Managing environmental AMR risks across agribusiness ecosystems

Antimicrobial resistance (AMR) is a recognised problem in healthcare, but its reach extends far beyond hospitals, clinics and aged care homes. Understanding how AMR develops in the environment and is transmitted between our water, wastewater, animal and plant systems is a globally important One Health challenge.

University of South Australia (UniSA) researchers are now working with the South Australian Environment Protection Authority (SA EPA) and other SAAFE partners on a project to determine how AMR microbes survive and spread and how best to manage them.

“Wastewater is a key starting point for following the impacts of AMR determinants,” said project lead Professor Nick Ashbolt from UniSA.

AMR determinants include the AMR genes, the vectors (or organisms) carrying the genes, and chemical stressors like pharmaceuticals or disinfectants that encourage AMR to develop. The project team is assessing these determinants in environmental sources such as wastewater, farm runoff, manures, soils and receiving stream sediments. The goal is to see if management is needed and, if so, where. For example, should healthcare sewage be treated before it is discharged to the municipal sewer, or does that make no difference to AMR risks via water reuse?

More than 99.99% of antimicrobial-resistant bacterial pathogens are typically removed during wastewater treatment, but those that survive are more likely to be multidrug-resistant. What is possibly most important are the subset of those pathogens that can grow in the environment.

“What we're finding is that pathogens of concern – such as bacteria that are resistant to the last-line antimicrobial drugs used in healthcare settings – appear not to amplify in the sewer or through wastewater treatment. But other organisms are,” Nick said. The danger is that these unexpected organisms, many of which are close relatives of pathogens of concern, could become vectors that transmit AMR genes to pathogens.

Once treated, wastewater can enter rivers and streams, where people swim, fish and extract water for drinking and irrigation. “Our concern is that those organisms might emerge as pathogens downstream and disseminate through environmental exposure routes to humans (and animals or plants), resulting in loss of drug treatability,” Nick said.

The researchers are using quantitative microbial risk assessment to determine the probability of infection or illness. They combine data on a reference pathogen, exposure routes and concentrations, known responses to infection, and the additional health burden and increased likelihood of death from antimicrobial-resistant infections.

With this approach, the researchers can pinpoint the combinations of AMR genes, vectors and stressors that pose unacceptable risks. The next step is to ask where such risks might best be mitigated.

Working with experts from SA EPA and other SAAFE partners, the researchers have mapped out all the steps in wastewater treatment and downstream uses of recycled water, as well as the potential interactions between the AMR determinants at each step. With this information, they can model how different interventions – such as changing when or how wastewater is treated – affect AMR risk.

The project team will soon carry out an expert elicitation process with different stakeholder groups, such as government regulators, health departments and utility companies. This will identify which steps are in their jurisdiction and under their control and what it may cost to implement various control strategies. This could help each group identify the most effective strategies for reducing AMR risk.

The researchers are now refining their modelling using as much local data as possible. “It's important that we use data from Australia,” said Dr Claire Hayward, a SAAFE Foundation Fellow from UniSA. “We can then determine what gaps there are and work with the SAAFE Monitoring Program and our other research partners to get the types of data we need.”

Claire is also expanding the list of reference pathogens to include microbes that might be more relevant to the development of environmental AMR hotspots. She is particularly interested in species that can grow outside clinical settings, such as in water, sediments or soil. “Microbial communities in the soil, for example, may help these bacteria share resistance genes and protect them from the elements.”

The project team hopes to apply the same approach to animal and plant pathogens of concern to relevant sectors. “Our initial focus has been on human exposure,” said Nick, “but we plan to follow the same logic for other industries involved in SAAFE, such as animal production, viticulture and horticulture.”