FAO/WHO Codex Alimentarius Commission. Codex texts on foodborne antimicrobial resistance. https://openknowledge.fao.org/server/api/core/bitstreams/4aff9afa-cd2b-47f0-af42-0aa1d86f9dd7/content (2015).
Lekagul, A., Tangcharoensathien, V. & Yeung, S. Patterns of antibiotic use in global pig production: A systematic review. Vet. Anim. Sci. 7, 100058 (2019).
The AMR One Health Surveillance Committee. Nippon AMR One Health Report (NAOR) 2023. https://www.mhlw.go.jp/content/10900000/001268945.pdf (2024).
European Food Safety Authority (EFSA) & European Centre for Disease Prevention and Control (ECDC) The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021–2022. EFSA J. 22, e8583 (2024)..
Aarestrup, F. M. The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward. Philos. Trans. R. Soc. B 370, 20140085 (2015).
Dorado-García, A. et al. Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the environment: a pooled analysis. J. Antimicrob. Chemother. 73, 339–347 (2018).
Day, M. J. et al. Extended-spectrum β-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study. Lancet Infect. Dis. 19, 1325–1335 (2019).
Mughini-Gras, L. et al. Attributable sources of community-acquired carriage of Escherichia coli containing β-lactam antibiotic resistance genes: a population-based modelling study. Lancet Planet. Heath 3, e357–e369 (2019).
Szmolka, A. & Nagy, B. Multidrug resistant commensal Escherichia coli in animals and its impact for public health. Front. Microbiol 4, 258 (2013).
Peng, Z. et al. Antimicrobial resistance and population genomics of multidrug-resistant Escherichia coli in pig farms in mainland China. Nat. Commun. 13, 1116 (2022).
Matakone, M. et al. Multi-drug resistant (MDR) and extended-spectrum β-lactamase (ESBL) producing Escherichia coli isolated from slaughtered pigs and slaughterhouse workers in Yaoundé, Cameroon. One Health 19, 100885 (2024).
Mulchandani, R., Wang, Y., Gilbert, M. & Boeckel, T. P. V. Global trends in antimicrobial use in food-producing animals: 2020 to 2030. PLOS Glob. Public Health 3, e0001305 (2023).
Aarestrup, F. M. Veterinary Drug Usage and Antimicrobial Resistance in Bacteria of Animal Origin. Basic Clin. Physiol. Pharmacol. 96, 271–281 (2005).
World Health Organization. WHO Guidelines on Use of Medically Important Antimicrobials in Food-Producing Animals. https://www.who.int/publications/i/item/9789241550130 (2017).
Etienne, F., Lurier, T., Yugueros-Marcos, J. & Pereira Mateus, A. L. Is use of antimicrobial growth promoters linked to antimicrobial resistance in food-producing animals? A systematic review. Int J. Antimicrob. Agents 66, 107505 (2025).
World Organisation for Animal Health. Use of antimicrobials as growth promoters. https://www.woah.org/app/uploads/2024/01/en-position-statement-use-of-antimicrobials-as-growth-promoters.pdf (2023).
Guardabassi, L., Apley, M., Olsen, J. E., Toutain, P.-L. & Weese, S. Optimization of Antimicrobial Treatment to Minimize Resistance Selection. Microbiol Spectr 6, 6.3.09 (2018).
World Health Organization. WHO global principles for the containment of antimicrobial resistance in animals intended for food: report of a WHO consultation with the participation of the Food and Agriculture Organization of the United Nations and the Office International des Epizooties, Geneva, Switzerland 5-9 June 2000. https://iris.who.int/handle/10665/68931 (2000).
Burow, E., Simoneit, C., Tenhagen, B.-A. & Käsbohrer, A. Oral antimicrobials increase antimicrobial resistance in porcine E. coli – A systematic review. Prev. Vet. Med. 113, 364–375 (2014).
Gibbons, J. F. et al. Antimicrobial Resistance of Faecal Escherichia coli Isolates from Pig Farms with Different Durations of In-feed Antimicrobial Use. Zoonoses Public Health 63, 241–250 (2016).
Lugsomya, K. et al. Routine Prophylactic Antimicrobial Use Is Associated with Increased Phenotypic and Genotypic Resistance in Commensal Escherichia coli Isolates Recovered from Healthy Fattening Pigs on Farms in Thailand. Microb. Drug Resist. 24, 213–223 (2018).
Callens, B. et al. Prophylactic and metaphylactic antimicrobial use in Belgian fattening pig herds. Prev. Vet. Med. 106, 53–62 (2012).
Stubberfield, E. et al. Use of whole genome sequencing of commensal Escherichia coli in pigs for antimicrobial resistance surveillance, United Kingdom, 2018. Eur. Surveill. 24, pii=1900136 (2019).
AbuOun, M. et al. Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain. Front. Microbiol. 11, 861 (2020).
The AACTING-network. Overview of Farm-level AMU Monitoring Systems. https://aacting.org/monitoring-systems/pig–data-collection-systems/?lid=1708.
Jensen, V. F., Jacobsen, E. & Bager, F. Veterinary antimicrobial-usage statistics based on standardized measures of dosage. Prev. Vet. Med. 64, 201–215 (2004).
Fujimoto, K. et al. Antimicrobial use on 74 Japanese pig farms in 2019: A comparison of Japanese and European defined daily doses in the field. PLoS One 16, e0255632 (2021).
Dorado-García, A. et al. Quantitative assessment of antimicrobial resistance in livestock during the course of a nationwide antimicrobial use reduction in the Netherlands. J. Antimicrob. Chemother. 71, 3607–3619 (2016).
Asai, T. et al. Correlation between the Usage Volume of Veterinary Therapeutic Antimicrobials and Resistance in Escherichia coli Isolated from the Feces of Food-Producing Animals in Japan. Jpn. J. Infect. Dis. 58, 369–372 (2005).
Li, X.-S. et al. Antimicrobial susceptibility and molecular detection of chloramphenicol and florfenicol resistance among Escherichia coli isolates from diseased chickens. J. Vet. Sci. 8, 243–247 (2007).
Schwarz, S., Kehrenberg, C., Doublet, B. & Cloeckaert, A. Molecular basis of bacterial resistance to chloramphenicol and florfenicol. FEMS Microbiol. Rev. 28, 519–542 (2004).
Bischoff, K. M., White, D. G., Hume, M. E., Poole, T. L. & Nisbet, D. J. The chloramphenicol resistance gene cmlA is disseminated on transferable plasmids that confer multiple-drug resistance in swine Escherichia coli. FEMS Microbiol. Lett. 243, 285–291 (2005).
Leverstein-van Hall, M. A. et al. Multidrug Resistance among Enterobacteriaceae Is Strongly Associated with the Presence of Integrons and Is Independent of Species or Isolate Origin. J. Infect. Dis. 187, 251–259 (2003).
Dawes, F. E. et al. Distribution of Class 1 Integrons with IS26-Mediated Deletions in Their 3′-Conserved Segments in Escherichia coli of Human and Animal Origin. PLoS ONE 5, e12754 (2010).
Reid, C. J. et al. Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS 26. Microb. Genomics 3, e000143 (2017).
Burow, E. et al. Antibiotic resistance in Escherichia coli from pigs from birth to slaughter and its association with antibiotic treatment. Prev. Vet. Med. 165, 52–62 (2019).
Marchant, M., Vinué, L., Torres, C. & Moreno, M. A. Change of integrons over time in Escherichia coli isolates recovered from healthy pigs and chickens. Vet. Microbiol. 163, 124–132 (2013).
Ingle, D. J., Levine, M. M., Kotloff, K. L., Holt, K. E. & Robins-Browne, R. M. Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa. Nat. Microbiol. 3, 1063–1073 (2018).
Wan, Y. et al. GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure. BMC Genomics 21, 658 (2020).
Toya, R., Sasaki, Y., Uemura, R. & Sueyoshi, M. Optimizing antimicrobial use by improving medication adherence among pig producers. Anim. Sci. J. 93, e13713 (2022).
Isomura, R., Matsuda, M. & Sugiura, K. Analyzing Pig Farmers’ and Veterinarians’ Perceptions and Intentions to Reduce Antimicrobial Usage in Japan. J. Vet. Epidemol. 21, 115–122 (2017).
Nakano, R. et al. Genetic relatedness of third-generation cephalosporin-resistant Escherichia coli among livestock, farmers, and patients in Japan. One Health 16, 100524 (2023).
Norizuki, C. et al. Detection of Escherichia coli Producing CTX-M-1-Group Extended-Spectrum β-Lactamases from Pigs in Aichi Prefecture, Japan, between 2015 and 2016. Jpn. J. Infect. Dis. 71, 33–38 (2018).
Kajitani, R. et al. Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process. DNA Res 27, dsaa014 (2020).
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25, 1043–1055 (2015).
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).
Hasman, H. et al. Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples. J. Clin. Microbiol. 52, 139–146 (2014).
Feldgarden, M. et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci. Rep. 11, 12728 (2021).
Ministry of Agriculture, Forestry and Fisheries. 2020 JVARM Japanese Veterinary Antimicrobial Resistance Monitoring Annual report. https://www.maff.go.jp/nval/yakuzai/pdf/Annual_Report_2020.pdf (2024).
World Health Organization. Defined Daily Dose (DDD). https://www.who.int/tools/atc-ddd-toolkit/about-ddd.
Toya, R., Sasaki, Y., Uemura, R. & Sueyoshi, M. Indications and patterns of antimicrobial use in pig farms in the southern Kyushu, Japan: large amounts of tetracyclines used to treat respiratory disease in post-weaning and fattening pigs. J. Vet. Med. Sci. 83, 322–328 (2021).
Csardi, G. & Nepusz, T. The igraph software package for complex network research. InterJ. Complex Syst. 1695, 1–9 (2006).
Kanda, Y. Investigation of the freely available easy-to-use software ‘EZR’ for medical statistics. Bone Marrow Transpl. 48, 452–458 (2013).
