Innovative Technology Enhances Antibiotic Resistance Surveillance in Indonesia

In a groundbreaking initiative aimed at combating the growing global crisis of antibiotic resistance, researchers from the Food and Agriculture Organization of the United Nations (FAO), Indonesia's Ministry of Agriculture, and Arizona State University (ASU) have successfully integrated a portable DNA sequencing device into the national antibiotic resistance surveillance system. This pilot project, conducted across six chicken slaughterhouses in the Greater Jakarta area, seeks to trace the transmission of drug-resistant E. coli, a critical indicator of antibiotic resistance, from agricultural settings to environmental waters.

Antibiotics have long been heralded as one of the greatest achievements in medical science; however, their overuse has led to the emergence of "superbugs"—pathogens that are resistant to standard treatments. In 2021 alone, antibiotic resistance was implicated in approximately 5 million deaths worldwide, a figure that is projected to double by 2050, according to a report by the World Health Organization (WHO) (WHO, 2021).

The study, published in the journal *Antibiotics* by R. Telussa and colleagues from the ASU Biodesign Institute, employed the MinION, a handheld nanopore DNA sequencing device capable of delivering laboratory-quality results in real-time at the point of sample collection. This innovation is particularly significant for Indonesia, an archipelago consisting of over 14,000 islands, where traditional laboratory testing faces logistical challenges.

"The MinION device allows for rapid analysis of genetic material without the need to transport samples to a laboratory, which is often impractical in remote areas," said Dr. Lee Voth-Gaeddert, a senior researcher at ASU and the study's lead author. The project found that antibiotic-resistant E. coli strains were prevalent in wastewater from slaughterhouses, with downstream river sites exhibiting higher resistance levels than upstream, indicating potential routes for resistance spread into the environment.

According to the Centers for Disease Control and Prevention (CDC), this strain of E. coli is a significant public health concern and serves as a proxy for tracking other dangerous resistant bacteria. The findings highlight the urgent need for enhanced surveillance and intervention strategies to mitigate the risks posed by antibiotic resistance.

The project revealed varying waste management practices among the slaughterhouses, with some employing treatment systems while others discharged untreated waste. The presence of antibiotic-resistant bacteria in both treated and untreated samples raises concerns about regulatory oversight and infrastructure efficacy. Researchers have noted that wastewater from agricultural, household, and healthcare sources significantly contributes to antibiotic contamination in rivers, particularly in Southeast Asia (Telussa et al., 2025).

The One Health approach, which underscores the interconnectedness of human, animal, and environmental health, is integral to addressing antibiotic resistance. Dr. Voth-Gaeddert emphasized the importance of broadening surveillance efforts, stating, "If we only use a narrow lens, we miss a lot of potential leverage points to control the spread of antibiotic resistance."

The implications of this research extend beyond Indonesia, as antibiotic resistance knows no borders. The successful application of the MinION device in this pilot project could pave the way for similar initiatives globally, enabling health authorities to respond more swiftly and effectively to microbial threats. The findings advocate for the integration of portable genomic technologies in national surveillance systems as a strategic move towards mitigating the antibiotic resistance crisis worldwide.

Future studies may expand the application of the MinION technology to track other pathogens, including avian influenza, thereby enhancing food safety and public health. As antibiotic resistance continues to escalate, adopting innovative surveillance methods will be crucial in safeguarding both human and environmental health.