Antimicrobial Resistance in Escherichia coli from the Broiler Farm Environment, with Detection of SHV-12-Producing Isolates.

Antimicrobial resistance is an important One Health challenge that encompasses the human, animal, and environmental fields. A total of 111 Escherichia coli isolates previously recovered from manure ( n = 57) and indoor air ( n = 54) samples from a broiler farm were analyzed to determine their phenotypes and genotypes of antimicrobial resistance and integron characterization; in addition, plasmid replicon analysis and molecular typing were performed in extended-spectrum-beta-lactamase (ESBL) producer isolates. A multidrug-resistance phenotype was detected in 46.8% of the isolates, and the highest rates of resistance were found for ampicillin, trimethoprim-sulfamethoxazole, and tetracycline (>40%); moreover, 15 isolates (13.5%) showed susceptibility to all tested antibiotics. None of the isolates showed imipenem and/or cefoxitin resistance. Twenty-three of the one hundred and eleven E. coli isolates (20.7%) were ESBL producers and carried the bla SHV-12 gene; one of these isolates was recovered from the air, and the remaining 22 were from manure samples. Most of ESBL-positive isolates carried the cmlA ( n = 23), tet (A) ( n = 19), and aac (6') -Ib-cr ( n = 11) genes. The following genetic lineages were identified among the ESBL-producing isolates (sequence type-phylogroup-clonotype): ST770-E-CH116-552 ( n = 12), ST117-B2-CH45-97 ( n = 4), ST68-E-CH26-382/49 ( n = 3), ST68-E-CH26-49 ( n = 1), and ST10992-A/B1-CH11-23/41/580 ( n = 4); the latter two were detected for the first time in the poultry sector. At least two plasmid replicon types were detected in the ESBL-producing E. coli isolates, with IncF, IncF1B, IncK, and IncHI1 being the most frequently found. The following antimicrobial resistance genes were identified among the non-ESBL-producing isolates (number of isolates): bla TEM (58), aac (6')-Ib-cr (6), qnrS (2), aac (3)-II (2), cmlA (6), tet (A)/ tet (B) (22), and sul1/2/3 (51). Four different gene-cassette arrays were detected in the variable region of class 1 ( dfrA1-aadA1 , dfrA12-aadA2 , and dfrA12-orf-aadA2-cmlA ) and class 2 integrons ( sat2-aadA1-orfX ). This work reveals the worrying presence of antimicrobial-resistant E. coli in the broiler farm environment, with ESBL-producing isolates of SHV-12 type being extensively disseminated.