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Full information on isolate 1059000105 (id:26162)

Provenance/meta data

id
26162
isolate
1059000105
alias
ERR405948
strain designation
Y: P1.5-1,2-2: F5-8: ST-23 (cc23)
country
Sweden
continent
Europe
year
2010
species
Neisseria meningitidis
serogroup
Y
capsule group
Y
ENA accession
ERR405948 www.ebi.ac.uk
sender
Paula Mölling, University Hospital Örebro, Sweden
curator
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update history
79 updates show details
date entered
2013-05-29
datestamp
2019-08-18

Vaccine coverage

Bexsero reactivity
none  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)

  • Törös B, Hedberg ST, Unemo M, Jacobsson S, Hill DM, Olcén P, Fredlund H, Bratcher HB, Jolley KA, Maiden MC, Mölling P (2015). Genome-Based Characterization of Emergent Invasive Neisseria meningitidis Serogroup Y Isolates in Sweden from 1995 to 2012. J Clin Microbiol 53:2154-62

Sequence bin

contigs
158
total length
2,109,960 bp
max length
89,913 bp
mean length
13,355 bp
N50 contig number
19
N50 length (L50)
34,852
N90 contig number
58
N90 length (L90)
12,352
N95 contig number
69
N95 length (L95)
7,052
loci tagged
2,114
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: 119 (79 isolates)
Nm_cgc_100N. meningitidis cgMLST v1.0Single-linkage100experimentalgroup: 159 (74 isolates)
Nm_cgc_50N. meningitidis cgMLST v1.0Single-linkage50experimentalgroup: 812 (20 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Analysis: