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Full information on isolate M18 240501 (id:63460)

Projects

This isolate is a member of the following project:

MRF Meningococcus 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.

Provenance/primary metadata

id
63460
isolate
M18 240501
strain designation
B: P1.7-2,4: F3-7: ST-41 (cc41/44)
country
UK [England]
continent
Europe
region
North West
year
2018
date sampled
2018-09-21
isoyear sampled
2018
week sampled
38
epidemiological year
07/2018-06/2019
disease
invasive (unspecified/other)
species
Neisseria meningitidis
serogroup
B
genogroup
B
genogroup notes
B backbone: csb fragmented (25.0% cov),csb fragmented (84.05% cov). Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
capsule group
B
ENA run accession
ERR3900335 www.ebi.ac.uk
sender
Holly Bratcher, University of Oxford
curator
Keith Jolley, University of Oxford, UK (E-mail: keith.jolley@zoo.ox.ac.uk)
update history
15 updates show details
date entered
2019-11-26
datestamp
2020-07-14

Secondary metadata

Vaccines

Bexsero reactivity
exact match 
notes
Bexsero notes
NHBA_peptide: 2 is exact match to vaccine variant - peptide sequence match (PMID:27521232);
PorA_VR2: 4 is exact match to vaccine variant - peptide sequence match (PMID:27521232)
Trumenba reactivity
cross-reactive 
notes
Trumenba notes
fHbp_peptide: 4 is cross-reactive to vaccine variant - data derived from MEASURE assays (PMID:29535195), and SBA assays (PMID:27846061, PMID:29236639)

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

Please note this work is in development and subject to change. When the final version is available the citation will be published here. 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

Please note this work is in development and subject to change. When the final version is available the citation will be published here. Please contact us if you have queries.

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Sequence bin

contigs
169
total length
2,190,235 bp
max length
175,768 bp
mean length
12,960 bp
N50 contig number
14
N50 length (L50)
48,771
N90 contig number
46
N90 length (L90)
10,557
N95 contig number
61
N95 length (L95)
4,291
loci tagged
2,154
detailed breakdown
Display

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
Nm_cgc_200N. meningitidis cgMLST v1.0Single-linkage200experimentalgroup: 930 (2 isolates)
Nm_cgc_100N. meningitidis cgMLST v1.0Single-linkage100experimentalgroup: 2036 (2 isolates)
Nm_cgc_50N. meningitidis cgMLST v1.0Single-linkage50experimentalgroup: 3018 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Analysis: