Full information on isolate F6854 (id:20)
Projects
This isolate is a member of the following project:
- Public isolates
- Isolates publicly available for consultation
Provenance/primary metadata
- id
- 20
- isolate
- F6854
- species
- L. monocytogenes
- sender
- Alexandra Moura, Institut Pasteur, France
- curator
- Auto Tagger
- update history
- 17876 updates show details
- date entered
- 2014-04-08
- datestamp
- 2025-09-22
- isolation year
- 1988
- country
- USA
- continent
- North America
- source
- Food
- source description
- Unknown
- phylogenetic lineage
- II
- serotype
- IIa; 1/2a
- clonal complex
- CC11
- sublineage
- SL11
- cgmlst type
- CT948
- accession number
- GCA_000167135.1
Publications (3)
- Maury MM, Tsai YH, Charlier C, Touchon M, Chenal-Francisque V, Leclercq A, Criscuolo A, Gaultier C, Roussel S, Brisabois A, Disson O, Rocha EPC, Brisse S, Lecuit M (2016). Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nat Genet 48:308-313
- Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A, Tarr C, Björkman JT, Dallman T, Reimer A, Enouf V, Larsonneur E, Carleton H, Bracq-Dieye H, Katz LS, Jones L, Touchon M, Tourdjman M, Walker M, Stroika S, Cantinelli T, Chenal-Francisque V, Kucerova Z, Rocha EP, Nadon C, Grant K, Nielsen EM, Pot B, Gerner-Smidt P, Lecuit M, Brisse S (2016). Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat Microbiol 2:16185
- Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM (2004). Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res 32:2386-95
Sequence bin
- method
- Unknown
- contigs
- 1
- length
- 2,963,485 bp
- %GC
- 37.85
- Ns
- 13200
- gaps
- 132
- loci tagged
- 2,213
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Similar isolates (determined by LIN codes)
- Scheme
- cgMLST1748_v2
- LIN code
- 0_0_0_19_1_8_3_0_0_0_3_0
- Lineage
- LII
- Sublineage
- SL11
- Genetic cluster
- GC169
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_0_19_1_8_3_0 | 7 | 12 |
| 0_0_0_19_1_8_3_0_0 | 4 | 11 |
| 0_0_0_19_1_8_3_0_0_0 | 2 | 7 |
| 0_0_0_19_1_8_3_0_0_0_3 | 1 | 1 |
| 0_0_0_19_1_8_3_0_0_0_3_0 | 0 | 1 |
| 0 | 1660 | 1992 |
| 0_0 | 1500 | 1990 |
| 0_0_0 | 1342 | 1979 |
| 0_0_0_19 | 1182 | 463 |
| 0_0_0_19_1 | 1020 | 460 |
| 0_0_0_19_1_8 | 200 | 40 |
| 0_0_0_19_1_8_3 | 50 | 14 |
| 0_0_0_19_1_8_3_0 | 7 | 12 |
| 0_0_0_19_1_8_3_0_0 | 4 | 11 |
| 0_0_0_19_1_8_3_0_0_0 | 2 | 7 |
| 0_0_0_19_1_8_3_0_0_0_3 | 1 | 1 |
| 0_0_0_19_1_8_3_0_0_0_3_0 | 0 | 1 |
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 |
|---|---|---|---|---|---|
| auto_cgclust_7 | cgMLST1748 | Single-linkage | 7 | experimental | 453 (4 isolates) |
| auto_cgclust_10 | cgMLST1748 | Single-linkage | 10 | experimental | 430 (4 isolates) |
| auto_cgclust_30 | cgMLST1748 | Single-linkage | 30 | experimental | 17 (7 isolates) |
| auto_cgclust_150 | cgMLST1748 | Single-linkage | 150 | experimental | 322 (7 isolates) |
| auto_cgclust_500 | cgMLST1748 | Single-linkage | 500 | experimental | 40 (53 isolates) |
| auto_cgclust_1000 | cgMLST1748 | Single-linkage | 1000 | experimental | 9 (337 isolates) |
| auto_cgclust_1500 | cgMLST1748 | Single-linkage | 1500 | experimental | 2 (1331 isolates) |
| auto_cgclust_4 | cgMLST1748 | Single-linkage | 4 | experimental | 17 (1 isolate) |
| auto_cgclust_7 | cgMLST1748 | Single-linkage | 7 | experimental | 453 (4 isolates) |
| auto_cgclust_10 | cgMLST1748 | Single-linkage | 10 | experimental | 430 (4 isolates) |
| auto_cgclust_30 | cgMLST1748 | Single-linkage | 30 | experimental | 17 (7 isolates) |
| auto_cgclust_150 | cgMLST1748 | Single-linkage | 150 | experimental | 322 (7 isolates) |
| auto_cgclust_500 | cgMLST1748 | Single-linkage | 500 | experimental | 40 (53 isolates) |
| auto_cgclust_1000 | cgMLST1748 | Single-linkage | 1000 | experimental | 9 (337 isolates) |
| auto_cgclust_1500 | cgMLST1748 | Single-linkage | 1500 | experimental | 2 (1331 isolates) |
Schemes and loci
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