{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T10:12:19Z","timestamp":1781863939664,"version":"3.54.5"},"reference-count":110,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,28]],"date-time":"2025-12-28T00:00:00Z","timestamp":1766880000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100013209","name":"European Union\u2013NextGenerationEU","doi-asserted-by":"publisher","award":["16560"],"award-info":[{"award-number":["16560"]}],"id":[{"id":"10.13039\/501100013209","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>Listeria monocytogenes is a major foodborne pathogen, responsible for severe listeriosis outbreaks associated with contaminated foods. This study reports the comparative genomic analysis of three novel L. monocytogenes strains C5, A2D9 and A2D10, obtained from dairy and clinical sources. Hybrid genome sequencing with Oxford-Nanopore and Illumina technologies provided high-quality complete chromosomes. Phylogenomic analysis revealed a highly conserved core genome alongside accessory genome diversity. Strain C5 belonged to sequence type ST2, while A2D9 and A2D10 were assigned to ST155 and ST1, respectively. All strains exhibited close genomic relatedness to isolates from dairy animals and\/or the dairy environment. Functional analysis identified conserved metabolic functions across all genomes. A total of 40 virulence genes were detected, including the LIPI-1 island in all strains and the LIPI-3 operon exclusively in A2D10, indicating a potential hypervirulent phenotype consistent with its ST1 background and the associated fatal clinical outcome. All strains exhibited similar antimicrobial resistance profiles typical of L. monocytogenes and diverse defense systems. The newly sequenced strains provide a valuable resource for functional analyses of the mechanisms underlying adaptation of L. monocytogenes to diverse environments.<\/jats:p>","DOI":"10.3390\/foods15010088","type":"journal-article","created":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T08:47:27Z","timestamp":1766998047000},"page":"88","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Hybrid Genome Sequencing and Comparative Analysis of Three Novel Listeria monocytogenes Strains: Insights into Lineage Diversity, Virulence, Antibiotic Resistance, and Defense Systems"],"prefix":"10.3390","volume":"15","author":[{"given":"Violeta","family":"Pemaj","sequence":"first","affiliation":[{"name":"Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-3104-4831","authenticated-orcid":false,"given":"Aleksandra","family":"Slavko","sequence":"additional","affiliation":[{"name":"Department of Food Science and Technology, University of the Peloponnese, 24100 Antikalamos, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantinos","family":"Konandreas","sequence":"additional","affiliation":[{"name":"Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0772-0812","authenticated-orcid":false,"given":"Dimitrios E.","family":"Pavlidis","sequence":"additional","affiliation":[{"name":"Department of Food Science and Technology, University of the Peloponnese, 24100 Antikalamos, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1880-7366","authenticated-orcid":false,"given":"Anastasios","family":"Ioannidis","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Microbiology, School of Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, Rimini 1, 12462 Chaidari, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantinos","family":"Panousopoulos","sequence":"additional","affiliation":[{"name":"Department of Food Science and Technology, University of the Peloponnese, 24100 Antikalamos, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikoletta","family":"Xydia","sequence":"additional","affiliation":[{"name":"2nd Indernal Medicine Clinic, General Hospital of Kalamata, 24100 Antikalamos, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vassiliki","family":"Antonopoulou","sequence":"additional","affiliation":[{"name":"Microbiology Department, General Hospital of Kalamata, 24100 Antikalamos, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Papadelli","sequence":"additional","affiliation":[{"name":"Department of Food Science and Technology, University of the Peloponnese, 24100 Antikalamos, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleftherios H.","family":"Drosinos","sequence":"additional","affiliation":[{"name":"Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7878-5897","authenticated-orcid":false,"given":"Panagiotis 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Rev. Dis. Primers"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"16185","DOI":"10.1038\/nmicrobiol.2016.185","article-title":"Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes","volume":"2","author":"Moura","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/nrmicro.2017.126","article-title":"Listeria monocytogenes: Towards a complete picture of its physiology and pathogenesis","volume":"16","author":"Radoshevich","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1016\/j.micinf.2007.05.011","article-title":"The epidemiology of human listeriosis","volume":"9","author":"Swaminathan","year":"2007","journal-title":"Microbes Infect."