PubMLST Database home Contents
Log in
Help

Full information on isolate TIGR4 (id:37765)

Provenance/meta data

id
37765
isolate
TIGR4
aliases
AE005672; ATCC BAA-334; JNR7/87; KNR.7/87; N4; NC_003028
country
Norway
continent
Europe
region
Kongsvinger
year
1991
serotype
4
age yr
30
sex
male
diagnosis1
bacteraemia
host
human
source
blood
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
2017-02-28
datestamp
2019-04-29

Publications (37)

  • Angiuoli SV, Salzberg SL (2011). Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27:334-42
  • Bidossi A, Mulas L, Decorosi F, Colomba L, Ricci S, Pozzi G, Deutscher J, Viti C, Oggioni MR (2012). A functional genomics approach to establish the complement of carbohydrate transporters in Streptococcus pneumoniae. PLoS One 7:e33320
  • 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
  • Croucher NJ, Vernikos GS, Parkhill J, Bentley SD (2011). Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics 12:120
  • Croucher NJ, Walker D, Romero P, Lennard N, Paterson GK, Bason NC, Mitchell AM, Quail MA, Andrew PW, Parkhill J, Bentley SD, Mitchell TJ (2009). Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81. J Bacteriol 191:1480-9
  • 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
  • Garbom S, Forsberg A, Wolf-Watz H, Kihlberg BM (2004). Identification of novel virulence-associated genes via genome analysis of hypothetical genes. Infect Immun 72:1333-40
  • 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
  • Hahn C, Harrison EM, Parkhill J, Holmes MA, Paterson GK (2015). Draft Genome Sequence of the Streptococcus pneumoniae Avery Strain A66. Genome Announc 3:
  • Hiller NL, Ahmed A, Powell E, Martin DP, Eutsey R, Earl J, Janto B, Boissy RJ, Hogg J, Barbadora K, Sampath R, Lonergan S, Post JC, Hu FZ, Ehrlich GD (2010). Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection. PLoS Pathog 6:e1001108
  • 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
  • Hiller NL, Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K, Hayes J, Barbadora K, Klimke W, Dernovoy D, Tatusova T, Parkhill J, Bentley SD, Post JC, Ehrlich GD, Hu FZ (2007). Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol 189:8186-95
  • Karlin S, Theriot J, Mrázek J (2004). Comparative analysis of gene expression among low G+C gram-positive genomes. Proc Natl Acad Sci U S A 101:6182-7
  • 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
  • Koeck JL, Njanpop-Lafourcade BM, Cade S, Varon E, Sangare L, Valjevac S, Vergnaud G, Pourcel C (2005). Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing. BMC Microbiol 5:66
  • 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 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
  • Marri PR, Hao W, Golding GB (2006). Gene gain and gene loss in streptococcus: is it driven by habitat? Mol Biol Evol 23:2379-91
  • Martín-Galiano AJ, Wells JM, de la Campa AG (2004). Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae. Microbiology 150:2313-25
  • Mrázek J, Gaynon LH, Karlin S (2002). Frequent oligonucleotide motifs in genomes of three streptococci. Nucleic Acids Res 30:4216-21
  • Muzzi A, Moschioni M, Covacci A, Rappuoli R, Donati C (2008). Pilus operon evolution in Streptococcus pneumoniae is driven by positive selection and recombination. PLoS One 3:e3660
  • Oggioni MR, Pozzi G (2001). Comparative genomics for identification of clone-specific sequence blocks in Streptococcus pneumoniae. FEMS Microbiol Lett 200:137-43
  • Piet JR, Geldhoff M, van Schaik BD, Brouwer MC, Valls Seron M, Jakobs ME, Schipper K, Pannekoek Y, Zwinderman AH, van der Poll T, van Kampen AH, Baas F, van der Ende A, van de Beek D (2014). Streptococcus pneumoniae arginine synthesis genes promote growth and virulence in pneumococcal meningitis. J Infect Dis 209:1781-91
  • 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
  • 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
  • Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM (2001). Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293:498-506
  • 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
  • Vetrivel U, Subramanian G, Dorairaj S (2011). A novel in silico approach to identify potential therapeutic targets in human bacterial pathogens. Hugo J 5:25-34
  • Williams TM, Loman NJ, Ebruke C, Musher DM, Adegbola RA, Pallen MJ, Weinstock GM, Antonio M (2012). Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa. PLoS One 7:e26742
  • Wyres KL, Lambertsen LM, Croucher NJ, McGee L, von Gottberg A, Liñares J, Jacobs MR, Kristinsson KG, Beall BW, Klugman KP, Parkhill J, Hakenbeck R, Bentley SD, Brueggemann AB (2012). The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success. Genome Biol 13:R103
  • 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
  • de Alvarenga Mudadu M, Carvalho V, Leclercq SY (2015). Nonclassically secreted proteins as possible antigens for vaccine development: a reverse vaccinology approach. Appl Biochem Biotechnol 175:3360-70

