A core genome MLST (cgMLST) scheme for Staphylococcus pseudintermedius

A core-genome MLST scheme for Staphylococcus pseudintermedius was developed using chewBBACA version 2.8.5 (Silva et al, 2018) with default settings (https://github.com/B-UMMI/chewBBACA_tutorial). A training file was generated using Prodigal version 2.6.3 (Hyatt et al, 2010). The scheme was generated using 74 complete genomes and is comprised of 1,356 genes present in 99% of the genomes. cgMLST types were designated relative to conventional MLST sequence types. Phylogenetic trees from the chewBBACA allele calls were constructed using GrapeTree version 1.5.0 and the RapidNJ algorithm (Zhou et al, 2018).

Due to format updates, two versions of the scheme are included: one usable with chewBBACA version 2.8.5, one updated for the most recent version in September 2024, version 3.3.10.

References:

- Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification. BMC Bioinformatics 2010;11:119. https://doi.org/10.1186/1471-2105-11-119. 

- Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, et al. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 2018;4: e000166 10.1099/mgen.0.000166.

- Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, et al. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res 2018;28(9):1395-404 10.1101/gr.232397.117.