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Kuenne, C., Billion, A., Mraheil, M.A., Strittmatter, A., Daniel, R., Goesmann, A., Barbuddhe, S., Hain, T., and Chakraborty, T. (2013). Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC Genom., 14.","DOI":"10.1186\/1471-2164-14-47"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Lachtara, B., Wieczorek, K., and Osek, J. (2022). Genetic diversity and relationships of Listeria monocytogenes serogroup IIa isolated in Poland. Microorganisms, 10.","DOI":"10.3390\/microorganisms10030532"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4229","DOI":"10.1128\/JCM.01032-06","article-title":"Listeria monocytogenes subgroups IIIA, IIIB, and IIIC delineate genetically distinct populations with varied pathogenic potential","volume":"44","author":"Liu","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.ijmm.2010.05.002","article-title":"Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics","volume":"301","author":"Orsi","year":"2011","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5058","DOI":"10.1111\/1462-2920.15111","article-title":"Lineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages","volume":"22","author":"Zamudio","year":"2020","journal-title":"Environ. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"5273","DOI":"10.1007\/s00253-016-7552-2","article-title":"Characteristics and distribution of Listeria spp., including Listeria species newly described since 2009","volume":"100","author":"Orsi","year":"2016","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.mib.2011.01.005","article-title":"Regulation of Listeria virulence: PrfA master and commander","volume":"14","author":"Cain","year":"2011","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e13186","DOI":"10.1111\/cmi.13186","article-title":"Listeria monocytogenes, a model in infection biology","volume":"22","author":"Lecuit","year":"2020","journal-title":"Cell Microbiol."},{"key":"ref_13","first-page":"10-1128","article-title":"Antimicrobial resistance in Listeria species","volume":"6","author":"Arroyo","year":"2018","journal-title":"Microbiol. Spectr."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Scortti, M., Han, L., Alvarez, S., Leclercq, A., Moura, A., Lecuit, M., and Vazquez-Boland, J. (2018). Epistatic control of intrinsic resistance by virulence genes in Listeria. PLoS Genet., 14.","DOI":"10.1371\/journal.pgen.1007727"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2433","DOI":"10.1128\/AEM.02480-08","article-title":"Temperature-dependent phage resistance of Listeria monocytogenes epidemic clone II","volume":"75","author":"Kim","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.chom.2020.04.001","article-title":"Listeria phages induce Cas9 degradation to protect lysogenic genomes","volume":"28","author":"Osuna","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Xu, X., and Gu, P. (2024). Overview of phage defense systems in bacteria and their applications. Mol. Sci., 25.","DOI":"10.3390\/ijms252413316"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/s41579-023-00934-x","article-title":"The highly diverse antiphage defence systems of bacteria","volume":"21","author":"Georjon","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Bobay, L.M., and Ochman, H. (2017). The evolution of bacterial genome architecture. Front. Genet., 8.","DOI":"10.3389\/fgene.2017.00072"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"113056","DOI":"10.1016\/j.foodres.2023.113056","article-title":"Studying the metabolic factors that may impact the growth of co-cultured Listeria monocytogenes strains at low temperature","volume":"171","author":"Gkerekou","year":"2023","journal-title":"Food Res. Int."},{"key":"ref_21","unstructured":"EUCAST (2025, January 10). European Committee on Antimicrobial Susceptibility Testing Disk Diffusion Test Methodology. Available online: https:\/\/www.eucast.org\/ast_of_bacteria\/disk_diffusion_methodology."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"33","DOI":"10.12688\/f1000research.29032.2","article-title":"Sustainable data analysis with Snakemake","volume":"10","author":"Jablonski","year":"2021","journal-title":"F1000Research"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"btad311","DOI":"10.1093\/bioinformatics\/btad311","article-title":"NanoPack2: Population-scale evaluation of long-read sequencing data","volume":"39","author":"Rademakers","year":"2023","journal-title":"Bioinformatics"},{"key":"ref_24","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_25","unstructured":"Andrews, S. (2025, July 08). FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"20740","DOI":"10.1038\/s41598-021-00178-w","article-title":"Comparative evaluation of Nanopore polishing tools for microbial genome assembly and