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Full information on isolate JJA (id:3776)

Provenance/meta data

South America
age yr
age mth
community acquired
microdilution; CID 2000, 30 (1): 78-86
Joice Reis,
Melissa Jansen van Rensburg, University of Oxford, UK (E-mail:
update history
15 updates show details
date entered

Publications (21)

  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Wadood A, Jamal A, Riaz M, Khan A, Uddin R, Jelani M, Azam SS (2018). Subtractive genome analysis for in silico identification and characterization of novel drug targets in Streptococcus pneumonia strain JJA. Microb Pathog 115:194-198
  • 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

Sequence bin

2120234 bp
loci tagged
detailed breakdown

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: 6 (48 isolates)
Sp_cgc_400cgMLSTSingle-linkage400experimentalgroup: 6 (40 isolates)
Sp_cgc_300cgMLSTSingle-linkage300experimentalgroup: 251 (40 isolates)
Sp_cgc_200cgMLSTSingle-linkage200experimentalgroup: 6 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations