Iron acquisition in the cystic fibrosis lung and potential for novel therapeutic strategies

Emerging strategies to target virulence in Pseudomonas aeruginosa respiratory infections

Pseudomonas aeruginosa is an opportunistic pathogen that is responsible for infections in people living with chronic respiratory conditions, such as cystic fibrosis (CF) and non-CF bronchiectasis (NCFB). Traditionally, in people with chronic respiratory disorders, P. aeruginosa infection has been managed with a combination of inhaled and intravenous antibiotic therapies. However, due in part to the prolonged use of antibiotics in these people, the emergence of multi-drug resistant P. aeruginosa strains is a growing concern. The development of anti-virulence therapeutics may provide a new means of treating P. aeruginosa lung infections whilst also combatting the AMR crisis, as these agents are presumed to exert reduced pressure for the emergence of drug resistance as compared to antibiotics. However, the pipeline for developing anti-virulence therapeutics is poorly defined, and it is currently unclear as to whether in vivo and in vitro models effectively replicate the complex pulmonary environment sufficiently to enable development and testing of such therapies for future clinical use. Here, we discuss potential targets for P. aeruginosa anti-virulence therapeutics and the effectiveness of the current models used to study them. Focus is given to the difficulty of replicating the virulence gene expression patterns of P. aeruginosa in the CF and NCFB lung under laboratory conditions and to the challenges this poses for anti-virulence therapeutic development.

Exploring the Biocontrol Potential of Phanerochaete chrysosporium against Wheat Crown Rot

The worldwide occurrence of wheat crown rot, predominantly caused by the pathogen Fusarium pseudograminearum, has a serious impact on wheat production. Numerous microorganisms have been employed as biocontrol agents, exhibiting effectiveness in addressing a wide array of plant pathogens through various pathways. The mycelium of the white-rot fungus Phanerochaete chrysosporium effectively inhibits the growth of F. pseudograminearum by tightly attaching to it and forming specialized penetrating structures. This process leads to the release of intracellular inclusions and the eventual disintegration of pathogen cells. Furthermore, volatile organic compounds and fermentation products produced by P. chrysosporium exhibit antifungal properties. A comprehensive understanding of the mechanisms and modalities of action will facilitate the advancement and implementation of this biocontrol fungus. In order to gain a deeper understanding of the mycoparasitic behavior of P. chrysosporium, transcriptome analyses were conducted to examine the interactions between P. chrysosporium and F. pseudograminearum at 36, 48, and 84 h. During mycoparasitism, the up-regulation of differentially expressed genes (DEGs) encoding fungal cell-wall-degrading enzymes (CWDEs), iron ion binding, and mycotoxins were mainly observed. Moreover, pot experiments revealed that P. chrysosporium not only promoted the growth and quality of wheat but also hindered the colonization of F. pseudograminearum in wheat seedlings. This led to a delay in the development of stem base rot, a reduction in disease severity and incidence, and the activation of the plant's self-defense mechanisms. Our study provides important insights into the biocontrol mechanisms employed by P. chrysosporium against wheat crown rot caused by F. pseudograminearum.

Mrs4 loss of function in fungi during adaptation to the cystic fibrosis lung

The genetic disease cystic fibrosis (CF) frequently leads to chronic lung infections by bacteria and fungi. We identified three individuals with CF with persistent lung infections dominated by Clavispora (Candida) lusitaniae. Whole-genome sequencing analysis of multiple isolates from each infection found evidence for selection for mutants in the gene MRS4 in all three distinct lung-associated populations. In each population, we found one or two unfixed, non-synonymous mutations in MRS4 relative to the reference allele found in multiple environmental and clinical isolates including the type strain. Genetic and phenotypic analyses found that all evolved alleles led to loss of function (LOF) of Mrs4, a mitochondrial iron transporter. RNA-seq analyses found that Mrs4 variants with decreased activity led to increased expression of genes involved in iron acquisition mechanisms in both low iron and replete iron conditions. Furthermore, surface iron reductase activity and intracellular iron were much higher in strains with Mrs4 LOF variants. Parallel studies found that a subpopulation of a CF-associated Exophiala dermatitidis infection also had a non-synonymous LOF mutation in MRS4. Together, these data suggest that MRS4 mutations may be beneficial during chronic CF lung infections in diverse fungi, perhaps, for the purposes of adaptation to an iron-restricted environment with chronic infections. IMPORTANCE The identification of MRS4 mutations in Clavispora (Candida) lusitaniae and Exophiala dermatitidis in individuals with cystic fibrosis (CF) highlights a possible adaptive mechanism for fungi during chronic CF lung infections. The findings of this study suggest that loss of function of the mitochondrial iron transporter Mrs4 can lead to increased activity of iron acquisition mechanisms, which may be advantageous for fungi in iron-restricted environments during chronic infections. This study provides valuable information for researchers working toward a better understanding of the pathogenesis of chronic lung infections and more effective therapies to treat them.

In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment

Individuals with cystic fibrosis (CF) are susceptible to chronic lung infections that lead to inflammation and irreversible lung damage. While most respiratory infections that occur in CF are caused by bacteria, some are dominated by fungi such as the slow-growing black yeast Exophiala dermatitidis. Here, we analyze isolates of E. dermatitidis cultured from two samples, collected from a single subject 2 years apart. One isolate genome was sequenced using long-read Nanopore technology as an in-population reference to use in comparative single nucleotide polymorphism and insertion-deletion variant analyses of 23 isolates. We then used population genomics and phylo-genomics to compare the isolates to each other as well as the reference genome strain E. dermatitidis NIH/UT8656. Within the CF lung population, three E. dermatitidis clades were detected, each with varying mutation rates. Overall, the isolates were highly similar suggesting that they were recently diverged. All isolates were MAT 1-1, which was consistent with their high relatedness and the absence of evidence for mating or recombination between isolates. Phylogenetic analysis grouped sets of isolates into clades that contained isolates from both early and late time points indicating there are multiple persistent lineages. Functional assessment of variants unique to each clade identified alleles in genes that encode transporters, cytochrome P450 oxidoreductases, iron acquisition, and DNA repair processes. Consistent with the genomic heterogeneity, isolates showed some stable phenotype heterogeneity in melanin production, subtle differences in antifungal minimum inhibitory concentrations, and growth on different substrates. The persistent population heterogeneity identified in lung-derived isolates is an important factor to consider in the study of chronic fungal infections, and the analysis of changes in fungal pathogens over time may provide important insights into the physiology of black yeasts and other slow-growing fungi in vivo.

Improved engineering of Pseudomonas aeruginosa to study the adaptation of pyoverdine production under intra- or inter- specific bacterial competition

Pseudomonas aeruginosa (PA) is a common cause of chronic infections, particularly feared by cystic fibrosis patients. PA colonizes the lung where it adapts to the local environment, and/or to treatments by drugs. This genotypic and phenotypic adaptation, in turns, influences its interaction with its environment, like bacteria from the microbiota. As an example, to access iron, PA produces and secretes two siderophores, pyoverdine and pyochelin that are iron chelators scavenging iron from the environment and bringing it back into the bacterial cells. Siderophores production depends on the level of iron starvation, on the presence of other bacteria, etc. this latter component being less well investigated. Even if studies on bacterial interactions, and their evolution, have been increasing since several years, we are still facing a lack of tools, for example, to specifically follow the growth of PA isolates in such competitive environments. We thus improved a cloning method to gain time in the cloning steps, to lower the polar effects, and to accurately follow the interactions of any PA isolate with other bacteria. For that, a fluorescent reporter gene was inserted between two genes, the glutamine-fructose-6-phosphate transaminase (glmS) and PA5548. This reporter was efficiently produced either from an inducible or a house-keeping promoter, and its expression did not lead to polar effects. We used this strain to study intra and inter-specific bacterial competitions for iron between different lung pathogens. We thus grew wild-type PA together either with an isogenic PA ΔpvdS variant, that does not produce the most efficient siderophore pyoverdine, or with Klebsiella pneumoniae or Acinetobacter baumanii, two other lung pathogens. We finally monitored the effect of the loss of pvdS on the competition between PA and the other bacterial species. These studies enabled us to differentiate intra from inter specific competitions, both arising in the lung environment, and pinpoint the importance of the bacterial specie for the adaptation of pyoverdine production.

Mrs4 loss of function in fungi during adaptation to the cystic fibrosis lung

The genetic disease cystic fibrosis (CF) frequently leads to chronic lung infections by bacteria and fungi. We identified three individuals with CF with persistent lung infections dominated by Clavispora ( Candida ) lusitaniae . Whole genome sequencing analysis of multiple isolates from each infection found evidence for selection for mutants in the gene MRS4 in all three distinct lung-associated populations. In each population, we found one or two unfixed, non-synonymous mutations in MRS4 relative to the reference allele found in multiple environmental and clinical isolates including the type strain. Genetic and phenotypic analyses found that all evolved alleles led to loss of function of Mrs4, a mitochondrial iron transporter. RNA Seq analyses found that Mrs4 variants with decreased activity led to increased expression of genes involved in iron acquisition mechanisms in both low iron and replete iron conditions. Furthermore, surface iron reductase activity and intracellular iron was much higher in strains with Mrs4 loss of function variants. Parallel studies found that a subpopulation of a CF-associated Exophiala dermatiditis infection also had a non-synonymous loss of function mutation in MRS4. Together, these data suggest that MRS4 mutations may be beneficial during chronic CF lung infections in diverse fungi perhaps for the purposes of adaptation to an iron restricted environment with chronic infections.

Interplay between biofilm microenvironment and pathogenicity of Pseudomonas aeruginosa in cystic fibrosis lung chronic infection

Pseudomonas aeruginosa (PA) is a highly, if not the most, versatile microorganism capable of colonizing diverse environments. One of the niches in which PA is able to thrive is the lung of cystic fibrosis (CF) patients. Due to a genetic aberration, the lungs of CF-affected patients exhibit impaired functions, rendering them highly susceptible to bacterial colonization. Once PA attaches to the epithelial surface and transitions to a mucoid phenotype, the infection becomes chronic, and antibiotic treatments become inefficient. Due to the high number of affected people and the severity of this infection, CF-chronic infection is a well-documented disease. Still, numerous aspects of PA CF infection remain unclear. The scientific reports published over the last decades have stressed how PA can adapt to CF microenvironmental conditions and how its surrounding matrix of extracellular polymeric substances (EPS) plays a key role in its pathogenicity. In this context, it is of paramount interest to present the nature of the EPS together with the local CF-biofilm microenvironment. We review how the PA biofilm microenvironment interacts with drugs to contribute to the pathogenicity of CF-lung infection. Understanding why so many drugs are inefficient in treating CF chronic infection while effectively treating planktonic PA is essential to devising better therapeutic targets and drug formulations.

Impact of CFTR Modulators on the Impaired Function of Phagocytes in Cystic Fibrosis Lung Disease

Cystic fibrosis (CF), the most common genetically inherited disease in Caucasian populations, is a multi-systemic life-threatening autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. In 2012, the arrival of CFTR modulators (potentiators, correctors, amplifiers, stabilizers, and read-through agents) revolutionized the therapeutic approach to CF. In this review, we examined the physiopathological mechanism of chronic dysregulated innate immune response in the lungs of CF patients with pulmonary involvement with particular reference to phagocytes, critically analyzing the role of CFTR modulators in influencing and eventually restoring their function. Our literature review highlighted that the role of CFTR in the lungs is crucial not only for the epithelial function but also for host defense, with particular reference to phagocytes. In macrophages and neutrophils, the CFTR dysfunction compromises both the intricate process of phagocytosis and the mechanisms of initiation and control of inflammation which then reverberates on the epithelial environment already burdened by the chronic colonization of pathogens leading to irreversible tissue damage. In this context, investigating the impact of CFTR modulators on phagocytic functions is therefore crucial not only for explaining the underlying mechanisms of pleiotropic effects of these molecules but also to better understand the physiopathological basis of this disease, still partly unexplored, and to develop new complementary or alternative therapeutic approaches.

Quick and wide-range taxonomical repertoire establishment of the cystic fibrosis lung microbiota by tandem mass spectrometry on sputum samples

Microorganisms proteotyping by tandem mass spectrometry has been recently shown as a powerful methodology to identify the wide-range taxonomy and biomass of microbiota. Sputum is the recommended specimen for routine microbiological monitoring of Cystic Fibrosis (CF) patients but has been rarely submitted to tandem mass spectrometry-based proteotyping. In this study, we compared the microbial components of spontaneous and induced sputum samples from three cystic fibrosis patients. Although the presence of microbial proteins is much lower than host proteins, we report that the microbiota’s components present in the samples can be identified, as well as host biomarkers and functional insights into the microbiota. No significant difference was found in microorganism abundance between paired spontaneous and induced sputum samples. Microbial proteins linked to resistance, iron uptake, and biofilm-forming ability were observed in sputa independently of the sampling method. This unbiased and enlarged view of the CF microbiome could be highly complementary to culture and relevant for the clinical management of CF patients by improving knowledge about the host-pathogen dynamics and CF pathophysiology.

Niche, not phylogeny, governs the response to oxygen availability among diverse Pseudomonas aeruginosa strains

Pseudomonas aeruginosa, a ubiquitous opportunistic pathogen, is a leading cause of chronic infection of airways in cystic fibrosis (CF) patients. Chronic infections typically arise from colonization by environmental strains, followed by adaptation of P. aeruginosa to the conditions within the CF airway. It has been suggested that oxygen availability can be an important source of selection causing trait changes associated with the transition to chronic infection, but little data exist on the response of P. aeruginosa to varying levels of oxygen. Here, we use a diverse collection of P. aeruginosa strains recovered from both CF patients and environmental sources to evaluate the role of oxygen availability in driving adaptation to the CF lung while also accounting for phylogenetic relatedness. While we can detect a signal of phylogeny in trait responses to oxygen availability, niche of origin is a far stronger predictor. Specifically, strains isolated from the lungs of CF patients are more sensitive to external oxidative stress but more resistant to antibiotics under anoxic conditions. Additionally, many, though not all, patho-adaptive traits we assayed are insensitive to oxygen availability. Our results suggest that inferences about trait expression, especially those associated with the transition to chronic infection, depend on both the available oxygen and niche of origin of the strains being studied.

Genomic and physiological evaluation of two root associated Pseudomonas from Coffea arabica

Many Pseudomonas species promote plant growth and colonize a wide range of environments. The annotation of a Coffea arabica ESTs database revealed a considerable number of Pseudomonas sequences. To evaluate the genomic and physiology of Pseudomonas that inhabit coffee plants, fluorescent Pseudomonas from C. arabica root environment were isolated. Two of them had their genomes sequenced; one from rhizospheric soil, named as MNR3A, and one from internal part of the root, named as EMN2. In parallel, we performed biochemical and physiological experiments to confirm genomic analyses results. Interestingly, EMN2 has achromobactin and aerobactin siderophore receptors, but does not have the genes responsible for the production of these siderophores, suggesting an interesting bacterial competition strategy. The two bacterial isolates were able to degrade and catabolize plant phenolic compounds for their own benefit. Surprisingly, MNR3A and EMN2 do not contain caffeine methylases that are responsible for the catabolism of caffeine. In fact, bench experiments confirm that the bacteria did not metabolize caffeine, but were resistant and chemically attracted to it. Furthermore, both bacteria, most especially MNR3A, were able to increase growth of lettuce plants. Our results indicate MNR3A as a potential plant growth promoting bacteria.

Emerging Concepts in Defective Macrophage Phagocytosis in Cystic Fibrosis

Cystic fibrosis (CF) is caused by mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Chronic inflammation and decline in lung function are major reasons for morbidity in CF. Mutant CFTR expressed in phagocytic cells such as macrophages contributes to persistent infection, inflammation, and lung disease in CF. Macrophages play a central role in innate immunity by eliminating pathogenic microbes by a process called phagocytosis. Phagocytosis is required for tissue homeostasis, balancing inflammation, and crosstalk with the adaptive immune system for antigen presentation. This review focused on (1) current understandings of the signaling underlying phagocytic mechanisms; (2) existing evidence for phagocytic dysregulation in CF; and (3) the emerging role of CFTR modulators in influencing CF phagocytic function. Alterations in CF macrophages from receptor initiation to phagosome formation are linked to disease progression in CF. A deeper understanding of macrophages in the context of CFTR and phagocytosis proteins at each step of phagosome formation might contribute to the new therapeutic development of dysregulated innate immunity in CF. Therefore, the review also indicates future areas of research in the context of CFTR and macrophages.

Dynamic alterations in the lung microbiota in a rat model of lipopolysaccharide-induced acute lung injury

The lung microbiota have been found to be substantially altered in numerous pulmonary disorders, and crosstalk between the host pathophysiology and lung microbiota plays critical roles in the regulation of disease states. The aim of this study was to investigate dynamic changes in the lung microbiota during different stages of acute lung injury and acute respiratory distress syndrome (ALI/ARDS). Rats receiving an intraperitoneal administration of lipopolysaccharide (LPS) were sacrificed at 12 and 48 h after injection, and the hematological parameters, serum cytokine levels, and histological characteristics of the lung tissue and lung microbiota were assessed. After LPS injection, along with fluctuations of systemic cytokine levels and the onset and regression of pulmonary edema, the diversity, components, and functionalities of the pulmonary microbiota underwent significant dynamic changes. The volatility of the α-diversity indices narrowed after LPS injection, and the indices significantly decreased 48 h later. The abundance of 18 genera and functionality of adenosine triphosphate–binding cassette (ABC) transporters, pentose phosphate, and bacterial chemotaxis pathways were found to significantly differ between specified time points. Several significant correlations between the components and functionalities of the lung microbiota and indicative symptoms of ALI/ARDS were also observed. Brevibacterium was correlated with cytokines tumor necrosis factor (TNF)-α, interleukin (IL)-10, and IL-6 and with hematological percentage of neutrophils (NEU%); Wnt, Notch, and chronic myeloid leukemia signaling pathways were correlated with IL-1β; mitogen-activated protein kinase (MAPK) signaling pathway–yeast was correlated with IL-10; and the pathways of ascorbate and aldarate metabolism and basal transcription factors were correlated with platelet-related indicators. The correlations between the lung microbiota and indicative symptoms of ALI/ARDS identified in this study support further investigation into the underlying mechanism of host–microbiota interactions during lung injury and repair.

OUP accepted manuscript

Burkholderia cenocepacia is an opportunistic pathogen that causes severe infections of the cystic fibrosis (CF) lung. To acquire iron, B. cenocepacia secretes the Fe(III)-binding compound, ornibactin. Genes for synthesis and utilisation of ornibactin are served by the iron starvation (IS) extracytoplasmic function (ECF) σ factor, OrbS. Transcription of orbS is regulated in response to the prevailing iron concentration by the ferric uptake regulator (Fur), such that orbS expression is repressed under iron-sufficient conditions. Here we show that, in addition to Fur-mediated regulation of orbS, the OrbS protein itself responds to intracellular iron availability. Substitution of cysteine residues in the C-terminal region of OrbS diminished the ability to respond to Fe(II) in vivo. Accordingly, whilst Fe(II) impaired transcription from and recognition of OrbS-dependent promoters in vitro by inhibiting the binding of OrbS to core RNA polymerase (RNAP), the cysteine-substituted OrbS variant was less responsive to Fe(II). Thus, the cysteine residues within the C-terminal region of OrbS contribute to an iron-sensing motif that serves as an on-board ‘anti-σ factor’ in the presence of Fe(II). A model to account for the presence two regulators (Fur and OrbS) that respond to the same intracellular Fe(II) signal to control ornibactin synthesis and utilisation is discussed.

Emerging role of ferrous iron in bacterial growth and host-pathogen interaction: New tools for chemical (micro)biology and antibacterial therapy

Chemical tools capable of detecting ferrous iron with oxidation-state specificity have only recently become available. Coincident with this development in chemical biology has been increased study and appreciation for the importance of ferrous iron during infection and more generally in host-pathogen interaction. Some of the recent findings are surprising and challenge long-standing assumptions about bacterial iron homeostasis and the innate immune response to infection. Here, we review these recent developments and their implications for antibacterial therapy.

Ferrous Iron-Dependent Pharmacology

The recent emergence of oxidation state selective probes of cellular iron has produced a more nuanced understanding of how cells utilize this crucial nutrient to empower enzyme function, and also how labile ferrous iron contributes to iron-dependent cell death (ferroptosis) and other disease pathologies including cancer, bacterial infections, and neurodegeneration. These findings, viewed in light of the Fenton chemistry promoted by ferrous iron, suggest a new category of therapeutics exhibiting ferrous iron-dependent pharmacology. While still in its infancy, this nascent field draws inspiration from the remarkable activity and tremendous clinical impact of the antimalarial artemisinin. Here, we review recent insights into the role of labile ferrous iron in biology and disease, and describe new therapeutic approaches designed to exploit this divalent transition metal.

Loss of a pyoverdine secondary receptor in Pseudomonas aeruginosa results in a fitter strain suitable for population invasion

The rapid emergence of antibiotic resistant bacterial pathogens constitutes a critical problem in healthcare and requires the development of novel treatments. Potential strategies include the exploitation of microbial social interactions based on public goods, which are produced at a fitness cost by cooperative microorganisms, but can be exploited by cheaters that do not produce these goods. Cheater invasion has been proposed as a 'Trojan horse' approach to infiltrate pathogen populations with strains deploying built-in weaknesses (e.g., sensitiveness to antibiotics). However, previous attempts have been often unsuccessful because population invasion by cheaters was prevented by various mechanisms including the presence of spatial structure (e.g., growth in biofilms), which limits the diffusion and exploitation of public goods. Here we followed an alternative approach and examined whether the manipulation of public good uptake and not its production could result in potential 'Trojan horses' suitable for population invasion. We focused on the siderophore pyoverdine produced by the human pathogen Pseudomonas aeruginosa MPAO1 and manipulated its uptake by deleting and/or overexpressing the pyoverdine primary (FpvA) and secondary (FpvB) receptors. We found that receptor synthesis feeds back on pyoverdine production and uptake rates, which led to strains with altered pyoverdine-associated costs and benefits. Moreover, we found that the receptor FpvB was advantageous under iron-limited conditions but revealed hidden costs in the presence of an antibiotic stressor (gentamicin). As a consequence, FpvB mutants became the fittest strain under gentamicin exposure, displacing the wildtype in liquid cultures, and in biofilms and during infections of the wax moth larvae Galleria mellonella, which both represent structured environments. Our findings reveal that an evolutionary trade-off associated with the costs and benefits of a versatile pyoverdine uptake strategy can be harnessed for devising a Trojan-horse candidate for medical interventions.

Iron at the host-microbe interface

Iron is an essential micronutrient for nearly all living organisms. In addition to facilitating redox reactions, iron is bound by metalloproteins that participate in a variety of biological processes. As the bioavailability of free iron in host environments is extremely low, iron lies at the center of a battle for nutrients between microbes and their host. Mucosal surfaces such as the respiratory and gastrointestinal tracts are constantly exposed to commensal and pathogenic microorganisms. Whereas a key strategy of mammalian antimicrobial defense is to deprive microbes of iron, pathogens and some commensals have evolved effective strategies to circumvent iron limitation. Here we provide an overview of mechanisms underpinning the tug-of-war for iron between microbes and their host, with a particular focus on mucosal surfaces.

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

AIMS

Relatively, few anti-biofilm polysaccharides against Pseudomonas aeruginosa were done to investigate the underlying molecular mechanism. Exopolysaccharide EPS273 can clearly reduce biofilm formation and infection of P. aeruginosa. This study aims to investigate its anti-biofilm and anti-infection mechanism on transcriptional level.

METHODS AND RESULTS

Herein, we used an RNA-Seq transcriptomic approach to investigate the underlying anti-biofilm and anti-infection mechanism of EPS273. The expression levels of a large number of genes were changed after P. aeruginosa PAO1 was treated with EPS273. Especially, the genes related to biofilm formation, such as gene involved in production of extracellular matrix and virulence factor, genes involved in flagella and cell motility and genes involved in iron acquisition. Notably, the expression levels of genes involved in regulatory and signal transduction were markedly downregulated, such as two-component system PhoP-PhoQ and quorum sensing (QS) system LasI/LasR and RhlI/RhlR. Furthermore, when genes phoP and phoQ were disrupted, respectively, the reduction of biofilm formation and cell motility in mutant △phoP or △phoQ was also detected.

CONCLUSION

EPS273 may exert its anti-biofilm and anti-infection function by downregulating gene expression of two-component system PhoP-PhoQ and QS systems LasI/LasR and RhlI/RhlR of P. aeruginosa, which further regulated expression of genes involved in biofilm formation.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our data will expand understanding of anti-biofilm mechanisms of polysaccharides on transcriptomic level.

Interplay between host-microbe and microbe-microbe interactions in cystic fibrosis

The respiratory tract of individuals with cystic fibrosis is host to polymicrobial infections that persist for decades and lead to significant morbidity and mortality. Improving our understanding of CF respiratory infections requires coordinated efforts from researchers in the fields of microbial physiology, genomics, and ecology, as well as epithelial biology and immunology. Here, we have highlighted examples from recent CF microbial pathogenesis literature of how the host nutritional environment, immune response, and microbe-microbe interactions can feedback onto each other, leading to diverse effects on lung disease pathogenesis in CF.

Targeting Mobilization of Ferrous Iron in Pseudomonas aeruginosa Infection with an Iron(II)-Caged LpxC Inhibitor

Iron is essential to all life, and competition for this vital nutrient is central to host-pathogen interactions during infection. The opportunistic Gram-negative pathogen Pseudomonas aeruginosa utilizes a diverse array of iron-acquisition strategies, including those enabling import of extracellular ferrous iron. We hypothesize that soluble and redox-active ferrous iron can be employed to activate caged antibiotics at sites of infection in vivo. Here we describe new chemistry that expands the application of our laboratory's Fe²⁺-activated-prodrug chemistry to cage hydroxamic acids, a class of drugs that present manifold development challenges. We synthesize the caged form of a known LpxC inhibitor and show that it is efficacious in an acute P. aeruginosa mouse-lung infection model, despite showing little activity in cell-culture experiments. Overall, our results are consistent with the Fe²⁺-promoted uncaging of an antibacterial payload at sites of infection in an animal and lend support to recent reports indicating that extracellular pools of ferrous iron can be utilized by bacterial pathogens like P. aeruginosa during infection.

Iron Homeostasis in the Lungs-A Balance between Health and Disease

A strong mechanistic link between the regulation of iron homeostasis and oxygen sensing is evident in the lung, where both systems must be properly controlled to maintain lung function. Imbalances in pulmonary iron homeostasis are frequently associated with respiratory diseases, such as chronic obstructive pulmonary disease and with lung cancer. However, the underlying mechanisms causing alterations in iron levels and the involvement of iron in the development of lung disorders are incompletely understood. Here, we review current knowledge about the regulation of pulmonary iron homeostasis, its functional importance, and the link between dysregulated iron levels and lung diseases. Gaining greater knowledge on how iron contributes to the pathogenesis of these diseases holds promise for future iron-related therapeutic strategies.

High-resolution in situ transcriptomics of Pseudomonas aeruginosa unveils genotype independent patho-phenotypes in cystic fibrosis lungs

Life-long bacterial infections in cystic fibrosis (CF) airways constitute an excellent model both for persistent infections and for microbial adaptive evolution in complex dynamic environments. Using high-resolution transcriptomics applied on CF sputum, we profile transcriptional phenotypes of Pseudomonas aeruginosa populations in patho-physiological conditions. Here we show that the soft-core genome of genetically distinct populations, while maintaining transcriptional flexibility, shares a common expression program tied to the lungs environment. We identify genetically independent traits defining P. aeruginosa physiology in vivo, documenting the connection between several previously identified mutations in CF isolates and some of the convergent phenotypes known to develop in later stages of the infection. In addition, our data highlight to what extent this organism can exploit its extensive repertoire of physiological pathways to acclimate to a new niche and suggest how alternative nutrients produced in the lungs may be utilized in unexpected metabolic contexts.

Unmet needs in cystic fibrosis: the next steps in improving outcomes

INTRODUCTION

Cystic fibrosis (CF) outcomes and survival have improved over the last century primarily due to advancements in antibiotics, nutritional, and pulmonary therapies. Reviewed here are the significant unmet needs that exist for individuals with CF. Areas covered: With the recent development of medications that address the underlying defect in the CF protein, there is hope that there will be continued improvement in CF outcomes. However, there remains a need to prevent or stop progression of CF-related complications, as the CF protein is important to several body systems. As end stage lung disease is the primary cause of mortality in CF, a need exists for advancements in pulmonary therapies to reduce time burden, identification of best practices for the treatment of pulmonary exacerbations, further development of anti-infective and anti-inflammatory therapies, and appropriately timed referral for lung transplantation at end-stage lung disease. Extra-pulmonary complications are increasingly recognized and better understanding of such problems as CF related liver disease is needed. Expert commentary: While CFTR modulators are available for the majority of CF patients, there remains a need for effective therapies to address infection, inflammation, irreversible lung disease, and extrapulmonary complications of CF.

Iron at the Centre of Candida albicans Interactions

Iron is an absolute requirement for both the host and most pathogens alike and is needed for normal cellular growth. The acquisition of iron by biological systems is regulated to circumvent toxicity of iron overload, as well as the growth deficits imposed by iron deficiency. In addition, hosts, such as humans, need to limit the availability of iron to pathogens. However, opportunistic pathogens such as Candida albicans are able to adapt to extremes of iron availability, such as the iron replete environment of the gastrointestinal tract and iron deficiency during systemic infection. C. albicans has developed a complex and effective regulatory circuit for iron acquisition and storage to circumvent iron limitation within the human host. As C. albicans can form complex interactions with both commensal and pathogenic co-inhabitants, it can be speculated that iron may play an important role in these interactions. In this review, we highlight host iron regulation as well as regulation of iron homeostasis in C. albicans. In addition, the review argues for the need for further research into the role of iron in polymicrobial interactions. Lastly, the role of iron in treatment of C. albicans infection is discussed.

The role of multispecies social interactions in shaping Pseudomonas aeruginosa pathogenicity in the cystic fibrosis lung

Pseudomonas aeruginosa is a major pathogen in the lungs of cystic fibrosis (CF) patients. However, it is now recognised that a diverse microbial community exists in the airways comprising aerobic and anaerobic bacteria as well as fungi and viruses. This rich soup of microorganisms provides ample opportunity for interspecies interactions, particularly when considering secreted compounds. Here, we discuss how P. aeruginosa-secreted products can have community-wide effects, with the potential to ultimately shape microbial community dynamics within the lung. We focus on three well-studied traits associated with worsening clinical outcome in CF: phenazines, siderophores and biofilm formation, and discuss how secretions can shape interactions between P. aeruginosa and other commonly encountered members of the lung microbiome: Staphylococcus aureus, the Burkholderia cepacia complex, Candida albicans and Aspergillus fumigatus. These interactions may shape the evolutionary trajectory of P. aeruginosa while providing new opportunities for therapeutic exploitation of the CF lung microbiome.

The bacterium Pseudomonas aeruginosa senses and gradually responds to interspecific competition for iron

Phenotypic plasticity in response to competition is a well-described phenomenon in higher organisms. Here, we show that also bacteria have the ability to sense the presence of competitors and mount fine-tuned responses to match prevailing levels of competition. In our experiments, we studied interspecific competition for iron between the bacterium Pseudomonas aeruginosa (PA) and its competitor Burkholderia cenocepacia (BC). We focused on the ability of PA to phenotypically adjust the production of pyoverdine, an iron-scavenging siderophore. We found that PA upregulates pyoverdine production early on during competition under condition of low iron availability. This plastic upregulation was fine-tuned in response to the level of competition imposed by BC, and seems to confer a relative fitness benefit to PA in the form of an earlier initiation of growth. At later time points, however, PA showed reduced growth in mixed compared to monoculture, suggesting that competitive responses are costly. Altogether, our results demonstrate that phenotypic plasticity in siderophore production plays an important role in interspecific competition for iron. Upregulating siderophore production may be a powerful strategy to lock iron away from competing species, and to reserve this nutrient for strain members possessing the compatible receptor for uptake.

Optimised chronic infection models demonstrate that siderophore 'cheating' in Pseudomonas aeruginosa is context specific

The potential for siderophore mutants of Pseudomonas aeruginosa to attenuate virulence during infection, and the possibility of exploiting this for clinical ends, have attracted much discussion. This has largely been based on the results of in vitro experiments conducted in iron-limited growth medium, in which siderophore mutants act as social 'cheats:' increasing in frequency at the expense of the wild type to result in low-productivity, low-virulence populations dominated by mutants. We show that insights from in vitro experiments cannot necessarily be transferred to infection contexts. First, most published experiments use an undefined siderophore mutant. Whole-genome sequencing of this strain revealed a range of mutations affecting phenotypes other than siderophore production. Second, iron-limited medium provides a very different environment from that encountered in chronic infections. We conducted cheating assays using defined siderophore deletion mutants, in conditions designed to model infected fluids and tissue in cystic fibrosis lung infection and non-healing wounds. Depending on the environment, siderophore loss led to cheating, simple fitness defects, or no fitness effect at all. Our results show that it is crucial to develop defined in vitro models in order to predict whether siderophores are social, cheatable and suitable for clinical exploitation in specific infection contexts.

Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa

Cystic fibrosis (CF) lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp) and 52 P. aeruginosa-negative (Pn) pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA) from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P. aeruginosa. RISA clusters Ip and IIIp contained CF sputa with a P. aeruginosa prevalence above 93%, and of 24.2% in cluster IIp. Clusters Ip and IIIp showed lower RISA genetic diversity and richness than IIp. Highly similar cluster IIp RISA profiles were obtained from two patients harboring isolates of a same P. aeruginosa clone, suggesting convergent evolution in the structure of their microbiota. CF patients of cluster IIp had received significantly less antibiotics than patients of clusters Ip and IIIp but harbored the most resistant P. aeruginosa strains. Patients of cluster IIIp were older than those of Ip. The effects of P. aeruginosa on the RISA structures could not be fully dissociated from the above two confounding factors but several trends in these datasets support the conclusion of a strong incidence of P. aeruginosa on the genetic structure of CF lung microbiota.

Cheating fosters species co-existence in well-mixed bacterial communities

Explaining the enormous biodiversity observed in bacterial communities is challenging because ecological theory predicts that competition between species occupying the same niche should lead to the exclusion of less competitive community members. Competitive exclusion should be particularly strong when species compete for a single limiting resource or live in unstructured habitats that offer no refuge for weaker competitors. Here, we describe the 'cheating effect', a form of intra-specific competition that can counterbalance between-species competition, thereby fostering biodiversity in unstructured habitats. Using experimental communities consisting of the strong competitor Pseudomonas aeruginosa (PA) and its weaker counterpart Burkholderia cenocepacia (BC), we show that co-existence is impossible when the two species compete for a single limiting resource, iron. However, when introducing a PA cheating mutant, which specifically exploits the iron-scavenging siderophores produced by the PA wild type, we found that biodiversity was preserved under well-mixed conditions where PA cheats could outcompete the PA wild type. Cheating fosters biodiversity in our system because it creates strong intra-specific competition, which equalizes fitness differences between PA and BC. Our study identifies cheating - typically considered a destructive element - as a constructive force in shaping biodiversity.

Transient Proteotoxicity of Bacterial Virulence Factor Pyocyanin in Renal Tubular Epithelial Cells Induces ER-Related Vacuolation and Can Be Efficiently Modulated by Iron Chelators

Persistent infections of biofilm forming bacteria, such as Pseudomonas aeruginosa, are common among human populations, due to the bacterial resistance to antibiotics and other adaptation strategies, including release of cytotoxic virulent factors such as pigment pyocyanin (PCN). Urinary tract infections harbor P. aeruginosa strains characterized by the highest PCN-producing capacity, yet no information is available on PCN cytotoxicity mechanism in kidney. We report here that renal tubular epithelial cell (RTEC) line NRK-52E responds to PCN treatments with paraptosis-like activity features. Specifically, PCN-treated cells experienced dilation of endoplasmic reticulum (ER) and an extensive development of ER-derived vacuoles after about 8 h. This process was accompanied with hyper-activation of proteotoxic stress-inducible transcription factors Nrf2, ATF6, and HSF-1. The cells could be rescued by withdrawal of PCN from the culture media before the vacuoles burst and cells die of non-programmed necrosis after about 24–30 h. The paraptosis-like activity was abrogated by co-treatment of the cells with metal-chelating antioxidants. A microscopic examination of cells co-treated with PCN and agents aiming at a variety of the cellular stress mediators and pathways have identified iron as a single most significant co-factor of the PCN cytotoxicity in the RTECs. Among biologically relevant metal ions, low micromolar Fe²⁺specifically mediated anaerobic oxidation of glutathione by PCN, but catechol derivatives and other strong iron complexing agents could inhibit the reaction. Our data suggest that iron chelation could be considered as a supplementary treatment in the PCN-positive infections.