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Full information on isolate 2059001 (id:387)

Projects

This isolate is a member of the following project:

107 global collection
This dataset was originally used to validate MLST and was chosen to represent global diversity of N. meningitidis in the latter half of the Twentieth Century. It has been used in many publications since and the isolates are available as the EMGM MLST reference collection.

Provenance/meta data

id
387
isolate
2059001
aliases
D60; NIBSC_2745; Z4421
strain designation
A: P1.7,13: F1-5: ST-4 (cc4)
country
Mali
continent
Africa
year
1990
disease
invasive (unspecified/other)
epidemiology
endemic
species
Neisseria meningitidis
serogroup
A
capsule group
A
MLEE designation
Subgroup IV-I
serotype
4,21
sero subtype
P1.7
ET no
72
ENA accession
ERS006929 www.ebi.ac.uk
comments
Pili I
sender
B Koumare, Service de Bacteriologie/Virologie, Institut national de recherche en Sante publique, Bamako, Mali
curator
Holly Bratcher, University of Oxford (E-mail: Holly.Bratcher@zoo.ox.ac.uk)
update history
123 updates show details
date entered
2001-02-07
datestamp
2018-12-06

Vaccine coverage

Bexsero reactivity
none  caveats
Trumenba reactivity
none  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

Publications (9)

  • Bennett JS, Jolley KA, Sparling PF, Saunders NJ, Hart CA, Feavers IM, Maiden MC (2007). Species status of Neisseria gonorrhoeae: evolutionary and epidemiological inferences from multilocus sequence typing. BMC Biol 5:35
  • Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MC (2014). A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics 15:1138
  • Didelot X, Urwin R, Maiden MC, Falush D (2009). Genealogical typing of Neisseria meningitidis. Microbiology 155:3176-86
  • Jolley KA, Sun L, Moxon ER, Maiden MC (2004). Dam inactivation in Neisseria meningitidis: prevalence among diverse hyperinvasive lineages. BMC Microbiol 4:34
  • Jolley KA, Wilson DJ, Kriz P, McVean G, Maiden MC (2005). The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis. Mol Biol Evol 22:562-9
  • Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998). Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140-5
  • Thompson EA, Feavers IM, Maiden MC (2003). Antigenic diversity of meningococcal enterobactin receptor FetA, a vaccine component. Microbiology 149:1849-58
  • Urwin R, Russell JE, Thompson EA, Holmes EC, Feavers IM, Maiden MC (2004). Distribution of surface protein variants among hyperinvasive meningococci: implications for vaccine design. Infect Immun 72:5955-62
  • Wang JF, Caugant DA, Li X, Hu X, Poolman JT, Crowe BA, Achtman M (1992). Clonal and antigenic analysis of serogroup A Neisseria meningitidis with particular reference to epidemiological features of epidemic meningitis in the People's Republic of China. Infect Immun 60:5267-82

Sequence bin

contigs
284
total length
2,078,511 bp
max length
99,092 bp
mean length
7,319 bp
N50 contig number
24
N50 length (L50)
25,837
N90 contig number
83
N90 length (L90)
6,314
N95 contig number
104
N95 length (L95)
3,512
loci tagged
2,165
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: 3 (15 isolates)
Nm_cgc_100N. meningitidis cgMLST v1.0Single-linkage100experimentalgroup: 4 (15 isolates)
Nm_cgc_50N. meningitidis cgMLST v1.0Single-linkage50experimentalgroup: 33 (3 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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