Identification of integrons and phylogenetic groups of drug-resistant Escherichia coli from broiler carcasses in China

• We investigated antibiotic resistance and integrons in phylogenetic groups of E. coli strains from broiler carcasses.
• The prevalence of class 1 and 2 integrons and their gene cassettes in the drug-resistant E. coli was characterized.
• It demonstrated that broiler products are potential sources of multi-drug resistant E. coli.

The dissemination of drug-resistant Escherichia coli in poultry products is becoming a public concern, as it endangers food security and human health. It is very common for E. coli to exhibit drug resistance in the poultry industry in China due to the excessive use of antibiotics. However, few studies have examined the drug resistance endowed by integrons and integron-associated gene cassettes in different phylogenetic groups of E. coli isolated from broiler carcasses. In this study, 373 antibiotic-resistant E. coli strains were isolated from the surfaces or insides of broiler carcasses from a slaughterhouse in Shandong Province, China. According to phylogenetic assays of chuA, yjaA, and an anonymous DNA fragment, TSPE4-C2, these isolates belong to four phylogenetic groups (A, B1, B2, and D) and seven subgroups (A0, A1, B1, B21, B22, D1, and D2). Of the tested isolates, 95.71% (n = 357) are multi-drug resistant, among which group B1 was predominant, accounting for 33.51% (n = 125) of the tested isolates. A high percentage of the E. coli isolates were resistant to amoxicillin–clavulanic acid (99.20%, n = 370), doxycycline (92.23%, n = 344), sulfamethoxazole–trimethoprim (90.88%, n = 339), ciprofloxacin, (64.61%, n = 241), sulbactam–cefoperazone (51.21%, n = 191), and amikacin (33.78%, n = 126). Furthermore, among the 373 isolates, class 1 and 2 integrons were identified in 292 (78.28%) and 49 (13.14%) of the isolates, respectively, while no class 3 integrons were detected. The most prevalent gene cassette arrays were dfrA17–aadA5 and dfrA12–orfF–aadA2 in the variable region of class 1 integrons, while only one gene cassette array (dfrA1–sat2–aadA1) was detected in the variable region of class 2 integrons. Class 1 integrons were distributed in various physiological subtypes, whereas no predominant phylogenetic groups could be identified. The presence of class 2 integrons in the B21 subtype was significantly higher than in the other subtypes, and it coexisted with the class 1 integron. This study suggests that broiler products are potential sources of multi-drug resistant E. coli, and that resistance genes could be spread by lateral gene transfer.