{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:38:40Z","timestamp":1760060320194,"version":"build-2065373602"},"reference-count":62,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,8,25]],"date-time":"2025-08-25T00:00:00Z","timestamp":1756080000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Vancomycin-resistant Enterococcus faecium (VREfm), particularly vanA-positive strains, represents a growing threat in hospital settings worldwide. These bacteria are able to survive under severe environmental conditions, including high temperatures and saline concentrations. High genome plasticity and advanced ability of inheriting antimicrobial resistance determinants defined the success of E. faecium as a hospital pathogen. Methods: This study presents the whole genomic characterization of vanA-positive VREfm isolates, analyzing 10 clinical isolates collected from three tertiary care hospitals in Moscow, Russia. Several typing approaches, including two MLST schemes and cgMLST profiles, were used to elucidate the relationship between the isolates. Phylogenetic analysis placed the isolates in context with global VREfm populations, demonstrating both local clonal expansion and possible international connections. Phenotypic and genomic antimicrobial resistance profiles were obtained, as well as data regarding the repertoire of virulence factors and plasmid content. Results: Whole genome sequencing revealed that all isolates belonged to the clinically significant CC17 lineage, specifically sequence types ST80 and ST552. Notably, two isolates possessed truncated Tn1546-type transposons lacking vanY and vanZ genes, representing a potentially emerging variant of the vanA operon in Russian clinical settings. A plasmid carrying a truncated vanA operon was reconstructed using long-read sequencing. Conclusions: The study highlights the utility of genomic investigation for tracking resistance mechanisms and strain dissemination, providing crucial baseline data for epidemiological surveillance of infections caused by VREfm in Russia. These findings emphasize the need for continued genomic monitoring to understand the evolution and spread of antimicrobial resistance in clinically important enterococcal lineages.<\/jats:p>","DOI":"10.3390\/antibiotics14090858","type":"journal-article","created":{"date-parts":[[2025,8,26]],"date-time":"2025-08-26T06:26:31Z","timestamp":1756189591000},"page":"858","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium Isolates with Full and Truncated vanA Operons from Russian Hospitals"],"prefix":"10.3390","volume":"14","author":[{"given":"Anna","family":"Slavokhotova","sequence":"first","affiliation":[{"name":"Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7409-077X","authenticated-orcid":false,"given":"Andrey","family":"Shelenkov","sequence":"additional","affiliation":[{"name":"Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5646-538X","authenticated-orcid":false,"given":"Yulia","family":"Mikhaylova","sequence":"additional","affiliation":[{"name":"Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lyudmila","family":"Petrova","sequence":"additional","affiliation":[{"name":"National Medical and Surgical Center Named After N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2900-1459","authenticated-orcid":false,"given":"Vitaly","family":"Gusarov","sequence":"additional","affiliation":[{"name":"National Medical and Surgical Center Named After N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikhail","family":"Zamyatin","sequence":"additional","affiliation":[{"name":"National Medical and Surgical Center Named After N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vasiliy","family":"Akimkin","sequence":"additional","affiliation":[{"name":"Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e2310852121","DOI":"10.1073\/pnas.2310852121","article-title":"Global diversity of enterococci and description of 18 previously unknown species","volume":"121","author":"Schwartzman","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1128\/MMBR.00023-12","article-title":"Enterococci in the environment","volume":"76","author":"Byappanahalli","year":"2012","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Hourigan, D., Stefanovic, E., Hill, C., and Ross, R.P. (2024). Promiscuous, persistent and problematic: Insights into current enterococcal genomics to guide therapeutic strategy. BMC Microbiol., 24.","DOI":"10.1186\/s12866-024-03243-2"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Li, G., Walker, M.J., and De Oliveira, D.M.P. (2022). Vancomycin Resistance in Enterococcus and Staphylococcus aureus. Microorganisms, 11.","DOI":"10.3390\/microorganisms11010024"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"101663","DOI":"10.1016\/j.cegh.2024.101663","article-title":"Vancomycin-resistant enterococci: A rising challenge to global health","volume":"28","author":"Iqbal","year":"2024","journal-title":"Clin. Epidemiol. Glob. Health"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/nrmicro2761","article-title":"The rise of the Enterococcus: Beyond vancomycin resistance","volume":"10","author":"Arias","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/s13073-021-00868-0","article-title":"The global dissemination of hospital clones of Enterococcus faecium","volume":"13","author":"Willems","year":"2021","journal-title":"Genome Med."