1
|
Coluccio A, Lopez Palomera F, Spero MA. Anaerobic bacteria in chronic wounds: Roles in disease, infection and treatment failure. Wound Repair Regen 2024. [PMID: 39129662 DOI: 10.1111/wrr.13208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/09/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024]
Abstract
Infection is among the most common factors that impede wound healing, yet standard treatments routinely fail to resolve chronic wound infections. The chronic wound environment is largely hypoxic/anoxic, and wounds are predominantly colonised by facultative and obligate anaerobic bacteria. Oxygen (O2) limitation is an underappreciated driver of microbiota composition and behaviour in chronic wounds. In this perspective article, we examine how anaerobic bacteria and their distinct physiologies support persistent, antibiotic-recalcitrant infections. We describe the anaerobic energy metabolisms bacteria rely on for long-term survival in the wound environment, and why many antibiotics become less effective under hypoxic conditions. We also discuss obligate anaerobes, which are among the most prevalent taxa to colonise chronic wounds, yet their potential roles in influencing the microbial community and wound healing have been overlooked. All of the most common obligate anaerobes found in chronic wounds are opportunistic pathogens. We consider how these organisms persist in the wound environment and interface with host physiology to hinder wound healing processes or promote chronic inflammation. Finally, we apply our understanding of anaerobic physiologies to evaluate current treatment practices and to propose new strategies for treating chronic wound infections.
Collapse
Affiliation(s)
- Alison Coluccio
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | | | - Melanie A Spero
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| |
Collapse
|
2
|
Stoodley P, Toelke N, Schwermer C, de Beer D. Bioenergetics of simultaneous oxygen and nitrate respiration and nitric oxide production in a Pseudomonas aeruginosa agar colony biofilm. Biofilm 2024; 7:100181. [PMID: 38425549 PMCID: PMC10902143 DOI: 10.1016/j.bioflm.2024.100181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/09/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Pseudomonas aeruginosa is a biofilm forming pathogen commonly associated with infection of the cystic fibrosis (CF) lung, chronic wounds and indwelling medical devices. P. aeruginosa is a facultative aerobe that can use nitrate (NO3-) found in healthy and infected tissues and body fluids to generate energy through denitrification. Further, P. aeruginosa the expression of denitrification genes has been found in specimens from people with CF. The main aim of this study was to determine the relative energy contribution of oxygen (O2) respiration and denitrification in single Pseudomonas aeruginosa PAO1 biofilm colonies under different O2 concentrations to estimate the possible relative importance of these metabolic processes in the context of biofilm infections. We showed that the used strain PAO1 in biofilms denitrified with nitrous oxide (N2O), and not nitrogen (N2), as the end product in our incubations. From simultaneous O2 and N2O microprofiles measured with high spatial resolution by microsensors in agar colony biofilms under air, N2 and pure O2, the rates of aerobic respiration and denitrification were calculated and converted to ATP production rates. Denitrification occurred both in the oxic and anoxic zones, and became increasingly dominant with decreasing O2 concentrations. At O2 concentrations characteristic for tissues and wounds (20-60 μM), denitrification was responsible for 50% of the total energy conservation in the biofilm. In addition the formation of nitric oxide (NO), a precursor of N2O and an important regulator of many cellular processes, was strongly influenced by the local O2 concentrations. NO production was inhibited under pure O2, present under anoxia (∼1 μM) and remarkably high (up to 6 μM) under intermediate O2 levels, which can be found in infected tissues. Possible impacts of such NO levels on both the host and the biofilm bacteria are discussed.
Collapse
Affiliation(s)
- Paul Stoodley
- National Centre for Advanced Tribology at Southampton, (NCATS), Mechanical Engineering, University of Southampton, Southampton, SO17 1BJ, UK
- Department of Microbial Infection and Immunity, Department of Orthopaedics, The Ohio State University, 716 Biomedical Research Tower (BRT), 460 W 12th Ave, Columbus OH, 43210, United States
| | - Nina Toelke
- Max Planck Institute for Marine Microbiology (MPI), Microsensor Group and Molecular Ecology Group, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Carsten Schwermer
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology (MPI), Microsensor Group and Molecular Ecology Group, Celsiusstrasse 1, D-28359, Bremen, Germany
| |
Collapse
|
3
|
Shen R, Borer B, Ciccarese D, Salek MM, Babbin AR. Microscale advection governs microbial growth and oxygen consumption in macroporous aggregates. mSphere 2024; 9:e0018524. [PMID: 38530018 PMCID: PMC11036798 DOI: 10.1128/msphere.00185-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Most microbial life on Earth is found in localized microenvironments that collectively exert a crucial role in maintaining ecosystem health and influencing global biogeochemical cycles. In many habitats such as biofilms in aquatic systems, bacterial flocs in activated sludge, periphyton mats, or particles sinking in the ocean, these microenvironments experience sporadic or continuous flow. Depending on their microscale structure, pores and channels through the microenvironments permit localized flow that shifts the relative importance of diffusive and advective mass transport. How this flow alters nutrient supply, facilitates waste removal, drives the emergence of different microbial niches, and impacts the overall function of the microenvironments remains unclear. Here, we quantify how pores through microenvironments that permit flow can elevate nutrient supply to the resident bacterial community using a microfluidic experimental system and gain further insights from coupled population-based and computational fluid dynamics simulations. We find that the microscale structure determines the relative contribution of advection vs diffusion, and even a modest flow through a pore in the range of 10 µm s-1 can increase the carrying capacity of a microenvironment by 10%. Recognizing the fundamental role that microbial hotspots play in the Earth system, developing frameworks that predict how their heterogeneous morphology and potential interstitial flows change microbial function and collectively alter global scale fluxes is critical.IMPORTANCEMicrobial life is a key driver of global biogeochemical cycles. Similar to the distribution of humans on Earth, they are often not homogeneously distributed in nature but occur in dense clusters that resemble microbial cities. Within and around these clusters, diffusion is often assumed as the sole mass-transfer process that dictates nutrient supply and waste removal. In many natural and engineered systems such as biofilms in aquatic environments, aggregates in bioremediation, or flocs in wastewater treatment plants, these clusters are exposed to flow that elevates mass transfer, a process that is often overlooked. In this study, we show that advective fluxes can increase the local growth of bacteria in a single microenvironment by up to 50% and shape their metabolism by disrupting localized anoxia or supplying nutrients at different rates. Collectively, advection-enhanced mass transport may thus regulate important biogeochemical transformations in both natural and engineered environments.
Collapse
Affiliation(s)
- Rachel Shen
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Davide Ciccarese
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - M. Mehdi Salek
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
4
|
Kuper TJ, Islam MM, Peirce-Cottler SM, Papin JA, Ford RM. Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment. PLoS Comput Biol 2024; 20:e1012031. [PMID: 38669236 PMCID: PMC11051585 DOI: 10.1371/journal.pcbi.1012031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
With the generation of spatially resolved transcriptomics of microbial biofilms, computational tools can be used to integrate this data to elucidate the multi-scale mechanisms controlling heterogeneous biofilm metabolism. This work presents a Multi-scale model of Metabolism In Cellular Systems (MiMICS) which is a computational framework that couples a genome-scale metabolic network reconstruction (GENRE) with Hybrid Automata Library (HAL), an existing agent-based model and reaction-diffusion model platform. A key feature of MiMICS is the ability to incorporate multiple -omics-guided metabolic models, which can represent unique metabolic states that yield different metabolic parameter values passed to the extracellular models. We used MiMICS to simulate Pseudomonas aeruginosa regulation of denitrification and oxidative stress metabolism in hypoxic and nitric oxide (NO) biofilm microenvironments. Integration of P. aeruginosa PA14 biofilm spatial transcriptomic data into a P. aeruginosa PA14 GENRE generated four PA14 metabolic model states that were input into MiMICS. Characteristic of aerobic, denitrification, and oxidative stress metabolism, the four metabolic model states predicted different oxygen, nitrate, and NO exchange fluxes that were passed as inputs to update the agent's local metabolite concentrations in the extracellular reaction-diffusion model. Individual bacterial agents chose a PA14 metabolic model state based on a combination of stochastic rules, and agents sensing local oxygen and NO. Transcriptome-guided MiMICS predictions suggested microscale denitrification and oxidative stress metabolic heterogeneity emerged due to local variability in the NO biofilm microenvironment. MiMICS accurately predicted the biofilm's spatial relationships between denitrification, oxidative stress, and central carbon metabolism. As simulated cells responded to extracellular NO, MiMICS revealed dynamics of cell populations heterogeneously upregulating reactions in the denitrification pathway, which may function to maintain NO levels within non-toxic ranges. We demonstrated that MiMICS is a valuable computational tool to incorporate multiple -omics-guided metabolic models to mechanistically map heterogeneous microbial metabolic states to the biofilm microenvironment.
Collapse
Affiliation(s)
- Tracy J. Kuper
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Mohammad Mazharul Islam
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Shayn M. Peirce-Cottler
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jason A. Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Roseanne M Ford
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| |
Collapse
|
5
|
De R, Whiteley M, Azad RK. A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1. mSystems 2023; 8:e0047323. [PMID: 37921470 PMCID: PMC10734507 DOI: 10.1128/msystems.00473-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE We present here a new systems-level approach to decipher genetic factors and biological pathways associated with virulence and/or antibiotic treatment of bacterial pathogens. The power of this approach was demonstrated by application to a well-studied pathogen Pseudomonas aeruginosa PAO1. Our gene co-expression network-based approach unraveled known and unknown genes and their networks associated with pathogenicity in P. aeruginosa PAO1. The systems-level investigation of P. aeruginosa PAO1 helped identify putative pathogenicity and resistance-associated genetic factors that could not otherwise be detected by conventional approaches of differential gene expression analysis. The network-based analysis uncovered modules that harbor genes not previously reported by several original studies on P. aeruginosa virulence and resistance. These could potentially act as molecular determinants of P. aeruginosa PAO1 pathogenicity and responses to antibiotics.
Collapse
Affiliation(s)
- Ronika De
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
| | - Marvin Whiteley
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children’s Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Rajeev K. Azad
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
- Department of Mathematics, University of North Texas, Denton, Texas, USA
| |
Collapse
|
6
|
Ambreetha S, Singh V. Genetic and environmental determinants of surface adaptations in Pseudomonas aeruginosa. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37276014 DOI: 10.1099/mic.0.001335] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pseudomonas aeruginosa
is a well-studied Gram-negative opportunistic bacterium that thrives in markedly varied environments. It is a nutritionally versatile microbe that can colonize a host as well as exist in the environment. Unicellular, planktonic cells of
P. aeruginosa
can come together to perform a coordinated swarming movement or turn into a sessile, surface-adhered population called biofilm. These collective behaviours produce strikingly different outcomes. While swarming motility rapidly disseminates the bacterial population, biofilm collectively protects the population from environmental stresses such as heat, drought, toxic chemicals, grazing by predators, and attack by host immune cells and antibiotics. The ubiquitous nature of
P. aeruginosa
is likely to be supported by the timely transition between planktonic, swarming and biofilm lifestyles. The social behaviours of this bacteria viz biofilm and swarm modes are controlled by signals from quorum-sensing networks, LasI-LasR, RhlI-RhlR and PQS-MvfR, and several other sensory kinases and response regulators. A combination of environmental and genetic cues regulates the transition of the
P. aeruginosa
population to specific states. The current review is aimed at discussing key factors that promote physiologically distinct transitioning of the
P. aeruginosa
population.
Collapse
Affiliation(s)
- Sakthivel Ambreetha
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, Karnataka - 560012, India
| | - Varsha Singh
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, Karnataka - 560012, India
| |
Collapse
|
7
|
Vaillancourt M, Galdino ACM, Limsuwannarot SP, Celedonio D, Dimitrova E, Broerman M, Bresee C, Doi Y, Lee JS, Parks WC, Jorth P. A compensatory RNase E variation increases Iron Piracy and Virulence in multidrug-resistant Pseudomonas aeruginosa during Macrophage infection. PLoS Pathog 2023; 19:e1010942. [PMID: 37027441 PMCID: PMC10115287 DOI: 10.1371/journal.ppat.1010942] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/19/2023] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
During chronic cystic fibrosis (CF) infections, evolved Pseudomonas aeruginosa antibiotic resistance is linked to increased pulmonary exacerbations, decreased lung function, and hospitalizations. However, the virulence mechanisms underlying worse outcomes caused by antibiotic resistant infections are poorly understood. Here, we investigated evolved aztreonam resistant P. aeruginosa virulence mechanisms. Using a macrophage infection model combined with genomic and transcriptomic analyses, we show that a compensatory mutation in the rne gene, encoding RNase E, increased pyoverdine and pyochelin siderophore gene expression, causing macrophage ferroptosis and lysis. We show that iron-bound pyochelin was sufficient to cause macrophage ferroptosis and lysis, however, apo-pyochelin, iron-bound pyoverdine, or apo-pyoverdine were insufficient to kill macrophages. Macrophage killing could be eliminated by treatment with the iron mimetic gallium. RNase E variants were abundant in clinical isolates, and CF sputum gene expression data show that clinical isolates phenocopied RNase E variant functions during macrophage infection. Together these data show how P. aeruginosa RNase E variants can cause host damage via increased siderophore production and host cell ferroptosis but may also be targets for gallium precision therapy.
Collapse
Affiliation(s)
- Mylene Vaillancourt
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Anna Clara Milesi Galdino
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Sam P. Limsuwannarot
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Diana Celedonio
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Elizabeth Dimitrova
- Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Matthew Broerman
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Catherine Bresee
- Biostatistics Core, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Yohei Doi
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Janet S. Lee
- Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - William C. Parks
- Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Peter Jorth
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Women’s Guild Lung Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| |
Collapse
|
8
|
Exposure of Aspergillus fumigatus to Klebsiella pneumoniae Culture Filtrate Inhibits Growth and Stimulates Gliotoxin Production. J Fungi (Basel) 2023; 9:jof9020222. [PMID: 36836336 PMCID: PMC9961802 DOI: 10.3390/jof9020222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen capable of inducing chronic and acute infection in susceptible patients. A. fumigatus interacts with numerous bacteria that compose the microbiota of the lung, including Pseudomonas aeruginosa and Klebsiella pneumoniae, both of which are common isolates from cystic fibrosis sputum. Exposure of A. fumigatus to K. pneumoniae culture filtrate reduced fungal growth and increased gliotoxin production. Qualitative proteomic analysis of the K. pneumoniae culture filtrate identified proteins associated with metal sequestering, enzymatic degradation and redox activity, which may impact fungal growth and development. Quantitative proteomic analysis of A. fumigatus following exposure to K. pneumoniae culture filtrate (25% v/v) for 24 h revealed a reduced abundance of 1,3-beta-glucanosyltransferase (-3.97 fold), methyl sterol monooxygenase erg25B (-2.9 fold) and calcium/calmodulin-dependent protein kinase (-4.2 fold) involved in fungal development, and increased abundance of glutathione S-transferase GliG (+6.17 fold), non-ribosomal peptide synthase GliP (+3.67 fold), O-methyltransferase GliM (+3.5 fold), gamma-glutamyl acyltransferase GliK (+2.89 fold) and thioredoxin reductase GliT (+2.33 fold) involved in gliotoxin production. These results reveal that exposure of A. fumigatus to K. pneumoniae in vivo could exacerbate infection and negatively impact patient prognosis.
Collapse
|
9
|
Lichtenberg M, Kvich L, Larsen SLB, Jakobsen TH, Bjarnsholt T. Inoculum Concentration Influences Pseudomonas aeruginosa Phenotype and Biofilm Architecture. Microbiol Spectr 2022; 10:e0313122. [PMID: 36354337 PMCID: PMC9769529 DOI: 10.1128/spectrum.03131-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2022] Open
Abstract
In infections, bacterial cells are often found as relatively small multicellular aggregates characterized by a heterogeneous distribution of phenotype, genotype, and growth rates depending on their surrounding microenvironment. Many laboratory models fail to mimic these characteristics, and experiments are often initiated from planktonic bacteria given optimal conditions for rapid growth without concerns about the microenvironmental characteristics during biofilm maturation. Therefore, we investigated how the initial bacterial concentration (henceforth termed the inoculum) influences the microenvironment during initial growth and how this affects the sizes and distribution of developed aggregates in an embedded biofilm model-the alginate bead biofilm model. Following 24 h of incubation, the viable biomass was independent of starting inoculum but with a radically different microenvironment which led to differences in metabolic activity depending on the inoculum. The inoculum also affected the number of cells surviving treatment with the antibiotic tobramycin, where the highest inoculum showed higher survival rates than the lowest inoculum. The change in antibiotic tolerance was correlated with cell-specific RNA content and O2 consumption rates, suggesting a direct role of metabolic activity. Thus, the starting number of bacteria results in different phenotypic trajectories governed by different microenvironmental characteristics, and we demonstrate some of the possible implications of such physiological gradients on the outcome of in vitro experiments. IMPORTANCE Biofilm aggregates grown in the alginate bead biofilm model bear resemblance to features of in vivo biofilms. Here, we show that changing the initial concentration of bacteria in the biofilm model leads to widely different behavior of the bacteria following an incubation period. This difference is influenced by the local conditions experienced by the bacteria during growth, which impact their response to antibiotic treatment. Our study provides a framework for manipulating aggregate sizes in in vitro biofilm models. It underlines the importance of how experiments are initiated, which can profoundly impact the outcomes and interpretation of microbiological experiments.
