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Full information on isolate R34-3071 (id:29176)

Provenance/primary metadata

id
29176
isolate
R34-3071
country
USA
continent
North America
region
Massachusetts
year
2004
serotype
11A
diagnosis
carriage
host
human
source
nasopharynx
penicillin
0.03
erythromycin
0.06
tetracycline
0.50
chloramphenicol
2.00
comments
6-24 months
ENA accession
ERR065326 www.ebi.ac.uk
rMLST database accession
31298
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
10 updates show details
date entered
2015-04-28
datestamp
2020-04-08

Publications (9)

  • 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

Sequence bin

contigs
79
total length
2,033,096 bp
max length
244,809 bp
mean length
25,736 bp
N50 contig number
9
N50 length (L50)
71,654
N90 contig number
26
N90 length (L90)
21,450
N95 contig number
32
N95 length (L95)
12,941
loci tagged
1,403
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: 4 (827 isolates)
Sp_cgc_500cgMLSTSingle-linkage500experimentalgroup: 4 (309 isolates)
Sp_cgc_400cgMLSTSingle-linkage400experimentalgroup: 4 (231 isolates)
Sp_cgc_300cgMLSTSingle-linkage300experimentalgroup: 4 (231 isolates)
Sp_cgc_200cgMLSTSingle-linkage200experimentalgroup: 4 (230 isolates)
Sp_cgc_100cgMLSTSingle-linkage100experimentalgroup: 315 (28 isolates)
Sp_cgc_50cgMLSTSingle-linkage50experimentalgroup: 578 (23 isolates)

Schemes and loci

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