Full information on isolate 2846 (id:669)
Projects
This isolate is a member of the following project:
- GMGL
- Global Meningitis Genome Library: curated isolate data sets of N. meningtidis causing meningitis and/or septicaemia
Provenance/primary metadata
- id
- 669
- isolate
- 2846
- strain designation
- C: P1.Δ,Δ: F1-30: ST-52 (cc11)
- alias
- M97/252836
- country
- UK
- continent
- Europe
- year
- 1997
- disease
- carrier
- epidemiology
- endemic
- species
- Neisseria meningitidis
- serogroup
- C
- genogroup
- C
- genogroup notes
- C backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
- capsule group
- C
- comments
- University outbreak, strain 4, carrier 3
Tracking
- ENA run accession
- ERR063494 www.ebi.ac.uk
- sender
- Ian Feavers, University of Oxford, UK
- curator
- Auto Tagger
- update history
- 164 updates show details
- date entered
- 2001-02-07
- datestamp
- 2021-10-16
Secondary metadata
Publications (4)
- Feavers IM, Gray SJ, Urwin R, Russell JE, Bygraves JA, Kaczmarski EB, Maiden MC (1999). Multilocus sequence typing and antigen gene sequencing in the investigation of a meningococcal disease outbreak. J Clin Microbiol 37:3883-7
- Jolley KA, Hill DM, Bratcher HB, Harrison OB, Feavers IM, Parkhill J, Maiden MC (2012). Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid Web-based analysis methods. J Clin Microbiol 50:3046-53
- Lucidarme J, Hill DM, Bratcher HB, Gray SJ, du Plessis M, Tsang RS, Vazquez JA, Taha MK, Ceyhan M, Efron AM, Gorla MC, Findlow J, Jolley KA, Maiden MC, Borrow R (2015). Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage. J Infect 71:544-52
- Lucidarme J, Lekshmi A, Parikh SR, Bray JE, Hill DM, Bratcher HB, Gray SJ, Carr AD, Jolley KA, Findlow J, Campbell H, Ladhani SN, Ramsay ME, Maiden MCJ, Borrow R (2017). Frequent capsule switching in 'ultra-virulent' meningococci - Are we ready for a serogroup B ST-11 complex outbreak? J Infect 75:95-103
Sequence bin
- contigs
- 465
- total length
- 2,056,804 bp
- max length
- 54,203 bp
- mean length
- 4,424 bp
- N50
- 16,562
- L50
- 41
- N90
- 3,374
- L90
- 145
- N95
- 1,670
- L95
- 188
- %GC
- 51.93
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,141
Annotation quality metrics
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 | 1403 | 98 |
Analysis
rMLST species identification
Rank | Taxon | Taxonomy | Support | Matches |
---|---|---|---|---|
SPECIES | Neisseria meningitidis | Proteobacteria > Betaproteobacteria > Neisseriales > Neisseriaceae > Neisseria > Neisseria meningitidis | 100% |
Analysis performed: 2022-12-20
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 | 696 (5334 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 796 (5327 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 917 (5308 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1121 (5175 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1599 (5071 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 156 (6579 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 1498 (41 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 696 (5334 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 796 (5327 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 917 (5308 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1121 (5175 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1599 (5071 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 156 (6579 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 1498 (41 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 80 (1 isolate) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 83 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 85 (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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Analysis: