Use RNA-seq to investigate the transcriptional response of Pseudomonas aeruginosa when adhering to different surfaces

Purpose: Use RNA-seq to investigate the transcriptional response of Pseudomonas aeruginosa when adhering to different surfaces. Methods: Coupons of silicone, glass, and polycarbonate plastic were purchased from Biosurfaces Technologies (Catalog numbers: RD128-Si, RD128-GL, RD128-PC). Coupons were placed into a 24-well plate and conditioned in LB for at least 10 min prior to bacterial addition. LB was removed and replaced with 2mL of logarithmic phase bacterial culture in LB (OD600 0.7). At the indicated time point, the coupon was rinsed twice in PBS and placed into 1 mL of Trizol. Trizol was collected and stored at -80°C for RNA isolation. HiSeq 4000 sequencing was performed, generating approximately 300 million total paired end 300 bp reads. Reads were aligned to the reference PAO1 genome using Rockhopper. Results: A total of 833 genes were differentially expressed across the three surfaces. Most genes were reduced (522 genes) rather than elevated (269 genes), with 42 genes showing both elevated and reduced RNA levels across two or more surfaces. Conclusion: Bacteria had a nearly unique transcriptional response on each surface, with the vast majority regulated on only one surface RNA-Seq analysis of wild type Pseudomonas aeruginosa adhered to three different medically relevant surfaces; silicone, glass, and polycarbonate plastic. Each time point was analyzed in triplicate