Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing

PLoS One. 2013 Sep 30;8(9):e77122. doi: 10.1371/journal.pone.0077122. eCollection 2013.

Abstract

Staphylococcus aureus strains of the 8325 lineage, especially 8325-4 and derivatives lacking prophage, have been used extensively for decades of research. We report herein the results of our deep sequence analysis of strain 8325-4. Assignment of sequence variants compared with the reference strain 8325 (NRS77/PS47) required correction of errors in the 8325 reference genome, and reassessment of variation previously attributed to chemical mutagenesis of the restriction-defective RN4220. Using an extensive strain pedigree analysis, we discovered that 8325-4 contains 16 single nucleotide polymorphisms (SNP) arising prior to the construction of RN4220. We identified 5 indels in 8325-4 compared with 8325. Three indels correspond to expected Φ11, 12, 13 excisions, one indel is explained by a sequence assembly artifact, and the final indel (Δ63bp) in the spa-sarS intergenic region is common to only a sub-lineage of 8325-4 strains including SH1000. This deletion was found to significantly decrease (75%) steady state sarS but not spa transcript levels in post-exponential phase. The sub-lineage 8325-4 was also found to harbor 4 additional SNPs. We also found large sequence variation between 8325, 8325-4 and RN4220 in a cluster of repetitive hypothetical proteins (SA0282 homologs) near the Ess secretion cluster. The overall 8325-4 SNP set results in 17 alterations within coding sequences. Remarkably, we discovered that all tested strains of the 8325-4 lineage lack phenol soluble modulin α3 (PSMα3), a virulence determinant implicated in neutrophil chemotaxis, biofilm architecture and surface spreading. Collectively, our results clarify and define the 8325-4 pedigree and reveal clear evidence that mutations existing throughout all branches of this lineage, including the widely used RN6390 and SH1000 strains, could conceivably impact virulence regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Computational Biology
  • Genetic Variation / genetics*
  • Genome, Bacterial / genetics*
  • High-Throughput Nucleotide Sequencing / methods
  • INDEL Mutation / genetics
  • Molecular Sequence Data
  • Pedigree
  • Polymorphism, Single Nucleotide / genetics
  • Real-Time Polymerase Chain Reaction
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Species Specificity
  • Staphylococcus aureus / genetics*

Grant support

This work was supported by grants from the Swiss National Science Foundation (3100A0-120428 and 310030-146540 to WLK), the Danish Council for Independent Research (12-132527 to KTB), the Nordic Joint Committee for Agricultural Research (to DF), a fellowship grant from the Swiss Society for Infectious Diseases (to NR), and the Canton of Geneva. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.