Full information on isolate LNP26048 (id:19771)

Projects

This isolate is a member of the following project:

gyrA sequence analysis
Analysis of gyrA sequences correlated with ciprofloxacin resistance published in Hong et al. 2013 Antimicrob Agents Chemother 57:1961-4.

Provenance/primary metadata

id
19771
isolate
LNP26048
strain designation
B: P1.7-2,16: F1-5: ST-1403 (cc41/44)
country
France
continent
Europe
region
37
year
2011
age yr
1
age range
1-4
disease
septicaemia
source
blood
species
Neisseria meningitidis
serogroup
B
genogroup
B
genogroup notes
B backbone: csb fragmented (53.05% cov). Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
capsule group
B

Antimicrobial resistance

cefotaxime mic
=0.06 μg/mL
cefotaxime SIR
S
ciprofloxacin mic
=0.003 μg/mL
ciprofloxacin SIR
S
penicillin mic
=0.023 μg/mL
penicillin SIR
S
rifampicin mic
=0.006 μg/mL
rifampicin SIR
S

Tracking

date sampled
2011-01-13
isoyear sampled
2011
week sampled
2
date received
2011-01-18
sender
Muhamed-Kheir Taha, National Reference Center for Meningococci and Haemophilus influenzae, Institut Pasteur, France
curator
Auto Tagger
update history
9 updates show details
date entered
2012-08-22
datestamp
2022-04-16

Secondary metadata

Vaccines

Bexsero reactivity
cross-reactive 
notes
Bexsero notes
fHbp_peptide: 14 is cross-reactive to vaccine variant - data derived from MATS assays (PMID:23414709, PMID:26686998, PMID:26950303, PMID:27083425, PMID:27355628, PMID:28366725, PMID:29152576, PMID:30135218, PMID:30592763)
Trumenba reactivity
cross-reactive 
notes
Trumenba notes
fHbp_peptide: 14 is cross-reactive to vaccine variant - data derived from MEASURE assays (PMID:29535195), and SBA assays (PMID:22569484, PMID:22718089, PMID:27846061, PMID:28196734, 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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Publication (1)

  • Hong E, Thulin Hedberg S, Abad R, Fazio C, Enríquez R, Deghmane AE, Jolley KA, Stefanelli P, Unemo M, Vazquez JA, Veyrier FJ, Taha MK (2013). Target gene sequencing to define the susceptibility of Neisseria meningitidis to ciprofloxacin. Antimicrob Agents Chemother 57:1961-4

Sequence bin

contigs
178
total length
2,075,336 bp
max length
81,052 bp
mean length
11,660 bp
N50
25,754
L50
26
N90
6,702
L90
86
N95
4,039
L95
106
%GC
51.90
Ns
0
gaps
0
loci tagged
2,096

Show sequence bin

Annotation quality metrics

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
rplF species11100
Finetyping antigens33100
Bexsero Antigen Sequence Typing (BAST)55100
MLST77100
Ribosomal MLST5353100
N. meningitidis cgMLST v21422140398

Analysis

rMLST species identification

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

Analysis performed: 2021-03-31

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_20Ribosomal MLSTSingle-linkage20experimental169 (25820 isolates)
Bact_rmlstc_10Ribosomal MLSTSingle-linkage10experimental476 (3832 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental698 (3506 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental799 (2989 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental921 (2680 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1173 (1576 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental1665 (1180 isolates)
Nm_cgc_200N. meningitidis cgMLST v2Single-linkage200experimental33 (1662 isolates)
Bact_rmlstc_20Ribosomal MLSTSingle-linkage20experimental169 (25820 isolates)
Bact_rmlstc_10Ribosomal MLSTSingle-linkage10experimental476 (3832 isolates)
Bact_rmlstc_5Ribosomal MLSTSingle-linkage5experimental698 (3506 isolates)
Bact_rmlstc_4Ribosomal MLSTSingle-linkage4experimental799 (2989 isolates)
Bact_rmlstc_3Ribosomal MLSTSingle-linkage3experimental921 (2680 isolates)
Bact_rmlstc_2Ribosomal MLSTSingle-linkage2experimental1173 (1576 isolates)
Bact_rmlstc_1Ribosomal MLSTSingle-linkage1experimental1665 (1180 isolates)
Nm_cgc_200N. meningitidis cgMLST v2Single-linkage200experimental33 (1662 isolates)
Nm_cgc_100N. meningitidis cgMLST v2Single-linkage100experimental352 (1 isolate)
Nm_cgc_50N. meningitidis cgMLST v2Single-linkage50experimental418 (1 isolate)
Nm_cgc_25N. meningitidis cgMLST v2Single-linkage25experimental441 (1 isolate)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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