{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,6]],"date-time":"2025-08-06T12:39:29Z","timestamp":1754483969837,"version":"3.41.2"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T00:00:00Z","timestamp":1728864000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p><jats:italic>Neisseria meningitidis<\/jats:italic> is a gram-negative bacterium responsible for life-threatening invasive infections known as invasive meningococcal disease and is associated with high fatality rates and serious lifelong disabilities among survivors.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>This study aimed to characterize <jats:italic>N. meningitidis<\/jats:italic> isolates cultured from blood and cerebrospinal fluid collected between 2009 and 2021 in Lithuania, assess their genomic relationships with European strains, and evaluate the possibility of using a cost-effective method for strain characterization, thus improving the national molecular surveillance of invasive meningococcal disease. In total, 321 <jats:italic>N. meningitidis<\/jats:italic> isolates were collected and analyzed using multilocus restriction typing (MLRT). Amplification of the <jats:italic>penA<\/jats:italic> gene and restriction fragment length polymorphism analysis were performed to identify the modified <jats:italic>penA<\/jats:italic> genes. Based on the MLRT genotyping results, we selected 10 strains for additional analysis using whole-genome sequencing. The sequenced genomes were incorporated into a dataset of publicly available <jats:italic>N. meningitidis<\/jats:italic> genomes to evaluate genomic diversity and establish phylogenetic relationships within the Lithuanian and European circulating strains.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We identified 83 different strains using MLRT genotyping. Genomic diversity of <jats:italic>N. meningitidis<\/jats:italic> genomes analysed revealed 21 different sequence types (STs) circulating in Lithuania. Among these, ST34 was the most prevalent. Notably, three isolates displayed unique combinations of seven housekeeping genes and were identified as novel STs: ST16969, ST16901, and ST16959. The analyzed strains were found to possess virulence factors not commonly found in <jats:italic>N. meningitidis<\/jats:italic>. Six distinct <jats:italic>penA<\/jats:italic> profiles were identified, each with different frequencies. In the present study, we also identified <jats:italic>N. meningitidis<\/jats:italic> strains with new <jats:italic>penA<\/jats:italic>, NEIS0123, NEIS1320, NEIS1525, NEIS1600, and NEIS1753 loci variants. In our study, using the cgMLST scheme, Minimum Spanning Tree (MST) analysis did not identify significant geographic relationships between Lithuanian <jats:italic>N.\u00a0meningitidis<\/jats:italic> isolates and strains from Europe.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>Discussion: To our knowledge, this is the first study to employ whole genome sequencing (WGS) method for a comprehensive genetic characterization of invasive <jats:italic>N. meningitidis<\/jats:italic> isolates from Lithuania. This approach provides a more detailed and precise analysis of genomic relationships and diversity compared to prior studies relying on traditional molecular typing methods and antigen analysis.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2024.1432197","type":"journal-article","created":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T10:13:39Z","timestamp":1728900819000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Genetic characterization of Neisseria meningitidis isolates recovered from patients with invasive meningococcal disease in Lithuania"],"prefix":"10.3389","volume":"14","author":[{"given":"An\u017eelika","family":"Slavinska","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Magdalena","family":"Kowalczyk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agn\u0117","family":"Kirkliauskien\u0117","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Greta","family":"Vizuje","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pawe\u0142","family":"Siedlecki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joana","family":"Bikul\u010dien\u0117","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristina","family":"Tamo\u0161i\u016bnien\u0117","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aurelija","family":"Petrutien\u0117","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nomeda","family":"Kuisiene","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2024,10,14]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1080\/14760584.2019.1557520","article-title":"The Global Meningococcal Initiative meeting on prevention of meningococcal disease worldwide: Epidemiology, surveillance, hypervirulent strains, antibiotic resistance and high-risk populations","volume":"18","author":"Acevedo","year":"2019","journal-title":"Expert Rev. Vaccines"},{"key":"B2","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/NAR\/GKZ935","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1016\/j.jinf.2021.11.016","article-title":"Surveillance and control of meningococcal disease in the COVID-19 era: A Global Meningococcal Initiative review","volume":"84","author":"Alderson","year":"2022","journal-title":"J. Infect."