GDA in staphylococci

Gen Duplication and Amplification in Staphylococcal populations

01/01/2016 to 31/12/2017

Bacterial pathogens possess the ability to adapt rapidly to changing environmental conditions which is especially
apparent in the hospital setting where bacteria acquire antibiotic resistances readily. Besides well studied
mechanisms such as horizontal gene transfer bacteria can alter the genetic material by acquiring gen duplications
and amplifications (GDA). Exemplarily an improved gene dosage of a minor resistance determinant can lead to
increased resistance to antibiotics. Due to the difficulties in their detection GDAs are almost exclusively studied in
model organisms and neglected in natural populations of clinically relevant species such as Staphylococcus aureus.
Accordingly many important questions about the frequency and clinical importance of GDAs remain unanswered.
State of the art sequencing technologies enable the identification of GDAs by analysis of the coverage scaffold and
groundbreaking experiments using 387 USA300 genome sequences showed promising results regarding putative copy
number variation of virulence factors. We will extend the GDA analysis to ca. 1200 already available EMRSA15
sequences. This will enable a comprising analysis of gen copy number variation in clinical isolates and might allow
identifying genomic regions under strong evolutionary pressure during infection. We will optimize experimental
setups for the rapid validation of GDAs by qPCR and develop techniques to study the effects of GDAs in S. aureus.
Furthermore we will sequence a selection ca. 70 S. aureus isolates causing chronic infections in patients suffering
from cystic fibrosis (CF). This will enable us to optimize the detection of GDAs by NGS and will allow investigating
the role of GDAs during adaption to the complex environment within the CF-lung. This project will show new
avenues to extract additional valuable biological information from NGS data and will investigate the importance of
GDAs during the adaption of S. aureus to the hospital setting and to the CF-lung.