High throughput robotics for the management and control of Antimicrobial resistance and endemic diseases in pigs

This project aimed to establish a high-throughput, fully automated robotic system to monitor and control antimicrobial resistance (AMR) and endemic bacterial diseases in Australian pigs. 

Using the Robotic Antimicrobial Susceptibility Platform (RASP), 30 pig herds nationwide were tested. A total of 77% of isolates were resistant to ampicillin and 79% to tetracycline. Multiclass resistance (MCR) was observed in 56.9% of isolates, with less than 1% showing resistance to critically important antimicrobials (CIAs). 

Pathogen-specific robotic workflows were developed and validated for Staphylococcus hyicus, Pasteurella multocida, Campylobacter coli, and Actinobacillus pleuropneumoniae (APP). The developed workflow had enabled an outbreak of S. hyicus associated with greasy pig disease to be investigated and confirmed.

Results showed that the S. hyicus isolates were 89% genetically identical. This had led to the development of a vaccine target strain to help with outbreak management.

Effluent testing was piloted on 26 farms to evaluate its utility for AMR surveillance. Effluent samples showed similar AMR patterns to individual animal samples, particularly for ampicillin, tetracycline, and ciprofloxacin-resistant E. coli. However, gentamicin-resistant isolates detected in faeces were not found in effluent. While promising, further optimisation is required to improve the sensitivity of this surveillance method.

This project has enabled the transition from semi-automated to fully automated AMR surveillance systems. The integration of robotics with high-resolution genomic tools has significantly improved diagnostic efficiency and scale, while reducing cost and labour. The outputs of this project directly support national surveillance objectives, current surveillance projects and provide tools for outbreak response, biosecurity, and the rational use of antimicrobials.

Value for producers

• Producers /veterinarians can assess if the pathogen(s) on their farm is resistant to certain antimicrobials and hence improve the treatment of sick pigs 
   

Key findings:

• E. coli surveillance data confirmed widespread resistance to ampicillin and tetracycline.
• Resistance to critically important antimicrobials (CIAs) such as cephalosporins and fluoroquinolones remained low.
• The RASP technology has been used successfully to investigate an outbreak of greasy pig disease due to Staphylococcus hyicus.
• Pasteurella multocida isolates collected between 2014 and 2019 revealed low overall resistance, with tetracycline being the most common resistance phenotype.
• The pilot study into effluent-based AMR detection demonstrated promising concordance with individual rectal sampling.