{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T09:28:10Z","timestamp":1793525290102,"version":"4.5.0"},"reference-count":34,"publisher":"Elsevier BV","issue":"11","license":[{"start":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T00:00:00Z","timestamp":1793491200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T00:00:00Z","timestamp":1793491200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014455","name":"University of Tennessee, Knoxville","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014455","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100030824","name":"AgResearch, University of Tennessee","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100030824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009260","name":"Institute of Agriculture, University of Tennessee","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009260","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Food Protection"],"published-print":{"date-parts":[[2026,11]]},"DOI":"10.1016\/j.jfp.2026.100931","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T06:36:15Z","timestamp":1790231775000},"page":"100931","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Long-Read Metagenomic Characterization of the Microbial DNA and Resistome Recovered from a Peracetic Acid Immersion Chiller in a Commercial Poultry Processing Facility: A Pilot Study"],"prefix":"10.1016","volume":"89","author":[{"given":"Wei","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Beever","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sohyun","family":"Cho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6023-8561","authenticated-orcid":false,"given":"Xiang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jfp.2026.100931_b0005","doi-asserted-by":"crossref","first-page":"5575","DOI":"10.1099\/ijsem.0.001485","volume":"66","author":"Adeolu","year":"2016","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"10.1016\/j.jfp.2026.100931_b0010","doi-asserted-by":"crossref","DOI":"10.3389\/fvets.2025.1683110","article-title":"The final frontier: Using carcasses for one health surveillance at the ecosystem interface","volume":"12","author":"Barton","year":"2025","journal-title":"Frontiers in Veterinary Science"},{"key":"10.1016\/j.jfp.2026.100931_b0015","doi-asserted-by":"crossref","first-page":"448","DOI":"10.4315\/JFP-21-301","article-title":"Metagenomics approaches for improving food safety: A review","volume":"85","author":"Billington","year":"2022","journal-title":"Journal of Food Protection"},{"key":"10.1016\/j.jfp.2026.100931_b0020","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.4315\/JFP-22-123","article-title":"Peroxyacetic acid effectiveness against Salmonella on raw poultry parts is not affected by organic matter","volume":"85","author":"Cano","year":"2022","journal-title":"Journal of Food Protection"},{"key":"10.1016\/j.jfp.2026.100931_b0025","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Molecular Biology and Evolution"},{"key":"10.1016\/j.jfp.2026.100931_b0030","doi-asserted-by":"crossref","DOI":"10.1111\/1541-4337.70445","article-title":"Application of peracetic acid in poultry processing: Effects of treatment dynamics and emerging risk of resistance development in Salmonella spp.","volume":"25","author":"Chapagain","year":"2026","journal-title":"Comprehensive Reviews in Food Science and Food Safety"},{"key":"10.1016\/j.jfp.2026.100931_b0035","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: A toolkit to classify genomes with the Genome Taxonomy Database","volume":"36","author":"Chaumeil","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2026.100931_b0040","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","article-title":"CheckM2: A rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","volume":"20","author":"Chklovski","year":"2023","journal-title":"Nature Methods"},{"key":"10.1016\/j.jfp.2026.100931_b0045","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1016\/j.csbj.2021.02.020","article-title":"Nanopore sequencing and its application to the study of microbial communities","volume":"19","author":"Ciuffreda","year":"2021","journal-title":"Computational and Structural Biotechnology Journal"},{"key":"10.1016\/j.jfp.2026.100931_b0050","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1007\/s11274-025-04397-5","article-title":"Proteomic analysis reveals phage-driven metabolic shifts and biofilm disruption in methicillin-resistant S. aureus (MRSA)","volume":"41","author":"Dakheel","year":"2025","journal-title":"World Journal of Microbiology and Biotechnology"},{"key":"10.1016\/j.jfp.2026.100931_b0055","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.biochi.2017.09.016","article-title":"Functional efficiency of MerA protein among diverse mercury resistant bacteria for efficient use in bioremediation of inorganic mercury","volume":"142","author":"Dash","year":"2017","journal-title":"Biochimie"},{"key":"10.1016\/j.jfp.2026.100931_b0060","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad311","article-title":"NanoPack2: Population-scale evaluation of long-read sequencing data","volume":"39","author":"De Coster","year":"2023","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2026.100931_b0065","doi-asserted-by":"crossref","DOI":"10.1016\/j.psj.2023.103003","article-title":"Peracetic acid application as an antimicrobial and its residual (HEDP): A holistic approach on the technological characteristics of chicken meat","volume":"102","author":"De Rezende","year":"2023","journal-title":"Poultry Science"},{"key":"10.1016\/j.jfp.2026.100931_b0070","doi-asserted-by":"crossref","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","article-title":"AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence","volume":"11","author":"Feldgarden","year":"2021","journal-title":"Scientific Reports"},{"key":"10.1016\/j.jfp.2026.100931_b0075","unstructured":"Food Safety and Inspection Service (FSIS), U.S. Department of Agriculture. (2024). Salmonella in not-ready-to-eat breaded stuffed chicken products. Final rule. Retrieved from: https:\/\/www.federalregister.gov\/. Accessed August 1, 2026."