Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections.
Romain GuérillotXenia KostouliasLiam DonovanLucy LiGlen P CarterAbderrahman HachaniKoen VandelannooteStefano GiulieriIan R MonkMayu KunimotoLora StarrsGaétan BurgioTorsten SeemannAnton Y PelegTimothy P StinearBenjamin Peter HowdenPublished in: Proceedings of the National Academy of Sciences of the United States of America (2019)
Staphylococcus aureus small-colony variants (SCVs) are associated with unusually chronic and persistent infections despite active antibiotic treatment. The molecular basis for this clinically important phenomenon is poorly understood, hampered by the instability of the SCV phenotype. Here we investigated the genetic basis for an unstable S. aureus SCV that arose spontaneously while studying rifampicin resistance. This SCV showed no nucleotide differences across its genome compared with a normal-colony variant (NCV) revertant, yet the SCV presented the hallmarks of S. aureus linked to persistent infection: down-regulation of virulence genes and reduced hemolysis and neutrophil chemotaxis, while exhibiting increased survival in blood and ability to invade host cells. Further genome analysis revealed chromosome structural variation uniquely associated with the SCV. These variations included an asymmetric inversion across half of the S. aureus chromosome via recombination between type I restriction modification system (T1RMS) genes, and the activation of a conserved prophage harboring the immune evasion cluster (IEC). Phenotypic reversion to the wild-type-like NCV state correlated with reversal of the chromosomal inversion (CI) and with prophage stabilization. Further analysis of 29 complete S. aureus genomes showed strong signatures of recombination between hsdMS genes, suggesting that analogous CI has repeatedly occurred during S. aureus evolution. Using qPCR and long-read amplicon deep sequencing, we detected subpopulations with T1RMS rearrangements causing CIs and prophage activation across major S. aureus lineages. Here, we have discovered a previously unrecognized and widespread mechanism of reversible genomic instability in S. aureus associated with SCV generation and persistent infections.
Keyphrases
- genome wide
- copy number
- staphylococcus aureus
- dna methylation
- biofilm formation
- wild type
- escherichia coli
- dna damage
- dna repair
- mycobacterium tuberculosis
- cell death
- contrast enhanced
- pseudomonas aeruginosa
- magnetic resonance imaging
- antimicrobial resistance
- cell cycle arrest
- bioinformatics analysis
- high resolution
- genome wide analysis
- cystic fibrosis
- pi k akt
- high speed
- pulmonary tuberculosis