Integrating Nanopore MinION Sequencing into National Animal Health AMR Surveillance Programs: An Indonesian Pilot Study of Chicken Slaughterhouse Effluent and Rivers

Antimicrobial resistance (AMR) poses significant risks to human and animal health while the environment can contribute to its spread. National AMR surveillance programs are pivotal for assessing AMR prevalence, trends, and intervention outcomes, however, integrating advanced surveillance tools can be difficult. This pilot study, conducted by FAO ECTAD Indonesia and DGLAHS, Indonesian Ministry of Agriculture, evaluated the costs and benefits of integrating the Nanopore MinION, Illumina MiSeq, and Sensititre system into a culture-based slaughterhouse-river surveillance system. Water samples were collected from six chicken slaughterhouses and adjacent rivers (pre- and post-treatment effluent, upstream, downstream). Culture-based ESBL and general E. coli concentrations were estimated via the WHO Tricycle Protocol, while isolates (n=42) were sequenced (MinION, MiSeq) and antimicrobial susceptibility testing conducted (Sensititre). The Tricycle Protocol results provided estimates of effluent and river concentrations of ESBL and general E. coli identifying ESBL-to-general E. coli ratios of 13.8% and 6.2%, respectively. Compared to hybrid sequencing assemblies, MinION had a higher concordance than MiSeq for ARG identification (98%), virulence genes (96%), and locations for both (predominately plasmids). Furthermore, MinION concordance with Sensititre AST was 91%. Cost-benefit comparisons suggest sequencing can complement culture-based methods but is dependent on the value placed on the additional information gained. Highlights: This study demonstrates the integration of Nanopore MinION sequencing into a national AMR surveillance program, highlighting its potential for monitoring antibiotic-resistant E. coli in slaughterhouse effluent and rivers. Our findings show that Nanopore MinION sequencing exhibits high concordance with hybrid sequencing assemblies, validating its effectiveness for genomic surveillance in decentralized settings. The study evaluates the cost-benefit of using Nanopore MinION, Illumina MiSeq, and Sensititre AST, comparing information gained with cost. Graphical Abstract