Transnational flow of E. coli ST354 into Australian poultry

Surveillance programs for measuring antimicrobial resistance (AMR) in the microbiota of food animals have a targeted emphasis on commensal Escherichia coli. Traditionally, only a very small number of E. coli isolates (from 100 to 600 per animal class) are assessed nationally each year and this severely limits the evaluation of risks posed to public health. Here we demonstrate an affordable approach for early detection of emergence of resistance on a broad scale that can also accurately characterise spatial and temporal changes in resistance. We produce a high-resolution picture of the epidemiology of AMR across 10 meat chicken flocks in Australia. Data are based on thousands of commensal E. coli from faeces of 27 to 30 birds per flock obtained by combining high-throughput robotics and advancements in agar-dilution assays. Within and between flock carriage of resistance was shown to vary with drug class. Ampicillin and tetracycline resistance is ubiquitous in all or most birds in all flocks with an average carriage rate of 5.8 log10 CFU/g. Gentamicin and ciprofloxacin-resistant E. coli were present in only some flocks, with fewer birds colonised, and an average carriage rate of 1.2 log10 CFU/g and 1.0 log10 CFU/g of faeces respectively. Resistance to extended-spectrum cephalosporins was not detected. These data amply demonstrate the ineffectiveness of commonly relied-on approaches to AMR surveillance for achieving early detection of emergence, or for measuring temporal trends or spatial or temporal clustering of resistance. Genetic analysis suggested that there has been a transnational flow of a ciprofloxacin-resistant strain into these poultry flocks, explaining their detection in a nation that prohibits fluoroquinolone use in poultry.