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The compost microcosm is a prime site for bacterial interaction that carries the inherent potential for disseminating antibiotic resistance through genetic exchange and subsequent land application. One hundred and thirty-six Escherichia coli isolates from compost heaps in South Carolina and California from a total of 277 compost samples were classified to phylogenetic groups, tested for resistance to 10 antibiotics, and screened for shiga toxins and integrons. Isolates that had identical antibiotic resistance patterns, grouped phylogenetically, and came from the same sample source were tested with pulsed-field gel electrophoresis. All isolates were negative for shiga toxins 1 and 2 as determined by polymerase chain reaction (PCR) assay. Resistance phenotypes comprised various combinations of seven antibiotics with a prevalence of ampicillin resistance in 63% of isolates (n = 56) from California, and tetracycline resistance in 37% of isolates (n = 62) from South Carolina. This disparity may be attributed to the differences in regional application of antibiotics as well as the origin of the waste materials in the compost itself. Phylogenetic PCR revealed that the majority of E. coli isolates (64%) belonged to groups A or B1. However, among these isolates, only 7% were resistant to two or more antibiotics as compared with 35% of isolates belonging to groups B2 and D. Integron detection by PCR revealed that nine (7.6%) E. coli isolates were positive for class I integrons, with six of the nine detected in isolates from groups B2 or D. Sequenced integrons (n = 5) were found to carry genes aadA, conferring reduced susceptibility to streptomycin, and dfrA, conferring resistance to trimethoprim. Our results suggest that E. coli isolates in compost belonging to phylogenetic groups B2 and D are more likely to contain integrons and higher levels of antibiotic resistance. The presence of multiple antibiotic resistances as well as integrons in E. coli implicates the potential for antibiotic resistance spread in the compost environment.