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Expression pattern of Pseudomonas aeruginosa biofilm-residing bacteria exposed to gentamicin or surface acoustic waves or gentamicin and surface acoustic waves combined

ABSTRACT: Bacteria are known to respond to various environmental stimuli including nutrient deprivation, osmotic stress, and exposure to antibiotics. Our experimental data showed that P. aeruginosa biofilm formed in urinary catheters is very suseptible to gentamicin treatment when combined with exposure to surface acoustic waves Our goal was to establish whether P. aeruginosa is capable of specifically sensing the surface acoustic waves as well as to try and decipher the molecular mechanism underlying the increased biofilm suseptibility to antibiotics treatment

ORGANISM(S): Pseudomonas aeruginosa PAO1 Pseudomonas aeruginosa

PROVIDER: GSE28081 | GEO | 2011/09/01

SECONDARY ACCESSION(S): PRJNA139731

REPOSITORIES: GEO

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Project description:Purpose: The goals of this study are to compare RNA-Seq transcriptomic data of P. aeruginosa PAO1 in response to chronic exposure of clindamycin and rifampicin eluted from antibiotic-impregnated catheters in a continuous biofilm culture condition. Methods: Transcriptomic profiles of P. aeruginosa PAO1 grown with catheters without antibiotic coating or with clindamycin/rifampicin coating were generated by deep sequencing, in quadruplicates, using Illumina NextSeq 550 sequencer with SE-75. FastQC and Trimmomatic (v0.39) were used for sequencing quality assessment. Raw read counts of the annotated genes were calculated using HTSeq-count. The log2 fold change and false discovery rate (FDR) were measured by edgeR. Genes with |log2FC| > 1.0 and FDR < 0.05 were considered as differential expression genes. Transcripts per million (TPM) was measured by Kallisto, which is an alignment free expression estimation tool. Results: P. aeruginosa PAO1 RNA sequencing using Illumina NextSeq 550 sequencer generated 5,205,190 of average number of reads with average read length of 65 bp and a mean coverage of 54X. Differentially regulated proteins of 877 in the planktonic cells were identified, 55 of which displayed up-regulation and 822 displayed down-regulation. On the other hand, 178 proteins were differentially expressed in the biofilm cells containing 152 up-regulated and 26 down-regulated. Conclusions: Our study represents the first detailed analysis of transcriptomes generated by RNA-seq technology after P. aeruginosa PAO1 planktonic and biofilm cells were continuously exposed to clindamycin/rifampicin-impregnated catheters. Our results show that RNA sequencing offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content of strain PAO1 cells. We conclude that RNA-seq based transcriptome characterization would help the understanding for the mechanism of antimicrobial resistance and virulence in P. aeruginosa after exposure of antimicrobial-coated catheter.

Dataset Information

Expression pattern of Pseudomonas aeruginosa biofilm-residing bacteria exposed to gentamicin or surface acoustic waves or gentamicin and surface acoustic waves combined

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