{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:32:26Z","timestamp":1787027546281,"version":"build-2736575974"},"reference-count":63,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T00:00:00Z","timestamp":1750377600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Food and Agriculture Organization of the United Nations","award":["UNJP\/RAS\/399\/EC"],"award-info":[{"award-number":["UNJP\/RAS\/399\/EC"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: 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, the Indonesian Ministry of Agriculture, evaluated the costs and benefits of integrating the Nanopore MinION, Illumina MiSeq, and Sensititre system into a culture-based slaughterhouse\u2013river surveillance system. Methods: Water samples were collected from six chicken slaughterhouses and adjacent rivers (pre- and post-treatment effluent, upstream, and 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). Results: 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%. Conclusions: Cost\u2013benefit comparisons suggest sequencing can complement culture-based methods but is dependent on the value placed on the additional information gained.<\/jats:p>","DOI":"10.3390\/antibiotics14070624","type":"journal-article","created":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T03:05:27Z","timestamp":1750388727000},"page":"624","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Integrating Nanopore MinION Sequencing into National Animal Health AMR Surveillance Programs: An Indonesian Pilot Study of Chicken Slaughterhouse Effluent and Rivers"],"prefix":"10.3390","volume":"14","author":[{"given":"Rallya","family":"Telussa","sequence":"first","affiliation":[{"name":"FAO Country Office for Indonesia, Jakarta 10250, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4707-7577","authenticated-orcid":false,"given":"Puji","family":"Rahayu","sequence":"additional","affiliation":[{"name":"Quality Control and Animal Product Certification Laboratory, Ministry of Agriculture, Jakarta 12550, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thufeil","family":"Yunindika","sequence":"additional","affiliation":[{"name":"Quality Control and Animal Product Certification Laboratory, Ministry of Agriculture, Jakarta 12550, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8735-1190","authenticated-orcid":false,"given":"Curtis J.","family":"Kapsak","sequence":"additional","affiliation":[{"name":"Theiagen Genomics, Highlands Ranch, CO 80129, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kanti Puji","family":"Rahayu","sequence":"additional","affiliation":[{"name":"Quality Control and Animal Product Certification Laboratory, Ministry of Agriculture, Jakarta 12550, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oli","family":"Susanti","sequence":"additional","affiliation":[{"name":"Quality Control and Animal Product Certification Laboratory, Ministry of Agriculture, Jakarta 12550, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Imron","family":"Suandy","sequence":"additional","affiliation":[{"name":"Quality Control and Animal Product Certification Laboratory, Ministry of Agriculture, Jakarta 12550, Indonesia"},{"name":"Directorate Veterinary Public Health, Ministry of Agriculture, Jakarta 12550, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuraini","family":"Triwijayanti","sequence":"additional","affiliation":[{"name":"Directorate Veterinary Public Health, Ministry of Agriculture, Jakarta 12550, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aji B.","family":"Niasono","sequence":"additional","affiliation":[{"name":"Directorate Veterinary Public Health, Ministry of Agriculture, Jakarta 12550, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Syamsul","family":"Ma\u2019arif","sequence":"additional","affiliation":[{"name":"Directorate Veterinary Public Health, Ministry of Agriculture, Jakarta 12550, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hendra","family":"Wibawa","sequence":"additional","affiliation":[{"name":"Disease Investigation Center Wates, Ministry of Agriculture, Yogyakarta 55651, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lestari","family":"Lestari","sequence":"additional","affiliation":[{"name":"Disease Investigation Center Wates, Ministry of Agriculture, Yogyakarta 55651, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunawan B.","family":"Utomo","sequence":"additional","affiliation":[{"name":"FAO Country Office for Indonesia, Jakarta 10250, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Farida C.","family":"Zenal","sequence":"additional","affiliation":[{"name":"FAO Country Office for Indonesia, Jakarta 10250, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luuk","family":"Schoonman","sequence":"additional","affiliation":[{"name":"FAO Country Office for Indonesia, Jakarta 10250, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9541-1958","authenticated-orcid":false,"given":"Lee E.","family":"Voth-Gaeddert","sequence":"additional","affiliation":[{"name":"Center for Health Through Microbiomes, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA"},{"name":"Global Health Engineering, LLC, Saint Louis, MO 63116, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/nrmicro3439","article-title":"Tackling antibiotic resistance: The environmental framework","volume":"13","author":"Berendonk","year":"2015","journal-title":"Nat. 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