{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T22:40:06Z","timestamp":1783032006114,"version":"3.54.6"},"reference-count":86,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2023,9,9]],"date-time":"2023-09-09T00:00:00Z","timestamp":1694217600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union and Greek national funds","award":["MIS 5045647"],"award-info":[{"award-number":["MIS 5045647"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Dairy products play a crucial role in human nutrition as they provide essential nutrients. However, the presence of diverse microorganisms in these products can pose challenges to food safety and quality. Here, we provide a comprehensive molecular characterization of a diverse collection of lactic acid bacteria (LAB) and staphylococci isolated from raw sheep\u2019s milk. Whole-genome sequencing, phenotypic characterization, and bioinformatics were employed to gain insight into the genetic composition and functional attributes of these bacteria. Bioinformatics analysis revealed the presence of various genetic elements. Important toxin-related genes in staphylococci that contribute to their pathogenic potential were identified and confirmed using phenotypic assays, while adherence-related genes, which are essential for attachment to host tissues, surfaces in the dairy environment, and the creation of biofilms, were also present. Interestingly, the Staphylococcus aureus isolates belonged to sequence type 5, which largely consists of methicillin-susceptible isolates that have been involved in severe nosocomial infections. Although genes encoding methicillin resistance were not identified, multiple resistance genes (RGs) conferring resistance to aminoglycosides, macrolides, and fluroquinolones were found. In contrast, LAB had few inherently present RGs and no virulence genes, suggesting their likely safe status as food additives in dairy products. LAB were also richer in bacteriocins and carbohydrate-active enzymes, indicating their potential to suppress pathogens and effectively utilize carbohydrate substrates, respectively. Additionally, mobile genetic elements, present in both LAB and staphylococci, may facilitate the acquisition and dissemination of genetic traits, including RGs, virulence genes, and metabolic factors, with implications for food quality and public health. The molecular and phenotypic characterization presented herein contributes to the effort to mitigate risks and infections (e.g., mastitis) and enhance the safety and quality of milk and products thereof.<\/jats:p>","DOI":"10.3390\/ijms241813883","type":"journal-article","created":{"date-parts":[[2023,9,11]],"date-time":"2023-09-11T09:00:52Z","timestamp":1694422852000},"page":"13883","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep\u2019s Milk"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9840-5318","authenticated-orcid":false,"given":"Ilias","family":"Apostolakos","sequence":"first","affiliation":[{"name":"Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization \u201cDIMITRA\u201d, 3rd Ethnikis Antistaseos St., 45221 Ioannina, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theodora","family":"Skarlatoudi","sequence":"additional","affiliation":[{"name":"Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization \u201cDIMITRA\u201d, 3rd Ethnikis Antistaseos St., 45221 Ioannina, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kornilia","family":"Vatavali","sequence":"additional","affiliation":[{"name":"Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization \u201cDIMITRA\u201d, 3rd Ethnikis Antistaseos St., 45221 Ioannina, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agathi","family":"Giannouli","sequence":"additional","affiliation":[{"name":"Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization \u201cDIMITRA\u201d, 3rd Ethnikis Antistaseos St., 45221 Ioannina, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1224-6759","authenticated-orcid":false,"given":"Loulouda","family":"Bosnea","sequence":"additional","affiliation":[{"name":"Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization \u201cDIMITRA\u201d, 3rd Ethnikis Antistaseos St., 45221 Ioannina, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0782-8954","authenticated-orcid":false,"given":"Marios","family":"Mataragas","sequence":"additional","affiliation":[{"name":"Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization \u201cDIMITRA\u201d, 3rd Ethnikis Antistaseos St., 45221 Ioannina, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,9,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Romero-Velarde, E., Delgado-Franco, D., Garc\u00eda-Guti\u00e9rrez, M., Gurrola-D\u00edaz, C., Larrosa-Haro, A., Montijo-Barrios, E., Muskiet, F.A.J., Vargas-Guerrero, B., and Geurts, J. (2019). The Importance of Lactose in the Human Diet: Outcomes of a Mexican Consensus Meeting. Nutrients, 11.","DOI":"10.3390\/nu11112737"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"K\u00f6nig, H., Unden, G., and Fr\u00f6hlich, J. (2017). Biology of Microorganisms on Grapes, in Must and in Wine, Springer International