Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen that thrives in diverse environments and causes a variety of human infections. Pseudomonas aeruginosa AG1 (PaeAG1) is a high-risk sequence type 111 (ST-111) strain isolated from a Costa Rican hospital in 2010. PaeAG1 has both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases, and it is resistant to β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. Ciprofloxacin (CIP) is an antibiotic commonly used to treat P. aeruginosa infections, and it is known to produce DNA damage, triggering a complex molecular response. In order to evaluate the effects of a sub-inhibitory CIP concentration on PaeAG1, growth curves using increasing CIP concentrations were compared. We then measured gene expression using RNA-Seq at three time points (0, 2.5 and 5 h) after CIP exposure to identify the transcriptomic determinants of the response (i.e. hub genes, gene clusters and enriched pathways). Changes in expression were determined using differential expression analysis and network analysis using a topdown systems biology approach. A hybrid model using database-based and co-expression analysis approaches was implemented to predict gene-gene interactions. We observed a reduction of the growth curve rate as the sub-inhibitory cip concentrations were increased. in the transcriptomic analysis, we detected that over time CIP treatment resulted in the differential expression of 518 genes, showing a complex impact at the molecular level. The transcriptomic determinants were 14 hub genes, multiple gene clusters at different levels (associated to hub genes or as co-expression modules) and 15 enriched pathways. Down-regulation of genes implicated in several metabolism pathways, virulence elements and ribosomal activity was observed. in contrast, amino acid catabolism, RpoS factor, proteases, and phenazines genes were up-regulated. Remarkably, > 80 resident-phage genes were up-regulated after CIP treatment, which was validated at phenomic level using a phage plaque assay. thus, reduction of the growth curve rate and increasing phage induction was evidenced as the CIP concentrations were increased. In summary, transcriptomic and network analyses, as well as the growth curves and phage plaque assays provide evidence that PaeAG1 presents a complex, concentration-dependent response to sub-inhibitory CIP exposure, showing pleiotropic effects at the systems level. Manipulation of these determinants, such as phage genes, could be used to gain

Enhanced Biosynthesis of Fatty Acids Contributes to Ciprofloxacin Resistance in Pseudomonas aeruginosa

“…Enhanced biosynthesis of fatty acids is associated with the acquisition of quinolone antibiotic resistance that has been revealed in bacteria, including Vibrio alginolyticus, Edwardsiella tarda , and Xanthomonas oryzae (Cheng et al, 2018 ; Su et al, 2021 ; Wang et al, 2021 ). In addition, RNA-Seq analysis of P. aeruginosa after treatment with a subinhibitory CIP concentration identifies 15 KEGG-enriched pathways, where biosynthesis of fatty acids and metabolism of fatty acids are included (Molina-Mora et al, 2020 ). The total cellular protein contents are decreased after sub-MIC of CIP treatment in company with the increase of total lipids and phospholipids and the decrease of neutral lipids in P. aeruginosa (Yehia et al, 2015 ).…”

Adaptive Resistance Mutations at Suprainhibitory Concentrations Independent of SOS Mutagenesis

“…7 B ). In other bacteria, prophages are induced after exposure to sub-MIC antibiotic concentrations ( Goerke et al 2006 ; Long et al 2016 ; Molina-Mora et al 2020 ). These results suggest that stressed cells could undergo DNA breaks (single- or double-strand breaks) due to the excision of induced phages ( Craig and Nash 1983 ; Ramisetty and Sudhakari 2019 ), all of this under a limited DNA repair capacity ( fig.…”

Antibiotic-producing Micrococcales govern the microbiome that inhabits the fur of two- and three-toed sloths

“…P. aeruginosa is an opportunistic pathogen that has shown an intrinsic resistance to a variety of antibiotics (Gellatly et al, 2013;Qiu et al, 2009;Thi et al, 2020). Nowadays, P. aeruginosa strains resistant to almost all antibiotics (Molina-Mora et al, 2020) have been isolated and represent a significant health problem; therefore, isolates that show the ability to inhibit its growth are interesting for future research to identify the compounds responsible for this activity.…”