Collapse
Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lasse Kvich
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Sara Louise Borregaard Larsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| |
Collapse
|
10
|
Spero MA, Jones J, Lomenick B, Chou TF, Newman DK. Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa. Mol Microbiol 2022; 118:321-335. [PMID: 36271736 PMCID: PMC9589919 DOI: 10.1111/mmi.14972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that often encounters hypoxic/anoxic environments within the host, which increases its tolerance to many conventional antibiotics. Toward identifying novel treatments, we explored the therapeutic potential of chlorate, a pro-drug that kills hypoxic/anoxic, antibiotic-tolerant P. aeruginosa populations. While chlorate itself is relatively nontoxic, it is enzymatically reduced to the toxic oxidizing agent, chlorite, by hypoxically induced nitrate reductase. To better assess chlorate's therapeutic potential, we investigated mechanisms of chlorate toxicity and resistance in P. aeruginosa. We used transposon mutagenesis to identify genes that alter P. aeruginosa fitness during chlorate treatment, finding that methionine sulfoxide reductases (Msr), which repair oxidized methionine residues, support survival during chlorate stress. Chlorate treatment leads to proteome-wide methionine oxidation, which is exacerbated in a ∆msrA∆msrB strain. In response to chlorate, P. aeruginosa upregulates proteins involved in a wide range of functions, including metabolism, DNA replication/repair, protein repair, transcription, and translation, and these newly synthesized proteins are particularly vulnerable to methionine oxidation. The addition of exogenous methionine partially rescues P. aeruginosa survival during chlorate treatment, suggesting that widespread methionine oxidation contributes to death. Finally, we found that mutations that decrease nitrate reductase activity are a common mechanism of chlorate resistance.
Collapse
Affiliation(s)
- Melanie A. Spero
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Jeff Jones
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| |
Collapse
|
11
|
Lichtenberg M, Kragh KN, Fritz B, Kirkegaard JB, Tolker-Nielsen T, Bjarnsholt T. Cyclic-di-GMP signaling controls metabolic activity in Pseudomonas aeruginosa. Cell Rep 2022; 41:111515. [DOI: 10.1016/j.celrep.2022.111515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 07/13/2022] [Accepted: 09/26/2022] [Indexed: 11/03/2022] Open
|
12
|
Ciofu O, Moser C, Jensen PØ, Høiby N. Tolerance and resistance of microbial biofilms. Nat Rev Microbiol 2022; 20:621-635. [PMID: 35115704 DOI: 10.1038/s41579-022-00682-4] [Citation(s) in RCA: 333] [Impact Index Per Article: 166.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 02/07/2023]
Abstract
Chronic infections caused by microbial biofilms represent an important clinical challenge. The recalcitrance of microbial biofilms to antimicrobials and to the immune system is a major cause of persistence and clinical recurrence of these infections. In this Review, we present the extent of the clinical problem, and the mechanisms underlying the tolerance of biofilms to antibiotics and to host responses. We also explore the role of biofilms in the development of antimicrobial resistance mechanisms.
Collapse
Affiliation(s)
- Oana Ciofu
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Claus Moser
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Peter Østrup Jensen
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Niels Høiby
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| |
Collapse
|
13
|
The Metabolic Adaptation in Response to Nitrate Is Critical for Actinobacillus pleuropneumoniae Growth and Pathogenicity under the Regulation of NarQ/P. Infect Immun 2022; 90:e0023922. [PMID: 35938858 PMCID: PMC9476948 DOI: 10.1128/iai.00239-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrate metabolism is an adaptation mechanism used by many bacteria for survival in anaerobic environments. As a by-product of inflammation, nitrate is used by the intestinal bacterial pathogens to enable gut infection. However, the responses of bacterial respiratory pathogens to nitrate are less well understood. Actinobacillus pleuropneumoniae is an important bacterial respiratory pathogen of swine. Previous studies have suggested that adaptation of A. pleuropneumoniae to anaerobiosis is important for infection. In this work, A. pleuropneumoniae growth and pathogenesis in response to the nitrate were investigated. Nitrate significantly promoted A. pleuropneumoniae growth under anaerobic conditions in vitro and lethality in mice. By using narQ and narP deletion mutants and single-residue-mutated complementary strains of ΔnarQ, the two-component system NarQ/P was confirmed to be critical for nitrate-induced growth, with Arg50 in NarQ as an essential functional residue. Transcriptome analysis showed that nitrate upregulated multiple energy-generating pathways, including nitrate metabolism, mannose and pentose metabolism, and glycerolipid metabolism via the regulation of NarQ/P. Furthermore, narQ, narP, and its target gene encoding the nitrate reductase Nap contributed to the pathogenicity of A. pleuropneumoniae. The Nap inhibitor tungstate significantly reduced the survival of A. pleuropneumoniae in vivo, suggesting that Nap is a potential drug target. These results give new insights into how the respiratory pathogen A. pleuropneumoniae utilizes the alternative electron acceptor nitrate to overcome the hypoxia microenvironment, which can occur in the inflammatory or necrotic infected tissues.