},{"key":"10.1016\/j.jfp.2026.100931_b0080","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2026.1724533","article-title":"From bioadsorption to biotransformation: A hypothesis for mercury bioremediation using genetically modified microalgae","volume":"17","author":"Hui","year":"2026","journal-title":"Frontiers in Microbiology"},{"key":"10.1016\/j.jfp.2026.100931_b0085","doi-asserted-by":"crossref","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"10.1016\/j.jfp.2026.100931_b0090","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nature Biotechnology"},{"key":"10.1016\/j.jfp.2026.100931_b0095","doi-asserted-by":"crossref","first-page":"e14","DOI":"10.1074\/jbc.O110.000237","article-title":"Mercury detoxification and natural product synthesis: The work of Christopher T. Walsh","volume":"285","author":"Kresge","year":"2010","journal-title":"Journal of Biological Chemistry"},{"key":"10.1016\/j.jfp.2026.100931_b0100","doi-asserted-by":"crossref","DOI":"10.1016\/j.psj.2023.103310","article-title":"Influence of peroxyacetic acid concentration, temperature, pH, and treatment time on antimicrobial efficacy against Salmonella on chicken wings","volume":"103","author":"Kroft","year":"2024","journal-title":"Poultry Science"},{"key":"10.1016\/j.jfp.2026.100931_b0105","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2026.100931_b0110","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2026.100931_b0115","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1128\/MMBR.63.3.507-522.1999","article-title":"Transposon Tn21, flagship of the floating genome","volume":"63","author":"Liebert","year":"1999","journal-title":"Microbiology and Molecular Biology Reviews"},{"key":"10.1016\/j.jfp.2026.100931_b0120","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.1038\/s41596-022-00738-y","article-title":"Metagenome analysis using the Kraken software suite","volume":"17","author":"Lu","year":"2022","journal-title":"Nature Protocols"},{"key":"10.1016\/j.jfp.2026.100931_b0125","doi-asserted-by":"crossref","first-page":"7046","DOI":"10.1128\/AEM.70.12.7046-7052.2004","article-title":"Diagnostic real-time PCR for detection of Salmonella in food","volume":"70","author":"Malorny","year":"2004","journal-title":"Applied and Environmental Microbiology"},{"key":"10.1016\/j.jfp.2026.100931_b0130","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1128\/AAC.45.4.1263-1270.2001","article-title":"Transposons Tn1696 and Tn21 and their integrons In4 and In2 have independent origins","volume":"45","author":"Partridge","year":"2001","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"10.1016\/j.jfp.2026.100931_b0135","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/s44259-025-00157-5","article-title":"The applications and advantages of nanopore sequencing in bacterial antimicrobial resistance surveillance and research","volume":"3","author":"Peng","year":"2025","journal-title":"npj Antimicrobials and Resistance"},{"key":"10.1016\/j.jfp.2026.100931_b0140","doi-asserted-by":"crossref","first-page":"2463","DOI":"10.1128\/JB.183.8.2463-2475.2001","article-title":"The alternative electron acceptor tetrathionate supports B12-dependent anaerobic growth of Salmonella enterica serovar Typhimurium on ethanolamine or 1,2-propanediol","volume":"183","author":"Price-Carter","year":"2001","journal-title":"Journal of Bacteriology"},{"key":"10.1016\/j.jfp.2026.100931_b0145","article-title":"Long-read sequencing revealed co-occurrence, host range, and potential mobility of antibiotic resistome in cow feces","volume":"118","author":"Qian","year":"2021","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/j.jfp.2026.100931_b0150","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02060-21","article-title":"TnCentral: a prokaryotic transposable element database and web portal for transposon analysis","volume":"12","author":"Ross","year":"2021","journal-title":"mBio"},{"key":"10.1016\/j.jfp.2026.100931_b0155","doi-asserted-by":"crossref","DOI":"10.1099\/mgen.0.000685","article-title":"Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microbial Genomics"},{"key":"10.1016\/j.jfp.2026.100931_b0160","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: A cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.jfp.2026.100931_b0165","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: Interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2026.100931_b0170","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biology"}],"container-title":["Journal of Food Protection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0362028X2600236X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0362028X2600236X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T08:34:30Z","timestamp":1793522070000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0362028X2600236X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,11]]},"references-count":34,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["S0362028X2600236X"],"URL":"https:\/\/doi.org\/10.1016\/j.jfp.2026.100931","relation":{},"ISSN":["0362-028X"],"issn-type":[{"value":"0362-028X","type":"print"}],"subject":[],"published":{"date-parts":[[2026,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Long-Read Metagenomic Characterization of the Microbial DNA and Resistome Recovered from a Peracetic Acid Immersion Chiller in a Commercial Poultry Processing Facility: A Pilot Study","name":"articletitle","label":"Article Title"},{"value":"Journal of Food Protection","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jfp.2026.100931","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc. on behalf of International Association for Food Protection.","name":"copyright","label":"Copyright"}],"article-number":"100931"}}