{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:20:49Z","timestamp":1787026849112,"version":"build-2736575974"},"reference-count":74,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T00:00:00Z","timestamp":1757980800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Mapping reservoirs of antimicrobial resistance (AMR) across food value chains and their environmental dissemination pathways is essential for limiting the spread and impact of AMR. The aim of this study was to investigate the prevalence of AMR genes and bacteria in sidestream materials, waste discharges, and processing environments of salmon and broiler. A targeted hybrid capture-based sequencing approach was used to characterize the resistome in samples collected from four processing plants, revealing a diverse range of AMR genes. Among these, we found several high-risk AMR genes, including the multidrug resistance genes\n                    <jats:italic>TolC<\/jats:italic>\n                    and\n                    <jats:italic>mdtE<\/jats:italic>\n                    , tetracycline genes\n                    <jats:italic>tet(L)<\/jats:italic>\n                    and\n                    <jats:italic>tet(M)<\/jats:italic>\n                    , aminoglycoside genes\n                    <jats:italic>APH(3\u2032)-IIIa<\/jats:italic>\n                    and\n                    <jats:italic>APH(6)-Id<\/jats:italic>\n                    , and beta-lactam genes\n                    <jats:italic>mecA<\/jats:italic>\n                    and\n                    <jats:italic>mecR1<\/jats:italic>\n                    . Overall, the highest numbers of AMR genes were found in samples of process wastewater and sludge, ranging from 32 to 330 unique genes. More than 300 bacterial isolates, including Enterobacterales,\n                    <jats:italic>Enterococcus<\/jats:italic>\n                    and\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    spp. were also collected and identified, and a subset was tested for antibiotic susceptibility. Antibiotic resistance among\n                    <jats:italic>Enterococcus<\/jats:italic>\n                    and\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    spp. was low. Quinolone-resistant\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    (QREC) were detected in waste discharges from two broiler processing plants, while multidrug resistant (MDR)\n                    <jats:italic>E. coli<\/jats:italic>\n                    were found only in one plant. Whole genome sequencing of MDR isolates revealed multiple plasmids and AMR genes such as\n                    <jats:italic>sul2<\/jats:italic>\n                    ,\n                    <jats:italic>ant(3\u2033)-Ia<\/jats:italic>\n                    ,\n                    <jats:italic>qnrS1<\/jats:italic>\n                    , and\n                    <jats:italic>\n                      bla\n                      <jats:sub>CTX-M-1<\/jats:sub>\n                    <\/jats:italic>\n                    . Our study highlights that wastewater from food industries can contribute to the release of AMR bacteria and genes to the environment. While the prevalence of AMR bacteria in sidestream materials was low among the isolates in our collection, numerous AMR genes were detected, which may be re-introduced to new production systems.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2025.1662113","type":"journal-article","created":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T05:34:21Z","timestamp":1758000861000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Antimicrobial resistance reservoirs in salmon and broiler processing environments, sidestreams, and waste discharges"],"prefix":"10.3389","volume":"16","author":[{"given":"Thorben","family":"Reiche","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anita Nordeng","family":"Jakobsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mihai","family":"Mares","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sunniva","family":"Hoel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"T\u00f8ndervik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tonje Marita Bjerkan","family":"Heggeset","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tone","family":"Haugen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas Husby","family":"T\u00f8mmerdal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunn","family":"Broli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Husnain Amir","family":"Butt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iris Olene","family":"B\u00e5rdsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunhild","family":"Hageskal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,9,16]]},"reference":[{"key":"ref1","year":"2022"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1016\/j.aquaculture.2016.10.031","article-title":"The development of large scale aquaculture production: a comparison of the supply chains for chicken and salmon","volume":"493","author":"Asche","year":"2018","journal-title":"Aquaculture"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/s13059-024-03198-7","article-title":"Rapid and sensitive detection of genome contamination at scale with FCS-GX","volume":"25","author":"Astashyn","year":"2024","journal-title":"Genome Biol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"e0010023","DOI":"10.1128\/msphere.00100-23","article-title":"Highly sensitive detection of antimicrobial resistance genes in hospital wastewater using the multiplex hybrid capture target enrichment","volume":"8","author":"Baba","year":"2023","journal-title":"mSphere"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1111\/j.1472-765X.2009.02625.x","article-title":"Detection of metallo-\u03b2-lactamases-encoding genes in environmental isolates of Aeromonas hydrophila and Aeromonas jandaei","volume":"49","author":"Balsalobre","year":"2009","journal-title":"Lett. Appl. Microbiol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"5400","DOI":"10.1038\/s41467-021-25679-0","article-title":"Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae","volume":"12","author":"Bharatham","year":"2021","journal-title":"Nat. Commun."