Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2023

Resistance is Futile: Technological Assimilation for Enhanced Surveillance of Antimicrobial Resistance in Food Animals (93953)

Alec AT Truswell 1 , Zheng Zhou Lee 1 , Marc Stegger 2 , John Blinco 1 , Rebecca Abraham 1 , David Jordan 1 , Marin Milotic 1 , Kylie Hewson 3 , Stanley Pang 1 , Sam Abraham 1
  1. Murdoch University, Murdoch, Western Australia
  2. Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
  3. Australian Chicken Meat Federation, Sydney, New South Wales

Standard surveillance of antimicrobial resistance (AMR) in commensal organisms from food animals assesses the proportion of isolates with phenotypic resistance to a comprehensive panel of drugs (1, 2). However, only a very small fraction of animals and isolates in the population are ever assessed leading to questions about adequacy for detecting emerging resistance and defining the distribution of resistance. This study draws on high-throughput robotics to demonstrate how the epidemiological relevance of surveillance can be boosted by examining more samples from more flocks and subjecting each sample to greater microbiological scrutiny through initial mass-screening to yield counts of resistant commensal per gram of sample, then combining this with genomic investigation of select isolates.

Caecal samples (n=295) from broiler chickens at slaughter were procured from ten flocks and processed via the robotic antimicrobial susceptibility platform (RASP) method (3). An optimised agar dilution method (4) was utilised for the initial mass screening and quantification of susceptible and non-susceptible E. coli (CFU/g) of samples using a combination of CHROMagar ECC and antimicrobial-infused CHROMagar plates (total number of plates = 5,310). Isolates identified as resistant to critically important antimicrobials proceeded to broth microdilution susceptibility testing for verification. A subset of these isolates representing unique phenotypes from each flock, were subjected to whole-genome sequencing (WGS) for genomic characterisation.

Ampicillin and tetracycline resistant E. coli were ubiquitous (mean log10 CFU/g 6.7 and 5.8 respectively). Ciprofloxacin and gentamicin resistant E. coli occurred in ten flocks and seven flocks respectively, and both at levels (mean log10 CFU/g 1.2 and 1.0 respectively) unlikely to be detected by standard surveillance. Fluoroquinolone resistant isolates (n=91) represented ten AMR phenotypes of which a WGS subset (n=28) revealed a dominant internationally disseminated sequence type ST354 (n=22), that appears to have been introduced to Australian poultry. The power of RASP was exemplified by the ability to distinguish patterns of distribution of resistance amongst commensal E.coli.

  1. 1. Food and Drug Administration (FDA). NARMS Now. Rockville, MD: U.S. Department of Health and Human Services. Available from URL: https://www.fda.gov/animal-veterinary/national-antimicrobial-resistance-monitoring-system/narms-now-integrated-data. Accessed 25/11/2022.
  2. 2. Duarte ASR, Høg BB, Korsgaard HB, Attauabi M, Boel J, Dalby T, et al. DANMAP 2020: Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark. 2021.
  3. 3. Truswell A, Abraham R, O’Dea M, Lee ZZ, Lee T, Laird T, et al. Robotic Antimicrobial Susceptibility Platform (RASP): a next-generation approach to One Health surveillance of antimicrobial resistance. J. Antimicrob. Chemother. 2021;76(7):1800-7.
  4. 4. Lee ZZ, Abraham R, O’Dea M, Harb A, Hunt K, Lee T, et al. Validation of Selective Agars for Detection and Quantification of Escherichia coli Strains Resistant to Critically Important Antimicrobials. Microbiol Spectr. 2021;9(3):e00664-21.