Full information on isolate 2843 (id:666)

Projects

This isolate is a member of the following project:

GMGL
Global Meningitis Genome Library: curated isolate data sets of N. meningtidis causing meningitis and/or septicaemia

Provenance/primary metadata

id
666
isolate
2843
alias
M97/252847
strain designation
C: P1.19-3,15: F5-5: ST-51 (cc11)
country
UK
continent
Europe
year
1997
disease
carrier
epidemiology
endemic
species
Neisseria meningitidis
serogroup
C
genogroup
C
genogroup notes
C backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
capsule group
C
comments
University outbreak, strain 5, carrier 4

Tracking

ENA run accession
ERR063497 www.ebi.ac.uk
sender
Ian Feavers, University of Oxford, UK
curator
Keith Jolley, University of Oxford, UK (E-mail: keith.jolley@zoo.ox.ac.uk)
update history
174 updates show details
date entered
2001-02-07
datestamp
2021-06-18

Secondary metadata

Vaccines

Bexsero reactivity
cross-reactive 
notes
Bexsero notes
NadA_peptide: 3 is cross-reactive to vaccine variant - data derived from MATS assays (PMID:23588089, PMID:26686998, PMID:26950303, PMID:27083425, PMID:29950334)
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.

  1. 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
  2. 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®.

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.

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.

  1. 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
  2. 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.

Click to close

Publications (4)

  • Feavers IM, Gray SJ, Urwin R, Russell JE, Bygraves JA, Kaczmarski EB, Maiden MC (1999). Multilocus sequence typing and antigen gene sequencing in the investigation of a meningococcal disease outbreak. J Clin Microbiol 37:3883-7
  • Jolley KA, Hill DM, Bratcher HB, Harrison OB, Feavers IM, Parkhill J, Maiden MC (2012). Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid Web-based analysis methods. J Clin Microbiol 50:3046-53
  • Lucidarme J, Lekshmi A, Parikh SR, Bray JE, Hill DM, Bratcher HB, Gray SJ, Carr AD, Jolley KA, Findlow J, Campbell H, Ladhani SN, Ramsay ME, Maiden MCJ, Borrow R (2017). Frequent capsule switching in 'ultra-virulent' meningococci - Are we¬†ready for a serogroup B ST-11 complex¬†outbreak? J Infect 75:95-103
  • Spinsanti M, Brignoli T, Bodini M, Fontana LE, De Chiara M, Biolchi A, Muzzi A, Scarlato V, Delany I (2021). Deconvolution of intergenic polymorphisms determining high expression of Factor H binding protein in meningococcus and their association with invasive disease. PLoS Pathog 17:e1009461

Sequence bin

contigs
252
total length
2,110,572 bp
max length
119,058 bp
mean length
8,376 bp
N50
38,378
L50
19
N90
8,212
L90
61
N95
3,965
L95
77
%GC
51.82
Ns
0
gaps
0
loci tagged
2,174

Show sequence bin

Annotation quality metrics

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
rplF species11100
Finetyping antigens33100
Bexsero Antigen Sequence Typing (BAST)55100
MLST77100
Ribosomal MLST5353100
N. meningitidis cgMLST v1.01605157398

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Neisseria meningitidis Proteobacteria > Betaproteobacteria > Neisseriales > Neisseriaceae > Neisseria > Neisseria meningitidis 100%

Analysis performed: 2021-03-31

Similar isolates (determined by classification schemes)

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

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Bact_rmlstc_20Ribosomal MLSTSingle-linkage20experimental169 (24212 isolates)
Bact_rmlstc_10Ribosomal MLSTSingle-linkage10experimental475 (6052 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental696 (4358 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental796 (4351 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental917 (4332 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1121 (4204 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental1601 (5 isolates)
Nm_cgc_200N. meningitidis cgMLST v1.0Single-linkage200experimental65 (3870 isolates)
Nm_cgc_100N. meningitidis cgMLST v1.0Single-linkage100experimental40 (5 isolates)
Nm_cgc_50N. meningitidis cgMLST v1.0Single-linkage50experimental48 (2 isolates)
Nm_cgc_25N. meningitidis cgMLST v1.0Single-linkage25experimental48 (2 isolates)
Bact_rmlstc_20Ribosomal MLSTSingle-linkage20experimental169 (24212 isolates)
Bact_rmlstc_10Ribosomal MLSTSingle-linkage10experimental475 (6052 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental696 (4358 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental796 (4351 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental917 (4332 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1121 (4204 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental1601 (5 isolates)
Nm_cgc_200N. meningitidis cgMLST v1.0Single-linkage200experimental65 (3870 isolates)
Nm_cgc_100N. meningitidis cgMLST v1.0Single-linkage100experimental40 (5 isolates)
Nm_cgc_50N. meningitidis cgMLST v1.0Single-linkage50experimental48 (2 isolates)
Nm_cgc_25N. meningitidis cgMLST v1.0Single-linkage25experimental48 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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