Full information on isolate OX0051350 (id:3193)
Projects
This isolate is a member of the following project:
- UKMenCar2
- United Kingdom Meningococcal Carriage Study - 2000
Provenance/primary metadata
- id
- 3193
- isolate
- OX0051350
- strain designation
- B: P1.7-2,4: F1-5: ST-2189 (cc41/44)
- country
- UK [England]
- continent
- Europe
- region
- South East
- year
- 2000
- age yr
- 17
- age range
- 15-24
- sex
- male
- disease
- carrier
- source
- throat swab
- epidemiology
- carrier
- species
- Neisseria meningitidis
- serogroup
- NG
- genogroup
- B
- capsule group
- B
- serotype
- NT
- comments
- Study Centre: Oxford
Tracking
- sender
- Ana-Belen Ibarz-Pavon, Centre de Recerca en Salut Internacional de Barcelona (CRESIB) & Centro de Investigacao em Saude da Manhica (CISM)
- curator
- Auto Tagger
- update history
- 121 updates show details
- date entered
- 2002-11-28
- datestamp
- 2023-05-19
Secondary metadata
Deduced vaccine reactivity
- Bexsero reactivity
- exact match notes
- Bexsero notes
- NHBA_peptide: 2 is exact match to vaccine variant - peptide sequence match (PMID:27521232); PorA_VR2: 4 is exact match to vaccine variant - peptide sequence match (PMID:27521232)
- Trumenba reactivity
- cross-reactive notes
- Trumenba notes
- fHbp_peptide: 4 is cross-reactive to vaccine variant - data derived from MEASURE assays (PMID:29535195), and SBA assays (PMID:27846061, PMID:29236639)
Risk factors
- UK school year
- 13
- persons in household
- 6
- antibiotic use
- no
- cigarettes per day
- 6-10
- passive smoking
- no
- pubs clubs per week
- 2-3
- persons kissed past week
- 2-3
Publications (2)
- 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
- Spinsanti M, Brignoli T, Bodini M, Fontana LE, De Chiara M, Biolchi A, Muzzi A, Scarlato V, Delany I (2021). Deconvolution of intergenic polymorphisms determining high expression of Factor H binding protein in meningococcus and their association with invasive disease. PLoS Pathog 17:e1009461
Sequence bin
- contigs
- 190
- total length
- 2,177,875 bp
- max length
- 103,936 bp
- mean length
- 11,463 bp
- N50
- 45,713
- L50
- 17
- N90
- 9,150
- L90
- 51
- N95
- 3,954
- L95
- 69
- %GC
- 51.44
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,222
Annotation quality metrics
Provenance information
Scheme completion
Scheme | Scheme loci | Designated loci | Annotation | |
---|---|---|---|---|
Score | Status | |||
rplF species | 1 | 1 | 100 | |
Finetyping antigens | 3 | 3 | 100 | |
Bexsero Antigen Sequence Typing (BAST) | 5 | 5 | 100 | |
MLST | 7 | 7 | 100 | |
Ribosomal MLST | 53 | 53 | 100 | |
N. meningitidis cgMLST v2 | 1422 | 1418 | 99 |
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 scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
---|---|---|---|---|---|
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 698 (3992 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 799 (3399 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 921 (3077 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1173 (1716 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1665 (1286 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 33 (1931 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 239 (2 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 269 (2 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 698 (3992 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 799 (3399 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 921 (3077 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1173 (1716 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1665 (1286 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 33 (1931 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 239 (2 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 269 (2 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 280 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 294 (1 isolate) |
Schemes and loci
- All loci
- Capsule
- Genetic Information Processing
- Genomic islands
- Lineage Schemes
- Metabolism
- Peptidoglycan Biosynthesis
- Pilin
- Typing
- Other schemes
- Loci not in schemes
Navigate and select schemes within tree to display allele designations
Tools
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