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The acquisition of stx prophages and associated regulatory mutations can impose adaptive restrictions on this phenotype. This study analyzed 216 whole-genome sequences (WGS) to investigate the genomic determinants of biofilm formation in a diverse collection of E. coli isolates (STEC and non-STEC) isolated from cattle feedlots. Genomes were characterized for serogroup, MLST, stx subtyping, integrity of the mlrA and rpoS regulators, single nucleotide polymorphisms (SNPs) in the csg\/bcs operons, antimicrobial resistance (AMR) genes, and plasmid replicons. The biofilm phenotype was quantitatively evaluated using a crystal violet assay at 15 \u00b0C for 96 h. Results demonstrated higher biofilm forming ability among non-STEC isolates compared to STEC strains, with strains simultaneously carrying both stx1 and stx2 exhibiting the lowest prevalence of biofilm formation (3.3%). Although the rpoS mutation did not show a significant overall association (p = 0.354) with biofilm formation, it was universally present across all O157:H7 isolates, and likely enhanced mlrA disruption toward csgD repression. In addition, stx-positive isolates accumulated significantly more SNPs in the curli (csg) and cellulose (bcs) structural genes. Exploratory gene-level association tests and multiple correspondence analysis further indicated that stx status was associated with broader differences in non-stx accessory gene composition. In addition, there was no statistical association between AMR classes and biofilm-forming capacity. Furthermore, STEC strains demonstrated a lower frequency of resistance to aminoglycosides, phenicols, and tetracyclines. Finally, the plasmid replicons IncX1 and IncFII(pSE11) were present and associated with biofilm-positive isolates. In conclusion, biofilm suppression in STEC suggests a multifactorial and evolutionary phage-induced regulatory trade-off, whereas biofilm persistence in non-STEC strains is independently driven by mobile genetic elements and potential accessory determinants.<\/jats:p>","DOI":"10.3390\/pathogens15080807","type":"journal-article","created":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T08:20:18Z","timestamp":1785486018000},"page":"807","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Phenotypic and Genomic Divergence in Biofilm Formation in STEC and Non-STEC Escherichia coli: The Impact of Genomic Plasticity on the Virulence and Persistence of Bovine Isolates"],"prefix":"10.3390","volume":"15","author":[{"given":"Vinicius Silva","family":"Castro","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada"},{"name":"Faculty of Nutrition, Federal University of Mato Grosso (UFMT), Cuiab\u00e1 78060-900, MT, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0292-2589","authenticated-orcid":false,"given":"Emmanuel W.","family":"Bumunang","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7794-581X","authenticated-orcid":false,"given":"Xianqin","family":"Yang","sequence":"additional","affiliation":[{"name":"Agriculture and Agri-Food Canada Research and Development Centre, Lacombe, AB T4L 1V8, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri Duarte","family":"Porto","sequence":"additional","affiliation":[{"name":"Faculty of Nutrition, Federal University of Mato Grosso (UFMT), Cuiab\u00e1 78060-900, MT, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2608-4324","authenticated-orcid":false,"given":"Eduardo Eust\u00e1quio","family":"de Souza Figueiredo","sequence":"additional","affiliation":[{"name":"Faculty of Nutrition, Federal University of Mato Grosso (UFMT), Cuiab\u00e1 78060-900, MT, Brazil"},{"name":"Faculty of Agronomy and Zootechnics, Federal University of Mato Grosso (UFMT), Cuiab\u00e1 78060-900, MT, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8784-0042","authenticated-orcid":false,"given":"Kim","family":"Stanford","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Engda, T., Tessema, B., Mesifin, N., Nuru, A., Belachew, T., and Moges, F. (2023). Shiga Toxin-Producing Escherichia coli O157:H7 among Diarrheic Patients and Their Cattle in Amhara National Regional State, Ethiopia. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0295266"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Edison, L.K., Kudva, I.T., and Kariyawasam, S. (2023). Comparative Transcriptome Analysis of Shiga Toxin-Producing Escherichia coli O157:H7 on Bovine Rectoanal Junction Cells and Human Colonic Epithelial Cells during Initial Adherence. Microorganisms, 11.","DOI":"10.20944\/preprints202309.1079.v1"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1111\/1541-4337.12929","article-title":"A Systematized Review and Qualitative Synthesis of Potential Risk Factors Associated with the Occurrence of Non-O157 Shiga Toxin-Producing Escherichia coli (STEC) in the Primary Production of Cattle","volume":"21","author":"Withenshaw","year":"2022","journal-title":"Compr. Rev. Food Sci. Food Saf."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Naidoo, N., and Zishiri, O.T. (2023). Comparative Genomics Analysis and Characterization of Shiga Toxin-Producing Escherichia coli O157:H7 Strains Reveal Virulence Genes, Resistance Genes, Prophages and Plasmids. BMC Genom., 24.","DOI":"10.1186\/s12864-023-09902-4"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1038\/s41589-023-01282-w","article-title":"Spatial Transcriptome Uncovers Rich Coordination of Metabolism in E. coli K12 Biofilm","volume":"19","author":"Wang","year":"2023","journal-title":"Nat. Chem. Biol."},{"key":"ref_6","first-page":"e83475","article-title":"A Comprehensive Review of the Role of Virulence Factors in Enteropathogenic Escherichia coli-Induced Intestinal Injury","volume":"17","author":"Ahmad","year":"2025","journal-title":"Cureus"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1007\/s10096-018-3384-6","article-title":"Implications of Stx Loss for Clinical Diagnostics of Shiga Toxin-Producing Escherichia coli","volume":"37","author":"Senthakumaran","year":"2018","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Ban-Cucerzan, A., Imre, K., Morar, A., Marcu, A., Hotea, I., Popa, S.-A., P\u0103tr\u00eenjan, R.-T., Bucur, I.-M., Ga\u0219par, C., and Plotuna, A.-M. (2025). Persistent Threats: A Comprehensive Review of Biofilm Formation, Control, and Economic Implications in Food Processing Environments. Microorganisms, 13.","DOI":"10.3390\/microorganisms13081805"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Yin, W., Wang, Y., Liu, L., and He, J. (2019). Biofilms: The Microbial \u201cProtective Clothing\u201d in Extreme Environments. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20143423"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2065","DOI":"10.1038\/s41467-017-01523-2","article-title":"Insights into the Structure and Assembly of a Bacterial Cellulose Secretion System","volume":"8","author":"Krasteva","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"3731","DOI":"10.1128\/JB.01780-05","article-title":"A Complex Transcription Network Controls the Early Stages of Biofilm Development by Escherichia coli","volume":"188","author":"Besemann","year":"2006","journal-title":"J. Bacteriol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"180066","DOI":"10.1098\/rsob.180066","article-title":"Spatial Organization of Different Sigma Factor Activities and C-Di-GMP Signalling within the Three-Dimensional Landscape of a Bacterial Biofilm","volume":"8","author":"Klauck","year":"2018","journal-title":"Open Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1111\/j.1574-6968.2010.02112.x","article-title":"Regulatory Role of MlrA in Transcription Activation of csgD, the Master Regulator of Biofilm Formation in Escherichia coli","volume":"312","author":"Ogasawara","year":"2010","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1099\/mic.0.000448","article-title":"Genome Amplification and Promoter Mutation Expand the Range of csgD-Dependent Biofilm Responses in an STEC Population","volume":"163","author":"Uhlich","year":"2017","journal-title":"Microbiology"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Chen, C.-Y., Hofmann, C.S., Cottrell, B.J., Strobaugh, T.P., Paoli, G.C., Nguyen, L.-H., Yan, X., and Uhlich, G.A. (2013). Phenotypic and Genotypic Characterization of Biofilm Forming Capabilities in Non-O157 Shiga Toxin-Producing Escherichia coli Strains. