Full information on isolate J0161 (id:11)
Projects
This isolate is a member of the following project:
- Public isolates
- Isolates publicly available for consultation
Provenance/primary metadata
- id
- 11
- isolate
- J0161
- species
- L. monocytogenes
- sender
- Alexandra Moura, Institut Pasteur, France
- curator
- Auto Tagger
- update history
- 17983 updates show details
- date entered
- 2014-04-08
- datestamp
- 2025-09-22
- isolation year
- 2000
- country
- USA
- continent
- North America
- outbreak info
- Outbreak 2000
- source
- Human
- source description
- Unknown
- phylogenetic lineage
- II
- serotype
- IIa; 1/2a
- clonal complex
- CC11
- sublineage
- SL11
- cgmlst type
- CT948
- accession number
- NC_017545
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
- Orsi RH, Borowsky ML, Lauer P, Young SK, Nusbaum C, Galagan JE, Birren BW, Ivy RA, Sun Q, Graves LM, Swaminathan B, Wiedmann M (2008). Short-term genome evolution of Listeria monocytogenes in a non-controlled environment. BMC Genomics 9:539
Sequence bin
- method
- Unknown
- contigs
- 1
- length
- 3,000,464 bp
- %GC
- 37.86
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,357
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_0_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_0 | 1 | 3 |
| 0_0_0_19_1_8_3_0_0_0_0_0 | 0 | 3 |
| 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_0 | 1 | 3 |
| 0_0_0_19_1_8_3_0_0_0_0_0 | 0 | 3 |
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 |
|---|---|---|---|---|---|
| auto_cgclust_4 | cgMLST1748 | Single-linkage | 4 | experimental | 486 (3 isolates) |
| 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 | 486 (3 isolates) |
| 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
Navigate and select schemes within tree to display allele designations
Tools
Export:
Analysis: