Full information on isolate 19679 (id:17196)

Projects

This isolate is a member of the following project:

penA sequence analysis
Analysis of penA sequences correlated with penicillin G resistance published in Taha et al. 2007 Antimicrob Agents Chemother 51:2784-92.

Provenance/primary metadata

id
17196
isolate
19679
strain designation
W: P1.5,2: F1-1: ST-11 (cc11)
country
Madagascar
continent
Africa
year
2002
source
throat swab
species
Neisseria meningitidis
serogroup
W
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
penicillin
0.064
penicillin range
>0.06 - 1 (intermediate)
amoxicillin
0.094
sender
Muhamed-Kheir Taha, National Reference Center for Meningococci and Haemophilus influenzae, Institut Pasteur, France
curator
Auto Tagger
update history
48 updates show details
date entered
2010-05-27
datestamp
2020-10-06

Secondary metadata

Vaccines

Bexsero reactivity
cross-reactive 
notes
Bexsero notes
NadA_peptide: 6 is cross-reactive to vaccine variant - data derived from MATS assays (PMID:29950334)

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, bioRxiv 2020.08.18.256834. Please contact us if you have queries.

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Publication (1)

  • Taha MK, Vázquez JA, Hong E, Bennett DE, Bertrand S, Bukovski S, Cafferkey MT, Carion F, Christensen JJ, Diggle M, Edwards G, Enríquez R, Fazio C, Frosch M, Heuberger S, Hoffmann S, Jolley KA, Kadlubowski M, Kechrid A, Kesanopoulos K, Kriz P, Lambertsen L, Levenet I, Musilek M, Paragi M, Saguer A, Skoczynska A, Stefanelli P, Thulin S, Tzanakaki G, Unemo M, Vogel U, Zarantonelli ML (2007). Target gene sequencing to characterize the penicillin G susceptibility of Neisseria meningitidis. Antimicrob Agents Chemother 51:2784-92

Sequence bin

contigs
109
total length
2,059,095 bp
max length
97,630 bp
mean length
18,891 bp
N50 contig number
18
N50 length (L50)
38,674
N90 contig number
55
N90 length (L90)
9,862
N95 contig number
68
N95 length (L95)
6,617
loci tagged
2,154

Show sequence bin

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: 65 (3469 isolates)
Nm_cgc_100N. meningitidis cgMLST v1.0Single-linkage100experimentalgroup: 87 (910 isolates)
Nm_cgc_50N. meningitidis cgMLST v1.0Single-linkage50experimentalgroup: 104 (892 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Analysis: