Full information on isolate 19121 (id:17192)
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
- 17192
- isolate
- 19121
- 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
- =0.064 μg/mL
- penicillin mic
- =0.094 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
- 53 updates show details
- date entered
- 2010-05-27
- datestamp
- 2022-10-16
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
- 118
- total length
- 2,063,391 bp
- max length
- 97,233 bp
- mean length
- 17,487 bp
- N50
- 40,699
- L50
- 17
- N90
- 9,109
- L90
- 58
- N95
- 6,425
- L95
- 71
- %GC
- 51.93
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,169
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 | 4 | 80 | |
MLST | 7 | 7 | 100 | |
Ribosomal MLST | 53 | 53 | 100 | |
N. meningitidis cgMLST v2 | 1422 | 1416 | 99 |
Analysis
rMLST species identification
Rank | Taxon | Taxonomy | Support | Matches |
---|---|---|---|---|
SPECIES | Neisseria meningitidis | Proteobacteria > Betaproteobacteria > Neisseriales > Neisseriaceae > Neisseria > Neisseria meningitidis | 98% |
Analysis performed: 2022-11-29
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 | 228 (4179 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 258 (1567 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 | 402 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 435 (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
Export:
Analysis: