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Updated: Jul 11, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Sequence analysis reveals genetic exchanges and intraspecific spread of SaPI2, a pathogenicity island involved in
Abhignya Subedi1, Carles Ubeda1, Rajan P Adhikari1
1Skirball Institute and Departments of Microbiology and Medicine, New York University Medical Center, New York, NY 10016, USA.
Abstract:
SaPIs are a family of homologous phage-related pathogenicity islands in staphylococci that carry superantigen and other virulence genes, and are responsible for a wide variety of superantigen-related diseases. SaPIs are induced to excise and replicate by particular staphylococcal phages and are encapsidated in infectious, small-headed, phage-like particles, which are transmitted at very high frequency among staphylococcal strains and species. SaPI2 is a prototypical member of this family that was identified in a typical menstrual toxic shock syndrome (TSS) strain of Staphylococcus aureus, the so-called Harrisburg strain, and found to be mobilizable by typing phage 80. Most menstrual TSS strains belong to a highly uniform agr group III clone of electrophoretic type (ET) 41, and this study was undertaken to determine whether such strains typically carry SaPI2, and whether it has spread beyond the ET41 clone. We report here the complete sequence of SaPI2, describe its relation to other known SaPIs, and show that it, or a very similar element, is carried by most ET41 strains but that it has disseminated to other strains that have also been implicated in TSS. We show additionally, that SaPIs are widespread among the staphylococci and that most TSS strains carry two or more, including SaPI2.
Insights
Staphylococcal pathogenicity islands (SaPIs) like SaPI2 carry virulence genes causing disease. This study reveals SaPI2 is common in toxic shock syndrome strains and widespread among staphylococci.
Area of Science:
- Microbiology
- Genetics
- Infectious Diseases
Background:
- Staphylococcal pathogenicity islands (SaPIs) are mobile genetic elements carrying virulence genes.
- SaPIs are implicated in various staphylococcal diseases, including toxic shock syndrome (TSS).
- SaPI2 was initially identified in a specific Staphylococcus aureus TSS strain.
Purpose of the Study:
- To determine the prevalence of SaPI2 in typical menstrual TSS strains (agr group III, ET41).
- To investigate the dissemination of SaPI2 beyond the ET41 clone.
- To analyze the relationship of SaPI2 to other SaPIs and its presence in other TSS-associated strains.
Main Methods:
- Complete genome sequencing of SaPI2.
- Comparative sequence analysis of SaPI2 with other SaPIs.
- Screening of various staphylococcal strains, including TSS isolates, for SaPI presence.
Main Results:
- The complete sequence of SaPI2 was determined and its relationship to other SaPIs elucidated.
- SaPI2, or a highly similar element, is present in most ET41 strains.
- SaPI2 has disseminated to other Staphylococcus aureus strains implicated in TSS.
- SaPIs are widespread in staphylococci, with most TSS strains carrying multiple SaPIs, including SaPI2.
Conclusions:
- SaPI2 is a common element in Staphylococcus aureus strains causing TSS, particularly within the ET41 clone.
- SaPI elements have significant horizontal transfer and are widespread among staphylococci.
- The presence of multiple SaPIs in TSS strains highlights their importance in staphylococcal pathogenesis.
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