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| Status |
Public on Jun 10, 2013 |
| Title |
Investigating the sRNA and mRNA transcriptional response to antibiotics in methicillin-resistant Staphylococcus aureus using Illumina RNAseq |
| Organism |
Staphylococcus aureus |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Coordinated protein-coding sequence transcriptional responses of Staphylococcus aureus to antimicrobial exposure are well described but little is known of the role of bacterial non-coding, small RNAs (sRNAs) in these responses. Here we used RNAseq to investigate the sRNA response of the epidemic multiresistant hospital ST239 S. Aureus strain JKD6009 and its vancomycin-intermediate clinical derivative, JKD6008, after exposure to four antibiotics representing the major classes of antimicrobials used to treat methicillin-resistant S. Aureus infections. These agents included vancomycin, linezolid, ceftobiprole, and tigecycline. We identified 410 potential sRNAs (sRNAs) and then compared global sRNA and mRNA expression profiles at 2 and 6 hours, without antibiotic exposure, and after exposure to 0.5 x MIC for each antibiotic, for both JKD6009 (VSSA), and JKD6008 (VISA).
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| Overall design |
Two strains were used (JKD6009, vancomycin-susceptible S. Aureus; JKD6008, in vivo derived vancomycin-intermediate S. Aureus). The complete JKD6008 genome seqeuce was used as the reference. Two time points, 2 hours and 6 hours after culture in Mueller Hinton broth. Strains were exposed to no antibiotic, or 0.5 x MIC for 10 mins for the following antibiotics; vancomycin, linezolid, ceftobiprole, tigecycline. RNA isolation procedures enriched for mRNA or sRNA. The 40 cDNA libraries were sequenced using a whole flowcell (8 lanes) in an Illumina genome analyzer GAII for 36 cycles. Data was analyzed using the BioConductor package limma, and by applying non-negative matrix factorization to determine the impact of antibiotic exposure on the sRNA and mRNA transcriptional profiles.
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| Contributor(s) |
Howden BP |
| Citation(s) |
23733475 |
| |
| Submission date |
Sep 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ben Howden |
| E-mail(s) |
bhowden@unimelb.edu.au
|
| Organization name |
Austin Health
|
| Department |
Infectious Diseases Department
|
| Lab |
Austin Centre for Infection Research
|
| Street address |
Austin Health
|
| City |
Heidelberg |
| State/province |
VIC |
| ZIP/Postal code |
3084 |
| Country |
Australia |
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| Platforms (1) |
| GPL16057 |
Illumina Genome Analyzer IIx (Staphylococcus aureus) |
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| Samples (40)
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| Relations |
| BioProject |
PRJNA175138 |
| SRA |
SRP015747 |
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