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Objectives: The aim of this study was to identify the prevalence of genes encoding resistance to three groups of antimicrobial agents in root canal samples from primary infection or post-treatment disease in Mexico., Methods: A total of 64 subjects requiring root canal treatment because of primary infection or post-treatment disease were enrolled in this cross-sectional analytical study. Root canal samples were obtained and DNA was isolated. Specific primers for six antimicrobial resistance genes (ARGs) and seven bacterial taxa (five genera and two species) were used. Student's t-test, χ 2 test and Fisher's exact test were applied where appropriate to detect statistical differences., Results: The bla TEM-1 , ermC and tetM genes were found more frequently in the post-treatment disease group compared with the primary infection group. The occurrence of assessed bacteria was similar in both groups, except for Enterococcus spp. and Porphyromonas endodontalis, which were found at a significantly higher frequency in the post-treatment disease group. It was observed that the post-treatment disease group harboured more ARGs. The most frequent ARG was tetW, whereas tetQ and cfxA were not detected in any case. With respect to bacterial taxa, Fusobacterium spp. was present in 100% of samples, whereas Porphyromonas gingivalis was not observed in any of the samples., Conclusions: At least one ARG was detected in all cases; moreover, 32.8% of samples were positive for four ARGs, 54.7% for three ARGs, 9.4% for two ARGs and only 3.1% for one ARG. This indicates a high prevalence and diversity of ARGs in these root canal samples., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)