Publishing.","DOI":"10.1007\/978-3-319-60021-5"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"202","DOI":"10.3390\/dairy1030015","article-title":"Lactic Acid Bacteria: Food Safety and Human Health Applications","volume":"1","author":"Ayivi","year":"2020","journal-title":"Dairy"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Zapa\u015bnik, A., Soko\u0142owska, B., and Bry\u0142a, M. (2022). Role of Lactic Acid Bacteria in Food Preservation and Safety. Foods, 11.","DOI":"10.3390\/foods11091283"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.ijfoodmicro.2007.08.016","article-title":"Safety Assessment of Dairy Microorganisms: Coagulase-Negative Staphylococci","volume":"126","author":"Irlinger","year":"2008","journal-title":"Int. J. Food Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.fm.2004.05.005","article-title":"Factors Affecting the Susceptibility of Staphylococcus aureus CCRC 12657 to Water Soluble Lactose Chitosan Derivative","volume":"22","author":"Chen","year":"2005","journal-title":"Food Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1099\/00207713-50-4-1521","article-title":"Staphylococcus Fleurettii Sp. Nov., Isolated from Goat\u2019s Milk Cheeses","volume":"50","author":"Mazuy","year":"2000","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Apostolakos, I., Paramithiotis, S., and Mataragas, M. (2023). Comparative Genomic Analysis Reveals the Functional Traits and Safety Status of Lactic Acid Bacteria Retrieved from Artisanal Cheeses and Raw Sheep Milk. Foods, 12.","DOI":"10.3390\/foods12030599"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"799","DOI":"10.3390\/dairy3040055","article-title":"Functional and Safety Characterization of Weissella Paramesenteroides Strains Isolated from Dairy Products through Whole-Genome Sequencing and Comparative Genomics","volume":"3","author":"Apostolakos","year":"2022","journal-title":"Dairy"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Apostolakos, I., Tsigkrimani, M., Paramithiotis, S., and Mataragas, M. (2022). Whole-Genome Sequencing and Comparative Genomic Analysis of Enterococcus Spp. Isolated from Dairy Products: Genomic Diversity, Functional Characteristics, and Pathogenic Potential. Appl. Sci., 12.","DOI":"10.3390\/app12199620"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"D678","DOI":"10.1093\/nar\/gkac1003","article-title":"ntroducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): A resource combining PATRIC, IRD and ViPR","volume":"51","author":"Olson","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"4","DOI":"10.3389\/fmicb.2019.00004","article-title":"Comparative Genome Analysis of Lactococcus Lactis Indicates Niche Adaptation and Resolves Genotype\/Phenotype Disparity","volume":"10","author":"Wels","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1111\/j.1365-2958.2006.05267.x","article-title":"LmrCD Is a Major Multidrug Resistance Transporter in Lactococcus Lactis","volume":"61","author":"Lubelski","year":"2006","journal-title":"Mol. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1128\/AEM.67.2.569-574.2001","article-title":"Identification of Bacteriocin-like Inhibitors from Rumen Streptococcus Spp. and Isolation and Characterization of Bovicin 255","volume":"67","author":"Whitford","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.foodcont.2012.11.015","article-title":"Molecular Cloning and Antimicrobial Activity of Enterolysin A and Helveticin J of Bacteriolysins from Metagenome of Chinese Traditional Fermented Foods","volume":"31","author":"Zhang","year":"2013","journal-title":"Food Control"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.ijfoodmicro.2013.12.019","article-title":"Purification and Characterization of Antimicrobial Peptides from Fish Isolate Carnobacterium Maltaromaticum C2: Carnobacteriocin X and Carnolysins A1 and A2","volume":"173","author":"Tulini","year":"2014","journal-title":"Int. J. Food Microbiol."},{"key":"ref_17","first-page":"317","article-title":"Inhibitory Effect of Lactococcin BZ Against Listeria Innocua and Indigenous Microbiota of Fresh Beef","volume":"54","author":"Yerlikaya","year":"2016","journal-title":"Food Technol. Biotechnol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1007\/s13205-018-1546-y","article-title":"Anti-Staphylococcal Activity of Bacteriocins of Food Isolates Enterococcus Hirae LD3 and Lactobacillus Plantarum LD4 in Pasteurized Milk","volume":"9","author":"Sheoran","year":"2019","journal-title":"3 Biotech"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1146\/annurev.biochem.76.061005.092322","article-title":"Glycosyltransferases: Structures, Functions, and Mechanisms","volume":"77","author":"Lairson","year":"2008","journal-title":"Annu. Rev. Biochem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"5094","DOI":"10.1128\/AEM.67.11.5094-5099.2001","article-title":"Characterization of Two New Glycosyl Hydrolases from the Lactic Acid Bacterium Carnobacterium Piscicola Strain