Collapse
|
14
|
De Giglio O, Narracci M, Apollonio F, Triggiano F, Acquaviva MI, Caroppo C, Diella G, Di Leo A, Fasano F, Giandomenico S, Spada L, Cavallo RA, Montagna MT. Microbiological and chemical characteristics of beaches along the Taranto Gulf (Ionian Sea, Southern Italy). ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:448. [PMID: 35604473 PMCID: PMC9165249 DOI: 10.1007/s10661-022-10103-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/15/2022] [Indexed: 06/14/2023]
Abstract
Coastal habitats provide important ecosystem services, such as the maintenance of ecological sustainability, water quality regulation, nutrient recycling, and sandy beaches which are important areas for recreation and tourism. The quality of seawater is generally measured by determining the concentrations of Escherichia coli and intestinal Enterococci, which might be affected by the persistent populations of these bacteria in sand. Sand might thus be a significant source of pathogen exposure to beachgoers. The quality of coastal recreational waters can also be affected by eutrophication, water discoloration, and harmful algal blooms, which pose additional human health risks. Here, we conducted a monitoring of the beaches quality along the Taranto Gulf by determining the concentrations of fecal indicator organisms, as well as other parameters that are not traditionally measured (physicochemical parameters, Pseudomonas aeruginosa, and harmful microalgae), in shallow seawater and sand sampled from three beaches. The concentrations of bacteria were determined using both standard microbiological methods and the IDEXX system. Our results demonstrate the utility of measuring a greater number of parameters in addition to those conventionally measured, as well as the importance of assessing the health risks posed by the sand matrix. Additional work is needed to develop rapid analytical techniques that could be used to monitor the microbiological parameters of solid matrices.
Collapse
Affiliation(s)
- Osvalda De Giglio
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Marcella Narracci
- National Research Council (CNR), Water Research Institute (IRSA), S.S. of Taranto, via Roma 3, 74123 Taranto, Italy
| | - Francesca Apollonio
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Francesco Triggiano
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Maria Immacolata Acquaviva
- National Research Council (CNR), Water Research Institute (IRSA), S.S. of Taranto, via Roma 3, 74123 Taranto, Italy
| | - Carmela Caroppo
- National Research Council (CNR), Water Research Institute (IRSA), S.S. of Taranto, via Roma 3, 74123 Taranto, Italy
| | - Giusy Diella
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Antonella Di Leo
- National Research Council (CNR), Water Research Institute (IRSA), S.S. of Taranto, via Roma 3, 74123 Taranto, Italy
| | - Fabrizio Fasano
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Santina Giandomenico
- National Research Council (CNR), Water Research Institute (IRSA), S.S. of Taranto, via Roma 3, 74123 Taranto, Italy
| | - Lucia Spada
- National Research Council (CNR), Water Research Institute (IRSA), S.S. of Taranto, via Roma 3, 74123 Taranto, Italy
| | - Rosa Anna Cavallo
- National Research Council (CNR), Water Research Institute (IRSA), S.S. of Taranto, via Roma 3, 74123 Taranto, Italy
| | - Maria Teresa Montagna
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy
| |
Collapse
|
15
|
Nitrate respiration occurs throughout the depth of mucoid and non-mucoid Pseudomonas aeruginosa submerged agar colony biofilms including the oxic zone. Sci Rep 2022; 12:8557. [PMID: 35595796 PMCID: PMC9123002 DOI: 10.1038/s41598-022-11957-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/19/2022] [Indexed: 11/15/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen and well characterized biofilm former. P. aeruginosa forms strong oxygen gradients inside biofilms due to rapid oxygen respiration in the top layers and the poor solubility of oxygen coupled with diffusion limited transport. Transcriptomic evidence from in vitro and ex vivo sampling suggests that denitrification is occurring in biofilms in ostensibly oxic environments. It is hypothesized that in the presence of nitrate there is stratification with aerobic respiration occurring in the outer oxic layer and denitrification in the lower anoxic zone. We used submerged agar colony biofilms grown from mucoid (FRD1) and non-mucoid (PAO1) strains to simultaneously measure depth microprofiles of oxygen and nitrous oxide in the same colony with microelectrodes. Oxygen respiration occurred at the top of the colony as expected but denitrification occurred throughout the entire depth, even in the oxic region. Local denitrification rates were highly variable suggesting heterogenous metabolic activity within the colony. We also assessed the short-term influence of tobramycin on aerobic respiration within a PAO1 colony. Although there was an immediate reduction in respiration it was never completely arrested over a 2 h period. On tobramycin removal the oxygen gradient steadily reestablished, demonstrating immediate recovery of metabolic activity.
Collapse
|
16
|
Visualization of mRNA Expression in Pseudomonas aeruginosa Aggregates Reveals Spatial Patterns of Fermentative and Denitrifying Metabolism. Appl Environ Microbiol 2022; 88:e0043922. [PMID: 35586988 DOI: 10.1128/aem.00439-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gaining insight into the behavior of bacteria at the single-cell level is important given that heterogeneous microenvironments strongly influence microbial physiology. The hybridization chain reaction (HCR) is a technique that provides in situ molecular signal amplification, enabling simultaneous mapping of multiple target RNAs at small spatial scales. To refine this method for biofilm applications, we designed and validated new probes to visualize the expression of key catabolic genes in Pseudomonas aeruginosa aggregates. In addition to using existing probes for the dissimilatory nitrate reductase (narG), we developed probes for a terminal oxidase (ccoN1), nitrite reductase (nirS), nitrous oxide reductase (nosZ), and acetate kinase (ackA). These probes can be used to determine gene expression levels across heterogeneous populations such as biofilms. Using these probes, we quantified gene expression across oxygen gradients in aggregate populations grown using the agar block biofilm assay (ABBA). We observed distinct patterns of catabolic gene expression, with upregulation occurring in particular ABBA regions both within individual aggregates and over the aggregate population. Aerobic respiration (ccoN1) showed peak expression under oxic conditions, whereas fermentation (ackA) showed peak expression in the anoxic cores of high metabolic activity aggregates near the air-agar interface. Denitrification genes narG, nirS, and nosZ showed peak expression in hypoxic and anoxic regions, although nirS expression remained at peak levels deeper into anoxic environments than other denitrification genes. These results reveal that the microenvironment correlates with catabolic gene expression in aggregates, and they demonstrate the utility of HCR in unveiling cellular activities at the microscale level in heterogeneous populations. IMPORTANCE To understand bacteria in diverse contexts, we must understand the variations in behaviors and metabolisms they express spatiotemporally. Populations of bacteria are known to be heterogeneous, but the ways this variation manifests can be challenging to characterize due to technical limitations. By focusing on energy conservation, we demonstrate that HCR v3.0 can visualize nuances in gene expression, allowing us to understand how metabolism in Pseudomonas aeruginosa biofilms responds to microenvironmental variation at high spatial resolution. We validated probes for four catabolic genes, including a constitutively expressed oxidase, acetate kinase, nitrite reductase, and nitrous oxide reductase. We showed that the genes for different modes of metabolism are expressed in overlapping but distinct subpopulations according to oxygen concentrations in a predictable fashion. The spatial transcriptomic technique described here has the potential to be used to map microbial activities across diverse environments.
Collapse
|
17
|
Baty JJ, Huffines JT, Stoner SN, Scoffield JA. A Commensal Streptococcus Dysregulates the Pseudomonas aeruginosa Nitrosative Stress Response. Front Cell Infect Microbiol 2022; 12:817336. [PMID: 35619650 PMCID: PMC9127344 DOI: 10.3389/fcimb.2022.817336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic infections in the cystic fibrosis (CF) airway are composed of both pathogenic and commensal bacteria. However, chronic Pseudomonas aeruginosa infections are the leading cause of lung deterioration in individuals with CF. Interestingly, oral commensals can translocate to the CF lung and their presence is associated with improved lung function, presumably due to their ability to antagonize P. aeruginosa. We have previously shown that one commensal, Streptococcus parasanguinis, produces hydrogen peroxide that reacts with nitrite to generate reactive nitrogen intermediates (RNI) which inhibit P. aeruginosa growth. In this study, we sought to understand the global impact of commensal-mediated RNI on the P. aeruginosa transcriptome. RNA sequencing analysis revealed that S. parasanguinis and nitrite-mediated RNI dysregulated expression of denitrification genes in a CF isolate of P. aeruginosa compared to when this isolate was only exposed to S. parasanguinis. Further, loss of a nitric oxide reductase subunit (norB) rendered an acute P. aeruginosa isolate more susceptible to S. parasanguinis-mediated RNI. Additionally, S. parasanguinis-mediated RNI inactivated P. aeruginosa aconitase activity. Lastly, we report that P. aeruginosa isolates recovered from CF individuals are uniquely hypersensitive to S. parasanguinis-mediated RNI compared to acute infection or environmental P. aeruginosa isolates. These findings illustrate that S. parasanguinis hinders the ability of P. aeruginosa to respond to RNI, which potentially prevents P. aeruginosa CF isolates from resisting commensal and host-induced RNI in the CF airway.
Collapse
|
18
|
Nitrate Water Contamination from Industrial Activities and Complete Denitrification as a Remediation Option. WATER 2022. [DOI: 10.3390/w14050799] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Freshwater is a scarce resource that continues to be at high risk of pollution from anthropogenic activities, requiring remediation in such cases for its continuous use. The agricultural and mining industries extensively use water and nitrogen (N)-dependent products, mainly in fertilizers and explosives, respectively, with their excess accumulating in different water bodies. Although removal of NO3 from water and soil through the application of chemical, physical, and biological methods has been studied globally, these methods seldom yield N2 gas as a desired byproduct for nitrogen cycling. These methods predominantly cause secondary contamination with deposits of chemical waste such as slurry brine, nitrite (NO2), ammonia (NH3), and nitrous oxide (N2O), which are also harmful and fastidious to remove. This review focuses on complete denitrification facilitated by bacteria as a remedial option aimed at producing nitrogen gas as a terminal byproduct. Synergistic interaction of different nitrogen metabolisms from different bacteria is highlighted, with detailed attention to the optimization of their enzymatic activities. A biotechnological approach to mitigating industrial NO3 contamination using indigenous bacteria from wastewater is proposed, holding the prospect of optimizing to the point of complete denitrification. The approach was reviewed and found to be durable, sustainable, cost effective, and environmentally friendly, as opposed to current chemical and physical water remediation technologies.
Collapse
|
19
|
Margalit A, Sheehan D, Carolan JC, Kavanagh K. Exposure to the Pseudomonas aeruginosa secretome alters the proteome and secondary metabolite production of Aspergillus fumigatus. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001164. [PMID: 35333152 PMCID: PMC9558348 DOI: 10.1099/mic.0.001164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/16/2022] [Indexed: 01/09/2023]
Abstract
The fungal pathogen Aspergillus fumigatus is frequently cultured from the sputum of cystic fibrosis (CF) patients along with the bacterium Pseudomonas aeruginosa. A. fumigatus secretes a range of secondary metabolites, and one of these, gliotoxin, has inhibitory effects on the host immune response. The effect of P. aeruginosa culture filtrate (CuF) on fungal growth and gliotoxin production was investigated. Exposure of A. fumigatus hyphae to P. aeruginosa cells induced increased production of gliotoxin and a decrease in fungal growth. In contrast, exposure of A. fumigatus hyphae to P. aeruginosa CuF led to increased growth and decreased gliotoxin production. Quantitative proteomic analysis was used to characterize the proteomic response of A. fumigatus upon exposure to P. aeruginosa CuF. Changes in the profile of proteins involved in secondary metabolite biosynthesis (e.g. gliotoxin, fumagillin, pseurotin A), and changes to the abundance of proteins involved in oxidative stress (e.g. formate dehydrogenase) and detoxification (e.g. thioredoxin reductase) were observed, indicating that the bacterial secretome had a profound effect on the fungal proteome. Alterations in the abundance of proteins involved in detoxification and oxidative stress highlight the ability of A. fumigatus to differentially regulate protein synthesis in response to environmental stresses imposed by competitors such as P. aeruginosa. Such responses may ultimately have serious detrimental effects on the host.
Collapse
Affiliation(s)
- Anatte Margalit
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - David Sheehan
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - James C. Carolan
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Kevin Kavanagh
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| |
Collapse
|
20
|
Webb K, Zain NMM, Stewart I, Fogarty A, Nash EF, Whitehouse JL, Smyth AR, Lilley AK, Knox A, Williams P, Cámara M, Bruce K, Barr HL. Porphyromonas pasteri and Prevotella nanceiensis in the sputum microbiota are associated with increased decline in lung function in individuals with cystic fibrosis. J Med Microbiol 2022; 71. [PMID: 35113780 PMCID: PMC8941952 DOI: 10.1099/jmm.0.001481] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Although anaerobic bacteria exist in abundance in cystic fibrosis (CF) airways, their role in disease progression is poorly understood. We hypothesized that the presence and relative abundance of the most prevalent, live, anaerobic bacteria in sputum of adults with CF were associated with adverse clinical outcomes. This is the first study to prospectively investigate viable anaerobic bacteria present in the sputum microbiota and their relationship with long-term outcomes in adults with CF. We performed 16S rRNA analysis using a viability quantitative PCR technique on sputum samples obtained from a prospective cohort of 70 adults with CF and collected clinical data over an 8 year follow-up period. We examined the associations of the ten most abundant obligate anaerobic bacteria present in the sputum with annual rate of FEV1 change. The presence of Porphyromonas pasteri and Prevotella nanceiensis were associated with a greater annual rate of FEV1 change; −52.3 ml yr−1 (95 % CI-87.7;−16.9), –67.9 ml yr−1 (95 % CI-115.6;−20.1), respectively. Similarly, the relative abundance of these live organisms were associated with a greater annual rate of FEV1 decline of −3.7 ml yr−1 (95 % CI: −6.1 to −1.3, P=0.003) and −5.3 ml yr−1 (95 % CI: −8.7 to −1.9, P=0.002) for each log2 increment of abundance, respectively. The presence and relative abundance of certain anaerobes in the sputum of adults with CF are associated with a greater rate of long-term lung function decline. The pathogenicity of anaerobic bacteria in the CF airways should be confirmed with further longitudinal prospective studies with a larger cohort of participants.
Collapse
Affiliation(s)
- Karmel Webb
- Division of Epidemiology and Public Health, University of Nottingham, City Hospital Campus, Nottingham, UK.,Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, UK
| | - Nur Masirah M Zain
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, UK.,Institute of Pharmaceutical Science, King's College London, UK
| | - Iain Stewart
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, UK.,Division of Respiratory Medicine, University of Nottingham, City Hospital Campus, Nottingham, UK
| | - Andrew Fogarty
- Division of Epidemiology and Public Health, University of Nottingham, City Hospital Campus, Nottingham, UK.,Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, UK
| | - Edward F Nash
- West Midlands Adult CF Centre, Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Joanna L Whitehouse
- West Midlands Adult CF Centre, Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Alan R Smyth
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, UK.,School of Medicine, University of Nottingham, Nottingham, UK
| | - Andrew K Lilley
- Institute of Pharmaceutical Science, King's College London, UK
| | - Alan Knox
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, UK.,Division of Respiratory Medicine, University of Nottingham, City Hospital Campus, Nottingham, UK
| | - Paul Williams
- National Biofilms Innovation Centre, Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Miguel Cámara
- National Biofilms Innovation Centre, Biodiscovery Institute, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Kenneth Bruce
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, UK.,Institute of Pharmaceutical Science, King's College London, UK
| | - Helen L Barr
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, UK.,Wolfson Cystic Fibrosis Centre, Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK
| |
Collapse
|
21
|
Lichtenberg M, Line L, Schrameyer V, Jakobsen TH, Rybtke ML, Toyofuku M, Nomura N, Kolpen M, Tolker-Nielsen T, Kühl M, Bjarnsholt T, Jensen PØ. Nitric-oxide-driven oxygen release in anoxic Pseudomonas aeruginosa. iScience 2021; 24:103404. [PMID: 34849468 PMCID: PMC8608891 DOI: 10.1016/j.isci.2021.103404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/29/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022] Open
Abstract
Denitrification supports anoxic growth of Pseudomonas aeruginosa in infections. Moreover, denitrification may provide oxygen (O2) resulting from dismutation of the denitrification intermediate nitric oxide (NO) as seen in Methylomirabilis oxyfera. To examine the prevalence of NO dismutation we studied O2 release by P. aeruginosa in airtight vials. P. aeruginosa rapidly depleted O2 but NO supplementation generated peaks of O2 at the onset of anoxia, and we demonstrate a direct role of NO in the O2 release. However, we were not able to detect genetic evidence for putative NO dismutases. The supply of endogenous O2 at the onset of anoxia could play an adaptive role when P. aeruginosa enters anaerobiosis. Furthermore, O2 generation by NO dismutation may be more widespread than indicated by the reports on the distribution of homologues genes. In general, NO dismutation may allow removal of nitrate by denitrification without release of the very potent greenhouse gas, nitrous oxide. Pseudomonas aeruginosa was found to release O2 at the onset of anoxia Peaks of O2 were amplified in a nitric oxide reductase (NOR) mutant The O2 release was mediated by nitric oxide (NO)
Collapse
Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Laura Line
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Verena Schrameyer
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Morten Levin Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Masanori Toyofuku
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8577 Tsukuba, Japan
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8577 Tsukuba, Japan
