{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T10:44:36Z","timestamp":1785926676778,"version":"3.56.0"},"reference-count":60,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:00:00Z","timestamp":1785888000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003827","name":"National Recovery Fund","doi-asserted-by":"publisher","award":["RRF-2.3.1-21-2022-00001"],"award-info":[{"award-number":["RRF-2.3.1-21-2022-00001"]}],"id":[{"id":"10.13039\/501100003827","id-type":"DOI","asserted-by":"publisher"}]},{"award":["RRF-2.3.1-21-2022-00001"],"award-info":[{"award-number":["RRF-2.3.1-21-2022-00001"]}],"id":[{"id":"https:\/\/ror.org\/01zza8h42","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Pseudomonas aeruginosa combines intrinsic resistance, adaptive plasticity, and biofilm formation, making treatment failure common in veterinary and human medicine. We examined whether geraniol and Tris-ethylenediaminetetraacetic acid (Tris-EDTA) modulate marbofloxacin activity during serial exposure and whether whole-genome sequencing detects genomic correlates of the observed phenotypic changes. Methods: A biofilm-producing reference P. aeruginosa ATCC 27853 strain was serially passaged for 10 days with marbofloxacin, geraniol, Tris-EDTA, and their double and triple combinations. Minimum inhibitory concentration (MIC) trajectories and fractional inhibitory concentration indices were determined. Efflux involvement was assessed by MIC testing with carbonyl cyanide 3-chlorophenylhydrazone (CCCP) in 22 canine isolates and the reference strain. Biofilm disruption was evaluated by crystal violet and MTS assays. Whole-genome sequencing was performed for day 0 controls and selected derivatives collected on days 2, 6, and 10. Results: Marbofloxacin alone showed a progressive MIC increase from 2 to 16 \u00b5g\/mL, whereas its MIC remained low in the triple combination and in the marbofloxacin\u2013Tris-EDTA combination. No antagonism was detected. The triple combination showed the most consistent interaction profile, meeting the prespecified synergy criterion on 7 of 10 passage days, compared with 5 of 10 days for marbofloxacin\u2013Tris-EDTA, 2 of 10 days for geraniol\u2013Tris-EDTA, and none for marbofloxacin\u2013geraniol. CCCP caused at most a single twofold-dilution-step decrease in MIC, not supporting a dominant efflux-driven phenotype. In MTS assays, MTS-derived relative EC50 values approximated planktonic inhibitory concentrations, whereas crystal violet results were poorly reproducible. Draft genomes remained highly conserved, and only one candidate nonsynonymous sequence difference in oprN was observed in a day 2 marbofloxacin\u2013Tris-EDTA derivative. Conclusions: Geraniol- and especially Tris-EDTA-containing combinations constrained in vitro marbofloxacin resistance escalation. The marked phenotypic separation despite minimal genomic divergence is consistent with a possible contribution from regulatory or transcriptional adaptation, although this mechanism requires direct experimental confirmation.<\/jats:p>","DOI":"10.3390\/antibiotics15080754","type":"journal-article","created":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T09:16:22Z","timestamp":1785921382000},"page":"754","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Combined Marbofloxacin-Geraniol-Tris-EDTA Exposure Delays Marbofloxacin Resistance Escalation in Pseudomonas aeruginosa While Early Genomic Changes Remain Limited"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3203-9458","authenticated-orcid":false,"given":"Merc\u00e9desz Adrienn","family":"Veres","sequence":"first","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Bodn\u00e1r","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Tak\u00e1ts","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5750-1872","authenticated-orcid":false,"given":"Eszter","family":"Kaszab","sequence":"additional","affiliation":[{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"Department of Bioinformatics, One Health Institute, Faculty of Health Sciences, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary"},{"name":"Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7778-9116","authenticated-orcid":false,"given":"Enik\u0151","family":"Feh\u00e9r","sequence":"additional","affiliation":[{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"National Laboratory of Virology, Szent\u00e1gothai Research Centre, University of P\u00e9cs, H-7624 P\u00e9cs, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7837-2459","authenticated-orcid":false,"given":"\u00c1d\u00e1m","family":"Kerek","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3380-0827","authenticated-orcid":false,"given":"\u00c1kos","family":"Jerzsele","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.2217\/fmb.15.48","article-title":"Pseudomonas aeruginosa: Arsenal of Resistance Mechanisms, Decades of Changing Resistance Profiles, and Future Antimicrobial Therapies","volume":"10","author":"Webster","year":"2015","journal-title":"Future Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"McVey, D.S., Kennedy, M., Chengappa, M.M., and Wilkes, R. (2022). \u00a0Pseudomonas. Veterinary Microbiology, Wiley-Blackwell. [4th ed.].","DOI":"10.1002\/9781119650836"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.biotechadv.2018.11.013","article-title":"Antibiotic Resistance in Pseudomonas aeruginosa: Mechanisms and Alternative Therapeutic Strategies","volume":"37","author":"Pang","year":"2019","journal-title":"Biotechnol. Adv."