Computational protocol: Genomic Recombination Leading to Decreased Virulence of Group B Streptococcus in a Mouse Model of Adult Invasive Disease

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Protocol publication

[…] The genomes of strains NGBS375 (ST297) and NGBS357 (ST1) were sequenced using PacBio sequencing (Pacific Biosciences, Menlo Park, CA, USA) as previously described []. Two cells of sequence were generated for each isolate. To assess base-calling accuracy in the PacBio assembly, Illumina short-reads for the two strains were generated. Genomic libraries were prepared using Nextera XT kits (Illumina, San Diego, CA, USA) and sequenced as paired-end reads in an Illumina HiSeq 2500 or MiSeq instrument (Illumina). Both genome assemblies were completely concordant with full length perfectly aligning Illumina short-reads. The genome of NGBS375 (ST297) was circularized. Circularization of NGBS357 could not be achieved due to the presence of a repetitive region of >80 kb in its genome. However, a single contig was obtained (). Genome assemblies are available in GenBank under Accession numbers CP012504 (NGBS357, ST1), and CP102503 (NGBS375, ST297). presents genome closure statistics. The genome sequences of strains NGBS128 (ST17), NGBS572 (ST452), NEM316 (ST23), A909 (ST7), NGBS061 (ST459), 2603VR (ST110) were retrieved from GenBank (Accession numbers CP012480, CP007632, AL732656, NC_007432, CP007631, and NC_004116, respectively). Short-read Illumina data for strain NGBS128 were retrieved from NCBI sequence-read archive (SRA, accession number SAMN04007140). Identification of tRNA-encoding regions and annotation were performed with Prokka []. Ortholog analysis was performed using PGAP []. Polymorphisms relative to strain NGBS375 were identified using VAAL [] for strains for which Illumina data was available, otherwise with Mauve []. Recombination analysis was performed using BRATNextGen [] run with 20 iterations and 100 replicates, with a p-value of 0.05 as the significance cut-off. Genome visualizations were created using BRIG []. Short reads have been made available at SRA under Study Accession PRJNA295774 and PRJNA274384 for the ST17 and ST1 strains, respectively. […]

Pipeline specifications

Software tools Prokka, PGAP, VAAL, Mauve, BRIG
Organisms Mus musculus
Diseases Infection, Neoplasm Metastasis, Lymphoma, B-Cell, Bacteremia