Full information on isolate M18 240603 (id:71108)

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
71108
isolate
M18 240603
strain designation
cnl: P1.7-2,13: F1-88: ST-1103 (cc41/44)
alias
WTCHG_734333_70465118
country
UK [England]
continent
Europe
region
North East
year
2018
epidemiological year
07/2018-06/2019
disease
invasive (unspecified/other)
species
Neisseria meningitidis
serogroup
NG
genogroup
cnl
genogroup notes
capsule null locus (cnl). Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
capsule group
cnl

Tracking

ENA run accession
ERR3664484 www.ebi.ac.uk
sender
Holly Bratcher, University of Oxford
curator
Auto Tagger
update history
20 updates show details
date entered
2019-12-19
datestamp
2021-06-18

Secondary metadata

Vaccines

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.

  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.

Click to close

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

Sequence bin

contigs
141
total length
2,108,057 bp
max length
138,376 bp
mean length
14,951 bp
N50
38,702
L50
16
N90
11,443
L90
50
N95
5,902
L95
62
%GC
51.79
Ns
0
gaps
0
loci tagged
2,100

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 v21422139397

Analysis

rMLST species identification

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

Analysis performed: 2021-03-03

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_20Ribosomal MLSTSingle-linkage20experimental169 (25907 isolates)
Bact_rmlstc_10Ribosomal MLSTSingle-linkage10experimental476 (3832 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental698 (3506 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental4661 (6 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental5401 (6 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental6641 (5 isolates)
Bact_rmlstc_20Ribosomal MLSTSingle-linkage20experimental169 (25907 isolates)
Bact_rmlstc_10Ribosomal MLSTSingle-linkage10experimental476 (3832 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental698 (3506 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental4661 (6 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental5401 (6 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental6641 (5 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental77754 (1 isolate)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Export:
Analysis: