Surface water, including rivers, lakes, and waterfalls, which are closely linked to daily human activities, is highly vulnerable to microbial contamination, particularly by Escherichia coli. This article reviews the role of specific E. coli marker genes in surface waters, molecular detection methods, and target genes used for E. coli identification in such environments. The review was conducted by synthesizing recent literature on the genetic detection of E. coli in surface water environments, using keyword searches such as Escherichia coli, identification methods, surface water, molecular markers, virulence genes, PCR, and water contamination. E. coli exhibits remarkable genetic diversity, driven by exceptional adaptability and shaped by horizontal gene transfer and extensive genomic variation. Approaches to E. coli identification have evolved from traditional culture techniques to molecular and integrated methods. The presence and activity of E. coli in water are influenced by the expression of specific genes that enable accurate detection and identification. Detection of universal markers such as 16S rRNA is essential for rapidly confirming bacterial presence and identity before conducting more specific analyses. Molecular detection of E. coli pathotypes relies on genetic markers closely associated with their virulence traits, such as EHEC, ETEC, EPEC, EAEC, DAEC, and ExPEC, highlighting the role of surface waters as significant reservoirs for the dissemination of enteric pathogenic bacteria

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