},{"key":"B4","doi-asserted-by":"publisher","first-page":"3625","DOI":"10.1128\/AAC.45.12.3625-3628.2001","article-title":"Nonculture prediction of neisseria meningitidis susceptibility to penicillin","volume":"45","author":"Antignac","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"B5","doi-asserted-by":"publisher","first-page":"781","DOI":"10.1099\/jmm.0.05225-0","article-title":"Multilocus restriction typing: A tool for Neisseria meningitidis strain discrimination","volume":"52","author":"Bennett","year":"2003","journal-title":"J. Med. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0228629","article-title":"Diversity of meningococci associated with invasive meningococcal disease in the Republic of Ireland over a 19 year period 1996-2015","volume":"15","author":"Bennett","year":"2020","journal-title":"PloS One"},{"key":"B7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-15-1138","article-title":"A gene-by-gene population genomics platform: De novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes","volume":"15","author":"Bratcher","year":"2014","journal-title":"BMC Genomics"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1016\/S2589-7500(21)00077-7","article-title":"Changes in the incidence of invasive disease due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis during the COVID-19 pandemic in 26 countries and territories in the Invasive Respiratory Infection Surveillance Initiative: a","volume":"3","author":"Brueggemann","year":"2021","journal-title":"Lancet Digit. Heal"},{"key":"B9","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1038\/s41579-019-0282-6","article-title":"Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis","volume":"18","author":"Caugant","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"B64","DOI":"10.1016\/J.VACCINE.2009.04.061","article-title":"Meningococcal carriage and disease\u2014Population biology and evolution","volume":"27","author":"Caugant","year":"2009","journal-title":"Vaccine"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01494-19","article-title":"Meningococcal quinolone resistance originated from several commensal neisseria species","volume":"64","author":"Chen","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PONE.0077302","article-title":"PathogenFinder - distinguishing friend from foe using bacterial whole genome sequence data","volume":"8","author":"Cosentino","year":"2013","journal-title":"PloS One"},{"key":"B13","doi-asserted-by":"publisher","first-page":"3208","DOI":"10.1128\/JCM.00221-08","article-title":"Neisseria meningitidis intermediately resistant to penicillin and causing invasive disease in South Africa in 2001 to 2005","volume":"46","author":"Du Plessis","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"B14","unstructured":"Surveillance Atlas of Infectious Diseases\n          \n          2023"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.19082\/5149","article-title":"Molecular epidemiology of infectious diseases","volume":"9","author":"Eybpoosh","year":"2017","journal-title":"Electron. Physician"},{"key":"B16","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1093\/oxfordjournals.molbev.a026203","article-title":"Horizontal Gene Transfer in Glycosyl Hydrolases Inferred from Codon Usage in Escherichia coli and Bacillus subtilis","volume":"16","author":"Garcia-Vallv\u00e9","year":"1999","journal-title":"Mol. Biol. Evol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1093\/GBE\/EVR119","article-title":"Extensive Genomic Variation within Clonal Complexes of Neisseria meningitidis","volume":"3","author":"Hao","year":"2011","journal-title":"Genome Biol. Evol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1128\/AAC.00994-08","article-title":"Antibiotic susceptibility and characteristics of neisseria meningitidis isolates from the african meningitis belt 2000 to 2006: phenotypic and genotypic perspectives","volume":"53","author":"Hedberg","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00831-18","article-title":"Acquisition of Beta-Lactamase by Neisseria meningitidis through Possible Horizontal Gene Transfer","volume":"62","author":"Hong","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.3390\/BIOLOGY2031054","article-title":"The biology of neisseria adhesins","volume":"2","author":"Hung","year":"2013","journal-title":"Biol. (Basel)"},{"key":"B21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12866-023-03111-5","article-title":"Molecular characteristics of Neisseria meningitidis carriage strains in university students in Lithuania","volume":"23","author":"Iva\u0161kevi\u010dien\u0117","year":"2023","journal-title":"BMC Microbiol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/WELLCOMEOPENRES.14826.1","article-title":"Open-access bacterial\u00a0population genomics: BIGSdb software, the PubMLST.org website and\u00a0their\u00a0applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"B23","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1111\/J.1574-6976.2006.00057.X","article-title":"Molecular typing of meningococci: recommendations for target choice and nomenclature","volume":"31","author":"Jolley","year":"2007","journal-title":"FEMS Microbiol. Rev."},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1016\/J.MEDMIC.2023.100087","article-title":"Survival and evasion of Neisseria meningitidis from macrophages","volume":"17","author":"Joshi","year":"2023","journal-title":"Med. Microecol"},{"key":"B25","doi-asserted-by":"publisher","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.\u00a0Mol. Biol."},{"key":"B26","doi-asserted-by":"publisher","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":"B27","doi-asserted-by":"publisher","first-page":"D687","DOI":"10.1093\/NAR\/GKY1080","article-title":"VFDB 2019: a comparative pathogenomic platform with an interactive web interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1155\/2019\/6015730","article-title":"Genus-wide comparative genomics analysis of neisseria to identify new genes associated with pathogenicity and niche adaptation of neisseria pathogens","volume":"2019","author":"Lu","year":"2019","journal-title":"Int. J. Genomics"},{"key":"B29","doi-asserted-by":"publisher","first-page":"3140","DOI":"10.1073\/PNAS.95.6.3140","article-title":"Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic\u2009microorganisms","volume":"95","author":"Maiden","year":"1998","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.3389\/FCIMB.2022.862935","article-title":"The host-pathogen interactions and epicellular lifestyle of neisseria meningitidis","volume":"12","author":"Mikucki","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/NAR\/GKAA913","article-title":"Pfam: The protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1099\/MGEN.0.000662","article-title":"Modelling evolutionary pathways for commensalism and hypervirulence in Neisseria meningitidis","volume":"7","author":"Mullally","year":"2021","journal-title":"Microb. Genomics"},{"key":"B33","doi-asserted-by":"publisher","first-page":"S21","DOI":"10.1016\/J.JADOHEALTH.2016.04.013","article-title":"Treatment of meningococcal disease","volume":"59","author":"Nadel","year":"2016","journal-title":"J. Adolesc. Heal"},{"key":"B34","doi-asserted-by":"publisher","first-page":"D206","DOI":"10.1093\/NAR\/GKT1226","article-title":"The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)","volume":"42","author":"Overbeek","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"B35","doi-asserted-by":"publisher","first-page":"D418","DOI":"10.1093\/NAR\/GKAC993","article-title":"InterPro in 2022","volume":"51","author":"Paysan-Lafosse","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B36","doi-asserted-by":"publisher","first-page":"9834","DOI":"10.3390\/IJMS23179834","article-title":"Combination of whole genome sequencing and metagenomics for microbiological diagnostics","volume":"23","author":"Purushothaman","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"B37","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1016\/j.jinf.2020.06.064","article-title":"The global meningitis genome partnership","volume":"81","author":"Rodgers","year":"2020","journal-title":"J. Infect."},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02161-20","article-title":"Meningococcal deduced vaccine antigen reactivity (MenDeVAR) index: a rapid and accessible tool that exploits genomic data in public health and clinical microbiology applications","volume":"59","author":"Rodrigues","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/J.IJMMB.2022.05.005","article-title":"A systematic review and meta-analysis on the antibiotic resistance of Neisseria meningitidis in the last 20 years in the world","volume":"40","author":"Rostamian","year":"2022","journal-title":"Indian J. Med. Microbiol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"B103","DOI":"10.1016\/J.VACCINE.2009.04.064","article-title":"Genome flexibility in Neisseria