polishing strategies for downstream analysis","volume":"11","author":"Lee","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_29","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_30","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1186\/s13059-015-0849-0","article-title":"Circlator: Automated circularization of genome assemblies using long sequencing reads","volume":"16","author":"Hunt","year":"2015","journal-title":"Genome Biol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Pellow, D., Mizrahi, I., and Shamir, R. (2020). PlasClass improves plasmid sequence classification. PLoS Comput. Biol., 16.","DOI":"10.1371\/journal.pcbi.1007781"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","article-title":"GTDB-Tk v2: Memory friendly classification with the genome taxonomy database","volume":"38","author":"Chaumeil","year":"2022","journal-title":"Bioinformatics"},{"key":"ref_33","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_34","doi-asserted-by":"crossref","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","article-title":"CheckM2: A rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","volume":"20","author":"Chklovski","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_36","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","author":"Goker","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: Multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2620","DOI":"10.1093\/bioinformatics\/btq484","article-title":"Circoletto: Visualizing sequence similarity with Circos","volume":"26","author":"Darzentas","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_40","unstructured":"Felsenstein, J. (2025, March 02). PHYLIP\u2014Phylogeny Inference Package. Available online: https:\/\/phylipweb.github.io\/phylip."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1093\/bioinformatics\/btv681","article-title":"JSpeciesWS: A web server for prokaryotic species circumscription based on pairwise genome comparison","volume":"32","author":"Richter","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_42","unstructured":"(2025, October 02). BIGSdb. Available online: http:\/\/bigsdb.pasteur.fr\/news\/."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences","volume":"428","author":"Kanehisa","year":"2016","journal-title":"J. Mol. Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"\u0395ggNOG-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_45","unstructured":"Seemann, T. (2025, September 05). Abricate. Available online: https:\/\/github.com\/tseemann\/abricate."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"D561","DOI":"10.1093\/nar\/gkz1010","article-title":"MEGARes 2.0: A database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data","volume":"48","author":"Doster","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: A general classification scheme for bacterial virulence factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2561","DOI":"10.1038\/s41467-022-30269-9","article-title":"Systematic and quantitative view of the antiviral arsenal of prokaryotes","volume":"13","author":"Tesson","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Qi, Y., Cao, Q., Zhao, X., Tian, C., Li, T., Shi, W., Wei, H., Song, C., Xue, H., and Gou, H. (2024). Comparative genomic analysis of pathogenic factors of Listeria spp. using whole-genome sequencing. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10849-3"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Lachtara, B., Osek, J., and Wieczorek, K. (2021). Molecular typing of Listeria monocytogenes IVb serogroup isolated from food and food production environments in Poland. Pathogens, 10.","DOI":"10.3390\/pathogens10040482"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"4284","DOI":"10.1128\/JB.05328-11","article-title":"Genome sequence of Listeria monocytogenes Scott A, a clinical isolate from a food-borne listeriosis outbreak","volume":"193","author":"Briers","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1099\/jmm.0.46495-0","article-title":"Identification, subtyping and virulence determination of Listeria monocytogenes, an important foodborne pathogen","volume":"55","author":"Liu","year":"2006","journal-title":"J. Med. Microbiol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/S0168-1605(01)00532-3","article-title":"Exposure of Listeria monocytogenes within an epidemic caused by butter in Finland","volume":"70","author":"Maijala","year":"2001","journal-title":"Int. J. Food Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Rychli, K., M\u00fcller, A., Zaiser, A., Schoder, D., Allerberger, F., Wagner, M., and Schmitz-Esser, S. (2014). Genome sequencing of Listeria monocytogenes \u201cQuargel\u201d listeriosis outbreak strains reveals two different strains with distinct in vitro virulence potential. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0089964"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"2386","DOI":"10.1093\/nar\/gkh562","article-title":"Whole genome comparisons of serotype 4b and 1\/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species","volume":"32","author":"Nelson","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"e01403-14","DOI":"10.1128\/genomeA.01403-14","article-title":"Complete genome sequence of Listeria monocytogenes NTSN, a serovar 4b and animal source strain","volume":"3","author":"Tan","year":"2015","journal-title":"Genome Announc."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"992","DOI":"10.15212\/ZOONOSES-2024-0050","article-title":"MLST evidence of two different sequence types of Listeria monocytogenes strains used for commercial veterinary listeriosis vaccines","volume":"5","author":"Kichemazova","year":"2025","journal-title":"Zoonoses"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1128\/JCM.41.2.757-762.2003","article-title":"Development of a multilocus sequence typing method for analysis of Listeria monocytogenes clones","volume":"41","author":"Salcedo","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Mafuna, T., Matle, I., Magwedere, K., Pierneef, R.E., and Reva, O.N. (2021). Whole genome-based characterization of Listeria monocytogenes isolates recovered from the food chain in South Africa. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.669287"},{"key":"ref_64","first-page":"1151E","article-title":"Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-to-eat (RTE) foods: Activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis","volume":"14","author":"Nielsen","year":"2017","journal-title":"EFSA Support. Publ."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Rychli, K., Stessl, B., Szakmary-Br\u00e4ndle, K., Strau\u00df, A., Wagner, M., and Schoder, D. (2018). Listeria monocytogenes isolated from illegally imported food products into the European Union harbor different virulence factor variants. Genes, 9.","DOI":"10.3390\/genes9090428"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Toledo, V., den Bakker, H.C., Hormaz\u00e1bal, J.C., Gonz\u00e1lez-Rocha, G., Bello-Toledo, H., Toro, M., and Moreno-Switt, A.I. (2018). Genomic diversity of Listeria monocytogenes isolated from clinical and non-clinical samples in Chile. Genes, 9.","DOI":"10.3390\/genes9080396"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Cabal, A., Pietzka, A., Huhulescu, S., Allerberger, F., Ruppitsch, W., and Schmid, D. (2019). Isolate-based surveillance of Listeria monocytogenes by whole genome sequencing in Austria. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.02282"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Wagner, E., Zaiser, A., Leitner, R., Quijada, N.M., Pracser, N., Pietzka, A., Ruppitsch, W., Schmitz-Esser, S., Wagner, M., and Rychli, K. (2020). Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains. BMC Genom., 21.","DOI":"10.1186\/s12864-020-07263-w"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"fyac021","DOI":"10.1093\/fqsafe\/fyac021","article-title":"Systematic review of Listeria monocytogenes from food and clinical samples in Chinese mainland from 2010 to 2019","volume":"6","author":"Cheng","year":"2022","journal-title":"Food Qual. Saf."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"36419","DOI":"10.1038\/srep36419","article-title":"Listeria monocytogenes sequence type 1 is predominant in ruminant rhombencephalitis","volume":"6","author":"Dreyer","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Silva, A., Silva, V., Gomes, J.P., Coelho, A., Batista, R., Saraiva, C., Esteves, A., Martins, \u00c2., Contente, D., and Diaz-Formoso, L. (2024). Listeria monocytogenes from food products and food associated environments: Antimicrobial resistance, genetic clustering and biofilm insights. Antibiotics, 13.","DOI":"10.3390\/antibiotics13050447"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Wieczorek, K., Bomba, A., and Osek, J. (2020). Whole-genome sequencing-based characterization of Listeria monocytogenes from fish and fish production environments in Poland. Mol. Sci., 21.","DOI":"10.3390\/ijms21249419"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Ragon, M., Wirth, T., Hollandt, F., Lavenir, R., Lecuit, M., Le Monnier, A., and Brisse, S. (2008). A new perspective on Listeria monocytogenes evolution. PLoS Pathog., 4.","DOI":"10.1371\/journal.ppat.1000146"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Li, H., Wang, P., Lan, R., Luo, L., Cao, X., Wang, Y., Wang, Y., Li, H., Zhang, L., and Ji, S. (2018). Risk factors and level of Listeria monocytogenes contamination of raw pork in retail markets in China. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01090"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1083\/jcb.200201081","article-title":"The Listeria monocytogenes hemolysin has an acidic pH optimum to compartmentalize activity and prevent damage to infected host cells","volume":"156","author":"Glomski","year":"2002","journal-title":"J. Cell Biol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2175","DOI":"10.1128\/IAI.00110-15","article-title":"Avoidance of autophagy mediated by PlcA or ActA is required for Listeria monocytogenes growth in macrophages","volume":"83","author":"Mitchell","year":"2015","journal-title":"Infect. Immun."