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Full information on isolate TCH8431 (id:35923)

Provenance/meta data

id
35923
isolate
TCH8431
aliases
ACJP00000000; CP001993; NC_014251; TCH8431/19A
country
Unknown
serotype
19A
host
human
sender
Angela Brueggemann, University of Oxford, UK
curator
Melissa Jansen van Rensburg, Imperial College London, UK (E-mail: m.jansen-van-rensburg@imperial.ac.uk)
update history
5 updates show details
date entered
2016-07-13
datestamp
2019-04-24

Publications (14)

  • Angiuoli SV, Salzberg SL (2011). Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27:334-42
  • 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
  • Croucher NJ, Vernikos GS, Parkhill J, Bentley SD (2011). Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics 12:120
  • Donner J, Bunk B, Schober I, Spröer C, Bergmann S, Jarek M, Overmann J, Wagner-Döbler I (2017). Complete Genome Sequences of Three Multidrug-Resistant Clinical Isolates of Streptococcus pneumoniae Serotype 19A with Different Susceptibilities to the Myxobacterial Metabolite Carolacton. Genome Announc 5:
  • Gámez G, Castro A, Gómez-Mejia A, Gallego M, Bedoya A, Camargo M, Hammerschmidt S (2018). The variome of pneumococcal virulence factors and regulators. BMC Genomics 19:10
  • Karlsson R, Gonzales-Siles L, Gomila M, Busquets A, Salvà-Serra F, Jaén-Luchoro D, Jakobsson HE, Karlsson A, Boulund F, Kristiansson E, Moore ERB (2018). Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics. PLoS One 13:e0208804
  • Kilian M, Riley DR, Jensen A, Brüggemann H, Tettelin H (2014). Parallel evolution of Streptococcus pneumoniae and Streptococcus mitis to pathogenic and mutualistic lifestyles. MBio 5:e01490-14
  • Li G, Hu FZ, Yang X, Cui Y, Yang J, Qu F, Gao GF, Zhang JR (2012). Complete genome sequence of Streptococcus pneumoniae strain ST556, a multidrug-resistant isolate from an otitis media patient. J Bacteriol 194:3294-5
  • Lin IH, Hsu MT, Chang CH (2012). Protein domain repetition is enriched in Streptococcal cell-surface proteins. Genomics 100:370-9
  • 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
  • Swetha RG, Sekar DK, Devi ED, Ahmed ZZ, Ramaiah S, Anbarasu A, Sekar K (2014). Streptococcus pneumoniae Genome Database (SPGDB): a database for strain specific comparative analysis of Streptococcus pneumoniae genes and proteins. Genomics 104:582-6
  • Valentino MD, McGuire AM, Rosch JW, Bispo PJ, Burnham C, Sanfilippo CM, Carter RA, Zegans ME, Beall B, Earl AM, Tuomanen EI, Morris TW, Haas W, Gilmore MS (2014). Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster. Nat Commun 5:5411
  • Zhao Y, Sun C, Zhao D, Zhang Y, You Y, Jia X, Yang J, Wang L, Wang J, Fu H, Kang Y, Chen F, Yu J, Wu J, Xiao J (2018). PGAP-X: extension on pan-genome analysis pipeline. BMC Genomics 19:36

Sequence bin

contigs
1
length
2088772 bp
loci tagged
60
detailed breakdown
Display

Schemes and loci

MLST

aroE 
4  S 
gdh 
16  S 
gki 
19  S 
recP 
15  S 
spi 
6  S 
xpt 
20  S 
ddl 
1  S 
ST
320
clonal complex
Not defined

Ribosomal MLST

BACT000001 (rpsA) 
112  S 
BACT000002 (rpsB) 
68  S 
BACT000003 (rpsC) 
61  S 
BACT000004 (rpsD) 
60  S 
BACT000005 (rpsE) 
23  S 
BACT000006 (rpsF) 
28  S 
BACT000007 (rpsG) 
24  S 
BACT000008 (rpsH) 
38  S 
BACT000009 (rpsI) 
48  S 
BACT000010 (rpsJ) 
48  S 
BACT000011 (rpsK) 
34  S 
BACT000012 (rpsL) 
33  S 
BACT000013 (rpsM) 
23  S 
BACT000014 (rpsN) 
29  S 
BACT000015 (rpsO) 
32  S 
BACT000016 (rpsP) 
27  S 
BACT000017 (rpsQ) 
20  S 
BACT000018 (rpsR) 
35  S 
BACT000019 (rpsS) 
17  S 
BACT000020 (rpsT) 
1557  S 
BACT000021 (rpsU) 
20  S 
BACT000030 (rplA) 
56  S 
BACT000031 (rplB) 
57  S 
BACT000032 (rplC) 
64  S 
BACT000033 (rplD) 
48  S 
BACT000034 (rplE) 
23  S 
BACT000035 (rplF) 
50  S 
BACT000036 (rplL) 
47  S 
BACT000038 (rplI) 
65  S 
BACT000039 (rplJ) 
19  S 
BACT000040 (rplK) 
30  S 
BACT000042 (rplM) 
25  S 
BACT000043 (rplN) 
16  S 
BACT000044 (rplO) 
16  S 
BACT000045 (rplP) 
17  S 
BACT000046 (rplQ) 
37  S 
BACT000047 (rplR) 
18  S 
BACT000048 (rplS) 
51  S 
BACT000049 (rplT) 
49  S 
BACT000050 (rplU) 
35  S 
BACT000051 (rplV) 
31  S 
BACT000052 (rplW) 
54  S 
BACT000053 (rplX) 
190  S 
BACT000056 (rpmA) 
222  S 
BACT000057 (rpmB) 
25  S 
BACT000058 (rpmC) 
14  S 
BACT000059 (rpmD) 
20  S 
BACT000060 (rpmE) 
17  S 
BACT000061 (rpmF) 
26  S 
BACT000062 (rpmG) 
23, 173, 732  S 
BACT000063 (rpmH) 
26  S 
BACT000064 (rpmI) 
19  S 
BACT000065 (rpmJ) 
16  S 
rST
572
genus
Streptococcus
species
Streptococcus pneumoniae
subspecies
Not defined
lineage
Not defined
sublineage
Not defined
other designation
Not defined
notes
Not defined

Tools

Analysis: