A national study confirms a low occurrence of antimicrobial resistance amongst Escherichia coli isolates from the caecae of Australian meat chickens

In meat chickens, Escherichia coli has been widely used as an indicator of overall carriage of antimicrobial resistance (AMR), with low levels of AMR found in Australia's 2016 national survey. This follow-up survey applied a high-throughput robotic antimicrobial-susceptibility platform to increase the probability of detecting rare but clinically significant forms of resistance, obtain higher-resolution prevalence estimates and assess possible temporal changes in amounts and types of resistance. Pooled caecal samples were collected at slaughter from 20 processing plants covering > 90% of Australian national chicken meat production. E. coli colonies were tested by broth micro-dilution against 14 antimicrobials and whole-genome sequencing was performed on all isolates that were clinically resistant to ciprofloxacin. Among 2,950 E. coli isolates, 56.8% were wild-type to every drug and all were susceptible to colistin and amikacin. Non-wild-type (NWT) rates were highest for tetracycline (23.3%, 95% CI 21.7-24.8%) and ampicillin (11.7%, 95% CI 10.5-12.9%); NWT prevalence for ciprofloxacin was 3.3% (2.6-4.0%, 95% CI 2.6-4.0%) but only 1.1% were resistant at the clinical breakpoint. Multi-class resistance was rare (2.9%). The genomes of 32 ciprofloxacin-resistant isolates were sequenced: 25 (78%) carried canonical gyrA/parC mutations and mainly clustered in two lineages, ST354 (n = 16) and ST752 (n = 9). When compared to contemporary European Union surveillance data, E. coli colonizing Australian meat-chickens continue to exhibit relatively low levels of resistance to first line and critically important antimicrobials. The stable but detectable presence of fluoroquinolone-resistant ST354 and ST752 underscores the need for regular large-scale, genomics-enabled surveillance.