Transcriptional profiling of Pseudomonas aeruginosa PAO1 in response to anti-biofilm and anti-infection agent exopolysaccharide EPS273

Characterization of Exopolysaccharides from Lactiplantibacillus plantarum PC715 and Their Antibiofilm Activity Against Hafnia alvei

Exopolysaccharides (EPSs) secreted by lactic acid bacteria have the potential to enhance human health by showing various biological functions. This study investigated the biological role and antibiofilm properties of EPS715, a new neutral EPS produced by pickled vegetables originating from Lactobacillus plantarum PC715. The results indicate that EPS715 is primarily composed of rhamnose, glucose, and mannose. Its molecular weight (Mw) is 47.87 kDa, containing an α-glucoside linkage and an α-pyranose ring. It showed an amorphous morphology without a triple helix structure. Furthermore, EPS715 showed improved antioxidant activity. Specifically, its scavenging capacity of ABTS+ radicals, DPPH radicals, and the hydroxyl (·OH) reduction capacity at 5 mg/mL was 98.64 ± 2.70%, 97.37 ± 0.79%, and 1.64 ± 0.05%, respectively. Its maximal scavenging capacity was >40%, and the hydroxyl (·OH) radical scavenging ability was dose-dependent. Moreover, the biofilm of various pathogens including S. aureus, B. cereus, S. saprophyticus, Acinetobacter spp., and H. alvei was substantially dispersed and affected by EPS715, with a maximum inhibition rate of 78.17% for H. alvei. The possible mechanism by which EPS715 shows antibiofilm properties against the H. alvei may be attributed to its effects on the auto-aggregation, hydrophilic characteristics, and motility of Hafnia spp. Thus, EPS715 has significant antioxidant and antibiofilm characteristics that may hold substantial potential for applications in food and medicinal products.

Molecular mechanisms of DNase inhibition of early biofilm formation Pseudomonas aeruginosa or Staphylococcus aureus: A transcriptome analysis

In vitro studies show that DNase can inhibit Pseudomonas aeruginosa and Staphylococcus aureus biofilm formation. However, the underlying molecular mechanisms remain poorly understood. This study used an RNA-sequencing transcriptomic approach to investigate the mechanism by which DNase I inhibits early P. aeruginosa and S. aureus biofilm formation on a transcriptional level, respectively. A total of 1171 differentially expressed genes (DEGs) in P. aeruginosa and 1016 DEGs in S. aureus enriched in a variety of biological processes and pathways were identified, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs were primarily involved in P. aeruginosa two-component system, biofilm formation, and flagellar assembly and in S. aureus biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and biosynthesis of amino acids, respectively. The transcriptional data were validated using quantitative real-time polymerase chain reaction (RT-qPCR), and the expression profiles of 22 major genes remained consistent. These findings suggested that DNase I may inhibit early biofilm formation by downregulating the expression of P. aeruginosa genes associated with flagellar assembly and the type VI secretion system, and by downregulating S. aureus capsular polysaccharide and amino acids metabolism gene expression, respectively. This study offers insights into the mechanisms of DNase treatment-based inhibition of early P. aeruginosa and S. aureus biofilm formation.

Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851

Introduction

Pseudomonas aeruginosa infections are one of the leading causes of death in immunocompromised patients with cystic fibrosis, diabetes, and lung diseases such as pneumonia and bronchiectasis. Furthermore, P. aeruginosa is one of the main multidrug-resistant bacteria responsible for nosocomial infections worldwide, including the multidrug-resistant CCBH4851 strain isolated in Brazil.

Methods

One way to analyze their dynamic cellular behavior is through computational modeling of the gene regulatory network, which represents interactions between regulatory genes and their targets. For this purpose, Boolean models are important predictive tools to analyze these interactions. They are one of the most commonly used methods for studying complex dynamic behavior in biological systems.

Results and discussion

Therefore, this research consists of building a Boolean model of the gene regulatory network of P. aeruginosa CCBH4851 using data from RNA-seq experiments. Next, the basins of attraction are estimated, as these regions and the transitions between them can help identify the attractors, representing long-term behavior in the Boolean model. The essential genes of the basins were associated with the phenotypes of the bacteria for two conditions: biofilm formation and polymyxin B treatment. Overall, the Boolean model and the analysis method proposed in this work can identify promising control actions and indicate potential therapeutic targets, which can help pinpoint new drugs and intervention strategies.

Disruption of the sensor kinase phoQ gene decreases acid resistance in plant growth-promoting rhizobacterium Rahnella aquatilis HX2

AIMS

Rahnella aquatilis HX2, a promising plant growth-promoting rhizobacterium (PGPR) in the field, contains genes homologous to the PhoP/PhoQ two-component regulatory system. Although this system regulates stress response in numerous pathogens, PhoP/PhoQ characterization in a PGPR has not received in-depth exploration.

METHODS AND RESULTS

The phoQ gene was mutated in strain HX2 using an in-frame deletion strategy. Compared to the wild type, the phoQ mutant exhibited increased sensitivity to acidic conditions (pH 4.0) in a chemically defined medium and in mild acidic natural soil (pH 5.7). The phoQ mutant also exhibited increased swimming motility under acidic conditions. Acid resistance was restored in the mutant by introducing the phoQ gene on a plasmid. Three acid resistance genes, add, cfa, and fur were downregulated significantly, whereas the chaperone encoding gene, dnak, was upregulated when the phoQ mutant was exposed to acid stress.

CONCLUSIONS

This study suggested that the PhoP/PhoQ system positively regulates the acid resistance of R. aquatilis HX2.

High-Throughput Transcriptomic Profiling Reveals the Inhibitory Effect of Hydroquinine on Virulence Factors in Pseudomonas aeruginosa

Hydroquinine is an organic alkaloid compound that exhibits antimicrobial activity against several bacterial strains including strains of both drug-sensitive and multidrug-resistant P. aeruginosa. Despite this, the effects of hydroquinine on virulence factors in P. aeruginosa have not yet been characterized. We therefore aimed to uncover the mechanism of P. aeruginosa hydroquinine-sensitivity using high-throughput transcriptomic analysis. We further confirmed whether hydroquinine inhibits specific virulence factors using RT-qPCR and phenotypic analysis. At half the minimum inhibitory concentration (MIC) of hydroquinine (1.250 mg/mL), 254 genes were differentially expressed (97 downregulated and 157 upregulated). We found that flagellar-related genes were downregulated by between −2.93 and −2.18 Log2-fold change. These genes were consistent with the analysis of gene ontology and KEGG pathway. Further validation by RT-qPCR showed that hydroquinine significantly suppressed expression of the flagellar-related genes. By analyzing cellular phenotypes, P. aeruginosa treated with ½MIC of hydroquinine exhibited inhibition of motility (30−54% reduction) and pyocyanin production (~25−27% reduction) and impaired biofilm formation (~57−87% reduction). These findings suggest that hydroquinine possesses anti-virulence factors, through diminishing flagellar, pyocyanin and biofilm formation.

Existence of a novel heavy metal-tolerant Pseudomonas aeruginosa strain Zambia SZK-17 Kabwe 1: the potential bioremediation agent in the heavy metal-contaminated area

Bacterial biomass may serve as an important environmental cleaning agent to toxic heavy metal ions at the expense of chemical processes which are not environmentally friendly. This study aimed at characterizing bacterial agents which could serve as a potential in situ bioremediation agent at the site of isolation. The characterization was performed using both phenotypic and molecular approaches. A novel Pseudomonas aeruginosa strain Pseudomonas aeruginosa Zambia SZK17 Kabwe1 was successfully isolated, identified, and characterized. The strain showed a promising tolerance to heavy metals such as copper (2 mM), zinc, nickel (2 mM), cobalt (1 mM), and cadmium (0.5 mM) at the laboratory level. The bacterium has shown the bioaccumulation of at least 60% of copper (II) sulfate (0.3655 mg/l) with R = 69.75%, cadmium (II) chloride (0.0241 mg/l) with R = 69.98%, zinc (II) chloride (0.1389 mg/l) with R = 69.91%, nickel (II) chloride (0.1155 mg/l) with R = 69.92%, and cobalt (II) chloride (0.593 mg/l) with R = 69.92%. The highest bioaccumulation has been observed in heavy metals cadmium, zinc, nickel, and cobalt. Characterization of the bacterium on pH has revealed that at a very high pH (≥ 9) and lower (≤ 5.5) pH, the bacterium tended to have reduced growth with optimum growth at pH 8. The high temperature at around 40 °C had a negative effect on the growth performance of the bacterium while optimum growth was observed at 28 °C. This novel P. aeruginosa strain has shown the phenotypic attributes to become a potential bioremediation agent; however, further investigation needs to be done to understand the genes and or molecular mechanisms that drive their tolerance to multiple heavy metals.

Treatment of Pseudomonas aeruginosa infectious biofilms: Challenges and strategies

Pseudomonas aeruginosa, a Gram-negative bacterium, is one of the major pathogens implicated in human opportunistic infection and a common cause of clinically persistent infections such as cystic fibrosis, urinary tract infections, and burn infections. The main reason for the persistence of P. aeruginosa infections is due to the ability of P. aeruginosa to secrete extracellular polymeric substances such as exopolysaccharides, matrix proteins, and extracellular DNA during invasion. These substances adhere to and wrap around bacterial cells to form a biofilm. Biofilm formation leads to multiple antibiotic resistance in P. aeruginosa, posing a significant challenge to conventional single antibiotic therapeutic approaches. It has therefore become particularly important to develop anti-biofilm drugs. In recent years, a number of new alternative drugs have been developed to treat P. aeruginosa infectious biofilms, including antimicrobial peptides, quorum-sensing inhibitors, bacteriophage therapy, and antimicrobial photodynamic therapy. This article briefly introduces the process and regulation of P. aeruginosa biofilm formation and reviews several developed anti-biofilm treatment technologies to provide new directions for the treatment of P. aeruginosa biofilm infection.

An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents

Bacterial biofilms are complex and highly antibiotic-resistant aggregates of microbes that form on surfaces in the environment and body including medical devices. They are key contributors to the growing antibiotic resistance crisis and account for two-thirds of all infections. Thus, there is a critical need to develop anti-biofilm specific therapeutics. Here we discuss mechanisms of biofilm formation, current anti-biofilm agents, and strategies for developing, discovering, and testing new anti-biofilm agents. Biofilm formation involves many factors and is broadly regulated by the stringent response, quorum sensing, and c-di-GMP signaling, processes that have been targeted by anti-biofilm agents. Developing new anti-biofilm agents requires a comprehensive systems-level understanding of these mechanisms, as well as the discovery of new mechanisms. This can be accomplished through omics approaches such as transcriptomics, metabolomics, and proteomics, which can also be integrated to better understand biofilm biology. Guided by mechanistic understanding, in silico techniques such as virtual screening and machine learning can discover small molecules that can inhibit key biofilm regulators. To increase the likelihood that these candidate agents selected from in silico approaches are efficacious in humans, they must be tested in biologically relevant biofilm models. We discuss the benefits and drawbacks of in vitro and in vivo biofilm models and highlight organoids as a new biofilm model. This review offers a comprehensive guide of current and future biological and computational approaches of anti-biofilm therapeutic discovery for investigators to utilize to combat the antibiotic resistance crisis.