Computational modeling of a Novel CTX-M β-lactamase Escherichia coli isolated from Yogyakarta, Indonesia Using I-TASSER and SWISS-MODEL

Extended-spectrum β-lactamases (ESBLs), particularly those of the CTX-M family, play a critical role in mediating antibiotic resistance in Escherichia coli. While CTX-M variants have been widely reported in clinical isolates, their genetic and structural diversity in foodborne E. coli from Indonesia remains poorly characterized. To address this gap, a single E. coli isolate (D4DU2-ESBL-EC) was selected. Genomic DNA was extracted and sequenced to obtain the complete nucleotide sequence. Furthermore, a total of 23 reference sequences from all of the CTX-M variant groups in Enterobacteriaceae were selected from NCBI. Phylogenetic reconstruction was carried out with MEGA11, and haplotype network analysis was conducted with DnaSP. Additionally, amino acid sequence comparisons were performed to assess the novelty of the D4DU2-ESBL-EC isolate. Three-dimensional` (3D) structure modeling was generated using the C-I-TASSER (Iterative Threading ASSEmbly Refinement) server and SWISS-MODEL for comparison. Structural validation was performed using the Structure Validation Server (SAVES v6.1) and MolProbity. The phylogenetic and haplotype analyses revealed that D4DU2-ESBL-EC is evolutionarily closest to E. coli CTX-M-15 but carries two amino acid substitutions (W253L and P254A) located near the enzyme�s active site. This suggests a potentially novel CTX-M variant. The predicted 3D model exhibited high stereochemical quality, with 78.4 of residues in the most favored regions and 20.5 in allowed regions. Based on these findings, it can be concluded that E. coli D4DU2-ESBL-EC represents a new CTX-M variant isolated from foodborne samples in Yogyakarta, Indonesia, closely related to blaCTX-M-15 variants reported in India. © 2026 The Author(s).