title: Genetic elements associated with antimicrobial resistance among avian pathogenic Escherichia coli.
abstract: BACKGROUND
  Avian-pathogenic Escherichia coli (APEC) are pathogenic strains of E. coli that are responsible for one of the most predominant bacterial disease affecting poultry worldwide called avian colibacillosis. This study describes the genetic determinants implicated in antimicrobial resistance among APEC isolated from different broiler farms in Egypt.
  
  
  METHODS
  A total of 116 APEC were investigated by serotyping, antimicrobial resistance patterns to 10 antimicrobials, and the genetic mechanisms underlying the antimicrobial-resistant phenotypes.
  
  
  RESULTS
  Antibiogram results showed that the highest resistance was observed for ampicillin, tetracycline, nalidixic acid, and chloramphenicol. The detected carriage rate of integron was 29.3% (34/116). Further characterization of gene cassettes revealed the presence gene cassettes encoding resistance to trimethoprim (dfrA1, dfrA5, dfrA7, dfrA12), streptomycin/spectinomycin (aadA1, aadA2, aadA5, aadA23), and streptothricin (sat2). To our knowledge, this the first description of the presence of aadA23 in APEC isolates. Analysis of other antimicrobial resistance types not associated with integrons revealed the predominance of resistance genes encoding resistance to tetracycline (tetA and tetB), ampicillin (blaTEM), chloramphenicol (cat1), kanamycin (aphA1), and sulphonamide (sul1 and sul2). Among ciprofloxacin-resistant isolates, the S83L mutation was the most frequently substitution observed in the quinolone resistance-determining region of gyrA (56.3%). The blaTEMand blaCTX-M-1genes were the most prevalent among APEC isolates producing extended-spectrum beta-lactamase (ESβL).
  
  
  CONCLUSIONS
  These findings provided important clues about the role of integron-mediated resistance genes together with other independent resistance genes and chromosomal mutations in shaping the epidemiology of antimicrobial resistance in E. coli isolates from poultry farms in Egypt.
authors.affiliation: Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt.
authors.forename: Amal
authors.initials: A
authors.lastname: Awad
authors.affiliation: Department of Poultry diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt.
authors.forename: Nagah
authors.initials: N
authors.lastname: Arafat
authors.affiliation: Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt. mm_elhadidy@mans.edu.eg.|Foodborne Pathogens, Scientific Institute of Public Health, Juliette Wytsmanstraat 14, 1050, Brussels, Belgium. mm_elhadidy@mans.edu.eg.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Elhadidy
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D002645:Chickens; D024881:Drug Resistance, Bacterial; D004926:Escherichia coli / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000382:microbiology / Q000662:veterinary*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D032023:Integrons; D011201:Poultry Diseases / Q000382:microbiology*
chemical_list: D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins
keywords: Antimicrobial resistance; E. coli; Genes; Integron; Poultry