DOI: 10.5281/zenodo.8211298
title: Supplemental material of "An annotated whole-genome multilocus sequence typing schema for scalable high resolution typing of Streptococcus pyogenes"

description: This supplemental material includes the genome assemblies, associated metadata and analysis results for five datasets used to define a publicly available annotated wgMLST schema for <em>S. pyogenes</em> and to evaluate its suitability for high resolution typing. A brief description for each file in the dataset is available in the included README file. Raw sequencing data and sample metadata for the 265 isolates included in Dataset1 have been deposited in the European Nucleotide Archive (ENA) under Project PRJEB49967. The wgMLST schema was created with chewBBACA and is publicly available at chewie-NS, where a more detailed description of schema creation, annotation and curation can be found.
description: RM was supported by Fundação para a Ciência e Tecnologia (grant 2020.08493.BD). Partial support was received from ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI – Fundos Europeus Estruturais e de Investimento from Programa Operacional Regional Lisboa 2020 and by national funds from FCT–Fundação para a Ciência e a Tecnologia, and by the LISBOA-01-0145-FEDER-007391 project, cofunded by FEDER through POR Lisboa 2020 –Programa Operacional Regional de Lisboa, PORTUGAL 2020, and Fundação para a Ciência e a Tecnologia.
description: {"references": ["Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carri\u00e7o JA. 2018. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 4:e000166.", "Mamede R, Vila-Cerqueira P, Silva M, Carri\u00e7o JA, Ramirez M. 2021. Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas. Nucleic Acids Res 49:D660\u2013D666.", "Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duch\u00eane S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ. 2019. Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics. Nat Genet 51:1035\u20131043.", "Coelho JM, Kapatai G, Jironkin A, Al-Shahib A, Daniel R, Dhami C, Laranjeira AM, Chambers T, Phillips S, Tewolde R, Underwood A, Chalker VJ. 2019. Genomic sequence investigation Streptococcus pyogenes clusters in England (2010-2015). Clin Microbiol Infect 25:96\u2013101.", "Lynskey NN, Jauneikaite E, Li HK, Zhi X, Turner CE, Mosavie M, Pearson M, Asai M, Lobkowicz L, Chow JY, Parkhill J, Lamagni T, Chalker VJ, Sriskandan S. 2019. Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study. Lancet Infect Dis 19:1209\u20131218.", "Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ. 2019. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Res 29:304\u2013316."]}