BA","volume":"67","author":"Coombs","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"871","DOI":"10.3389\/fbioe.2020.00871","article-title":"Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms","volume":"8","author":"Sidar","year":"2020","journal-title":"Front. Bioeng. Biotechnol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"6032","DOI":"10.1128\/AEM.69.10.6032-6040.2003","article-title":"IS Lpl1 Is a Functional IS 30 -Related Insertion Element in Lactobacillus Plantarum That Is Also Found in Other Lactic Acid Bacteria","volume":"69","author":"Nicoloff","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"7463","DOI":"10.1128\/jb.174.22.7463-7469.1992","article-title":"Molecular Characterization of a Second Abortive Phage Resistance Gene Present in Lactococcus Lactis Subsp. Lactis ME2","volume":"174","author":"Durmaz","year":"1992","journal-title":"J. Bacteriol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e0054621","DOI":"10.1128\/MRA.00546-21","article-title":"Genome Sequences of Lactococcus Garvieae and Lactococcus Petauri Strains Isolated from Traditional Montenegrin Brine Cheeses","volume":"10","author":"Martinovic","year":"2021","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s13100-020-00221-z","article-title":"IS982 and Kin: New Insights into an Old IS Family","volume":"11","author":"Fayad","year":"2020","journal-title":"Mob. DNA"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.gene.2014.11.019","article-title":"Insertion Sequence Elements in Lactococcus Garvieae","volume":"555","author":"Eraclio","year":"2015","journal-title":"Gene"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"S20","DOI":"10.1186\/1475-2859-10-S1-S20","article-title":"Bacteriophages of Lactic Acid Bacteria and Their Impact on Milk Fermentations","volume":"10","author":"Garneau","year":"2011","journal-title":"Microb. Cell Fact."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2032","DOI":"10.3389\/fmicb.2018.02032","article-title":"Characterization of a Prophage-Free Derivative Strain of Lactococcus Lactis Ssp. Lactis IL1403 Reveals the Importance of Prophages for Phenotypic Plasticity of the Host","volume":"9","author":"Aucouturier","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.lwt.2017.05.055","article-title":"Identification, Characterization, and Probiotic Potential of Lactobacillus Rhamnosus Isolated from Human Milk","volume":"84","author":"Mehwish","year":"2017","journal-title":"LWT"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"658031","DOI":"10.3389\/fvets.2021.658031","article-title":"Non-Aureus Staphylococci and Bovine Udder Health: Current Understanding and Knowledge Gaps","volume":"8","author":"Ha","year":"2021","journal-title":"Front. Vet. Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2329","DOI":"10.3168\/jds.2010-3741","article-title":"Some Coagulase-Negative Staphylococcus Species Affect Udder Health More than Others","volume":"94","author":"Haesebrouck","year":"2011","journal-title":"J. Dairy Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1080\/22221751.2020.1868950","article-title":"Increasing Prevalence of Hypervirulent ST5 Methicillin Susceptible Staphylococcus aureus Subtype Poses a Serious Clinical Threat","volume":"10","author":"Jian","year":"2021","journal-title":"Emerg. Microbes Infect."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"710","DOI":"10.3389\/fgene.2018.00710","article-title":"Genetic Diversity of NorA, Coding for a Main Efflux Pump of Staphylococcus aureus","volume":"9","author":"Costa","year":"2019","journal-title":"Front. Genet."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2766","DOI":"10.1093\/jac\/dkt286","article-title":"Association of NorB Overexpression and Fluoroquinolone Resistance in Clinical Isolates of Staphylococcus aureus from Korea","volume":"68","author":"Kwak","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1128\/JB.182.3.664-671.2000","article-title":"Expression of the Multidrug Resistance Transporter NorA from Staphylococcus aureus Is Modified by a Two-Component Regulatory System","volume":"182","author":"Fournier","year":"2000","journal-title":"J. Bacteriol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1128\/JB.187.7.2395-2405.2005","article-title":"MgrA Is a Multiple Regulator of Two New Efflux Pumps in Staphylococcus aureus","volume":"187","author":"Dunman","year":"2005","journal-title":"J. Bacteriol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1074\/jbc.M112.385138","article-title":"Characterization of the Staphylococcus aureus RRNA Methyltransferase Encoded by OrfX, the Gene Containing the Staphylococcal Chromosome Cassette Mec (SCCmec) Insertion Site","volume":"288","author":"Boundy","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"108536","DOI":"10.1016\/j.vetmic.2019.108536","article-title":"Impact of Selective and Non-Selective Media on Prevalence and Genetic Makeup of ESBL\/PAmpC-Producing Escherichia Coli in the Broiler Production Pyramid","volume":"240","author":"Apostolakos","year":"2020","journal-title":"Vet. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1128\/IAI.70.7.3389-3395.2002","article-title":"Overproduction of Type 8 Capsular Polysaccharide Augments Staphylococcus aureus Virulence","volume":"70","author":"Luong","year":"2002","journal-title":"Infect. Immun."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"511","DOI":"10.3389\/fmicb.2017.00511","article-title":"Molecular Characterization of Staphylococcus aureus Isolated from Bovine Mastitis and Close Human Contacts in South African Dairy Herds: Genetic Diversity and Inter-Species Host Transmission","volume":"8","author":"Schmidt","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Xiao, M., Zhao, R., Zhang, Q., Fan, X., O\u2019Sullivan, M.V.N., Li, D.-F., Wang, X.-Y., Wu, H.-L., Kong, F., and Xu, Y.-C. (2016). Genotypic Diversity of Staphylococcus aureus \u03b1-Hemolysin Gene (Hla) and Its Association with Clonal Background: Implications for Vaccine Development. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0149112"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"5438","DOI":"10.1038\/ncomms6438","article-title":"The Staphylococcal Toxins \u03b3-Haemolysin AB and CB Differentially Target Phagocytes by Employing Specific Chemokine Receptors","volume":"5","author":"Spaan","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"100992","DOI":"10.1016\/j.nmni.2022.100992","article-title":"Identification of Nuc Nuclease and Sea Enterotoxin Genes in Staphylococcus aureus Isolates from Nasal Mucosa of Burn Hospital Staff: A Cross-Sectional Study","volume":"47","author":"Karimzadeh","year":"2022","journal-title":"New Microbes New Infect."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Tam, K., and Torres, V.J. (2019). Staphylococcus aureus Secreted Toxins and Extracellular Enzymes. Microbiol. Spectr., 7.","DOI":"10.1128\/microbiolspec.GPP3-0039-2018"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1337","DOI":"10.2217\/fmb.09.102","article-title":"Structural and Functional Role of Staphylococcus aureus Surface Components Recognizing Adhesive Matrix Molecules of the Host","volume":"4","author":"Speziale","year":"2009","journal-title":"Future Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1111\/j.1574-6968.2007.00688.x","article-title":"Ica and beyond: Biofilm Mechanisms and Regulation in Staphylococcus Epidermidis and Staphylococcus aureus","volume":"270","year":"2007","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1021\/acsinfecdis.9b00002","article-title":"Simplified Autoinducing Peptide Mimetics with Single-Nanomolar Activity Against the Staphylococcus aureus AgrC Quorum Sensing Receptor","volume":"5","author":"Vasquez","year":"2019","journal-title":"ACS Infect. Dis."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"17080","DOI":"10.1038\/nmicrobiol.2017.80","article-title":"Surface-Attached Molecules Control Staphylococcus aureus Quorum Sensing and Biofilm Development","volume":"2","author":"Kim","year":"2017","journal-title":"Nat. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"574923","DOI":"10.3389\/fmicb.2020.574923","article-title":"Comparative Genomics of Plasmid-Bearing Staphylococcus aureus Strains Isolated From Various Retail Meats","volume":"11","author":"Karki","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"3057","DOI":"10.1007\/s00018-010-0389-4","article-title":"Mobile Genetic Elements of Staphylococcus aureus","volume":"67","author":"Malachowa","year":"2010","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"2061","DOI":"10.3389\/fmicb.2020.02061","article-title":"The Genome of Staphylococcus Epidermidis O47","volume":"11","author":"Raue","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1038\/s43856-022-00200-w","article-title":"Cfr and FexA Genes in Methicillin-Resistant Staphylococcus aureus from Humans and Livestock in the Netherlands","volume":"2","author":"Schouls","year":"2022","journal-title":"Commun. Med."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Dini, M., Shokoohizadeh, L., Jalilian, F.A., Moradi, A., and Arabestani, M.R. (2019). Genotyping and Characterization of Prophage Patterns in Clinical Isolates of Staphylococcus aureus. BMC Res. Notes, 12.","DOI":"10.1186\/s13104-019-4711-4"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"771","DOI":"10.4142\/jvs.2018.19.6.771","article-title":"Molecular Prophage Typing of Staphylococcus aureus Isolates from Bovine Mastitis","volume":"19","author":"Ko","year":"2018","journal-title":"J. Vet. Sci."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Syrokou, M.K., Themeli, C., Paramithiotis, S., Mataragas, M., Bosnea, L., Argyri, A.A., Chorianopoulos, N.G., Skandamis, P.N., and Drosinos, E.H. (2020). Microbial Ecology of Greek Wheat Sourdoughs, Identified by a Culture-Dependent and a Culture-Independent Approach. Foods, 9.","DOI":"10.3390\/foods9111603"},{"key":"ref_56","unstructured":"Andrews, S. (2023, January 10). FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1038\/nbt.4163","article-title":"KBase: The United States Department of Energy Systems Biology Knowledgebase","volume":"36","author":"Arkin","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref_58","first-page":"e000132","article-title":"Completing Bacterial Genome Assemblies with Multiplex MinION Sequencing","volume":"3","author":"Wick","year":"2017","journal-title":"Microb. Genom."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., and Young, S.K. (2014). Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0112963"},{"key":"ref_60","first-page":"D606","article-title":"The PATRIC Bioinformatics Resource Center: Expanding Data and Analysis Capabilities","volume":"48","author":"Davis","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"2443","DOI":"10.1093\/bioinformatics\/btv171","article-title":"MeDuSa: A Multi-Draft Based Scaffolder","volume":"31","author":"Bosi","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Lu, J., and Salzberg, S.L. (2020). SkewIT: The Skew Index Test for Large-Scale GC Skew Analysis of Bacterial Genomes. PLoS Comput. Biol., 16.","DOI":"10.1371\/journal.pcbi.1008439"},{"key":"ref_64","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_65","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_66","doi-asserted-by":"crossref","first-page":"2182","DOI":"10.1038\/s41467-019-10210-3","article-title":"TYGS Is an Automated High-Throughput Platform for State-of-the-Art Genome-Based Taxonomy","volume":"10","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1099\/ijsem.0.000760","article-title":"OrthoANI: An Improved Algorithm and Software for Calculating Average Nucleotide Identity","volume":"66","author":"Lee","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid Prokaryotic Genome Annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_69","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":"Mol. Biol. Evol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1560","DOI":"10.1093\/bib\/bbx121","article-title":"PHAST, PHASTER and PHASTEST: Tools for Finding Prophage in Bacterial Genomes","volume":"20","author":"Arndt","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_71","unstructured":"Seemann, T. (2023, June 27). Abricate, Github 2020. Available online: https:\/\/github.com\/tseemann\/abricate."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: Hierarchical and Refined Dataset for Big Data Analysis\u201410 Years On","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_73","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."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of Acquired Antimicrobial Resistance Genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In Silico Detection and Typing of Plasmids Using Plasmidfinder and Plasmid Multilocus Sequence Typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"W95","DOI":"10.1093\/nar\/gky418","article-title":"DbCAN2: A Meta Server for Automated Carbohydrate-Active Enzyme Annotation","volume":"46","author":"Zhang","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_77","doi-asserted-by":"crossref","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":"ref_78","doi-asserted-by":"crossref","first-page":"4305","DOI":"10.1128\/JCM.01979-14","article-title":"Comparing Whole-Genome Sequencing with Sanger Sequencing for Spa Typing of Methicillin-Resistant Staphylococcus aureus","volume":"52","author":"Bartels","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC) (2009). Classification of Staphylococcal Cassette Chromosome Mec (SCCmec): Guidelines for Reporting Novel SCCmec Elements. Antimicrob. Agents Chemother., 53, 4961\u20134967.","DOI":"10.1128\/AAC.00579-09"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Cosentino, S., Voldby Larsen, M., M\u00f8ller Aarestrup, F., and Lund, O. (2013). PathogenFinder\u2014Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data. PLoS ONE, 8.","DOI":"10.1371\/annotation\/b84e1af7-c127-45c3-be22-76abd977600f"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: Rapid Large-Scale Prokaryote Pan Genome Analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/molbev\/msp077","article-title":"FastTree: Computing Large Minimum Evolution Trees with Profiles Instead of a Distance Matrix","volume":"26","author":"Price","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (ITOL) v5: An Online Tool for Phylogenetic Tree Display and Annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy Platform for Accessible, Reproducible and Collaborative Biomedical Analyses: 2018 Update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"e5","DOI":"10.1002\/imt2.5","article-title":"ImageGP: An Easy-to-use Data Visualization Web Server for Scientific Researchers","volume":"1","author":"Chen","year":"2022","journal-title":"iMeta"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1080\/10942912.2021.1900233","article-title":"Partial Characterization of Probiotic Lactic Acid Bacteria Isolated from Chinese Dairy Products","volume":"24","author":"Huang","year":"2021","journal-title":"Int. J. Food Prop."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/18\/13883\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T20:47:53Z","timestamp":1760129273000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/18\/13883"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,9,9]]},"references-count":86,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2023,9]]}},"alternative-id":["ijms241813883"],"URL":"https:\/\/doi.org\/10.3390\/ijms241813883","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,9,9]]}}}