Study reveals that antibiotic-resistant bacteria are still present in Indonesia’s egg production
- Dec 6, 2023
- 4 min read
Updated: Dec 8, 2023

A new study conducted by researchers at the Faculty of Veterinary Medicine Universitas Gadjah Mada in Indonesia found that Salmonella, a type of bacteria that causes illness and death worldwide, is present in eggs sold at supermarkets.
In total, the study tested 160 eggs collected from retail outlets and farms in Yogyakarta. A total of 87.5% of the eggs tested positive for Salmonella were resistant to oxytetracycline, an important antibiotic used for the treatment of various conditions, including relapsing fever, malaria, respiratory infection, and acne. Even more concerning, the study also found eggs with bacteria, on both shell and internally, that are resistant to several drugs which is called “multi-drug resistance.”
“We are deeply concerned about these findings, as they strongly suggest that the antibiotic-resistant bacteria are a result of irresponsible use of antibiotics. Eggs contaminated with Salmonella bacteria can make people sick if not well cooked or if they contaminate other surfaces and spread to other foods. Infections with drug-resistant Salmonella can be more severe and have higher rates of hospitalization and death,” said Aisah Nurul Fitri. Fitri is the Animal Welfare Manager at Act for Farmed Animals, a coalition between Indonesian animal protection organization Animal Friends Jogja and international NGO Sinergia Animal.
Drug-resistant bacteria are a major public health threat caused by the misuse of antibiotics and other antimicrobial medicines. At least 700,000 people die each year due to drug-resistant diseases.
According to the World Health Organization (WHO), animal agriculture accounts for up to 80% of the total use of medically important antibiotics in some countries. The WHO states that the misuse of antibiotics, which occurs at a large scale in factory farms, could lead to more deaths than cancer in the near future. A study published in The Lancet estimates that 4.95 million people died of diseases associated with antimicrobial resistance in 2019 alone. This number could rise to 10 million deaths annually by 2050 if the trend continues.
Factory farms, which are a major culprit of antibiotic misuse, are industrial facilities in which millions of animals are confined. Cramming large populations of animals at high densities in barren environments promotes the development of high levels of microbial disease. Further, confined animals are under chronic stress, which results in a weakened immune response and less natural protection against infection. “In these systems, healthy animals receive long-term low-dose antibiotics to prevent diseases. Such treatment facilitates the evolution of antibiotic-resistant ‘superbugs,’ which then circulate in the environment and infect other animals and humans,” explains Fitri.
The vast majority of laying hens in Indonesia are raised in battery cages, a very intensive egg-production system that confines several hens together in small wire or bamboo cages. Each hen spends her life in a space smaller than an A4 sheet of paper and cannot walk freely nor properly open her wings. The extreme confinement and lack of physical exercise commonly cause high frustration levels and painful bone fractures.
Battery cages can also be a risk to public health. The European Food Safety Authority (EFSA) has conducted the world’s largest study on this issue and concluded that cage systems have a higher prevalence of Salmonella than cage-free systems. According to the WHO, “non-typhoidal Salmonella spp. are estimated to cause 93.8 million cases of acute gastroenteritis and 155,000 deaths globally each year, approximately 85% of which are estimated to be foodborne.”
“It is time that egg producers and food companies in Indonesia move away from very intensive animal production systems that have higher rates of Salmonella contamination and that irresponsibly use long-term antibiotics,” says Fitri. “It is also time that Indonesia starts phasing out the use of battery cages, a cruel system that confines hens in tiny spaces where they can barely move and that deeply compromises their welfare.”
Act For Farmed Animals Coalition (AFFA), uses dialogues, negotiations, and awareness campaigns to push for cage-free commitments from major food companies in the country. Kerry Group, Ascott, Hokkaido Baby, Ismaya Group, and Potato Head are a few examples of Indonesian companies that have already committed to eliminating caged eggs from their supply chains.
Sinergia Animal works to promote healthy, sustainable food choices and to improve animal welfare in countries of the Global South, including in Indonesia.
The study “Antibiogram Profile of Salmonella Spp. and Antimicrobial Residue of Chicken Egg in Yogyakarta: Implication to Public Health” was published in the Indonesian Journal of Veterinary Sciences and conducted by drh. M. Th. Khrisdiana Putri, M.P., PhD (Staff at Faculty of Veterinary Medicine, Universitas Gadjah Mada). Sinergia Animal sponsored the study with the support of the Tiny Beam Fund.
Reasons for seeking a Tiny Beam Fund awards
Sinergia Animal recognizes that basing the animal protection movement on science increases its credibility, thereby also increasing the potential to leverage actions that will lessen animal suffering. Our campaigns and messaging are more trusted, and our progress is more effective if they are based on scientific and technical information. Instead of being seen only as an activist NGO, we also want to be seen as a science-based organization with a higher power to influence public opinion and more conservative stakeholders, such as mainstream media, government officials, and major food companies.
Seeking Award funds to sponsor academic research has therefore been essential to the organization’s missions of helping animals more effectively, using more accurate information, and avoiding exaggerations and misconceptions.
During the grant period, for example, we learned that many people in the countries where we offered animal welfare workshops (academics, producers, other NGOs, and industry stakeholders) are interested in animal welfare science. Many are willing to collaborate with us to strengthen the animal welfare movement and networking in their countries, and this grant was essential in facilitating such connections.










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This is such an important and unsettling piece. The findings underline how decisions made on farms and in supply chains don’t stay “on the farm” – they follow us right onto our plates and eventually into healthcare and HMS environments that are already under pressure from antibiotic-resistant infections. I really appreciate how you connect resistant bacteria in eggs with broader public‑health risks and the urgent need to rethink intensive production models, not just individual consumption choices. Work like this makes the case for stronger regulation, better welfare standards, and far more transparency for consumers in Indonesia and beyond.