Comparative genomic analysis and identification of pathogenicity islands of hypervirulent ST-17 Streptococcus agalactiae Brazilian strain

Infect Genet Evol. 2020 Jun;80:104195. doi: 10.1016/j.meegid.2020.104195. Epub 2020 Jan 15.


Streptococcus agalactiae are important pathogenic bacteria that cause severe infections in humans, especially neonates. The mechanism by which ST-17 causes invasive infections than other STs is not well understood. In this study, we sequenced the first genome of a S. agalactiae ST-17 strain isolated in Brazil using the Illumina HiSeq 2500 technology. S. agalactiae GBS90356 ST-17 belongs to the capsular type III and was isolated from a neonatal with a fatal case of meningitis. The genome presented a size of 2.03 Mbp and a G + C content of 35.2%. S. agalactiae has 706 genes in its core genome and an open pan-genome with a size of 5.020 genes, suggesting a high genomic plasticity. GIPSy software was used to identify 10 Pathogenicity islands (PAIs) which corresponded to 15% of the genome size. IslandViewer4 corroborated the prediction of six PAIs. The pathogenicity islands showed important virulence factors genes for S. agalactiae e.g. neu, cps, dlt, fbs, cfb, lmb. SignalP detected 20 proteins with signal peptides among the 352 proteins found in PAIs, which 60% were located in the SagPAI_5. SagPAI_2 and 5 were mainly detected in ST-17 strains studied. Moreover, we identified 51 unique genes, 9 recombination regions and a large number of SNPs with an average of 760.3 polymorphisms, which can be related with high genomic plasticity and virulence during host-pathogen interactions. Our results showed implications for pathogenesis, evolution, concept of species and in silico analysis value to understand the epidemiology and genome plasticity of S. agalactiae.

Keywords: Comparative genomic; Hypervirulent; Pan-genome; Pathogenicity islands; ST-17; Streptococcus agalactiae.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Brazil / epidemiology
  • Computational Biology / methods
  • Genome, Bacterial*
  • Genomics* / methods
  • Humans
  • Molecular Sequence Annotation
  • Phylogeny
  • Public Health Surveillance
  • Streptococcal Infections / epidemiology*
  • Streptococcal Infections / microbiology*
  • Streptococcus agalactiae / classification*
  • Streptococcus agalactiae / genetics*
  • Streptococcus agalactiae / isolation & purification
  • Streptococcus agalactiae / pathogenicity
  • Virulence / genetics
  • Virulence Factors / genetics


  • Virulence Factors