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Full information on isolate 12033-13 (id:30720)

Provenance/meta data

id
30720
isolate
12033-13
strain designation
B: P1.12-1,16: F1-5: ST-485 (cc41/44)
country
Ireland
continent
Europe
region
MAYO
year
2013
epidemiological year
07/2013-06/2014
age yr
0
age mth
4
disease
invasive (unspecified/other)
source
CSF
species
Neisseria meningitidis
serogroup
B
genogroup
B
capsule group
B
ENA accession
ERR654781 www.ebi.ac.uk
sender
Carina Brehony, HSE, Ireland
curator
Charlene Rodrigues, University of Oxford, UK (E-mail: charlene.rodrigues@gtc.ox.ac.uk)
update history
88 updates show details
date entered
2014-08-27
datestamp
2019-04-15

Phenotypic fields

    Bexsero reactivity
    cross-reactive  caveats
    Trumenba reactivity
    cross-reactive  caveats

Bexsero Antigen Sequence Typing (1) was developed to allow high-throughput analysis of whole genome sequence data and cataloguing of vaccine antigenic variants.

  • There are 5 components to the BAST: fHbp, NHBA, NadA, PorAVR1 and PorAVR2.
  • Only 4 are used in determining the likelihood of coverage by the Bexsero vaccine:fHbp, NHBA, NadA, and PorAVR2. Of these, only fHbp and NadA variants are considered potentially cross-reactive.
  • You can find the BAST antigenic profile for this isolate by selecting the Typing → Bexsero Antigen Sequence Typing (BAST) link in the scheme tree at the bottom of the page.
  • Bexsero contains: fHbp 1; NHBA: 2; NadA 8; PorA VR2: 4.

The traffic light system was devised to help users of the BAST system to determine the potential genomic coverage of a given isolate by Bexsero.

  • isolate contains exact antigenic variants found in the vaccine.
  • isolate contains cross-reactive antigenic variants.
  • isolate contains no antigenic variants that are either exact matches or cross-reactive to those found in the vaccine.

It is important to understand the caveats to the estimates made using genomic data as below:

  • These are genomic estimates of vaccine coverage based on the presence or absence of genes encoding vaccine antigenic variants.
  • We have not inferred the cross-reactivity of antigenic variants based on genomic data alone.
  • We have used published literature to obtain information about cross reactivity of the antigens, which demonstrates that vaccinee sera can directly kill meningococci in serum bactericidal antibody assays or through the Meningococcal Antigen Typing System (MATS) assay (2,3), an indirect measure of the potential to be killed by vaccinees’ sera.
  • We have not inferred protein expression from the genomic data, therefore there may be isolates that possess genes but do not express the protein in vivo.
  • The age of the vaccinees included in the published trials needs to be considered when interpreting potential coverage of an isolate with Bexsero or Trumenba, and deciding which vaccine to administer.

  1. Brehony et al. Vaccine 2016 34:4690-7
  2. Vogel et al. Lancet Infect Dis 2013 13:416-25
  3. Medini et al. Vaccine 2015 33:2629-36

Click to close

Trumenba is a bivalent fHbp-containing vaccine.

  • The vaccine contains fHbp protein variants 45 and 55.

The traffic light system was devised to help users of PubMLST to determine the potential genomic coverage of a given isolate by Trumenba.
  • isolate contains exact antigenic variants found in the vaccine.
  • isolate contains cross-reactive antigenic variants.
  • isolate contains no antigenic variants that are either exact matches or cross-reactive to those found in the vaccine.

It is important to understand the caveats to the estimates made using genomic data as below:

  • These are genomic estimates of vaccine coverage based on the presence or absence of genes encoding vaccine antigenic variants.
  • We have not inferred the cross-reactivity of antigenic variants based on genomic data alone.
  • We have used published literature to obtain information about cross reactivity of the antigens, which demonstrates that vaccinee sera can directly kill meningococci in serum bactericidal antibody assays (1-4) or through the Meningococcal Antigen Typing System (MATS) assay (5), an indirect measure of the potential to be killed by vaccinees’ sera.
  • We have not inferred protein expression from the genomic data, therefore there may be isolates that possess genes but do not express the protein in vivo.
  • The age of the vaccinees included in the published trials needs to be considered when interpreting potential coverage of an isolate with Bexsero or Trumenba, and deciding which vaccine to administer.

  1. Harris et al. Pediatr Infect Dis J 2017 36:216-223
  2. Lujan et al. Clin Vaccine Immunol 2017 24:e00121-17
  3. Taha et al. Vaccine 35:1530-37
  4. Ostergaard et al. N Engl J Med 2017 377:2349-2362
  5. Medini et al. Vaccine 2015 33:2629-36

Click to close

Publication (1)

  • Brehony C, Rodrigues CM, Borrow R, Smith A, Cunney R, Moxon ER, Maiden MC (2016). Distribution of Bexsero® Antigen Sequence Types (BASTs) in invasive meningococcal disease isolates: Implications for immunisation. Vaccine 34:4690-7

Sequence bin

contigs
116
total length
2,139,539 bp
max length
117,061 bp
mean length
18,445 bp
N50 contig number
14
N50 length (L50)
52,992
N90 contig number
42
N90 length (L90)
15,052
N95 contig number
52
N95 length (L95)
9,665
loci tagged
2,195
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: 123 (516 isolates)
Nm_cgc_100N. meningitidis cgMLST v1.0Single-linkage100experimentalgroup: 184 (61 isolates)
Nm_cgc_50N. meningitidis cgMLST v1.0Single-linkage50experimentalgroup: 211 (52 isolates)
Nm_cgc_25N. meningitidis cgMLST v1.0Single-linkage25experimentalgroup: 1901 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Analysis: