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Aim: To investigate the nucleotide sequences associated with transposable elements carrying bla CTX-M allelic variants as potential markers for the transmission of antimicrobial resistance genes between domestic animals, humans and the environment., Materials & Methods: We conducted whole-genome sequencing and analyzed the nucleotide sequences of most abundant bla CTX-M allelic variants (bla CTX-M-27 , bla CTX-M-55 , and bla CTX-M-65 ) in commensal Escherichia coli ( n  = 20) from household members in Quito and uropathogenic E. coli (UPEC) ( n  = 149) isolated from nine clinics in Quito, Ecuador., Results: The Ecuadorian commensal E. coli and UPEC displayed identical nucleotide sequences surrounding the bla CTX-M gene and the synteny was similar to those found in other parts of the world; however phylogenetic analysis indicated that the genetic environments in Ecuadorian isolates were unique., Conclusion: These findings suggest that the nucleotide sequences flanking the bla CTX-M genes may be useful for resolving ARG transmission pathways, especially inter-regional analyses.