Full information on isolate 18581 (id:17191)
Projects
This isolate is a member of the following project:
- penA sequence analysis
- Analysis of penA sequences correlated with penicillin G resistance published in Taha et al. 2007 Antimicrob Agents Chemother 51:2784-92.
Provenance/primary metadata
- id
- 17191
- isolate
- 18581
- strain designation
- W: P1.5,2: F1-1: ST-11 (cc11)
- country
- Madagascar
- continent
- Africa
- year
- 2001
- disease
- invasive (unspecified/other)
- source
- CSF
- species
- Neisseria meningitidis
- serogroup
- W
- genogroup
- W
- genogroup notes
- W backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
- capsule group
- W
- serotype
- 2a
- sero subtype
- P1.5,2
Antimicrobial resistance
- amoxicillin mic
- =0.094 μg/mL
- penicillin mic
- =0.064 μg/mL
- penicillin SIR
- S
Tracking
- sender
- Muhamed-Kheir Taha, National Reference Center for Meningococci and Haemophilus influenzae, Institut Pasteur, France
- curator
- Auto Tagger
- update history
- 51 updates show details
- date entered
- 2010-05-27
- datestamp
- 2022-04-16
Secondary metadata
Publication (1)
- Taha MK, Vázquez JA, Hong E, Bennett DE, Bertrand S, Bukovski S, Cafferkey MT, Carion F, Christensen JJ, Diggle M, Edwards G, Enríquez R, Fazio C, Frosch M, Heuberger S, Hoffmann S, Jolley KA, Kadlubowski M, Kechrid A, Kesanopoulos K, Kriz P, Lambertsen L, Levenet I, Musilek M, Paragi M, Saguer A, Skoczynska A, Stefanelli P, Thulin S, Tzanakaki G, Unemo M, Vogel U, Zarantonelli ML (2007). Target gene sequencing to characterize the penicillin G susceptibility of Neisseria meningitidis. Antimicrob Agents Chemother 51:2784-92
Sequence bin
- contigs
- 125
- total length
- 2,063,912 bp
- max length
- 100,189 bp
- mean length
- 16,512 bp
- N50
- 36,212
- L50
- 19
- N90
- 8,837
- L90
- 63
- N95
- 6,357
- L95
- 77
- %GC
- 51.92
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,181
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 | 1420 | 99 |
Analysis
rMLST species identification
Rank | Taxon | Taxonomy | Support | Matches |
---|---|---|---|---|
SPECIES | Neisseria meningitidis | Proteobacteria > Betaproteobacteria > Neisseriales > Neisseriaceae > Neisseria > Neisseria meningitidis | 100% |
Analysis performed: 2022-11-29
Similar isolates (determined by classification schemes)
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 | 228 (4179 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 258 (1567 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 269 (292 isolates) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 283 (157 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 | 228 (4179 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 258 (1567 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 269 (292 isolates) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 283 (157 isolates) |
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: