The global food supply plays a quiet yet critical role in how resistant bacteria spread. Australia remains in a strong position, with relatively low levels of resistance in food compared with many other countries. But data gaps and a lack of coordinated surveillance leave weak points in our defences.
To understand how resistance in food is monitored, managed and misunderstood, we spoke with Dr Stanley Chen, who is the former co-lead of the National Surveillance of Antimicrobial Resistant Bacteria in Retail Foods when working at the Food Standards Australia New Zealand (FSANZ). During that time, he also served as an Australia’s technical representative, working with the World Health Organization (WHO), Food and Agriculture Organization of the United Nations (FAO) and Asia-Pacific Economic Cooperation (APEC) countries on AMR and food safety. Dr Chen is currently the AgriFutures Chicken Meat Consortium Manager and an expert advisory consultant to the Investment of Climate Resilient Communities Program in the Indo-Pacific with the Department of Foreign Affairs and Trade (DFAT).
Drawing on his experience in both government and agricultural research, he sheds light on the misconceptions surrounding livestock production and explains changes that need to occur to safeguard Australia’s food safety and public health.
The food chain: An overlooked part of the AMR puzzle
Food sits where humans, animals and the environment meet: at the heart of what’s known as the One Health approach. Antibiotic use in people, animals or crops can put pressure on bacteria to develop antimicrobial resistance. Those resistant bacteria can then move within and between sectors: from animal to animal, farm to fork, through the environment, and back again.
Foodborne illness or ‘food poisoning’ is one of the most direct ways resistant bacteria can affect us. If resistant bacteria are present on food that isn’t cooked thoroughly enough to kill them, those bacteria can cause foodborne illness.
Eating food contaminated with common culprits such as Salmonella and Campylobacter bacteria may causes unpleasant, but usually short-term gastrointestinal illness, such as diarrhoea, cramps, vomiting and fever. For others, these infections can trigger long-term complications such as arthritis or kidney failure, and in rare cases, can be fatal.
AMR makes these infections harder to treat. If bacteria on food are resistant to the antibiotics normally used for treating infection, treatments may fail or require stronger, or more toxic, drugs and routine cases can become severe. Vulnerable people — older adults, young children, pregnant women, and those with weakened immunity — face increased risk of severe illness and death from these infections.
Proper cooking, handling and hygiene can prevent most foodborne pathogens that cause infections. Undercooked or cross-contaminated foods — which don’t kill bacteria — can allow bacteria possessing certain levels of AMR to enter the digestive system.
Once in the gut, they can share their genes, which confer resistance capabilities, with other microbes that naturally reside there through ‘horizontal gene transfer’, a process where bacteria swap DNA fragments.
Even after recovery from a resistant infection, those genes can remain in the gut, potentially influencing how future infections respond to antibiotics.
“It’s a twofold risk,” Chen explains. “One, you might get an infection that’s harder to treat. Two, resistant genes can establish in your gut microbiome, making future infections more difficult to manage.”
Many AMR infections affect both humans and animals and are treated with the same antibiotics. Monitoring and controlling AMR levels in bacteria transmitted via food has implications for the ability to successfully treat infections in humans.
How does Australia monitor and test for AMR in food?
Australia has made progress in understanding AMR in its food supply, but efforts remain sporadic.
The first nationwide AMR surveillance of retail meat began only recently, led by FSANZ, in 2022. Funded by the Department of Health, the National Surveillance of Antimicrobial Resistance in Retail Foods collected samples of chicken, beef and pork from across all states and territories. The report is anticipated to be released towards the end of 2025, and it is expected to reveal encouraging AMR data in Australia.
Scientists tested common bacteria that cause foodborne infections, Escherichia coli (E. coli), Salmonella, Campylobacter and Enterococcus, for resistance to key antibiotics that have human clinical significance, producing the first comprehensive national dataset since an earlier CSIRO project in 2007.
In contrast, other regions run continuous programs. The U.S, the Centre for Disease Control (CDC) operates National Antimicrobial Resistance Monitoring System (NARMS), which links data from people, retail meat and farm animals. In Europe, the European Food Safety Authority (EFSA) monitors AMR in food and animals across Europe and assisted by the Network for zoonoses monitoring data, which gathers and shares data on zoonotic diseases (those that can be transmitted to humans from animals).
Continuous surveillance to identify emerging trends or sudden outbreaks is critical. Without it, Australia risks missing early warning signs of emerging resistance.
“If we don’t have ongoing monitoring and evaluation, we will likely miss emerging infections until they are at a later stage, once they already have certain levels of resistance. But if we can get ahead of that curve and identify those potential risks early, we can act before that infection gets out of control.”
Currently, there is no nationally coordinated, continuous surveillance testing for resistant bacteria in food in Australia. State and territory agriculture departments regulate antimicrobial use in animals. Industry groups collect on-farm data testing during animal production in farms or at processing plants. However, these tests are not ongoing microbiological monitoring of AMR, nor are they integrated across the entire food chain.
“We can learn from the countries who have government-led, national programs tracking AMR across the entire food chain, from the farm to retail outlets, and link it with human clinical data for better public health outcomes.”
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Today, antimicrobials can only be used for animal health and disease management purposes in Australia when animals are sick under very strict vet practices and recording of use.
Dr Stanley Chen
Misconceptions about AMR and food
Few topics in food safety attract more confusion than how antibiotics are used in livestock. Australian consumers increasingly expect transparency about where their food comes from, how it is produced and whether it is safe.
One of the most persistent myths is that Australian farmers routinely use antibiotics to boost growth.
Australia has legislation that prohibits the use of antimicrobials as growth promoters in livestock industries. From as early as 1987, codes of practice for the responsible prescription of antibiotics have been in place. The chicken meat industry was the first to formally implement an antimicrobial stewardship (AMS) framework, which was followed by beef and pork. In Australia, antimicrobials that are important for human health and are of significant concern overseas are either not registered or banned for use in animals.
“Today, antimicrobials can only be used for animal health and disease management purposes in Australia when animals are sick under very strict vet practices and recording of use.”
More than 80% of E. coli found in Australian beef cattle are considered ‘wild-type’, meaning they have never been exposed to antibiotics. Pig production has slightly higher rates of resistance because pigs are more susceptible to respiratory and gut infections, which can require antibiotics, but usage remain closely controlled.
“Our livestock industries are often undervalued and under-appreciated for their commitment and effort to responsible antimicrobial use. They’ve worked hard to reduce reliance, improve biosecurity and invest in animal health.” Dr Chen.
This explains why Australia reports some of the lowest levels of AMR in food-producing animals anywhere in the world. But low risk doesn’t mean no risk, especially in a globalised food system.
Another myth is that AMR is caused by eating antibiotics in food. This is not true.
AMR is the capability that microbes have to withstand antibiotic treatment. It is bacteria’s natural ability to adapt and survive antibiotics, a process accelerated by antibiotic overuse in humans, animals and agriculture. Eating undercooked food can introduce bacteria with resistance to our guts.
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In the EU, resistance to fluoroquinolone (ciprofloxacin) is so high that the report states that it’s no longer recommended for treating Campylobacter infections in humans
Dr Stanley Chen
Australia leads the world in low AMR in food: a Campylobacter case study
Around the world, resistance levels in foodborne microorganisms vary. Australia reports some of the lowest AMR levels in food.
One example is Campylobacter, the leading cause of foodborne bacterial infection in humans worldwide. Campylobacter can be transmitted between and within animals and humans.
Anyone who has had a Campylobacter infection — like I have — will tell you that it can be awful. I needed three rounds of antibiotics over a month of misery to treat it.
Australia has one of the highest rates of Campylobacter infections of industrialised countries, with 147 reported cases per 100,000 people in 2024[1]. Campylobacter costs Australia an estimated $368 million annually[2].
The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2022–2023 recently reported extremely high rates of resistance to the antibiotic fluoroquinolone in Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli)[3]with human and animal origin. Ciprofloxacin, a type of fluoroquinolone, is used for treating Campylobacter infections in humans but its effectiveness is declining due to widespread resistance.
It showed that resistance to ciprofloxacin in C. coli isolates ranged from 54.3% in pigs to 84.1% in turkeys, and resistance in C. jejuni isolates in poultry ranged from 70.9% in broilers to 78.1% in turkeys. In humans, the overall resistance of ciprofloxacin in C. jejuni in the EU was 71.9%, ranging from 28% in Ireland to nearly 100% in Poland, Portugal, Cyprus and Lithuania. The overall resistance in C. coli was at a similar level (75%).
In Australia, the picture looks very different. The Australian Chicken Meat Federation’s 2022 survey found ciprofloxacin resistance in C. jejuni at 24% and in C. coli at just 2%[4]. Importantly, these findings suggest the Australian chicken meat industry’s AMS efforts to reduce and refine the use of antibiotics are successfully keeping the rates of AMR low. Studies show only 13.7% to 20.1% Campylobacter isolates in humans are resistant to ciprofloxacin in Australia.
“In the EU, resistance to fluoroquinolone (ciprofloxacin) is so high that the report states that it’s no longer recommended for treating Campylobacter infections in humans,” Chen says. “Across EU member states, resistance rates can range from 40% to almost 80%, and on an upward trend. In Australia, they’re a fraction of that.”
Genetic analysis revealed that resistant isolates carried mutations linked to globally circulating strains. This implies introduction from external sources rather than domestic misuse of antibiotics.
This highlights a key vulnerability. Imported foods can introduce resistant bacteria into local ecosystems in Australia. Even strong domestic controls cannot prevent resistant bacteria from arriving via trade or global supply chains.
A truly One Health approach would require a nationally coordinated system that links human, animal and environmental data.
Challenges to coordinated AMR surveillance in food
Australia’s livestock industries invest heavily in AMS, biosecurity and animal health. Yet because much of the data is industry-led and not nationally coordinated, it isn’t always shared across sectors. The absence of a centralised, continuous AMR monitoring program is both a scientific and policy gap.
“The biggest challenge is coordination,” Chen explains. “Each state and territory has its own food safety legislation, its own priorities and resources. Industry bodies collect valuable data, but it’s often siloed. Without a national-led coordination, we can’t integrate information from farm, processing plant and retail and compare the findings from the human health space.”
A truly One Health approach would require a nationally coordinated system that links human, animal and environmental data.
Another issue is the lack of standardised data collection and harmonised interpretation methods. Australia lacks data standardisation and integration. It needs to develop methods for sampling, testing and reporting AMR across the food chain that are aligned with human and environmental data.
“Before we can properly assess AMR risk in humans or animals,” Chen concludes, “we need a reliable, consistent way to collect and harmonised approach to interpret the data. Otherwise, our management plans and policies won’t be evidence-based.”
Dr Chen argues for reforming how antimicrobial usage is recorded and reported. Data harmonisation must consider differences in animal species, lifespan, body weight and production cycles. A kilogram of antibiotic used in chicken production (life cycle 4–6 weeks) cannot be equated with the same quantity used in cattle (life cycle 18–24 months). Nor should total antibiotic mass obscure the classes of drugs involved: the World Health Organization (WHO)’s AWaRe classification distinguishes between critically important, high, medium and low-priority antimicrobials. These categorisations must also be considered.
“Even when we do have data, comparing across species, sectors or time periods is extremely difficult,” he notes. “Different studies use different metrics — grams per kilogram, per biomass, per production cycle — so we end up comparing apples with oranges.”
Where to from here?
Australia’s low AMR rates are a major achievement, but they shouldn’t make us complacent. We face blind spots in how resistance is tracked across our food supply. Enhanced AMR surveillance would allow earlier detection of resistance trends, targeted interventions, and timely public health responses.
A truly One Health surveillance network would connect data from human health, agriculture, food safety and environmental monitoring. It would enable Australia to track resistance trends across the continuum, from farm and feed to processing plants, retail shelves and consumers.
Demonstrating low resistance levels backed by robust national data would strengthen public confidence and trust in Australian foods.
As resistant bacteria continue to evolve and global food systems grow more connected, Australia must strengthen its defences now to stay ahead. To meet this challenge, Australia needs to ensure that AMR surveillance efforts are standardised, measurable and integrated across the food chain.
Melissa Waine swapped Petri dishes for prose, transforming her love of science into compelling health and medical writing. She is passionate about antimicrobial resistance (AMR) and communicating the looming threat it will pose if we exhaust our supply of effective treatments.
[1] Australian Government Department of Health and Aged Care. National notifiable disease surveillance system—national communicable disease surveillance dashboard. 2025. Available from: https://nindss.health.gov.au/pbi-dashboard/ [Last accessed: Nov, 2025].
[2] Glass K, McLure A, Bourke S, et al. The cost of foodborne illness and its sequelae in Australia Circa 2019. Foodborne Pathog Dis2023;20(10):419–426;
[3] EFSA and ECDC (European Food Safety Authority and European Centre for Disease Prevention and Control), (2025). The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2022–2023. EFSA Journal, 23(3), e9237. https://doi.org/10.2903/j.efsa.2025.9237
[4] Australian Chicken Meat Federation. Surveillance for antimicrobial resistance in enteric commensals and pathogens in Australian meat chickens. Australia Chicken Meat Federation; 2022.
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