Full information on isolate MenAfriCar7061590 (id:120902)

Projects

This isolate is a member of the following project:

MenAfriCar
The African Meningococcal Carriage (MenAfriCar) consortium was established in 2009 to investigate the pattern of meningococcal carriage in countries of the African meningitis belt prior to and after the introduction of meningococcal serogroup A polysaccharide/tetanus toxoid conjugate vaccine.

Provenance/primary metadata

id
120902
isolate
MenAfriCar7061590
strain designation
W: P1.5,2: F1-1: ST-11 (cc11)
aliases
10.0-13210.0-XS3-784; 10-13210-XS3-1
country
Senegal
continent
Africa
year
2012
sex
male
disease
carrier
source
throat swab
epidemiology
carrier
species
Neisseria meningitidis
genogroup
W
genogroup notes
W backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
capsule group
W

Tracking

date sampled
2012-04-19
isoyear sampled
2012
week sampled
16
bioproject accession
ERP024462 www.ebi.ac.uk
biosample accession
ERS4395866 www.ebi.ac.uk
ENA run accession
ERR4162225 www.ebi.ac.uk
sender
Neil MacAlasdair, WSI/University of Oslo
curator
Auto Tagger
update history
14 updates show details
date entered
2022-09-27
datestamp
2023-05-19

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.

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
58
total length
2,135,348 bp
max length
255,337 bp
mean length
36,817 bp
N50
80,382
L50
8
N90
28,489
L90
24
N95
26,337
L95
28
%GC
51.76
Ns
193
gaps
3
loci tagged
2,195

Show sequence bin

Annotation quality metrics

Provenance information

Fields used in metricFields completedAnnotation
ScoreStatus
5 480

Missing field values for: age_range

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
rplF species11100
Finetyping antigens33100
Bexsero Antigen Sequence Typing (BAST)55100
MLST77100
Ribosomal MLST5353100
N. meningitidis cgMLST v21422141699

Analysis

rMLST species identification

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

Analysis performed: 2022-11-30

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 (5549 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental796 (5542 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental917 (5521 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1121 (5387 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental1599 (5279 isolates)
Nm_cgc_200N. meningitidis cgMLST v2Single-linkage200experimental156 (6897 isolates)
Nm_cgc_100N. meningitidis cgMLST v2Single-linkage100experimental228 (4381 isolates)
Nm_cgc_50N. meningitidis cgMLST v2Single-linkage50experimental258 (1571 isolates)
Nm_cgc_25N. meningitidis cgMLST v2Single-linkage25experimental2693 (1209 isolates)
Nm_cgc_10N. meningitidis cgMLST v2Single-linkage10experimental3175 (932 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental696 (5549 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental796 (5542 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental917 (5521 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1121 (5387 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental1599 (5279 isolates)
Nm_cgc_200N. meningitidis cgMLST v2Single-linkage200experimental156 (6897 isolates)
Nm_cgc_100N. meningitidis cgMLST v2Single-linkage100experimental228 (4381 isolates)
Nm_cgc_50N. meningitidis cgMLST v2Single-linkage50experimental258 (1571 isolates)
Nm_cgc_25N. meningitidis cgMLST v2Single-linkage25experimental2693 (1209 isolates)
Nm_cgc_10N. meningitidis cgMLST v2Single-linkage10experimental3175 (932 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Export:
Analysis: