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Globally, avian colibacillosis is a leading cause of morbidity and mortality in poultry, associated with economic losses and welfare problems. Here, clinical avian pathogenic  E. coli  isolates (CEC;  n  = 50) and faecal  E. coli  isolates from healthy (FEC;  n  = 187) Australian meat chickens collected between 2006 and 2014 were subjected to antimicrobial susceptibility testing, phylogenetic grouping, plasmid replicon (PR) typing, multilocus sequence typing, and virulence gene (VG) profiling. Extended-spectrum cephalosporin (ESC)- and fluoroquinolone (FQ)-resistant  E. coli  isolates underwent further genetic characterization. Significant proportions of CEC and FEC were, respectively, susceptible (13/50; 48/187) or MDR (9/50; 26/187) to 20 tested antimicrobials. Phylogenetic groups A and C, and PR types IncFIB and IncFrep were most represented. Five tested CEC-associated VGs were more prevalent in CEC (≥ 90%) than FEC (≤ 58%). Some isolates (CEC  n  = 3; FEC  n  = 7) were resistant to ESCs and/or FQs and possessed signature mutations in chromosomal FQ target genes and plasmid-mediated  qnrS ,  blaCMY-2 , and  blaDHA-1  genes. Sequence type 354 ( n  = 4), associated with extraintestinal infections in a broad range of hosts, was prevalent among ESC- and/or FQ-resistant FEC. This study confirmed existence of a small reservoir of ESC- and FQ-resistant  E. coli  in Australian commercial meat chickens despite absence of use in the industry of these drugs. Otherwise, diversity of VGs and PR types in both FEC and CEC populations was identified. We hypothesize that the source of ESC- and FQ-resistant  E. coli  is external to poultry production facilities. RESEARCH HIGHLIGHTSLow-level resistance to older and newer generation antimicrobial drugs detected.The most common sequence type (ST) associated with FQ resistance was ST354 (4/10).A small proportion of CEC ( n  = 3) and FEC ( n  = 7) were resistant to ESCs and/or FQs. Low-level resistance to older and newer generation antimicrobial drugs detected. The most common sequence type (ST) associated with FQ resistance was ST354 (4/10). A small proportion of CEC ( n  = 3) and FEC ( n  = 7) were resistant to ESCs and/or FQs.

avian pathology

Antimicrobial susceptibility, plasmid replicon typing, phylogenetic grouping, and virulence potential of avian pathogenic and faecal  Escherichia coli  isolated from meat chickens in Australia