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.mimet.2010.08.018","article-title":"In Vitro and In Vivo Model Systems to Study Microbial Biofilm Formation","volume":"83","author":"Coenye","year":"2010","journal-title":"J. Microbiol. Methods"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Thi, M.T.T., Wibowo, D., and Rehm, B.H.A. (2020). Pseudomonas aeruginosa Biofilms. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21228671"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"20983","DOI":"10.3390\/ijms141020983","article-title":"Biofilm Matrix and Its Regulation in Pseudomonas aeruginosa","volume":"14","author":"Wei","year":"2013","journal-title":"Int. J. Mol. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1136\/inp.j892","article-title":"Pseudomonas Otitis in Dogs: A General Practitioner\u2019s Guide to Treatment","volume":"39","author":"Barnard","year":"2017","journal-title":"Practice"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s40575-021-00106-1","article-title":"Frequency and Predisposing Factors for Canine Otitis Externa in the UK\u2014A Primary Veterinary Care Epidemiological View","volume":"8","author":"Volk","year":"2021","journal-title":"Canine Med. Genet."},{"key":"ref_9","first-page":"1231","article-title":"Pseudomonas Otitis Externa in Dogs","volume":"59","author":"Pye","year":"2018","journal-title":"Can. Vet. J."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/s15010-016-0905-z","article-title":"In Vitro and In Vivo Activity of EDTA and Antibacterial Agents against the Biofilm of Mucoid Pseudomonas aeruginosa","volume":"45","author":"Liu","year":"2017","journal-title":"Infection"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Bhagirath, A.Y., Li, Y., Somayajula, D., Dadashi, M., Badr, S., and Duan, K. (2016). Cystic Fibrosis Lung Environment and Pseudomonas aeruginosa Infection. BMC Pulm. Med., 16.","DOI":"10.1186\/s12890-016-0339-5"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41392-022-01056-1","article-title":"Pseudomonas aeruginosa: Pathogenesis, Virulence Factors, Antibiotic Resistance, Interaction with Host, Technology Advances and Emerging Therapeutics","volume":"7","author":"Qin","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_13","unstructured":"Antimicrobial Resistance Collaborators (2022). Global Burden of Bacterial Antimicrobial Resistance in 2019: A Systematic Analysis. Lancet, 399, 629\u2013655."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1556\/004.2024.00988","article-title":"Resistome Analysis of Escherichia coli Isolates from Layers in Hungary","volume":"72","author":"Kerek","year":"2024","journal-title":"Acta Vet. Hung."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1556\/004.2024.01051","article-title":"Antimicrobial Susceptibility of Pasteurella multocida Strains Isolated from Different Host Species","volume":"72","author":"Gantelet","year":"2024","journal-title":"Acta Vet. Hung."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1556\/004.2023.00990","article-title":"Distribution of Antimicrobial Resistance and Virulence Markers in Chicken Originated Proteus mirabilis Isolates","volume":"72","author":"Akan","year":"2024","journal-title":"Acta Vet. Hung."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1024\/0036-7281.149.6.265","article-title":"In Vitro Antimicrobial Activity of Marbofloxacin and Enrofloxacin against Bacterial Strains Isolated from Companion Animals","volume":"149","author":"Farca","year":"2007","journal-title":"Schweiz. Arch. Tierheilkd."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1111\/jvp.13077","article-title":"Pseudomonas aeruginosa Susceptibility, Antibiogram and Clinical Interpretation, and Antimicrobial Prescribing Behaviors for Dogs with Otitis in the Midwestern United States","volume":"45","author":"KuKanich","year":"2022","journal-title":"J. Vet. Pharmacol. Ther."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1556\/amicr.62.2015.1.4","article-title":"Evaluating Synergy between Marbofloxacin and Gentamicin in Pseudomonas aeruginosa Strains Isolated from Dogs with Otitis Externa","volume":"62","author":"Jerzsele","year":"2015","journal-title":"Acta Microbiol. Immunol. Hung."