Computational protocol: Complete Genome of the Attenuated Sparfloxacin-Resistant Streptococcus agalactiae Strain 138spar

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Protocol publication

[…] The Gram-positive bacterium Streptococcus agalactiae (group B streptococcus [GBS]) causes streptococcosis in fish (), resulting in significant economic losses. For example, GBS was responsible for a massive disease outbreak in the Kuwait Bay in 2011, killing 2,500 metric tons of wild mullet (Liza klunzingeri) (). In addition, large-scale streptococcal outbreaks occurred frequently in tilapia farms in China from 2009 to 2011, involving >95% of farms, with a cumulative mortality rate of 30 to 80% (). GBS also causes meningitis (), neonatal sepsis (), and pneumonia () in humans. GBS is a major cause of bovine mastitis, a dominant health disorder affecting milk production (, ). A virulent GBS strain, S. agalactiae 138P, was isolated from infected Nile tilapia during a 2007 disease outbreak in Idaho. To develop an attenuated bacterial vaccine, a sparfloxacin resistance strategy was used to modify GBS strain 138P, resulting in the isolation of an attenuated GBS 138spar () that was 2,048-fold resistant to sparfloxacin. However, whether changes occurred at the genomic DNA level is unknown. Therefore, the whole-genome sequence of GBS 138spar was determined in this study.The genome of GBS 138spar was sequenced using the Illumina 1500 HiSeq platform. BioNumerics (Applied Maths) was used to assemble a total of 2,743,316 sequence reads, with an average length of 100 bp. The whole genome of the virulent GBS strain 138P was reported recently (). Using similar assembly methods as described previously (), the whole genome of GBS 138spar was obtained, which is 1,838,126 bp in length. The RAST server () predicted 1,892 coding sequences, including all the subsystems reported in its parent strain, GBS 138P (). RNAmmer () predicted 5 copies of 5S rRNA, 6 copies of 16S rRNA, and 6 copies of 23S rRNA, similar to those in the genome of GBS 138P and in the reference genome GBS 2-22 (GenBank accession no. FO393392). Compared to the whole genome of GBS 138P (), GBS 138spar has a deletion >6 bp in 22 places. In addition, single-nucleotide changes (deletion, insertion, and point mutation) were found in 26 places in the GBS 138P genome compared to in the GBS 138spar genome. […]

Pipeline specifications

Software tools BioNumerics, RAST, RNAmmer
Application WGS analysis
Organisms Streptococcus agalactiae