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"3488","DOI":"10.3390\/ani13223488","article-title":"Prevalence and antimicrobial resistance of Escherichia coli isolates from chicken meat in Romania","volume":"13","author":"Br\u0103tfelan","year":"2023","journal-title":"Animals (Basel)"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"e42724","DOI":"10.1371\/journal.pone.0042724","article-title":"Salmon aquaculture and antimicrobial resistance in the marine environment","volume":"7","author":"Buschmann","year":"2012","journal-title":"PLoS One"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"102392","DOI":"10.1016\/j.plasmid.2018.12.001","article-title":"Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in enterobacteriaceae","volume":"118","author":"Carattoli","year":"2021","journal-title":"Plasmid"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/aac.02412-14","article-title":"Plasmidfinder and pMLST: in silico detection and typing of plasmids","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-018-2336-6","article-title":"Rapid and precise alignment of raw reads against redundant databases with KMA","volume":"19","author":"Clausen","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1186\/s40168-021-01131-9","article-title":"Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity","volume":"9","author":"Cobo-D\u00edaz","year":"2021","journal-title":"Microbiome"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"e77302","DOI":"10.1371\/journal.pone.0077302","article-title":"PathogenFinder-distinguishing friend from foe using bacterial whole genome sequence data","volume":"8","author":"Cosentino","year":"2013","journal-title":"PLoS One"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1186\/s12864-022-08695-2","article-title":"Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence","volume":"23","author":"Daeschel","year":"2022","journal-title":"BMC Genomics"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"035","DOI":"10.3855\/jidc.4958","article-title":"Antibiotic susceptibility and prevalence of foodborne pathogens in poultry meat in Romania","volume":"9","author":"Dan","year":"2015","journal-title":"J. Infect. Dev. Ctries."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"e0179771","DOI":"10.1371\/journal.pone.0179771","article-title":"MRSA infections in Norway: a study of the temporal evolution, 2006-2015","volume":"12","author":"Di Ruscio","year":"2017","journal-title":"PLoS One"},{"key":"ref19","year":"2022"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1417","DOI":"10.1007\/s10096-025-05113-9","article-title":"Large DNA fragment ISEc9-mediated transposition during natural transformation allows interspecies dissemination of antimicrobial resistance genes","volume":"44","author":"Domingues","year":"2025","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"541972","DOI":"10.3389\/fmicb.2020.541972","article-title":"Metagenomic characterization of the microbiome and resistome of retail ground beef products","volume":"11","author":"Doster","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref22","year":"2023"},{"key":"ref23","year":"2022"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"e04872","DOI":"10.2903\/j.efsa.2017.4872","article-title":"ECDC\/EFSA\/EMA second joint report on the integrated analysis of the consumption of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals","volume":"15","year":"2017","journal-title":"EFSA J."},{"key":"ref25","year":"2020"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1007\/s12199-015-0468-0","article-title":"Understanding the contribution of environmental factors in the spread of antimicrobial resistance","volume":"20","author":"Fletcher","year":"2015","journal-title":"Environ. Health Prev. Med."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1881","DOI":"10.3389\/fmicb.2016.01881","article-title":"Antibiotic resistance in the food chain: a developing country-perspective","volume":"7","author":"Founou","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"120848","DOI":"10.1016\/j.envpol.2022.120848","article-title":"Prevalence and distribution of antimicrobial resistance in effluent wastewater from animal slaughter facilities: a systematic review","volume":"318","author":"Foyle","year":"2023","journal-title":"Environ. Pollut."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"100620","DOI":"10.1016\/j.gfs.2022.100620","article-title":"Aquaculture: the missing contributor in the food security agenda","volume":"32","author":"Garlock","year":"2022","journal-title":"Glob. Food Sec."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"516","DOI":"10.3389\/fvets.2020.00516","article-title":"Challenges to the poultry industry: current perspectives and strategic future after the COVID-19 outbreak","volume":"7","author":"Hafez","year":"2020","journal-title":"Front. Vet. Sci."