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"111188","DOI":"10.1016\/j.ijfoodmicro.2025.111188","article-title":"Comparative analysis of virulence in Listeria monocytogenes: Insights from genomic variations and in vitro cell-based studies","volume":"435","author":"Song","year":"2025","journal-title":"Int. J. Food Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Wiktorczyk-Kapischke, N., Skowron, K., and Wa\u0142ecka-Zacharska, E. (2023). Genomic and pathogenicity islands of Listeria monocytogenes\u2014Overview of selected aspects. Front. Mol. Biosci., 10.","DOI":"10.3389\/fmolb.2023.1161486"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Pedroni, L., Ghidini, S., Vazquez, J., Luque, F.J., and Dellafiora, L. (2025). Modeling the anti-adhesive role of punicalagin against Listeria monocytogenes from the analysis of the interaction between internalin a and e-cadherin. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26157327"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"2827","DOI":"10.1038\/sj.emboj.7600750","article-title":"Gp96 is a receptor for a novel Listeria monocytogenes virulence factor, Vip, a surface protein","volume":"24","author":"Cabanes","year":"2005","journal-title":"Embo J."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"379","DOI":"10.4161\/viru.2.5.17703","article-title":"The arsenal of virulence factors deployed by Listeria monocytogenes to promote its cell infection cycle","volume":"2","author":"Camejo","year":"2011","journal-title":"Virulence"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1126\/science.1200120","article-title":"A Bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response","volume":"331","author":"Lebreton","year":"2011","journal-title":"Science"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"e00743-24","DOI":"10.1128\/mbio.00743-24","article-title":"The chaperone PrsA2 regulates the secretion, stability, and folding of listeriolysin O during Listeria monocytogenes infection","volume":"15","author":"Agbavor","year":"2024","journal-title":"mBio"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"5062","DOI":"10.1128\/IAI.00516-10","article-title":"Listeria monocytogenes uses Listeria adhesion protein (LAP) to promote bacterial transepithelial translocation and induces expression of LAP receptor Hsp60","volume":"78","author":"Burkholder","year":"2010","journal-title":"Infect. Immun."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/S0923-2508(00)01166-9","article-title":"Detection and quantification of the iap gene of Listeria monocytogenes and Listeria innocua by a new real-time quantitative PCR assay","volume":"152","author":"Ingeborg","year":"2001","journal-title":"Res. Microbiol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"2509","DOI":"10.1080\/21505594.2021.1975526","article-title":"Pathogenicity and virulence of Listeria monocytogenes: A trip from environmental to medical microbiology","volume":"12","author":"Quereda","year":"2021","journal-title":"Virulence"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1368","DOI":"10.1128\/IAI.01519-07","article-title":"The Listeria monocytogenes virulence factor InlJ is specifically expressed in vivo and behaves as an adhesin","volume":"76","author":"Sabet","year":"2008","journal-title":"Infect. Immun."},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Parra-Flores, J., Daza-Prieto, B., Chavarria, P., Troncoso, M., Stoger, A., Figueroa, G., Mancilla-Rojano, J., Cruz-Cordova, A., Martinovic, A., and Ruppitsch, W. (2025). From traditional typing to genomic precision: Whole-genome sequencing of Listeria monocytogenes isolated from refrigerated foods in Chile. Foods, 14.","DOI":"10.3390\/foods14020290"},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Pyz-Lukasik, R., Paszkiewicz, W., Kielbus, M., Ziomek, M., Gondek, M., Domaradzki, P., Michalak, K., and Pietras-Ozga, D. (2022). Genetic diversity and potential virulence of Listeria monocytogenes isolates originating from polish artisanal cheeses. Foods, 11.","DOI":"10.3390\/foods11182805"},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Fern Tan, M., Siow, C.C., Dutta, A., Mutha, N.V., Wee, W.Y., Heydari, H., Tan, S.Y., Ang, M.Y., Wong, G.J., and Choo, S.W. (2015). Development of ListeriaBase and comparative analysis of Listeria monocytogenes. BMC Genom., 16.","DOI":"10.1186\/s12864-015-1959-5"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1111\/j.1365-2958.2001.02208.x","article-title":"The autolysin Ami contributes to the adhesion of Listeria monocytogenes to eukaryotic cells via its cell wall anchor","volume":"39","author":"Milohanic","year":"2001","journal-title":"Mol. Microbiol."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Lee, S. (2020). Bacteriocins of Listeria monocytogenes and their potential as a virulence factor. Toxins, 12.","DOI":"10.3390\/toxins12020103"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"e2108155118","DOI":"10.1073\/pnas.2108155118","article-title":"Listeriolysin S: A bacteriocin from Listeria monocytogenes that induces membrane permeabilization in a contact-dependent manner","volume":"118","author":"Lelek","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1128\/AAC.01139-07","article-title":"Activity of daptomycin against Listeria monocytogenes isolates from cerebrospinal fluid","volume":"52","author":"Spanjaard","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1128\/AAC.43.9.2103","article-title":"Antibiotic resistance in Listeria spp.","volume":"43","author":"Charpentier","year":"1999","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1697","DOI":"10.1128\/AAC.01211-07","article-title":"Comparison of the in vitro efficacies of moxifloxacin and amoxicillin against Listeria monocytogenes","volume":"52","author":"Grayo","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/j.ijfoodmicro.2008.10.018","article-title":"Characterization of antimicrobial resistance of foodborne Listeria monocytogenes","volume":"128","author":"Conter","year":"2009","journal-title":"Int. J. Food Microbiol."},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Manqele, A., Adesiyun, A., Mafuna, T., Pierneef, R., Moerane, R., and Gcebe, N. (2024). Virulence potential and antimicrobial resistance of Listeria monocytogenes isolates obtained from beef and beef-based products deciphered using whole-genome sequencing. Microorganisms, 12.","DOI":"10.3390\/microorganisms12061166"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/j.ijmm.2019.05.010","article-title":"MprF-mediated daptomycin resistance","volume":"309","author":"Ernst","year":"2019","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1111\/jam.12989","article-title":"The intrinsic cephalosporin resistome of Listeria monocytogenes in the context of stress response, gene regulation, pathogenesis and therapeutics","volume":"120","author":"Markiewicz","year":"2016","journal-title":"J. Appl. Microbiol."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.anaerobe.2008.08.001","article-title":"Growth, survival, proliferation and pathogenesis of Listeria monocytogenes under low oxygen or anaerobic conditions: A review","volume":"15","author":"Lungu","year":"2009","journal-title":"Anaerobe"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"10618","DOI":"10.1093\/nar\/gku734","article-title":"The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts","volume":"42","author":"Oliveira","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"8223","DOI":"10.1093\/nar\/gkr543","article-title":"Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI","volume":"39","author":"Shen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1016\/j.mib.2005.06.003","article-title":"The biology of restriction and anti-restriction","volume":"8","author":"Tock","year":"2005","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1126\/science.aba0372","article-title":"Diverse enzymatic activities mediate antiviral immunity in prokaryotes","volume":"369","author":"Gao","year":"2020","journal-title":"Science"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1016\/j.cell.2020.09.065","article-title":"Bacterial retrons function in anti-phage defense","volume":"183","author":"Millman","year":"2020","journal-title":"Cell"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"1560","DOI":"10.1111\/j.1365-2958.2008.06387.x","article-title":"RloC: A wobble nucleotide-excising and zinc-responsive bacterial tRNase","volume":"69","author":"Davidov","year":"2008","journal-title":"Mol. Microbiol."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1016\/j.tim.2023.05.002","article-title":"Abortive infection antiphage defense systems: Separating mechanism and phenotype","volume":"31","author":"Aframian","year":"2023","journal-title":"Trends Microbiol."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"6084","DOI":"10.1093\/nar\/gkac467","article-title":"UG\/Abi: A highly diverse family of prokaryotic reverse transcriptases associated with defense functions","volume":"50","author":"Mestre","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"4590","DOI":"10.1093\/nar\/gkt1419","article-title":"A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism","volume":"42","author":"Dy","year":"2014","journal-title":"Nucleic Acids Res."}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/1\/88\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T09:14:05Z","timestamp":1766999645000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/1\/88"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,28]]},"references-count":110,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["foods15010088"],"URL":"https:\/\/doi.org\/10.3390\/foods15010088","relation":{},"ISSN":["2304-8158"],"issn-type":[{"value":"2304-8158","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,28]]}}}