<![CDATA[ABSTRACT Background: Antimicrobial resistance mediated by the blaCTX-M gene in Escherichia coli represents a major global public health threat, while molecular epidemiological surveillance data from environmental sources in Indonesia remain highly limited. This is study aimed to analyze the molecular epidemiology of the blaCTX-M gene in environmental Escherichia coli isolates from Indonesia using a genomic surveillance approach based on publicly available genome data and Linux-based bioinformatics pipeline. Method: This quantitative descriptive study employed a comparative genomics and phylogenomic analysis design based on an in silico approach. The study included 86 Escherichia coli genome assemblies retrieved from the EnteroBase database using the selection criteria of Environment as the source niche and Indonesia as the country of origin. Data analysis was performed using QUAST, Prokka, AMRFinderPlus, ABRicate, MLST, Snippy, IQ-TREE, and FastTree on the Ubuntu 22.04 LTS operating system. Result: All isolates met the assembly quality criteria, and the analytical pipeline was validated using both positive and negative controls. Most isolates originated from water and river samples, with the highest number collected in 2019. The blaCTX-M subtypes were predominantly assigned to the CTX-M-1 group (88,2%), particularly CTX-M-15 and CTX-M-55, while resistome profiling revealed a multidrug-resistant pattern. Sequence type ST2 and ST471 were the most prevalent, and although the genomic population was highly heterogeneous, four clonal clusters were identified. Conclusion: These findings highlight the need for sustained deposition of environmental Escherichia coli genome data from Indonesia with more balanced temporal and geographic representation to strengthen the national One Health-based genomic surveillance system for antimicrobial resistance.]]>
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