Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13 by Belman, S, Soeng, S, Soputhy, C, Gladstone, R, Hawkins, PA, Breiman, RF, McGee, L, Bentley, SD, Lo, SW, Turner, P

“…We sequenced pre-PCV13 (01/2013–12/2015, N=258) and post-PCV13 carriage isolates (01/2016–02/2017, N=428) and used PopPUNK and SeroBA to determine lineage prevalence and serotype composition. …”

Novel multilocus sequence typing and global sequence clustering schemes for characterizing the population diversity of Streptococcus mitis by Kalizang’oma, A, Kwambana-Adams, B, Chan, JM, Viswanath, A, Gori, A, Richard, D, Jolley, KA, Lees, J, Goldblatt, D, Beleza, S, Bentley, SD, Heyderman, RS, Chaguza, C

“…We used internal 450-bp sequence fragments of seven housekeeping genes (<em>accA</em>,&nbsp;<em>gki</em>,&nbsp;<em>hom</em>,&nbsp;<em>oppC</em>,&nbsp;<em>patB</em>,&nbsp;<em>rlmN</em>, and&nbsp;<em>tsf</em>) to define the MLST scheme and derived the global&nbsp;S. mitis&nbsp;sequence clusters using the PopPUNK clustering algorithm. We identified an initial set of 259 sequence types (STs) and 258 global sequence clusters. …”

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates by Gladstone, RA, Lo, SW, Goater, R, Yeats, C, Taylor, B, Hadfield, J, Lees, JA, Croucher, NJ, van Tonder, AJ, Bentley, LJ, Quah, FX, Blaschke, AJ, Pershing, NL, Byington, CL, Balaji, V, Hryniewicz, W, Sigauque, B, Ravikumar, KL, Almeida, SCG, Ochoa, TJ, Ho, PL, du Plessis, M, Ndlangisa, KM, Cornick, JE, Kwambana-Adams, B, Benisty, R, Nzenze, SA, Madhi, SA, Hawkins, PA, Pollard, AJ, Everett, DB, Antonio, M, Dagan, R, Klugman, KP, von Gottberg, A, Metcalf, BJ, Li, Y, Beall, BW, McGee, L, Breiman, RF, Aanensen, DM, Bentley, SD, The Global Pneumococcal Sequencing Consortium

“…We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. …”