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0084863"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"fnw123","DOI":"10.1093\/femsle\/fnw123","article-title":"Stx1 Prophage Excision in Escherichia coli Strain PA20 Confers Strong Curli and Biofilm Formation by Restoring Native mlrA","volume":"363","author":"Uhlich","year":"2016","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Poulin, M.B., and Kuperman, L.L. (2021). Regulation of Biofilm Exopolysaccharide Production by Cyclic Di-Guanosine Monophosphate. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.730980"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1099\/mic.0.2007\/010454-0","article-title":"Type 3 Fimbriae, Encoded by the Conjugative Plasmid pOLA52, Enhance Biofilm Formation and Transfer Frequencies in Enterobacteriaceae Strains","volume":"154","author":"Bahl","year":"2008","journal-title":"Microbiology"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"0012","DOI":"10.1128\/microbiolspec.PLAS-0012-2013","article-title":"The Influence of Biofilms in the Biology of Plasmids","volume":"2","author":"Cook","year":"2014","journal-title":"Microbiol. Spectr."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Bianconi, I., Aschbacher, R., and Pagani, E. (2023). Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology. Antibiotics, 12.","DOI":"10.3390\/antibiotics12111580"},{"key":"ref_21","first-page":"000650","article-title":"Gene-Gene Relationships in an Escherichia coli Accessory Genome Are Linked to Function and Mobility","volume":"7","author":"Hall","year":"2021","journal-title":"Microb. Genom."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Stanford, K., Johnson, R.P., Alexander, T.W., McAllister, T.A., and Reuter, T. (2016). Influence of Season and Feedlot Location on Prevalence and Virulence Factors of Seven Serogroups of Escherichia coli in Feces of Western-Canadian Slaughter Cattle. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0159866"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"104267","DOI":"10.1016\/j.fm.2023.104267","article-title":"Association of Resistance to Quaternary Ammonium Compounds and Organic Acids with Genetic Markers and Their Relationship to Escherichia coli Serogroup","volume":"113","author":"Castro","year":"2023","journal-title":"Food Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Castro, V.S., Polo, R.O., Figueiredo, E.E.d.S., Bumunange, E.W., McAllister, T., King, R., Conte-Junior, C.A., and Stanford, K. (2021). Inconsistent PCR Detection of Shiga Toxin-Producing Escherichia coli: Insights from Whole Genome Sequence Analyses. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0257168"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Bumunang, E.W., Castro, V.S., Alexander, T., Zaheer, R., McAllister, T.A., Guan, L.L., and Stanford, K. (2024). In Silico Analysis of Shiga Toxin-Producing Escherichia coli O157:H7 Strains from Presumptive Super- and Low-Shedder Cattle. Toxins, 16.","DOI":"10.3390\/toxins16020086"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1089\/fpd.2023.0005","article-title":"Efficacy of Quaternary Ammonium Compounds for Control of Individual and Mixed Cultures of Escherichia coli with High- and Low-Quaternary Ammonium Compounds Resistance","volume":"20","author":"Castro","year":"2023","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_28","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_29","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_30","doi-asserted-by":"crossref","unstructured":"Ma, Z., Bumunang, E.W., Stanford, K., Bie, X., Niu, Y.D., and McAllister, T.A. (2019). Biofilm Formation by Shiga Toxin-Producing Escherichia coli on Stainless Steel Coupons as Affected by Temperature and Incubation Time. Microorganisms, 7.","DOI":"10.3390\/microorganisms7040095"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e01126-21","DOI":"10.1128\/AEM.01126-21","article-title":"Biofilm-Forming Capacity of Escherichia coli Isolated from Cattle and Beef Packing Plants: Relation to Virulence Attributes, Stage of Processing, Antimicrobial Interventions, and Heat Tolerance","volume":"87","author":"Stanford","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_32","first-page":"e000064","article-title":"EcOH: In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages","volume":"2","author":"Ingle","year":"2016","journal-title":"Microb. Genom."