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Full information on isolate M11 240802 (id:21206)

Projects

This isolate is a member of the following projects:

MRF Meningococcal Genome Library
MRF

The MRF Meningococcus Genome Library is a collaboration between Public Health England, the Scottish Haemophilus, Legionella, Meningococcus and Pneumococcus Reference (SHLMPR) Laboratory, The Wellcome Trust Sanger Institute and the University of Oxford, funded by the Meningitis Research Foundation.

Use of the MRF Genome Library data must be cited in any publication or presentation making use of it.

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

Provenance/primary metadata

id
21206
isolate
M11 240802
strain designation
W: P1.5,2: F1-1: ST-11 (cc11)
aliases
ERR294410; SC_RUN_9472_6#31
country
UK [England]
continent
Europe
region
North East
year
2011
epidemiological year
07/2011-06/2012
disease
invasive (unspecified/other)
species
Neisseria meningitidis
serogroup
W
genogroup
W
capsule group
W
type strain
0

Tracking

bioproject accession
PRJEB2712 www.ebi.ac.uk
biosample accession
SAMEA1904443; ERS209134 www.ebi.ac.uk
ENA run accession
ERR294410 www.ebi.ac.uk
sender
Dorothea Hill, University of Oxford, UK
curator
Auto Tagger
update history
168 updates show details
date entered
2013-04-12
datestamp
2023-07-10

Secondary metadata

Deduced vaccine reactivity

Bexsero reactivity
cross-reactive  notes
Bexsero notes
NadA_peptide: 6 is cross-reactive to vaccine variant - data derived from MATS assays (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 (10)

  • Brehony C, Rodrigues CM, Borrow R, Smith A, Cunney R, Moxon ER, Maiden MC (2016). Distribution of Bexsero® Antigen Sequence Types (BASTs) in invasive meningococcal disease isolates: Implications for immunisation. Vaccine 34:4690-7
  • Cayrou C, Akinduko AA, Mirkes EM, Lucidarme J, Clark SA, Green LR, Cooper HJ, Morrissey J, Borrow R, Bayliss CD (2018). Clustered intergenic region sequences as predictors of factor H Binding Protein expression patterns and for assessing Neisseria meningitidis strain coverage by meningococcal vaccines. PLoS One 13:e0197186
  • Green LR, Dave N, Adewoye AB, Lucidarme J, Clark SA, Oldfield NJ, Turner DPJ, Borrow R, Bayliss CD (2019). Potentiation of Phase Variation in Multiple Outer-Membrane Proteins During Spread of the Hyperinvasive Neisseria meningitidis Serogroup W ST-11 Lineage. J Infect Dis 220:1109-1117
  • Hill DM, Lucidarme J, Gray SJ, Newbold LS, Ure R, Brehony C, Harrison OB, Bray JE, Jolley KA, Bratcher HB, Parkhill J, Tang CM, Borrow R, Maiden MC (2015). Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. Lancet Infect Dis 15:1420-8
  • Lucidarme J, Hill DM, Bratcher HB, Gray SJ, du Plessis M, Tsang RS, Vazquez JA, Taha MK, Ceyhan M, Efron AM, Gorla MC, Findlow J, Jolley KA, Maiden MC, Borrow R (2015). Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage. J Infect 71:544-52
  • Retchless AC, Chen A, Chang HY, Blain AE, McNamara LA, Mustapha MM, Harrison LH, Wang X (2021). Using Neisseria meningitidis genomic diversity to inform outbreak strain identification. PLoS Pathog 17:e1009586
  • Rodrigues CMC, Chan H, Vipond C, Jolley K, Harrison OB, Wheeler J, Whiting G, Feavers IM, Maiden MCJ (2018). Typing complex meningococcal vaccines to understand diversity and population structure of key vaccine antigens. Wellcome Open Res 3:151
  • Rodrigues CMC, Lucidarme J, Borrow R, Smith A, Cameron JC, Moxon ER, Maiden MCJ (2018). Genomic Surveillance of 4CMenB Vaccine Antigenic Variants among Disease-Causing Neisseria meningitidis Isolates, United Kingdom, 2010-2016. Emerg Infect Dis 24:673-682
  • 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
  • Wanford JJ, Holmes JC, Bayliss CD, Green LR (2020). Meningococcal core and accessory phasomes vary by clonal complex. Microb Genom 6:

Sequence bin

contigs
154
total length
2,116,760 bp
max length
131,326 bp
mean length
13,746 bp
N50
42,809
L50
18
N90
9,334
L90
56
N95
6,603
L95
69
%GC
51.81
Ns
0
gaps
0
loci tagged
2,165

Show sequence bin

Annotation quality metrics

Provenance information

Fields used in metricFields completedAnnotation
ScoreStatus
5 360

Missing field values for: age_range, source

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
rplF species11100
Finetyping antigens33100
Bexsero Antigen Sequence Typing (BAST)55100
MLST77100
Ribosomal MLST5353100
N. meningitidis cgMLST v21422141899

Analysis

rMLST species identification

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

Analysis performed: 2022-11-29

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_5Ribosomal MLSTSingle-linkage5experimental696 (5588 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental796 (5580 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental917 (5559 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1121 (5425 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental1599 (5312 isolates)
Nm_cgc_200N. meningitidis cgMLST v2Single-linkage200experimental156 (6950 isolates)
Nm_cgc_100N. meningitidis cgMLST v2Single-linkage100experimental228 (4415 isolates)
Nm_cgc_50N. meningitidis cgMLST v2Single-linkage50experimental429 (2521 isolates)
Nm_cgc_25N. meningitidis cgMLST v2Single-linkage25experimental452 (532 isolates)
Nm_cgc_10N. meningitidis cgMLST v2Single-linkage10experimental670 (208 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental696 (5588 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental796 (5580 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental917 (5559 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1121 (5425 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental1599 (5312 isolates)
Nm_cgc_200N. meningitidis cgMLST v2Single-linkage200experimental156 (6950 isolates)
Nm_cgc_100N. meningitidis cgMLST v2Single-linkage100experimental228 (4415 isolates)
Nm_cgc_50N. meningitidis cgMLST v2Single-linkage50experimental429 (2521 isolates)
Nm_cgc_25N. meningitidis cgMLST v2Single-linkage25experimental452 (532 isolates)
Nm_cgc_10N. meningitidis cgMLST v2Single-linkage10experimental670 (208 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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