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Garcia-Solache, M., and Rice, L.B. (2019). The Enterococcus: A Model of Adaptability to Its Environment. Clin. Microbiol. Rev., 32.","DOI":"10.1128\/CMR.00058-18"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"10.1128\/mbio.00151-12","DOI":"10.1128\/mBio.00151-12","article-title":"Restricted gene flow among hospital subpopulations of Enterococcus faecium","volume":"3","author":"Willems","year":"2012","journal-title":"Mbio"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.jgar.2018.08.016","article-title":"Antimicrobial-resistant CC17 Enterococcus faecium: The past, the present and the future","volume":"16","author":"Lee","year":"2019","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_11","unstructured":"WHO (2024). WHO Bacterial Priority Pathogens List, 2024: Bacterial Pathogens of Public Health Importance to Guide Research, Development and Strategies to Prevent and Control Antimicrobial Resistance, World Health Organization."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.jgar.2025.01.016","article-title":"Vancomycin-resistant Enterococcus faecium: A current perspective on resilience, adaptation, and the urgent need for novel strategies","volume":"41","author":"Novais","year":"2025","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Guffey, A.A., and Loll, P.J. (2021). Regulation of Resistance in Vancomycin-Resistant Enterococci: The VanRS Two-Component System. Microorganisms, 9.","DOI":"10.3390\/microorganisms9102026"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1963","DOI":"10.1128\/JCM.40.6.1963-1971.2002","article-title":"Multilocus sequence typing scheme for Enterococcus faecium","volume":"40","author":"Homan","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Bezdicek, M., Hanslikova, J., Nykrynova, M., Dufkova, K., Kocmanova, I., Kubackova, P., Mayer, J., and Lengerova, M. (2023). New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data. Microbiol. Spectr., 11.","DOI":"10.1128\/spectrum.05107-22"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"6978","DOI":"10.1128\/AAC.03648-14","article-title":"Enterococcus faecium PBP5-S\/R, the missing link between PBP5-S and PBP5-R","volume":"58","author":"Pietta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Anyanwu, M.U., Nwobi, O.C., Okpala, C.O.R., and Ezeonu, I.M. (2022). Mobile Tigecycline Resistance: An Emerging Health Catastrophe Requiring Urgent One Health Global Intervention. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.808744"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Korczak, L., Majewski, P., Iwaniuk, D., Sacha, P., Matulewicz, M., Wieczorek, P., Majewska, P., Wieczorek, A., Radziwon, P., and Tryniszewska, E. (2024). Molecular mechanisms of tigecycline-resistance among Enterobacterales. Front. Cell Infect. Microbiol., 14.","DOI":"10.3389\/fcimb.2024.1289396"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Kim, D., Kang, D.Y., Choi, M.H., Hong, J.S., Kim, H.S., Kim, Y.R., Kim, Y.A., Uh, Y., Shin, K.S., and Shin, J.H. (2024). Fitness costs of Tn1546-type transposons harboring the vanA operon by plasmid type and structural diversity in Enterococcus faecium. Ann. Clin. Microbiol. Antimicrob., 23.","DOI":"10.1186\/s12941-024-00722-2"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Mbanga, J., Amoako, D.G., Abia, A.L.K., Allam, M., Ismail, A., and Essack, S.Y. (2021). Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.648454"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Cho, S., McMillan, E.A., Barrett, J.B., Hiott, L.M., Woodley, T.A., House, S.L., Frye, J.G., and Jackson, C.R. (2022). Distribution and Transfer of Plasmid Replicon Families among Multidrug-Resistant Enterococcus faecalis and Enterococcus faecium from Poultry. Microorganisms, 10.","DOI":"10.3390\/microorganisms10061244"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1016\/j.jgar.2022.03.013","article-title":"Novel linear plasmids carrying vanA cluster drives the spread of vancomycin resistance in Enterococcus faecium in India","volume":"29","author":"Bakthavatchalam","year":"2022","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Tadesse, B.T., Svetlicic, E., Zhao, S., Berhane, N., Jers, C., Solem, C., and Mijakovic, I. (2024). Bad to the bone?\u2014Genomic analysis of Enterococcus isolates from diverse environments reveals that most are safe and display potential as food fermentation microorganisms. Microbiol. Res., 283.","DOI":"10.1016\/j.micres.2024.127702"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.2147\/IDR.S358248","article-title":"Prevalence of CRISPR-Cas Systems and Their Possible Association with Antibiotic Resistance in Enterococcus faecalis and Enterococcus faecium Collected from Hospital Wastewater","volume":"15","author":"Alduhaidhawi","year":"2022","journal-title":"Infect. Drug Resist."