meningitidis","volume":"27","author":"Schoen","year":"2009","journal-title":"Vaccine"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.3389\/FCIMB.2023.1136211\/BIBTEX","article-title":"Molecular characterization of invasive Neisseria meningitidis isolates collected in Lithuania, (2009-2019) and estimation of serogroup B meningococcal vaccine 4CMenB and MenB-Fhbp coverage","volume":"13","author":"Sereikait\u0117","year":"2023","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"434","DOI":"10.3201\/EID2503.181574","article-title":"University-based outbreaks of meningococcal disease caused by serogroup B, United States 2013\u20132018","volume":"25","author":"Soeters","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"B43","doi-asserted-by":"publisher","first-page":"2196","DOI":"10.1016\/S0140-6736(07)61016-2","article-title":"Epidemic meningitis, meningococcaemia, and Neisseria meningitidis","volume":"369","author":"Stephens","year":"2007","journal-title":"Lancet"},{"key":"B44","doi-asserted-by":"publisher","first-page":"3651","DOI":"10.1128\/AAC.00315-10","article-title":"Multicenter Study for Defining the Breakpoint for Rifampin Resistance in Neisseria meningitidis by rpoB Sequencing. Antimicrob","volume":"54","author":"Taha","year":"2010","journal-title":"Agents Chemother."},{"key":"B45","doi-asserted-by":"publisher","first-page":"2784","DOI":"10.1128\/AAC.00412-07","article-title":"Target gene sequencing to characterize the penicillin G susceptibility of neisseria meningitidis. Antimicrob","volume":"51","author":"Taha","year":"2007","journal-title":"Agents Chemother."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2018.23.28.1700590","article-title":"Community outbreak of serogroup B invasive meningococcal disease in Beaujolais, France, February to June 2016: from alert to targeted vaccination","volume":"23","author":"Thabuis","year":"2018","journal-title":"Eurosurveillance"},{"key":"B47","unstructured":"Breakpoint Tables for Interpretation of MICs and Zone Diameters. Version 13.1\n          \n          2023"},{"key":"B48","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1093\/JAC\/DKY391","article-title":"WGS analysis of a penicillin-resistant Neisseria meningitidis strain containing a chromosomal ROB-1 \u03b2-lactamase gene","volume":"74","author":"Tsang","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9030519","article-title":"A narrative review of the W, X, Y, E, and NG of meningococcal disease: emerging capsular groups, pathotypes, and global control","volume":"9","author":"Tzeng","year":"2021","journal-title":"Microorganisms"},{"key":"B50","doi-asserted-by":"publisher","first-page":"951","DOI":"10.1111\/MMI.14197","article-title":"Streptococcal dTDP\u2010L\u2010rhamnose biosynthesis enzymes: functional characterization and lead compound identification","volume":"111","author":"van der Beek","year":"2019","journal-title":"Mol. Microbiol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1093\/BIOINFORMATICS\/BTP033","article-title":"Jalview Version 2\u2014a multiple sequence alignment editor and analysis workbench","volume":"25","author":"Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"B52","doi-asserted-by":"publisher","first-page":"2275","DOI":"10.1128\/JB.00094-12","article-title":"Prevalence and detailed mapping of the gonococcal genetic island in neisseria meningitidis","volume":"194","author":"Woodhams","year":"2012","journal-title":"J. Bacteriol"},{"key":"B53","doi-asserted-by":"publisher","first-page":"1608","DOI":"10.1093\/BIOINFORMATICS\/BTQ249","article-title":"PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"key":"B54","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1128\/JCM.00918-11","article-title":"Development of a multiplex PCR assay for detection and genogrouping of neisseria meningitidis","volume":"50","author":"Zhu","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"B55","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1080\/14760584.2023.2225596","article-title":"Invasive meningococcal disease epidemiology and vaccination strategies in four Southern European countries: a review of the available data","volume":"22","author":"Zografaki","year":"2023","journal-title":"Expert Rev. Vaccines"}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1432197\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T10:13:44Z","timestamp":1728900824000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1432197\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,14]]},"references-count":55,"alternative-id":["10.3389\/fcimb.2024.1432197"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2024.1432197","relation":{},"ISSN":["2235-2988"],"issn-type":[{"type":"electronic","value":"2235-2988"}],"subject":[],"published":{"date-parts":[[2024,10,14]]},"article-number":"1432197"}}