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"8665","DOI":"10.1007\/s11356-019-04303-1","article-title":"Detecting antibiotic resistance genes and human potential pathogenic Bacteria in fishmeal by culture-independent method","volume":"26","author":"Han","year":"2019","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"109526","DOI":"10.1016\/j.foodcont.2022.109526","article-title":"Assessment of poultry process hygiene and bacterial dynamics along two broiler slaughter lines in Norway","volume":"146","author":"Hauge","year":"2023","journal-title":"Food Control"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1440","DOI":"10.3390\/antibiotics10121440","article-title":"Assessing the impact of heat treatment of food on antimicrobial resistance genes and their potential uptake by other bacteria\u2014a critical review","volume":"10","author":"James","year":"2021","journal-title":"Antibiotics"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1128\/jcm.03617-13","article-title":"Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli","volume":"52","author":"Joensen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"2410","DOI":"10.1128\/jcm.00008-15","article-title":"Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data","volume":"53","author":"Joensen","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder","volume":"76","author":"Johansson","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"e1004557","DOI":"10.1371\/journal.pcbi.1004557","article-title":"High-specificity targeted functional profiling in microbial communities with ShortBRED","volume":"11","author":"Kaminski","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.vetmic.2018.02.022","article-title":"Occurrence of quinolone resistant E. coli originating from different animal species in Norway","volume":"217","author":"Kaspersen","year":"2018","journal-title":"Vet. Microbiol."},{"key":"ref39","author":"Kassambara","year":"2025"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"e06651","DOI":"10.2903\/j.efsa.2021.6651","article-title":"Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain","volume":"19","author":"Koutsoumanis","year":"2021","journal-title":"EFSA J."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/jcm.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1380","DOI":"10.1111\/jam.14865","article-title":"Aeromonas spp. isolated from ready-to-eat seafood on the Norwegian market: prevalence, putative virulence factors and antimicrobial resistance","volume":"130","author":"Lee","year":"2021","journal-title":"J. Appl. Microbiol."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"1175304","DOI":"10.3389\/fmicb.2023.1175304","article-title":"Whole genome sequence analysis of Aeromonas spp. isolated from ready-to-eat seafood: antimicrobial resistance and virulence factors","volume":"14","author":"Lee","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"129261","DOI":"10.1016\/j.jhazmat.2022.129261","article-title":"Temporal variation of antibiotic resistome and pathogens in food waste during short-term storage","volume":"436","author":"Lin","year":"2022","journal-title":"J. Hazard. Mater."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"112715","DOI":"10.1016\/j.envres.2022.112715","article-title":"Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries","volume":"208","author":"Luiken","year":"2022","journal-title":"Environ. Res."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"10.1128\/jcm. 01269-01220","DOI":"10.1128\/jcm.01269-20","article-title":"In silico genotyping of Escherichia coli isolates for extraintestinal virulence genes by use of whole-genome sequencing data","volume":"58","author":"Malberg Tetzschner","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"103823","DOI":"10.1016\/j.fm.2021.103823","article-title":"The changing microbiome of poultry meat; from farm to fridge","volume":"99","author":"Marmion","year":"2021","journal-title":"Food Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"640923","DOI":"10.3389\/fmicb.2021.640923","article-title":"Biocide-induced emergence of antibiotic resistance in Escherichia coli","volume":"12","author":"Merchel","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"114842","DOI":"10.1016\/j.foodres.2024.114842","article-title":"Dynamics of microbiome and resistome in a poultry burger processing line","volume":"193","author":"Merino","year":"2024","journal-title":"Food Res. Int."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"1284","DOI":"10.3389\/fmicb.2018.01284","article-title":"Current status of the use of antibiotics and the antimicrobial resistance in the Chilean salmon farms","volume":"9","author":"Miranda","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis","volume":"399","author":"Murray","year":"2022","journal-title":"Lancet"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"52","DOI":"10.2527\/af.2013-0008","article-title":"The role of sustainable commercial pig and poultry breeding for food security","volume":"3","author":"Neeteson-van Nieuwenhoven","year":"2013","journal-title":"Animal Front."},{"key":"ref54","year":"2023"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"e1416","DOI":"10.1002\/vms3.1416","article-title":"Climate change and broiler production","volume":"10","author":"Oke","year":"2024","journal-title":"Vet. Med. Sci."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"739972","DOI":"10.1016\/j.aquaculture.2023.739972","article-title":"Production growth, company size, and concentration: the case of salmon","volume":"577","author":"Pandey","year":"2023","journal-title":"Aquaculture"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1186\/s12917-020-02407-2","article-title":"Genomic analysis of Escherichia coli strains isolated from diseased chicken in the Czech Republic","volume":"16","author":"Papouskova","year":"2020","journal-title":"BMC Vet. Res."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"110853","DOI":"10.1016\/j.ijfoodmicro.2024.110853","article-title":"Disinfection in a salmon processing plant: impact on bacterial communities and efficacy towards foodborne bacteria and biofilms","volume":"424","author":"Reiche","year":"2024","journal-title":"Int. J. Food Microbiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"e0240124","DOI":"10.1128\/aem.02401-24","article-title":"Shifts in surface microbiota after cleaning and disinfection in broiler processing plants: incomplete biofilm eradication revealed by robotic high-throughput screening","volume":"91","author":"Reiche","year":"2025","journal-title":"Appl. Environ. Microbiol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.3389\/fmicb.2017.01650","article-title":"Resistance to antibiotics, biocides, preservatives and metals in bacteria isolated from seafoods: co-selection of strains resistant or tolerant to different classes of compounds","volume":"8","author":"Romero","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"578","DOI":"10.3390\/antibiotics14060578","article-title":"Phenotypic and genotypic characterization of ESBL and AmpC \u03b2-lactamase-producing E. coli isolates from poultry in northwestern Romania","volume":"14","author":"Rus","year":"2025","journal-title":"Antibiotics"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"138788","DOI":"10.1016\/j.scitotenv.2020.138788","article-title":"Antibiotic-resistant bacteria and antimicrobial residues in wastewater and process water from German pig slaughterhouses and their receiving municipal wastewater treatment plants","volume":"727","author":"Savin","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1186\/s12866-024-03412-3","article-title":"Comparative genomics of quinolone-resistant Escherichia coli from broilers and humans in Norway","volume":"24","author":"Sletteme\u00e5s","year":"2024","journal-title":"BMC Microbiol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"1420","DOI":"10.3390\/microorganisms10071420","article-title":"Antibiotic resistance properties among Pseudomonas spp. associated with Salmon processing environments","volume":"10","author":"Thomassen","year":"2022","journal-title":"Microorganisms"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"fnu062","DOI":"10.1093\/femsle\/fnu062","article-title":"Draft genome sequence of the Chilean isolate Aeromonas salmonicida strain CBA100","volume":"362","author":"Valdes","year":"2015","journal-title":"FEMS Microbiol. Lett."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"119870","DOI":"10.1016\/j.envpol.2022.119870","article-title":"Distribution, sources, and potential risks of antibiotic resistance genes in wastewater treatment plant: a review","volume":"310","author":"Wang","year":"2022","journal-title":"Environ. Pollut."},{"key":"ref67","year":"2022"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1002\/wics.147","article-title":"ggplot2. WIREs Comp Stat","volume":"3","author":"Wickham","year":"2011"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1111\/j.1365-2958.2006.05172.x","article-title":"Sex and virulence in Escherichia coli: an evolutionary perspective","volume":"60","author":"Wirth","year":"2006","journal-title":"Mol. Microbiol."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"133811","DOI":"10.1016\/j.jhazmat.2024.133811","article-title":"Insights into microbial contamination and antibiotic resistome traits in pork wholesale market: an evaluation of the disinfection effect of sodium hypochlorite","volume":"468","author":"Xiao","year":"2024","journal-title":"J. Hazard. Mater."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"e0185824","DOI":"10.1128\/aac.01858-24","article-title":"Contribution of RND superfamily multidrug efflux pumps AdeABC, AdeFGH, and AdeIJK to antimicrobial resistance and virulence factors in multidrug-resistant Acinetobacter baumannii AYE","volume":"69","author":"Xie","year":"2025","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"4765","DOI":"10.1038\/s41467-021-25096-3","article-title":"An omics-based framework for assessing the health risk of antimicrobial resistance genes","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"1553","DOI":"10.1038\/s41467-022-29283-8","article-title":"Assessment of global health risk of antibiotic resistance genes","volume":"13","author":"Zhang","year":"2022","journal-title":"Nat. Commun."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1101\/gr.251678.119","article-title":"The enterobase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity","volume":"30","author":"Zhou","year":"2020","journal-title":"Genome Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1662113\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T05:34:22Z","timestamp":1758000862000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1662113\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,16]]},"references-count":74,"alternative-id":["10.3389\/fmicb.2025.1662113"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1662113","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,16]]},"article-number":"1662113"}}