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Faury, H., Le Guen, R., Demontant, V., Rodriguez, C., Souhail, B., Galy, A., Jolivet, S., Lepeule, R., Decousser, J.W., and Fihman, V. (2023). Ampicillin-susceptible Enterococcus faecium infections: Clinical features, causal clades, and contribution of MALDI-TOF to early detection. Microbiol. Spectr., 11.","DOI":"10.1128\/spectrum.04545-22"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Monteiro Marques, J., Coelho, M., Santana, A.R., Pinto, D., and Semedo-Lemsaddek, T. (2023). Dissemination of Enterococcal Genetic Lineages: A One Health Perspective. Antibiotics, 12.","DOI":"10.3390\/antibiotics12071140"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"17","DOI":"10.46234\/ccdcw2021.277","article-title":"Antimicrobial-Resistant Evolution and Global Spread of Enterococcus faecium Clonal Complex (CC) 17: Progressive Change from Gut Colonization to Hospital-Adapted Pathogen","volume":"4","author":"Peng","year":"2022","journal-title":"China CDC Wkly."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Lee, S.Y., Nam, J.H., Kim, J.W., Kim, S.H., and Yoo, J.S. (2024). Prevalence of Vancomycin-Variable Enterococci from the Bloodstream in the Korea Global Antibiotic Resistance Surveillance System, 2017\u20132022. Antibiotics, 13.","DOI":"10.3390\/antibiotics13121210"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Rios, R., Reyes, J., Carvajal, L.P., Rincon, S., Panesso, D., Echeverri, A.M., Dinh, A., Kolokotronis, S.O., Narechania, A., and Tran, T.T. (2020). Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure. Sci. Rep., 10.","DOI":"10.1038\/s41598-020-62371-7"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"7795","DOI":"10.1128\/AAC.01732-15","article-title":"High Prevalence of vanM in Vancomycin-Resistant Enterococcus faecium Isolates from Shanghai, China","volume":"59","author":"Chen","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1016\/j.bjid.2017.07.001","article-title":"Clonal dissemination of vancomycin-resistant Enterococcus faecium ST412 in a Brazilian region","volume":"21","author":"Alves","year":"2017","journal-title":"Braz. J. Infect. Dis."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/j.jgar.2024.06.005","article-title":"Clonal expansion of Tn1546-like transposon-carrying vancomycin-resistant Enterococcus faecium, a nationwide study in Taiwan, 2004\u20132018","volume":"39","author":"Huang","year":"2024","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1007\/s10123-023-00441-2","article-title":"Molecular characterization and biofilm formation ability of Enterococcus faecium and Enterococcus faecalis bloodstream isolates from a Chinese tertiary hospital in Beijing","volume":"27","author":"Yang","year":"2024","journal-title":"Int. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"305","DOI":"10.36488\/cmac.2021.3.305-313","article-title":"Genetic diversity of vancomycinresistant Enterococcus faecium isolated from blood culture in patients with hematological malignancies","volume":"23","author":"Khrulnova","year":"2021","journal-title":"Clin. Microbiol. Antimicrob. Chemother."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/s41467-022-28156-4","article-title":"Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings","volume":"13","author":"Higgs","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"4110","DOI":"10.1128\/IAI.00375-08","article-title":"A functional collagen adhesin gene, acm, in clinical isolates of Enterococcus faecium correlates with the recent success of this emerging nosocomial pathogen","volume":"76","author":"Nallapareddy","year":"2008","journal-title":"Infect. Immun."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Ullah, M.A., Islam, M.S., Rana, M.L., Ferdous, F.B., Neloy, F.H., Firdous, Z., Hassan, J., and Rahman, M.T. (2023). Resistance Profiles and Virulence Determinants in Biofilm-Forming Enterococcus faecium Isolated from Raw Seafood in Bangladesh. Pathogens, 12.","DOI":"10.3390\/pathogens12091101"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Kiruthiga, A., Padmavathy, K., Shabana, P., Naveenkumar, V., Gnanadesikan, S., and Malaiyan, J. (2020). Improved detection of esp, hyl, asa1, gelE, cylA virulence genes among clinical isolates of Enterococci. BMC Res. Notes, 13.","DOI":"10.1186\/s13104-020-05018-0"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e0119621","DOI":"10.1128\/AAC.01196-21","article-title":"Prediction of Antimicrobial Resistance in Clinical Enterococcus faecium Isolates Using a Rules-Based Analysis of Whole-Genome Sequences","volume":"66","author":"Anahtar","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Bender, J.K., Fleige, C., Funk, F., Moreto-Castellsague, C., Fischer, M.A., and Werner, G. (2024). Linezolid Resistance Genes and Mutations among Linezolid-Susceptible Enterococcus spp.