Sequence bin

contigs
1
length
2160842 bp
loci tagged
53
detailed breakdown
Display

Schemes and loci

MLST

aroE 
10
gdh 
5
gki 
4
recP 
5
spi 
13
xpt 
10
ddl 
18
ST
205
clonal complex
Not defined

Ribosomal MLST

BACT000001 (rpsA) 
94  S 
BACT000002 (rpsB) 
71  S 
BACT000003 (rpsC) 
61  S 
BACT000004 (rpsD) 
63  S 
BACT000005 (rpsE) 
23  S 
BACT000006 (rpsF) 
28  S 
BACT000007 (rpsG) 
46  S 
BACT000008 (rpsH) 
38  S 
BACT000009 (rpsI) 
50  S 
BACT000010 (rpsJ) 
48  S 
BACT000011 (rpsK) 
34  S 
BACT000012 (rpsL) 
33  S 
BACT000013 (rpsM) 
27  S 
BACT000014 (rpsN) 
28  S 
BACT000015 (rpsO) 
31  S 
BACT000016 (rpsP) 
20  S 
BACT000017 (rpsQ) 
20  S 
BACT000018 (rpsR) 
21  S 
BACT000019 (rpsS) 
17  S 
BACT000020 (rpsT) 
50  S 
BACT000021 (rpsU) 
20  S 
BACT000030 (rplA) 
24  S 
BACT000031 (rplB) 
57  S 
BACT000032 (rplC) 
61  S 
BACT000033 (rplD) 
48  S 
BACT000034 (rplE) 
18  S 
BACT000035 (rplF) 
51  S 
BACT000036 (rplL) 
43  S 
BACT000038 (rplI) 
33  S 
BACT000039 (rplJ) 
19  S 
BACT000040 (rplK) 
30  S 
BACT000042 (rplM) 
46  S 
BACT000043 (rplN) 
16  S 
BACT000044 (rplO) 
16  S 
BACT000045 (rplP) 
17  S 
BACT000046 (rplQ) 
38  S 
BACT000047 (rplR) 
18  S 
BACT000048 (rplS) 
50  S 
BACT000049 (rplT) 
47  S 
BACT000050 (rplU) 
19  S 
BACT000051 (rplV) 
31  S 
BACT000052 (rplW) 
52  S 
BACT000053 (rplX) 
190  S 
BACT000056 (rpmA) 
29  S 
BACT000057 (rpmB) 
25  S 
BACT000058 (rpmC) 
25  S 
BACT000059 (rpmD) 
20  S 
BACT000060 (rpmE) 
17  S 
BACT000061 (rpmF) 
34  S 
BACT000062 (rpmG) 
35, 4289  S 
BACT000063 (rpmH) 
26  S 
BACT000064 (rpmI) 
19  S 
BACT000065 (rpmJ) 
16  S 
rST
569
genus
Streptococcus
species
Streptococcus pneumoniae
subspecies
Not defined
lineage
Not defined
sublineage
Not defined
other designation
Not defined
notes
Not defined

Tools

Analysis: