A new pilot study demonstrates how portable DNA sequencing can support antimicrobial resistance (AMR) surveillance in settings where traditional lab infrastructure poses logistical challenges. Researchers from Arizona State University, Indonesia’s Ministry of Agriculture, and the Food and Agriculture Organization of the United Nations tested handheld nanopore sequencing at six poultry slaughterhouses around Jakarta. Samples from wastewater and nearby river sites were collected to assess whether Escherichia coli resistant to multiple antibiotics was present and spreading.
Using Oxford Nanopore’s MinION device, the team generated genetic data onsite. The approach allowed for real-time detection of resistance genes, virulence factors, and strain types with accuracy comparable to conventional lab-based methods. The study focused on a strain of E. coli listed by the CDC as a significant AMR threat and commonly used as a proxy for other resistant bacteria.
Most wastewater samples contained antibiotic-resistant E. coli, and downstream river sites mirrored these resistance patterns, unlike upstream sites. “This wasn’t overly surprising,” said lead author Lee Voth-Gaeddert of ASU’s Biodesign Center. “A lot of these slaughterhouses are positioned right next to rivers.”
The researchers observed inconsistent waste treatment practices across sites. Some facilities had systems in place, but resistant bacteria were still found regardless of treatment status. Many resistance genes were plasmid-borne, highlighting the potential for horizontal gene transfer.
In addition to pathogen detection, the study suggests portable sequencing tools could expand AMR monitoring to remote or underserved areas. “In certain settings, diarrhea isn’t just uncomfortable, it’s life-threatening,” Voth-Gaeddert said. The findings reinforce the need for integrated surveillance strategies that align with the One Health framework.
Publication Details
Telussa R, Rahayu P, Yunindika T, Kapsak CJ, Rahayu KP, Susanti O, Suandy I, Triwijayanti N, Niasono AB, Ma’arif S, et al. Integrating Nanopore MinION Sequencing into National Animal Health AMR Surveillance Programs: An Indonesian Pilot Study of Chicken Slaughterhouse Effluent and Rivers. Antibiotics. 2025; 14(7):624. https://doi.org/10.3390/antibiotics14070624
Using Oxford Nanopore’s MinION device, the team generated genetic data onsite. The approach allowed for real-time detection of resistance genes, virulence factors, and strain types with accuracy comparable to conventional lab-based methods. The study focused on a strain of E. coli listed by the CDC as a significant AMR threat and commonly used as a proxy for other resistant bacteria.
Most wastewater samples contained antibiotic-resistant E. coli, and downstream river sites mirrored these resistance patterns, unlike upstream sites. “This wasn’t overly surprising,” said lead author Lee Voth-Gaeddert of ASU’s Biodesign Center. “A lot of these slaughterhouses are positioned right next to rivers.”
The researchers observed inconsistent waste treatment practices across sites. Some facilities had systems in place, but resistant bacteria were still found regardless of treatment status. Many resistance genes were plasmid-borne, highlighting the potential for horizontal gene transfer.
In addition to pathogen detection, the study suggests portable sequencing tools could expand AMR monitoring to remote or underserved areas. “In certain settings, diarrhea isn’t just uncomfortable, it’s life-threatening,” Voth-Gaeddert said. The findings reinforce the need for integrated surveillance strategies that align with the One Health framework.
Publication Details
Telussa R, Rahayu P, Yunindika T, Kapsak CJ, Rahayu KP, Susanti O, Suandy I, Triwijayanti N, Niasono AB, Ma’arif S, et al. Integrating Nanopore MinION Sequencing into National Animal Health AMR Surveillance Programs: An Indonesian Pilot Study of Chicken Slaughterhouse Effluent and Rivers. Antibiotics. 2025; 14(7):624. https://doi.org/10.3390/antibiotics14070624