Database Authors
Anamika Kothari1, Suzanne Paley1, Ron Caspi1, Anahit Penesyan2, Brendan Wilson-Mortier2, Ian Paulsen2, Peter D Karp1
1SRI International, 2Macquarie University
Summary This manually curated PGDB represents the genome of the serogroup B strain Neisseria meningitidis MC58, the reference genome of N. meningitidis [Tettelin00]. N. meningitidis is a Gram-negative diplococcus of the Neisseriaceae family and the etiological agent of invasive meningococcal disease (IMD) [Yazdankhah04, Stephens07, Rouphael12]. N. meningitidis commensally colonizes the nasopharynx of approximately 10% of healthy adults, though carriage rates of up to 55% have been reported in some subpopulations [Yazdankhah04, Read14].

IMD arises from a limited set of hyperinvasive clonal complexes, most of which are associated with serogroups A, B, C, W, X and Y; these isolates are capable of invading the bloodstream, resulting in potentially life-threatening septicemia and/or meningitis [Yazdankhah04, Hill10, Coureuil12, Caugant20]. Modelled global estimates suggest that the total burden of IMD may have exceeded 700,000 cases in 2019, with high incidence rates in infants and young adolescents [Caugant20, Shen24]. Fatality rates vary by serogroup, clinical presentation, age and comorbidity, but range from approximately 4-20% [Hill10, Wang19d].

An array of virulence factors facilitate pathogenesis in N. meningitidis, including the capsular polysaccharide, lipooligosaccharide (LOS), type IV pili, adhesive outer-membrane proteins, and iron acquisition systems [Hill10, Rouphael12, Pizza15, Tzeng16, Caugant20]. As with its close relative Neisseria gonorrhoeae, many of these surface structures undergo high-frequency phase variation. This results in substantial population heterogeneity, effective antigenic variation, and subsequent immune evasion [Saunders00, Martin03, Snyder01]. High rates of intraspecies and interspecies recombination amongst N. meningitidis and related Neisseria species also contribute to its genomic diversity and plasticity [Maiden08, Kong13, Joseph11].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp16, Karp11] component of Pathway Tools software version 29.5 and MetaCyc [Caspi18] version 29.5 on 26-Aug-2025 21:04:37.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
GEN-EL14979592,0812,006751842,272,360NCBI Assembly:GCF_000008805.1
Ortholog data available?Yes
Database Contents
Genes2,087
Pathways171
Enzymatic Reactions1,227
Transport Reactions70
Polypeptides2,025
Protein Complexes77
Enzymes641
Transporters159
Compounds971
Transcription Units1,657
tRNAs59
Transcriptional Regulation278
Protein Features2,597
GO Annotations16,492
Database Version29.6
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Betaproteobacteria
Neisseriales
Neisseriaceae
Neisseria
Neisseria meningitidis
Neisseria meningitidis serogroup B
Neisseria meningitidis MC58
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603997
NCBI BioProjectPRJNA224116
NCBI-Taxonomy122586
Annotation ProviderNCBI RefSeq
Annotation Date2025-01-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.9
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Caugant20: Caugant DA, Brynildsrud OB (2020). "Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis." Nat Rev Microbiol 18(2);84-96. PMID: 31705134

Coureuil12: Coureuil M, Join-Lambert O, Lecuyer H, Bourdoulous S, Marullo S, Nassif X (2012). "Mechanism of meningeal invasion by Neisseria meningitidis." Virulence 3(2);164-72. PMID: 22366962

Hill10: Hill DJ, Griffiths NJ, Borodina E, Virji M (2010). "Cellular and molecular biology of Neisseria meningitidis colonization and invasive disease." Clin Sci (Lond) 118(9);547-64. PMID: 20132098

Joseph11: Joseph B, Schwarz RF, Linke B, Blom J, Becker A, Claus H, Goesmann A, Frosch M, Muller T, Vogel U, Schoen C (2011). "Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome." PLoS One 6(4);e18441. PMID: 21541312

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Kong13: Kong Y, Ma JH, Warren K, Tsang RS, Low DE, Jamieson FB, Alexander DC, Hao W (2013). "Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis." Genome Biol Evol 5(9);1611-27. PMID: 23902748

Maiden08: Maiden MC (2008). "Population genomics: diversity and virulence in the Neisseria." Curr Opin Microbiol 11(5);467-71. PMID: 18822386

Martin03: Martin P, van de Ven T, Mouchel N, Jeffries AC, Hood DW, Moxon ER (2003). "Experimentally revised repertoire of putative contingency loci in Neisseria meningitidis strain MC58: evidence for a novel mechanism of phase variation." Mol Microbiol 50(1);245-57. PMID: 14507378

Pizza15: Pizza M, Rappuoli R (2015). "Neisseria meningitidis: pathogenesis and immunity." Curr Opin Microbiol 23;68-72. PMID: 25461575

Read14: Read RC (2014). "Neisseria meningitidis; clones, carriage, and disease." Clin Microbiol Infect 20(5);391-5. PMID: 24766477

Rouphael12: Rouphael NG, Stephens DS (2012). "Neisseria meningitidis: biology, microbiology, and epidemiology." Methods Mol Biol 799;1-20. PMID: 21993636

Saunders00: Saunders NJ, Jeffries AC, Peden JF, Hood DW, Tettelin H, Rappuoli R, Moxon ER (2000). "Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58." Mol Microbiol 37(1);207-15. PMID: 10931317

Shen24: Shen S, Findlow J, Peyrani P (2024). "Global Epidemiology of Meningococcal Disease-Causing Serogroups Before and After the COVID-19 Pandemic: A Narrative Review." Infect Dis Ther 13(12);2489-2507. PMID: 39509011

Snyder01: Snyder LAS, Butcher SA, Saunders NJ (2001). "Comparative whole-genome analyses reveal over 100 putative phase-variable genes in the pathogenic Neisseria spp." Microbiology (Reading) 147(Pt 8);2321-2332. PMID: 11496009

Stephens07: Stephens DS, Greenwood B, Brandtzaeg P (2007). "Epidemic meningitis, meningococcaemia, and Neisseria meningitidis." Lancet 369(9580);2196-2210. PMID: 17604802

Tettelin00: Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC (2000). "Complete genome sequence of Neisseria meningitidis serogroup B strain MC58." Science 287(5459);1809-15. PMID: 10710307

Tzeng16: Tzeng YL, Thomas J, Stephens DS (2016). "Regulation of capsule in Neisseria meningitidis." Crit Rev Microbiol 42(5);759-72. PMID: 26089023

Wang19d: Wang B, Santoreneos R, Giles L, Haji Ali Afzali H, Marshall H (2019). "Case fatality rates of invasive meningococcal disease by serogroup and age: A systematic review and meta-analysis." Vaccine 37(21);2768-2782. PMID: 30987851

Yazdankhah04: Yazdankhah SP, Caugant DA (2004). "Neisseria meningitidis: an overview of the carriage state." J Med Microbiol 53(Pt 9);821-832. PMID: 15314188

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Page generated by Pathway Tools version 29.5 (software by SRI International) on Tue Jun 16, 2026, BIOCYC15.