Designing Antimicrobial Resistance Biosurveillance at the Ellinbank Smartfarm

Program snapshot

• Collaborated with Agriculture Victoria Research (AVR) on an environmental testing pilot at the Ellinbank Smartfarm

• Designed and implemented a comprehensive sampling approach across various sites at a dairy farm

• Used an enrichment-based metagenomic sequencing approach on collected samples to identify antimicrobial resistance (AMR) genes and circulating bacterial pathogens

Notable outcomes

• Designed a custom sampling approach for the Ellinbank Smartfarm

• Provided data on the volume and diversity of AMR genes across various sampling sites

• Established a proof-of-concept method for future AMR biosurveillance in large-scale agricultural settings

A Need for Agricultural Biosurveillance

The World Health Organization considers AMR to be “one of the top global public health and development threats.” In light of this, Agriculture Victoria Research (AVR)—an organization that sits under the state of Victoria’s government in Australia—sought to improve their diagnostic capability for detecting AMR genes and gain a better understanding of the prevalence of AMR in a dairy production system. They chose to partner with Concentric to run a pilot program at the Ellinbank Smartfarm, Australia’s leading dairy innovation facility.

Finding the Farm’s Pulse

Concentric’s team worked with AVR to set up a pilot environmental sampling program. Concentric and AVR visited the farm to identify optimal sampling sites (such as wastewater ponds, milk filters, weigh stations, and water and feeding troughs) and select sampling equipment that would provide optimal samples to represent the presence of AMR genes and bacterial pathogens on farm. After sample collection, an enrichment-based metagenomic sequencing approach was applied to pull out targeted bacterial pathogens and AMR genes present in those samples.

A Map for Biosecure Farming

With this collaboration, Concentric and AVR have created a model for future farm-based AMR biosurveillance. Using innovative enrichment sequencing and metagenomic analysis approaches on the samples collected, the pilot study has generated highly impactful data on the prevalence of AMR genes and bacterial pathogens across the Ellinbank Smartfarm that could be used to inform future antimicrobial use in the dairy herd. The pilot established the viability of this type of targeted, high-throughput metagenomic sequencing strategy for examining resistance patterns in a working dairy farm.