-A Loose Cannon?. Antibiotics, 13.","DOI":"10.3390\/antibiotics13010101"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Dadashi, M., Sharifian, P., Bostanshirin, N., Hajikhani, B., Bostanghadiri, N., Khosravi-Dehaghi, N., van Belkum, A., and Darban-Sarokhalil, D. (2021). The Global Prevalence of Daptomycin, Tigecycline, and Linezolid-Resistant Enterococcus faecalis and Enterococcus faecium Strains From Human Clinical Samples: A Systematic Review and Meta-Analysis. Front. Med., 8.","DOI":"10.3389\/fmed.2021.720647"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.jgar.2023.12.002","article-title":"The first tigecycline resistant Enterococcus faecium in Norway was related to tigecycline exposure","volume":"36","author":"Hegstad","year":"2024","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Zaheer, R., Cook, S.R., Barbieri, R., Goji, N., Cameron, A., Petkau, A., Polo, R.O., Tymensen, L., Stamm, C., and Song, J. (2020). Surveillance of Enterococcus spp. reveals distinct species and antimicrobial resistance diversity across a One-Health continuum. Sci. Rep., 10.","DOI":"10.1038\/s41598-020-61002-5"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e0166721","DOI":"10.1128\/AAC.01667-21","article-title":"Activity of Oritavancin against Gram-Positive Pathogens Causing Bloodstream Infections in the United States over 10 Years: Focus on Drug-Resistant Enterococcal Subsets (2010\u20132019)","volume":"66","author":"Carvalhaes","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"3351","DOI":"10.1093\/jac\/dkw312","article-title":"Multilevel population genetic analysis of vanA and vanB Enterococcus faecium causing nosocomial outbreaks in 27 countries (1986\u20132012)","volume":"71","author":"Freitas","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.drup.2018.10.002","article-title":"Update on prevalence and mechanisms of resistance to linezolid, tigecycline and daptomycin in enterococci in Europe: Towards a common nomenclature","volume":"40","author":"Bender","year":"2018","journal-title":"Drug Resist. Updates"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1016\/j.cmi.2017.12.016","article-title":"Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches","volume":"24","author":"Schurch","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"5229","DOI":"10.2147\/IDR.S494327","article-title":"CRISPR-Cas Systems in the Fight Against Antimicrobial Resistance: Current Status, Potentials, and Future Directions","volume":"17","author":"Ahmed","year":"2024","journal-title":"Infect. Drug Resist."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Rodriguez-Lucas, C., and Ladero, V. (2023). Enterococcal Phages: Food and Health Applications. Antibiotics, 12.","DOI":"10.3390\/antibiotics12050842"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_51","first-page":"e000146","article-title":"MentaLiST\u2014A fast MLST caller for large MLST schemes","volume":"4","author":"Feijao","year":"2018","journal-title":"Microb. Genom."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"3788","DOI":"10.1128\/JCM.01946-15","article-title":"Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium","volume":"53","author":"Pinholt","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_55","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_56","first-page":"e000224","article-title":"Mlplasmids: A user-friendly tool to predict plasmid- and chromosome-derived sequences for single species","volume":"4","author":"Rogers","year":"2018","journal-title":"Microb. Genom."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Zhu, Q., Gao, S., Xiao, B., He, Z., and Hu, S. (2023). Plasmer: An Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features. Microbiol. Spectr., 11.","DOI":"10.1128\/spectrum.04645-22"},{"key":"ref_58","first-page":"e000435","article-title":"Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance","volume":"6","author":"Robertson","year":"2020","journal-title":"Microb. Genom."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Ross, K., Varani, A.M., Snesrud, E., Huang, H., Alvarenga, D.O., Zhang, J., Wu, C., McGann, P., and Chandler, M. (2021). TnCentral: A Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. Mbio, 12.","DOI":"10.1128\/mBio.02060-21"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"W246","DOI":"10.1093\/nar\/gky425","article-title":"CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins","volume":"46","author":"Couvin","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Egorova, A., Mikhaylova, Y., Saenko, S., Tyumentseva, M., Tyumentsev, A., Karbyshev, K., Chernyshkov, A., Manzeniuk, I., Akimkin, V., and Shelenkov, A. (2021). Comparative Whole-Genome Analysis of Russian Foodborne Multidrug-Resistant Salmonella Infantis Isolates. Microorganisms, 10.","DOI":"10.3390\/microorganisms10010089"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Shelenkov, A., Petrova, L., Fomina, V., Zamyatin, M., Mikhaylova, Y., and Akimkin, V. (2020). Multidrug-Resistant Proteus mirabilis Strain with Cointegrate Plasmid. Microorganisms, 8.","DOI":"10.3390\/microorganisms8111775"}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/9\/858\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:32:43Z","timestamp":1760034763000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/9\/858"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,25]]},"references-count":62,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["antibiotics14090858"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics14090858","relation":{},"ISSN":["2079-6382"],"issn-type":[{"type":"electronic","value":"2079-6382"}],"subject":[],"published":{"date-parts":[[2025,8,25]]}}}