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: Expanded Curation, Support for Machine Learning, and Resistome Prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Park, Y., Oh, J., Park, S., Sum, S., Song, W., Chae, J., and Park, H. (2020). Antimicrobial Resistance and Novel Mutations Detected in the gyrA and parC Genes of Pseudomonas aeruginosa Strains Isolated from Companion Dogs. BMC Vet. Res., 16.","DOI":"10.1186\/s12917-020-02328-0"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"59","DOI":"10.2174\/1568026013395605","article-title":"Multidrug Efflux in Pseudomonas aeruginosa: Components, Mechanisms and Clinical Significance","volume":"1","author":"Poole","year":"2001","journal-title":"Curr. Top. Med. Chem."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"103","DOI":"10.56385\/magyallorv.2026.2.103-120","article-title":"Prudent Use of Antibiotics in Pig Farming: National and International Practices and Regulatory Framework","volume":"148","author":"Gombos","year":"2026","journal-title":"Magy. \u00c1llatorvosok Lapja"},{"key":"ref_24","first-page":"131","article-title":"Changes in Antibiotic Use in Hungarian Large Pig Farms Between 2022 and 2024","volume":"148","author":"Gombos","year":"2026","journal-title":"Magy. \u00c1llatorvosok Lapja"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Li, W.-R., Zeng, T.-H., Zhang, Z.-Q., Shi, Q.-S., and Xie, X.-B. (2023). Geraniol Attenuates Virulence Factors by Inhibiting Quorum Sensing of Pseudomonas aeruginosa. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1190619"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Shariati, A., Noei, M., Askarinia, M., Khoshbayan, A., Farahani, A., and Chegini, Z. (2024). Inhibitory Effect of Natural Compounds on Quorum Sensing System in Pseudomonas aeruginosa: A Helpful Promise for Managing Biofilm Community. Front. Pharmacol., 15.","DOI":"10.3389\/fphar.2024.1350391"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Aelenei, P., Miron, A., Trifan, A., Bujor, A., Gille, E., and Aprotosoaie, A.C. (2016). Essential Oils and Their Components as Modulators of Antibiotic Activity against Gram-Negative Bacteria. Medicines, 3.","DOI":"10.3390\/medicines3030019"},{"key":"ref_28","first-page":"1629","article-title":"An In Vitro Antibacterial Study of Savory Essential Oil and Geraniol in Combination with Standard Antimicrobials","volume":"9","year":"2014","journal-title":"Nat. Prod. Commun."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Chouhan, S., Sharma, K., and Guleria, S. (2017). Antimicrobial Activity of Some Essential Oils\u2014Present Status and Future Perspectives. Medicines, 4.","DOI":"10.3390\/medicines4030058"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"519-e122","DOI":"10.1111\/vde.12071","article-title":"Tris-EDTA Significantly Enhances Antibiotic Efficacy against Multidrug-Resistant Pseudomonas aeruginosa In Vitro","volume":"24","author":"Buckley","year":"2013","journal-title":"Vet. Dermatol."},{"key":"ref_31","first-page":"421","article-title":"The Role of Tris in EDTA Toxicity and Lysozyme Lysis","volume":"47","author":"Goldschmidt","year":"1967","journal-title":"Microbiology"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"545","DOI":"10.56385\/magyallorv.2025.9.545-554","article-title":"A Classic Disinfectant Reimagined: The Role of Stabilized Hypochlorous Acid (HOCl) in Modern Hygiene","volume":"147","author":"Jerzsele","year":"2025","journal-title":"Magy. \u00c1llatorvosok Lapja"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"415","DOI":"10.56385\/magyallorv.2026.7.415-426","article-title":"The Role of Quorum Sensing in the Population Dynamics of Antimicrobial Resistance","volume":"148","author":"Kerek","year":"2026","journal-title":"Magy. \u00c1llatorvosok Lapja"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"fnx161","DOI":"10.1093\/femsle\/fnx161","article-title":"Comparative Genomics of a Drug-Resistant Pseudomonas aeruginosa Panel and the Challenges of Antimicrobial-Resistance Prediction from Genomes","volume":"364","author":"Jeukens","year":"2017","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1016\/j.devcel.2004.08.020","article-title":"A Signaling Network Reciprocally Regulates Genes Associated with Acute Infection and Chronic Persistence in Pseudomonas aeruginosa","volume":"7","author":"Goodman","year":"2004","journal-title":"Dev. Cell"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e00138-18","DOI":"10.1128\/CMR.00138-18","article-title":"Cystic Fibrosis and Pseudomonas aeruginosa: The Host-Microbe Interface","volume":"32","author":"Malhotra","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Shukla, S., and Toleti, S.R. (2017). An Improved Crystal Violet Assay for Biofilm Quantification in 96-Well Micro-Titre Plate. bioRxiv, 100214.","DOI":"10.1101\/100214"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Sykes, J.E. (2022). Greene\u2019s Infectious Diseases of the Dog and Cat, Saunders\/Elsevier. [5th ed.].","DOI":"10.1016\/B978-0-323-50934-3.02004-8"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Kim, C.-M., Ko, Y.J., Lee, S.-B., and Jang, S.J. (2022). Adjuvant Antimicrobial Activity and Resensitization Efficacy of Geraniol in Combination with Antibiotics on Acinetobacter baumannii Clinical Isolates. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0271516"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1097\/01.don.0000157994.49432.67","article-title":"In Vitro Evaluation of the Cytotoxic Effects of Acid Solutions Used as Canal Irrigants","volume":"31","author":"Malheiros","year":"2005","journal-title":"J. Endod."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1111\/j.1365-2885.2005.00672.x","article-title":"Ototoxicity and Tolerance Assessment of a TrisEDTA and Polyhexamethylene Biguanide Ear Flush Formulation in Dogs","volume":"28","author":"Mills","year":"2005","journal-title":"J. Vet. Pharmacol. Ther."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/jac\/dkg301","article-title":"Synergy, Antagonism, and What the Chequerboard Puts between Them","volume":"52","author":"Odds","year":"2003","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_43","first-page":"e2437","article-title":"Microtiter Dish Biofilm Formation Assay","volume":"47","year":"2011","journal-title":"J. Vis. Exp."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"207","DOI":"10.3727\/095535491820873191","article-title":"Use of an Aqueous Soluble Tetrazolium\/Formazan Assay for Cell Growth Assays in Culture","volume":"3","author":"Cory","year":"1991","journal-title":"Cancer Commun."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1002\/pst.426","article-title":"Guidelines for Accurate EC50\/IC50 Estimation","volume":"10","author":"Sebaugh","year":"2011","journal-title":"Pharm. Stat."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Ritz, C., Baty, F., Streibig, J.C., and Gerhard, D. (2015). Dose\u2013Response Analysis Using R. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0146021"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Bali, K., B\u00e1lint, \u00c1., Farsang, A., Marton, S., Nagy, B., Kaszab, E., Bel\u00e1k, S., Palya, V., and B\u00e1nyai, K. (2021). Recombination Events Shape the Genomic Evolution of Infectious Bronchitis Virus in Europe. Viruses, 13.","DOI":"10.3390\/v13040535"},{"key":"ref_48","unstructured":"Andrews, S. (2026, April 25). FastQC a Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_50","unstructured":"Benoit, G., Lavenier, D., Lemaitre, C., and Rizk, G. (2014, January 7\u201310). Bloocoo, a Memory-Efficient Read Corrector. Proceedings of the 13th European Conference on Computational Biology (ECCB 2014), Strasbourg, France. Available online: https:\/\/inria.hal.science\/hal-01092960."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An Ultra-Fast Single-Node Solution for Large and Complex Metagenomics Assembly via Succinct de Bruijn Graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Vicedomini, R., Vezzi, F., Scalabrin, S., Arvestad, L., and Policriti, A. (2013). GAM-NGS: Genomic Assemblies Merger for next Generation Sequencing. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-S7-S6"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality Assessment Tool for Genome Assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_55","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 Biol."},{"key":"ref_56","unstructured":"Seemann, T. (2026, July 05). ABRicate: Mass Screening of Contigs for Antimicrobial Resistance and Virulence Genes. Available online: https:\/\/github.com\/tseemann\/abricate."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: A Reference Database for Bacterial Virulence Factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"W443","DOI":"10.1093\/nar\/gkad382","article-title":"PHASTEST: Faster than PHASTER, Better than PHAST","volume":"51","author":"Wishart","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"e35","DOI":"10.1093\/nar\/gkx1321","article-title":"PlasFlow: Predicting Plasmid Sequences in Metagenomic Data Using Genome Signatures","volume":"46","author":"Krawczyk","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_60","doi-asserted-by":"crossref","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":"2021","journal-title":"J. Antimicrob. Chemother."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/8\/754\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T09:54:33Z","timestamp":1785923673000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/8\/754"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,5]]},"references-count":60,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["antibiotics15080754"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics15080754","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,5]]}}}