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Full information on isolate R34-3094 (id:29264)

Provenance/meta data

id
29264
isolate
R34-3094
country
USA
continent
North America
region
Massachusetts
year
2004
serotype
19F
diagnosis
carriage
host
human
source
nasopharynx
penicillin
2.00
erythromycin
0.50
tetracycline
4.00
chloramphenicol
2.00
comments
6-24 months
ENA accession
ERR067999 www.ebi.ac.uk
rMLST database accession
31347
sender
Angela Brueggemann, University of Oxford, UK
curator
Melissa Jansen van Rensburg, University of Oxford, UK (E-mail: Melissa.JansenvanRensburg@ndph.ox.ac.uk)
update history
8 updates show details
date entered
2015-04-28
datestamp
2020-03-03

Publications (10)

  • Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill J (2014). Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes. PLoS Genet 10:e1004547
  • Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP (2014). Diversification of bacterial genome content through distinct mechanisms over different timescales. Nat Commun 5:5471
  • Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP, Lipsitch M (2013). Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet 45:656-63
  • Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WP (2015). Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae. Sci Data 2:150058
  • Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP (2015). Selective and genetic constraints on pneumococcal serotype switching. PLoS Genet 11:e1005095
  • Lees JA, Kendall M, Parkhill J, Colijn C, Bentley SD, Harris SR (2018). Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study. Wellcome Open Res 3:33
  • Li Y, Croucher NJ, Thompson CM, TrzciƄski K, Hanage WP, Lipsitch M (2015). Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity. BMC Genomics 16:369
  • Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P (2017). Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations. Mol Biol Evol 34:1167-1182
  • Rezaei Javan R, van Tonder AJ, King JP, Harrold CL, Brueggemann AB (2018). Genome Sequencing Reveals a Large and Diverse Repertoire of Antimicrobial Peptides. Front Microbiol 9:2012
  • Rockett RJ, Oftadeh S, Bachmann NL, Timms VJ, Kong F, Gilbert GL, Sintchenko V (2018). Genome-wide analysis of Streptococcus pneumoniae serogroup 19 in the decade after the introduction of pneumococcal conjugate vaccines in Australia. Sci Rep 8:16969

Sequence bin

contigs
98
total length
2,084,533 bp
max length
172,225 bp
mean length
21,271 bp
N50 contig number
13
N50 length (L50)
58,762
N90 contig number
37
N90 length (L90)
19,883
N95 contig number
43
N95 length (L95)
13,458
loci tagged
1,407
detailed breakdown
Display

Similar isolates (determined by classification schemes)

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Sp_cgc_1000cgMLSTSingle-linkage1000experimentalgroup: 7 (4508 isolates)
Sp_cgc_500cgMLSTSingle-linkage500experimentalgroup: 1 (718 isolates)
Sp_cgc_400cgMLSTSingle-linkage400experimentalgroup: 1 (718 isolates)
Sp_cgc_300cgMLSTSingle-linkage300experimentalgroup: 1 (717 isolates)
Sp_cgc_200cgMLSTSingle-linkage200experimentalgroup: 1 (717 isolates)
Sp_cgc_100cgMLSTSingle-linkage100experimentalgroup: 238 (337 isolates)
Sp_cgc_50cgMLSTSingle-linkage50experimentalgroup: 307 (37 isolates)

Schemes and loci

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