Genome Sequencing and Typing of Group B Streptococcus

Genome sequences were assembled using the Velvet software^{47 (link)} with an optimized k-value and a minimal coverage of 10. MLST types were determined by extracting the sequences of the seven genes of the GBS MLST system^{5 (link)} and comparing them with the known STs from the GBS MLST web server (http://pubmlst.org/sagalactiae/). Serotypes were determined by BLASTn similarity search using as query the nucleotide sequences of the ten cps loci corresponding to the 10 known GBS serotypes. Antibiotic resistance genes were searched by BLASTx search with the protein sequences of 38 resistance genes from Gram-positive bacteria for tetracycline, macrolides, streptomycin, kanamycin, spectinomycin, streptothrycin, lincosamides and chloramphenicol. Genomic islands encoding antibiotic resistance genes were analysed by extracting the sequences surrounding the antibiotic resistance genes. Tn916 and Tn5801 insertion sites were determined by analysing the chromosome–transposon junctions (Table 4).