods: Urine culture samples were obtained from 678 patients suspected of having UTIs, and 21 samples yielded positive culture results. This study further analyzed 11 E. coli isolates, consisting of eight TMP-SMX-resistant isolates, two susceptible isolates, and one E. coli ATCC 25922 strain as a control. The clinical isolates were provided by the Clinical Microbiology Laboratory, Faculty of Medicine, Universitas Indonesia. PCR amplification and agarose gel electrophoresis were used to identify dfr and sul genes, followed by Sanger sequencing of selected amplicons. Sequence data were analyzed with BioEdit software and aligned against reference sequences from NCBI. Results: The distribution of resistance genes varies among resistant isolates. Some isolates carry the dfrA5 gene, while dfrA1 was detected in one isolate. The sul2 gene was present in a number of resistant isolates, while sul1 was identified but showed no differences from the reference sequence. Further sequence analysis revealed amino acid changes in the dfrA1, dfrA5, and sul2 genes, although these changes were not consistently found in all isolates. Conclusion: This study characterizes the distribution of dfr and sul genes and their sequence variations in a limited number of E. coli isolates. The results suggest that TMP-SMX-resistant isolates may contain diverse genetic determinants associated with resistance. Nevertheless, the limited isolate number restricts the broader interpretation of these findings. Larger-scale studies, supported by functional analyses, are required to determine the contribution of these genes and their sequence variations to antibiotic resistance. https://ijm.tums.ac.ir/index.php/ijm/article/view/5473 https://ijm.tums.ac.ir/index.php/ijm/article/download/5473/1914