Full information on isolate 0091/93 (id:991)

Provenance/primary metadata

id
991
isolate
0091/93
strain designation
B: P1.5-1,2-2: F1-7: ST-112 (cc41/44)
country
Czech Republic
continent
Europe
region
OC
year
1993
age yr
21
age range
15-24
sex
male
disease
carrier
source
throat swab
epidemiology
carrier
species
Neisseria meningitidis
serogroup
B
genogroup
B
capsule group
B
serotype
15
sero subtype
P1.5,2,12

Antimicrobial resistance

cefotaxime mic
=0.004 μg/mL
cefotaxime SIR
S
penicillin mic
=0.008 μg/mL
penicillin SIR
S
rifampicin mic
=0.008 μg/mL
rifampicin SIR
S
sulphonamide mic
=4 μg/mL

Tracking

bioproject accession
PRJEB2090 www.ebi.ac.uk
biosample accession
SAMEA1402016; ERS094674 www.ebi.ac.uk
ENA run accession
ERR133734 www.ebi.ac.uk
sender
Pavla Křížová, Pavla Křížová and Keith Jolley
curator
James Bray, University of Oxford, UK (E-mail: james.bray@biology.ox.ac.uk)
update history
121 updates show details
date entered
2007-03-29
datestamp
2023-06-07

Secondary metadata

Deduced vaccine reactivity

Bexsero reactivity
insufficient data  notes
Trumenba reactivity
cross-reactive  notes
Trumenba notes
fHbp_peptide: 19 is cross-reactive to vaccine variant - data derived from MEASURE assays (PMID:29535195), and SBA assays (PMID:22569484, PMID:22718089, PMID:22871351, PMID:23114369, PMID:23352429, PMID:26407272, PMID:26707218, PMID:26803328, PMID:26835974, PMID:26974889, PMID:27745812, PMID:27846061, PMID:28196734, PMID:28566335, PMID:29236639)

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.

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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.

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Publications (5)

  • 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
  • Buckee CO, Jolley KA, Recker M, Penman B, Kriz P, Gupta S, Maiden MC (2008). Role of selection in the emergence of lineages and the evolution of virulence in Neisseria meningitidis. Proc Natl Acad Sci U S A 105:15082-7
  • Earle SG, Lobanovska M, Lavender H, Tang C, Exley RM, Ramos-Sevillano E, Browning DF, Kostiou V, Harrison OB, Bratcher HB, Varani G, Tang CM, Wilson DJ, Maiden MCJ (2021). Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis. PLoS Pathog 17:e1009992
  • Jolley KA, Kalmusova J, Feil EJ, Gupta S, Musilek M, Kriz P, Maiden MC (2000). Carried meningococci in the Czech Republic: a diverse recombining population. J Clin Microbiol 38:4492-8
  • 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

Sequence bin

contigs
181
total length
2,117,925 bp
max length
142,250 bp
mean length
11,702 bp
N50
44,627
L50
17
N90
9,268
L90
52
N95
4,255
L95
68
%GC
51.73
Ns
0
gaps
0
loci tagged
2,171

Show sequence bin

Annotation quality metrics

Provenance information

Fields used in metricFields completedAnnotation
ScoreStatus
5 5100

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
rplF species11100
Finetyping antigens33100
Bexsero Antigen Sequence Typing (BAST)55100
MLST77100
Ribosomal MLST5353100
N. meningitidis cgMLST v21422141399

Analysis

rMLST species identification

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

Analysis performed: 2023-05-15

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental698 (3992 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental799 (3399 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental921 (3077 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1193 (557 isolates)
Nm_cgc_200N. meningitidis cgMLST v2Single-linkage200experimental89 (2 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental698 (3992 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental799 (3399 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental921 (3077 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1193 (557 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental2094 (1 isolate)
Nm_cgc_200N. meningitidis cgMLST v2Single-linkage200experimental89 (2 isolates)
Nm_cgc_100N. meningitidis cgMLST v2Single-linkage100experimental136 (1 isolate)
Nm_cgc_50N. meningitidis cgMLST v2Single-linkage50experimental151 (1 isolate)
Nm_cgc_25N. meningitidis cgMLST v2Single-linkage25experimental155 (1 isolate)
Nm_cgc_10N. meningitidis cgMLST v2Single-linkage10experimental163 (1 isolate)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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