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Jolley, K.A., and Maiden, M.C. (2010). BIGSdb: Scalable Analysis of Bacterial Genome Variation at the Population Level. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-595"},{"key":"ref_34","unstructured":"(2026, June 27). R: The R Project for Statistical Computing. Available online: https:\/\/www.r-project.org\/."},{"key":"ref_35","unstructured":"(2026, April 09). Libxls. Available online: https:\/\/github.com\/libxls\/libxls."},{"key":"ref_36","unstructured":"Ooms, J., and Denney, B. (2026, July 22). writexl: Export Data Frames to Excel \u2018xlsx\u2019 Format. R Package Version 1.5.4.9000. Available online: https:\/\/ropensci.r-universe.dev\/writexl."},{"key":"ref_37","unstructured":"Wickham, H., Fran\u00e7ois, R., Henry, L., M\u00fcller, K., and Vaughan, D. (2026, July 22). Dplyr: A Grammar of Data Manipulation; R Package Version 1.2.1. Available online: https:\/\/dplyr.tidyverse.org."},{"key":"ref_38","unstructured":"Wickham, H., Vaughan, D., Girlich, M., and Ushey, K. (2026, July 22). Tidyr Tidy Messy Data; R Package Version 1.3.2. Available online: https:\/\/tidyr.tidyverse.org."},{"key":"ref_39","unstructured":"M\u00fcller, K., Wickham, H., Francois, R., and Bryan, J. (2026, July 22). Tibble: Simple Data Frames; R Package Version 3.3.1. Available online: https:\/\/tibble.tidyverse.org\/."},{"key":"ref_40","unstructured":"Wickham, H. (2026, July 22). Stringr: Simple, Consistent Wrappers for Common String Operations, Version 1.6.0. Available online: https:\/\/github.com\/tidyverse\/stringr."},{"key":"ref_41","unstructured":"Husson, F., Josse, J., Le, S., and Mazet, J. (2026, July 22). FactoMineR: Multivariate Exploratory Data Analysis and Data Mining, FactoMineR 2.16. Available online: http:\/\/factominer.free.fr\/."},{"key":"ref_42","unstructured":"(2026, June 27). Create Elegant Data Visualisations Using the Grammar of Graphics. Available online: https:\/\/ggplot2.tidyverse.org\/."},{"key":"ref_43","unstructured":"Slowikowski, K., van den Brand, T., Schep, A., Hughes, S., Dang, T.K., Lukauskas, S., Irisson, J.-O., Kamvar, Z.N., Ryan, T., and Christophe, D. (2026, July 22). Ggrepel: Automatically Position Non-Overlapping Text Labels with \u201cggplot2\u201d; R Package v. 0.9.6. Available online: https:\/\/github.com\/slowkow\/ggrepel."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"001324","DOI":"10.1099\/mic.0.001324","article-title":"E. coli ST11 (O157:H7) Does Not Encode a Functional AcrF Efflux Pump","volume":"169","author":"Pugh","year":"2023","journal-title":"Microbiology"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1099\/mic.0.066118-0","article-title":"Phage Insertion in mlrA and Variations in rpoS Limit Curli Expression and Biofilm Formation in Escherichia coli Serotype O157:H7","volume":"159","author":"Uhlich","year":"2013","journal-title":"Microbiology"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1111\/j.1365-2958.1993.tb01143.x","article-title":"The RpoS Sigma Factor Relieves H-NS-Mediated Transcriptional Repression of csgA, the Subunit Gene of Fibronectin-Binding Curli in Escherichia coli","volume":"7","author":"Arnqvist","year":"1993","journal-title":"Mol. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Schellhorn, H.E. (2020). Function, Evolution, and Composition of the RpoS Regulon in Escherichia coli. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.560099"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"8331","DOI":"10.1128\/AEM.02149-12","article-title":"Role of rpoS in Escherichia coli O157:H7 Strain H32 Biofilm Development and Survival","volume":"78","author":"Sheldon","year":"2012","journal-title":"Appl. Env. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Reichhardt, C. (2024). Cellulose and Cellulose Secretion in Bacterial Biofilms. Biofilm Matrix, Springer Nature.","DOI":"10.1007\/978-3-031-70476-5"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.jmb.2007.07.037","article-title":"Structure and Function of the Escherichia coli Protein YmgB: A Protein Critical for Biofilm Formation and Acid-Resistance","volume":"373","author":"Lee","year":"2007","journal-title":"J. Mol. Biol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1128\/AEM.02809-07","article-title":"The R1 Conjugative Plasmid Increases Escherichia coli Biofilm Formation through an Envelope Stress Response","volume":"74","author":"Yang","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1609","DOI":"10.1111\/mmi.14386","article-title":"The Escherichia coli MarA Protein Regulates the ycgZ-ymgABC Operon to Inhibit Biofilm Formation","volume":"112","author":"Kettles","year":"2019","journal-title":"Mol. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1462-2920.2008.01768.x","article-title":"Insights on Escherichia Coli Biofilm Formation and Inhibition from Whole-Transcriptome Profiling","volume":"11","author":"Wood","year":"2009","journal-title":"Environ. Microbiol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Lee, J., Jayaraman, A., and Wood, T.K. (2007). Indole Is an Inter-Species Biofilm Signal Mediated by SdiA. BMC Microbiol., 7.","DOI":"10.1186\/1471-2180-7-42"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"3051","DOI":"10.1128\/JB.01832-06","article-title":"YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity","volume":"189","author":"Zhang","year":"2007","journal-title":"J. Bacteriol."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Hansen, S., Vuli\u0107, M., Min, J., Yen, T.-J., Schumacher, M.A., Brennan, R.G., and Lewis, K. (2012). Regulation of the Escherichia coli HipBA Toxin-Antitoxin System by Proteolysis. PLoS ONE, 7.","DOI":"10.1371\/annotation\/e608601c-eadd-4c11-adb2-7b605aba9c44"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"e01058-21","DOI":"10.1128\/mBio.01058-21","article-title":"Phylogeny Reveals Novel HipA-Homologous Kinase Families and Toxin-Antitoxin Gene Organizations","volume":"12","author":"Gerdes","year":"2021","journal-title":"mBio"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"12541","DOI":"10.1073\/pnas.1004333107","article-title":"Regulation of Phenotypic Variability by a Threshold-Based Mechanism Underlies Bacterial Persistence","volume":"107","author":"Rotem","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_59","first-page":"267","article-title":"Persister Cells and the Riddle of Biofilm Survival","volume":"70","author":"Lewis","year":"2005","journal-title":"Biochemistry"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Ma, D., Gu, H., Shi, Y., Huang, H., Sun, D., and Hu, Y. (2021). Edwardsiella Piscicida YefM-YoeB: A Type II Toxin-Antitoxin System That Is Related to Antibiotic Resistance, Biofilm Formation, Serum Survival, and Host Infection. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.646299"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"9549","DOI":"10.1093\/nar\/gkt742","article-title":"YoeB\u2013Ribosome Structure: A Canonical RNase That Requires the Ribosome for Its Specific Activity","volume":"41","author":"Feng","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Das, B., and Bhadra, R.K. (2020). (p)ppGpp Metabolism and Antimicrobial Resistance in Bacterial Pathogens. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.563944"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1139\/w02-060","article-title":"NoteThe Stringent Response Genes relA and spoT Are Important for Escherichia coli Biofilms under Slow-Growth Conditions","volume":"48","author":"Balzer","year":"2002","journal-title":"Can. J. Microbiol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e00124-24","DOI":"10.1128\/msphere.00124-24","article-title":"The Yad and Yeh Fimbrial Loci Influence Gene Expression and Virulence in Enterohemorrhagic Escherichia coli O157:H7","volume":"9","author":"Gonyar","year":"2024","journal-title":"mSphere"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.ebiom.2019.11.014","article-title":"Compounds Targeting YadC of Uropathogenic Escherichia coli and Its Host Receptor Annexin A2 Decrease Bacterial Colonization in Bladder","volume":"50","author":"Li","year":"2019","journal-title":"eBioMedicine"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"53","DOI":"10.2174\/1874285801711010053","article-title":"Understanding the Mechanism of Bacterial Biofilms Resistance to Antimicrobial Agents","volume":"11","author":"Singh","year":"2017","journal-title":"Open Microbiol. J."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1903","DOI":"10.1016\/j.cub.2018.04.046","article-title":"Division of Labor during Biofilm Matrix Production","volume":"28","author":"Kiesewalter","year":"2018","journal-title":"Curr. Biol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2503","DOI":"10.1128\/AEM.70.4.2503-2507.2004","article-title":"Frequency and Distribution of Tetracycline Resistance Genes in Genetically Diverse, Nonselected, and Nonclinical Escherichia coli Strains Isolated from Diverse Human and Animal Sources","volume":"70","author":"Bryan","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1038\/s41564-019-0496-4","article-title":"Plasmid-Encoded Tet(X) Genes That Confer High-Level Tigecycline Resistance in Escherichia coli","volume":"4","author":"Sun","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"San Millan, A., and MacLean, R.C. (2017). Fitness Costs of Plasmids: A Limit to Plasmid Transmission. Microbiol. Spectr., 5.","DOI":"10.1128\/microbiolspec.MTBP-0016-2017"},{"key":"ref_71","first-page":"20231088","article-title":"Prophages and Plasmids Can Display Opposite Trends in the Types of Accessory Genes They Carry","volume":"290","author":"Takeuchi","year":"2023","journal-title":"Proc. Biol. Sci."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Douarre, P.-E., Mallet, L., Radomski, N., Felten, A., and Mistou, M.-Y. (2020). Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00483"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.plasmid.2017.02.006","article-title":"Carriage of Type II Toxin-Antitoxin Systems by the Growing Group of IncX Plasmids","volume":"91","author":"Bustamante","year":"2017","journal-title":"Plasmid"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1093\/dnares\/dsn026","article-title":"Complete Genome Sequence and Comparative Analysis of the Wild-Type Commensal Escherichia coli Strain SE11 Isolated from a Healthy Adult","volume":"15","author":"Oshima","year":"2008","journal-title":"DNA Res."},{"key":"ref_75","first-page":"249","article-title":"Escherichia Coli Biofilms","volume":"322","author":"Beloin","year":"2008","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1600431","DOI":"10.1002\/pmic.201600431","article-title":"Autotransporter Adhesins in Escherichia coli Pathogenesis","volume":"17","author":"Vo","year":"2017","journal-title":"Proteomics"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1111\/j.1462-2920.2007.01479.x","article-title":"EhaA Is a Novel Autotransporter Protein of Enterohemorrhagic Escherichia coli O157:H7 That Contributes to Adhesion and Biofilm Formation","volume":"10","author":"Wells","year":"2008","journal-title":"Environ. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1128\/CMR.00022-13","article-title":"Recent Advances in Understanding Enteric Pathogenic Escherichia coli","volume":"26","author":"Croxen","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1007\/s10142-015-0433-4","article-title":"Insights from 20 Years of Bacterial Genome Sequencing","volume":"15","author":"Land","year":"2015","journal-title":"Funct. Integr. Genom."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/j.tim.2015.05.005","article-title":"Bacterial Cellulose Biosynthesis: Diversity of Operons, Subunits, Products, and Functions","volume":"23","author":"Galperin","year":"2015","journal-title":"Trends Microbiol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1128\/MMBR.69.1.12-50.2005","article-title":"The Acetate Switch","volume":"69","author":"Wolfe","year":"2005","journal-title":"Microbiol. Mol. Biol. Rev."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/8\/807\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,2]],"date-time":"2026-08-02T04:18:38Z","timestamp":1785644318000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/8\/807"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,31]]},"references-count":81,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["pathogens15080807"],"URL":"https:\/\/doi.org\/10.3390\/pathogens15080807","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,31]]}}}