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Full information on isolate P1041 (id:3217)

Provenance/meta data

id
3217
isolate
P1041
aliases
C5371; CACE01000000
country
Ghana
continent
Africa
serotype
1
age yr
6
sex
male
host
human
penicillin
S
chloramphenicol
S
cefotaxime
S
comments
meningitis
sender
Julia Leimkugel, Molecular Immunology; Swiss Tropical Institute; Socinstr. 57; CH-4051 Basel; Switzerland
curator
Melissa Jansen van Rensburg, University of Oxford, UK (E-mail: Melissa.JansenvanRensburg@ndph.ox.ac.uk)
update history
15 updates show details
date entered
2005-12-22
datestamp
2020-03-26

Publications (7)

  • Bogaardt C, van Tonder AJ, Brueggemann AB (2015). Genomic analyses of pneumococci reveal a wide diversity of bacteriocins - including pneumocyclicin, a novel circular bacteriocin. BMC Genomics 16:554
  • Brueggemann AB, Harrold CL, Rezaei Javan R, van Tonder AJ, McDonnell AJ, Edwards BA (2017). Pneumococcal prophages are diverse, but not without structure or history. Sci Rep 7:42976
  • Crisafulli G, Guidotti S, Muzzi A, Torricelli G, Moschioni M, Masignani V, Censini S, Donati C (2013). An extended multi-locus molecular typing schema for Streptococcus pneumoniae demonstrates that a limited number of capsular switch events is responsible for serotype heterogeneity of closely related strains from different countries. Infect Genet Evol 13:151-61
  • Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V (2010). Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 11:R107
  • Hiller NL, Eutsey RA, Powell E, Earl JP, Janto B, Martin DP, Dawid S, Ahmed A, Longwell MJ, Dahlgren ME, Ezzo S, Tettelin H, Daugherty SC, Mitchell TJ, Hillman TA, Buchinsky FJ, Tomasz A, de Lencastre H, Sá-Leão R, Post JC, Hu FZ, Ehrlich GD (2011). Differences in genotype and virulence among four multidrug-resistant Streptococcus pneumoniae isolates belonging to the PMEN1 clone. PLoS One 6:e28850
  • 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
  • Sanguinetti L, Toti S, Reguzzi V, Bagnoli F, Donati C (2012). A novel computational method identifies intra- and inter-species recombination events in Staphylococcus aureus and Streptococcus pneumoniae. PLoS Comput Biol 8:e1002668

Sequence bin

contigs
52
total length
2,097,342 bp
max length
179,939 bp
mean length
40,334 bp
N50 contig number
9
N50 length (L50)
78,864
N90 contig number
28
N90 length (L90)
22,123
N95 contig number
34
N95 length (L95)
12,401
loci tagged
1,395
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: 3 (14 isolates)
Sp_cgc_500cgMLSTSingle-linkage500experimentalgroup: 5 (8 isolates)
Sp_cgc_400cgMLSTSingle-linkage400experimentalgroup: 5 (8 isolates)
Sp_cgc_300cgMLSTSingle-linkage300experimentalgroup: 5 (8 isolates)
Sp_cgc_200cgMLSTSingle-linkage200experimentalgroup: 5 (8 isolates)
Sp_cgc_100cgMLSTSingle-linkage100experimentalgroup: 5 (2 isolates)
Sp_cgc_50cgMLSTSingle-linkage50experimentalgroup: 5 (2 isolates)
Sp_cgc_25cgMLSTSingle-linkage25experimentalgroup: 5 (2 isolates)

Schemes and loci

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