Full information on isolate M21 240025 (id:115345)

Projects

This isolate is a member of the following project:

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.

Provenance/primary metadata

id
115345
isolate
M21 240025
strain designation
B: P1.12-1,16: F1-5: ST-485 (cc41/44)
country
UK [England]
continent
Europe
town or city
London
year
2021
epidemiological year
07/2020-06/2021
disease
invasive (unspecified/other)
species
Neisseria meningitidis
serogroup
B
genogroup
B
genogroup notes
B backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
capsule group
B
type strain
0

Town or city

London

Aerial view Recentre

Tracking

bioproject accession
PRJEB9481 www.ebi.ac.uk
biosample accession
SAMEA13635372; ERS11237220 www.ebi.ac.uk
run accession
ERR9389329 www.ebi.ac.uk
sender
Aiswarya Lekshmi, Public Health England
curator
Auto Tagger
update history
107 updates show details
date entered
2022-03-23
datestamp
2024-12-13

Secondary metadata

Deduced vaccine reactivity

Bexsero reactivity
exact match  notes
Bexsero notes
NHBA_peptide: 2 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

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.

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Sequence bin

method
Illumina
contigs
176
total length
2,130,629 bp
max length
91,102 bp
mean length
12,106 bp
N50
25,728
L50
24
N90
6,025
L90
82
N95
3,822
L95
104
%GC
51.66
Ns
0
gaps
0
loci tagged
2,128

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 v31329131498
N. meningitidis cgMLST v21422140798

Analysis

rMLST species identification

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

Analysis performed: 2024-12-01

Similar isolates (determined by LIN codes)

Scheme
N. meningitidis cgMLST v3
LIN code
0_14_0_0_0_1_54_6_0_0_0_0_0_0

Show all thresholds

PrefixThresholdMatching isolates
0_14_0_0_0_1_54_6_0_071
0_14_0_0_0_1_54_6_0_0_031
0_14_0_0_0_1_54_6_0_0_0_021
0_14_0_0_0_1_54_6_0_0_0_0_011
0_14_0_0_0_1_54_6_0_0_0_0_0_001
0121837672
0_149706314
0_14_06915419
0_14_0_05453224
0_14_0_0_03853185
0_14_0_0_0_12792851
0_14_0_0_0_1_54156389
0_14_0_0_0_1_54_6671
0_14_0_0_0_1_54_6_0141
0_14_0_0_0_1_54_6_0_071
0_14_0_0_0_1_54_6_0_0_031
0_14_0_0_0_1_54_6_0_0_0_021
0_14_0_0_0_1_54_6_0_0_0_0_011
0_14_0_0_0_1_54_6_0_0_0_0_0_001

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups

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

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental698 (5147 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental799 (4359 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental921 (4009 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1173 (2134 isolates)
Nm_cgc3_200N. meningitidis cgMLST v3Single-linkage200experimental38 (2584 isolates)
Nm_cgc3_100N. meningitidis cgMLST v3Single-linkage100experimental506 (385 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental698 (5147 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental799 (4359 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental921 (4009 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1173 (2134 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental113482 (1 isolate)
Nm_cgc3_200N. meningitidis cgMLST v3Single-linkage200experimental38 (2584 isolates)
Nm_cgc3_100N. meningitidis cgMLST v3Single-linkage100experimental506 (385 isolates)
Nm_cgc3_50N. meningitidis cgMLST v3Single-linkage50experimental14477 (1 isolate)
Nm_cgc3_25N. meningitidis cgMLST v3Single-linkage25experimental19424 (1 isolate)
Nm_cgc3_10N. meningitidis cgMLST v3Single-linkage10experimental25655 (1 isolate)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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