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Full information on isolate Z2491 (id:613)

Projects

This isolate is a member of the following projects:

107 global collection: This dataset was originally used to validate MLST and was chosen to represent global diversity of N. meningitidis in the latter half of the Twentieth Century. It has been used in many publications since and the isolates are available as the EMGM MLST reference collection.
GMGL: Global Meningitis Genome Library: curated isolate data sets of N. meningtidis causing meningitis and/or septicaemia

Provenance/primary metadata

id: 613
isolate: Z2491
strain designation: A: P1.7,13-1: F1-5: ST-4 (cc4)
aliases: BennettTree09; C751; NIBSC_2763; Z6244
country: The Gambia
continent: Africa
year: 1983
disease: meningitis
source: CSF
epidemiology: epidemic
species: Neisseria meningitidis
serogroup: A
genogroup: A
genogroup notes: A backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
capsule group: A
serotype: 4,21
sero subtype: P1.7b,13a
type strain: 0
comments: Genome sequenced at Sanger Institute.

Tracking

bioproject accession: PRJEB2090 www.ebi.ac.uk
biosample accession: ERS006949; SAMEA678433 www.ebi.ac.uk
sender: Mark Achtman, Max-Planck Institut fur Infektionsbiologie, Schumannstr. 21/22, Berlin, Germany
curator: Auto Tagger
update history: 315 updates show details
date entered: 2001-02-07
datestamp: 2023-08-25

Secondary metadata

Deduced vaccine reactivity

Bexsero reactivity: insufficient data notes
Trumenba reactivity: insufficient data notes

Bexsero^® (4CMenB) is a multicomponent vaccine.

Protein-based meningococcal vaccines contain surface proteins as vaccine antigens, these proteins demonstrate nucleotide and amino acid sequence diversity.
Peptide sequence diversity can be analysed using the Bexsero Antigen Sequence Typing (BAST) scheme¹.
Bexsero^® contains: fHbp peptide 1; NHBA peptide 2; NadA peptide 8; PorA VR2 4.

The Deduced Vaccine Antigen Reactivity (MenDeVAR) Index was developed to combine multiple, complex data that inform the reactivity of each vaccine against specific antigenic variants.

The MenDeVAR Index:

isolate contains ≥1 exact sequence match to antigenic variants found in the vaccine.
isolate contains ≥1 antigenic variant deemed cross-reactive to vaccine variants through experimental studies.
all the isolate's antigenic variants have been deemed not cross-reactive to vaccine variants through experimental studies.
isolate contains antigens for which there is insufficient data from or are yet to be tested in experimental studies.

It is important to understand the caveats to interpreting the MenDeVAR Index:

Source of data - These data combine multiple sources of information including: peptide sequence identity through whole genome sequencing; experimental assays developed as indirect measures of the breadth of vaccine protection against diverse meningococci; and assays developed to assess immunogenicity. The Meningococcal Antigen Typing System (MATS)² assay was used for Bexsero^®.

Cross-reactivity definition - An antigenic variant was considered cross-reactive if it had been tested in ≥5 isolates/subjects and was above the accepted threshold in ≥75% of those isolates. This was established through combined analysis of published experimental studies (PMID provided for each variant), not from genomic data. These assays were based on serogroup B disease isolates.

Protein expression - We have not inferred from genomic data, therefore there may be isolates that possess genes but do no express the protein in vivo.

Age of vaccinees - For MATS assay development², Bexsero^® vaccine recipients were infants who had received 3 doses of vaccine and then a booster at 12 months. The pooled sera used for the MATS assay were taken from the toddlers at 13 months of age.

Brehony C, Rodrigues CMC, Borrow R, et al. Distribution of Bexsero^® Antigen Sequence Types (BASTs) in invasive meningococcal disease isolates: Implications for immunisation. Vaccine 2016 34(39):4690-7
Donnelly J, Medini D, Boccadifuoco G, et al. Qualitative and quantitative assessment of meningococcal antigens to evaluate the potential strain coverage of protein-based vaccines. Proc Natl Acad Sci USA 2010;107(45):19490-19495

MenDeVAR is described in Rodrigues et al. 2020, J Clin Microbiol 59(1):e02161-20. Please contact us if you have queries.

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Trumenba^® (rLP2086) is a bivalent fHbp-containing vaccine.

Protein-based meningococcal vaccines contain surface proteins as vaccine antigens, these proteins demonstrate nucleotide and amino acid sequence diversity.
Peptide sequence diversity can be analysed using the fhbp peptide locus.
Trumenba^® vaccine contains fHbp peptides 45 and 551.

The Deduced Vaccine Antigen Reactivity (MenDeVAR) Index was developed to combine multiple, complex data that inform the reactivity of each vaccine against specific antigenic variants.

The MenDeVAR Index:

isolate contains ≥1 exact sequence match to antigenic variants found in the vaccine.
isolate contains ≥1 antigenic variant deemed cross-reactive to vaccine variants through experimental studies.
all the isolate's antigenic variants have been deemed not cross-reactive to vaccine variants through experimental studies.
isolate contains antigens for which there is insufficient data from or are yet to be tested in experimental studies.

It is important to understand the caveats to interpreting the MenDeVAR Index:

Source of data - These data combine multiple sources of information including: peptide sequence identity through whole genome sequencing; experimental assays developed as indirect measures of the breadth of vaccine protection against diverse meningococci; and assays developed to assess immunogenicity. The meningococcal antigen surface expression (MEASURE)² and serum bactericidal activity (SBA) assays were used for Trumenba^®.

Age of vaccinees - The age of vaccine recipients in the experimental studies varies widely, ranging from toddlers to adults, and needs to be taken into consideration when interpreting results. Vaccine studies used different schedules and doses of vaccines.

Jiang HQ, Hoiseth SK, Harris SL, et al. Broad vaccine coverage predicted for a bivalent recombinant factor H binding protein based vaccine to prevent serogroup B meningococcal disease. Vaccine 2010;28(37):6086-93
McNeil LK, Donald RGK, Gribenko A, et al. Predicting the Susceptibility of Meningococcal Serogroup B Isolates to Bactericidal Antibodies Elicited by Bivalent rLP2086, a Novel Prophylactic Vaccine. mBio 2018;9(2):e00036-18

MenDeVAR is described in Rodrigues et al. 2020, J Clin Microbiol 59(1):e02161-20. Please contact us if you have queries.

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Publications (20)

Bennett JS, Bentley SD, Vernikos GS, Quail MA, Cherevach I, White B, Parkhill J, Maiden MC (2010). Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06. BMC Genomics 11:652
Bennett JS, Jolley KA, Earle SG, Corton C, Bentley SD, Parkhill J, Maiden MC (2012). A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria. Microbiology 158:1570-80
Bennett JS, Jolley KA, Maiden MC (2013). Genome sequence analyses show that Neisseria oralis is the same species as 'Neisseria mucosa var. heidelbergensis'. Int J Syst Evol Microbiol 63:3920-6
Bennett JS, Jolley KA, Sparling PF, Saunders NJ, Hart CA, Feavers IM, Maiden MC (2007). Species status of Neisseria gonorrhoeae: evolutionary and epidemiological inferences from multilocus sequence typing. BMC Biol 5:35
Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MC (2014). A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics 15:1138
Brik A, Terrade A, Hong E, Deghmane A, Taha MK, Bouafsoun A, Khmiri M, Boussetta K, Boukhir S, Jaballah NB, Kechrid A, Smaoui H (2020). Phenotypic and genotypic characterization of meningococcal isolates in Tunis, Tunisia: High diversity and impact on vaccination strategies. Int J Infect Dis 91:73-78
Budroni S, Siena E, Dunning Hotopp JC, Seib KL, Serruto D, Nofroni C, Comanducci M, Riley DR, Daugherty SC, Angiuoli SV, Covacci A, Pizza M, Rappuoli R, Moxon ER, Tettelin H, Medini D (2011). Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination. Proc Natl Acad Sci U S A 108:4494-9
Dempsey JA, Wallace AB, Cannon JG (1995). The physical map of the chromosome of a serogroup A strain of Neisseria meningitidis shows complex rearrangements relative to the chromosomes of the two mapped strains of the closely related species N. gonorrhoeae. J Bacteriol 177:6390-400
Diallo K, MacLennan J, Harrison OB, Msefula C, Sow SO, Daugla DM, Johnson E, Trotter C, MacLennan CA, Parkhill J, Borrow R, Greenwood BM, Maiden MCJ (2019). Genomic characterization of novel Neisseria species. Sci Rep 9:13742
Didelot X, Urwin R, Maiden MC, Falush D (2009). Genealogical typing of Neisseria meningitidis. Microbiology 155:3176-86
Jolley KA, Sun L, Moxon ER, Maiden MC (2004). Dam inactivation in Neisseria meningitidis: prevalence among diverse hyperinvasive lineages. BMC Microbiol 4:34
Jolley KA, Wilson DJ, Kriz P, McVean G, Maiden MC (2005). The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis. Mol Biol Evol 22:562-9
Katz LS, Sharma NV, Harcourt BH, Thomas JD, Wang X, Mayer LW, Jordan IK (2011). Using single-nucleotide polymorphisms to discriminate disease-associated from carried genomes of Neisseria meningitidis. J Bacteriol 193:3633-41
Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998). Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140-5
Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, Klee SR, Morelli G, Basham D, Brown D, Chillingworth T, Davies RM, Davis P, Devlin K, Feltwell T, Hamlin N, Holroyd S, Jagels K, Leather S, Moule S, Mungall K, Quail MA, Rajandream MA, Rutherford KM, Simmonds M, Skelton J, Whitehead S, Spratt BG, Barrell BG (2000). Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404:502-6
Shaskolskiy B, Kravtsov D, Kandinov I, Dementieva E, Gryadunov D (2022). Genomic Diversity and Chromosomal Rearrangements in Neisseria gonorrhoeae and Neisseria meningitidis. Int J Mol Sci 23:
Stabler RA, Marsden GL, Witney AA, Li Y, Bentley SD, Tang CM, Hinds J (2005). Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Neisseria species. Microbiology 151:2907-22
Thompson EA, Feavers IM, Maiden MC (2003). Antigenic diversity of meningococcal enterobactin receptor FetA, a vaccine component. Microbiology 149:1849-58
Urwin R, Russell JE, Thompson EA, Holmes EC, Feavers IM, Maiden MC (2004). Distribution of surface protein variants among hyperinvasive meningococci: implications for vaccine design. Infect Immun 72:5955-62
Watkins ER, Maiden MC (2017). Metabolic shift in the emergence of hyperinvasive pandemic meningococcal lineages. Sci Rep 7:41126

Sequence bin

contigs: 1
length: 2,184,406 bp
%GC: 51.81
Ns: 0
gaps: 0
loci tagged: 2,224

Show sequence bin

Annotation quality metrics

Provenance information

Fields used in metric	Fields completed	Annotation
Fields used in metric	Fields completed	Score	Status
5 country year age_range disease source	4	80

Missing field values for: age_range

Scheme completion

Scheme	Scheme loci	Designated loci	Annotation
Scheme	Scheme loci	Designated loci	Score	Status
rplF species	1	1	100
Finetyping antigens	3	3	100
Bexsero Antigen Sequence Typing (BAST)	5	5	100
MLST	7	7	100
Ribosomal MLST	53	53	100
N. meningitidis cgMLST v2	1422	1417	99

Analysis

rMLST species identification

Rank	Taxon	Taxonomy	Support	Matches
SPECIES	Neisseria meningitidis	Pseudomonadota > Betaproteobacteria > Neisseriales > Neisseriaceae > Neisseria > Neisseria meningitidis	100%

Analysis performed: 2023-09-28

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups Hide single groups

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification scheme	Underlying scheme	Clustering method	Mismatch threshold	Status	Group
Bact_rmlstc_5	Ribosomal MLST	Single-linkage	5	experimental	691 (461 isolates)
Bact_rmlstc_4	Ribosomal MLST	Single-linkage	4	experimental	789 (461 isolates)
Bact_rmlstc_3	Ribosomal MLST	Single-linkage	3	experimental	967 (461 isolates)
Bact_rmlstc_2	Ribosomal MLST	Single-linkage	2	experimental	1110 (23 isolates)
Bact_rmlstc_1	Ribosomal MLST	Single-linkage	1	experimental	1579 (20 isolates)
Nm_cgc_200	N. meningitidis cgMLST v2	Single-linkage	200	experimental	3 (17 isolates)
Nm_cgc_100	N. meningitidis cgMLST v2	Single-linkage	100	experimental	4 (17 isolates)
Nm_cgc_50	N. meningitidis cgMLST v2	Single-linkage	50	experimental	53 (5 isolates)
Bact_rmlstc_5	Ribosomal MLST	Single-linkage	5	experimental	691 (461 isolates)
Bact_rmlstc_4	Ribosomal MLST	Single-linkage	4	experimental	789 (461 isolates)
Bact_rmlstc_3	Ribosomal MLST	Single-linkage	3	experimental	967 (461 isolates)
Bact_rmlstc_2	Ribosomal MLST	Single-linkage	2	experimental	1110 (23 isolates)
Bact_rmlstc_1	Ribosomal MLST	Single-linkage	1	experimental	1579 (20 isolates)
Nm_cgc_200	N. meningitidis cgMLST v2	Single-linkage	200	experimental	3 (17 isolates)
Nm_cgc_100	N. meningitidis cgMLST v2	Single-linkage	100	experimental	4 (17 isolates)
Nm_cgc_50	N. meningitidis cgMLST v2	Single-linkage	50	experimental	53 (5 isolates)
Nm_cgc_25	N. meningitidis cgMLST v2	Single-linkage	25	experimental	59 (1 isolate)
Nm_cgc_10	N. meningitidis cgMLST v2	Single-linkage	10	experimental	60 (1 isolate)

Schemes and loci

All loci

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