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Peter Østrup Jensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
- Center for Rheumatology and Spine Diseases, Institute for Inflammation Research, Rigshospitalet, 2100 Copenhagen, Denmark
- Corresponding author
| |
Collapse
|
22
|
Asimakopoulou E, Εkonomou SΙ, Papakonstantinou P, Doran O, Stratakos AC. Inhibition of corrosion causing Pseudomonas aeruginosa using plasma-activated water. J Appl Microbiol 2021; 132:2781-2794. [PMID: 34846774 DOI: 10.1111/jam.15391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/28/2022]
Abstract
AIMS The cost of Microbiologically Influenced Corrosion (MIC) significantly affects a wide range of sectors. This study aims to assess the efficiency of a novel technology based on the use of plasma-activated water (PAW) in inhibiting corrosion caused by bacteria. METHODS AND RESULTS This study evaluated the effectiveness of PAW, produced by a plasma bubble reactor, in reducing corrosion causing Pseudomonas aeruginosa planktonic cells in tap water and biofilms were grown onto stainless steel (SS) coupons. Planktonic cells and biofilms were treated with PAW at different discharge frequencies (500-1500 Hz) and exposure times (0-20 min). P. aeruginosa cells in tap water were significantly reduced after treatment, with higher exposure times and discharge frequencies achieving higher reductions. Also, PAW treatment led to a gradual reduction for young and mature biofilms, achieving >4-Log reductions after 20 min. Results were also used to develop two predictive inactivation models. CONCLUSIONS This work presents evidence that PAW can be used to inactivate both planktonic cells and biofilms of P. aeruginosa. Experimental and theoretical results also demonstrate that reduction is dependent on discharge frequency and exposure time. SIGNIFICANCE AND IMPACT OF THE STUDY This work demonstrates the potential of using PAW as means to control MIC.
Collapse
Affiliation(s)
| | - Sotiriοs Ι Εkonomou
- Faculty of Health and Applied Sciences (HAS), Centre for Research in Biosciences, University of the West of England, Bristol, UK
| | | | - Olena Doran
- Faculty of Health and Applied Sciences (HAS), University of the West of England, Coldharbour Ln, Bristol, UK
| | - Alexandros Ch Stratakos
- Centre for Research in Biosciences, Faculty of Health and Applied Sciences (HAS), University of the West of England, Bristol, UK
| |
Collapse
|
23
|
Nolan C, Behrends V. Sub-Inhibitory Antibiotic Exposure and Virulence in Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10111393. [PMID: 34827331 PMCID: PMC8615142 DOI: 10.3390/antibiotics10111393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa is a prime opportunistic pathogen, one of the most important causes of hospital-acquired infections and the major cause of morbidity and mortality in cystic fibrosis lung infections. One reason for the bacterium's pathogenic success is the large array of virulence factors that it can employ. Another is its high degree of intrinsic and acquired resistance to antibiotics. In this review, we first summarise the current knowledge about the regulation of virulence factor expression and production. We then look at the impact of sub-MIC antibiotic exposure and find that the virulence-antibiotic interaction for P. aeruginosa is antibiotic-specific, multifaceted, and complex. Most studies undertaken to date have been in vitro assays in batch culture systems, involving short-term (<24 h) antibiotic exposure. Therefore, we discuss the importance of long-term, in vivo-mimicking models for future work, particularly highlighting the need to account for bacterial physiology, which by extension governs both virulence factor expression and antibiotic tolerance/resistance.
Collapse
|
24
|
Van den Bossche S, De Broe E, Coenye T, Van Braeckel E, Crabbé A. The cystic fibrosis lung microenvironment alters antibiotic activity: causes and effects. Eur Respir Rev 2021; 30:30/161/210055. [PMID: 34526313 DOI: 10.1183/16000617.0055-2021] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Chronic airway colonisation by Pseudomonas aeruginosa, a hallmark of cystic fibrosis (CF) lung disease, is associated with increased morbidity and mortality and despite aggressive antibiotic treatment, P. aeruginosa is able to persist in CF airways. In vitro antibiotic susceptibility assays are poor predictors of antibiotic efficacy to treat respiratory tract infections in the CF patient population and the selection of the antibiotic(s) is often made on an empirical base. In the current review, we discuss the factors that are responsible for the discrepancies between antibiotic activity in vitro and clinical efficacy in vivo We describe how the CF lung microenvironment, shaped by host factors (such as iron, mucus, immune mediators and oxygen availability) and the microbiota, influences antibiotic activity and varies widely between patients. A better understanding of the CF microenvironment and population diversity may thus help improve in vitro antibiotic susceptibility testing and clinical decision making, in turn increasing the success rate of antibiotic treatment.
Collapse
Affiliation(s)
| | - Emma De Broe
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Eva Van Braeckel
- Dept of Respiratory Medicine, Cystic Fibrosis Reference Centre, Ghent University Hospital, Ghent, Belgium.,Dept of Internal Medicine and Paediatrics, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
25
|
Alford MA, Baquir B, An A, Choi KYG, Hancock REW. NtrBC Selectively Regulates Host-Pathogen Interactions, Virulence, and Ciprofloxacin Susceptibility of Pseudomonas aeruginosa. Front Cell Infect Microbiol 2021; 11:694789. [PMID: 34249781 PMCID: PMC8264665 DOI: 10.3389/fcimb.2021.694789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/03/2021] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is a metabolically versatile opportunistic pathogen capable of infecting distinct niches of the human body, including skin wounds and the lungs of cystic fibrosis patients. Eradication of P. aeruginosa infection is becoming increasingly difficult due to the numerous resistance mechanisms it employs. Adaptive resistance is characterized by a transient state of decreased susceptibility to antibiotic therapy that is distinct from acquired or intrinsic resistance, can be triggered by various environmental stimuli and reverted by removal of the stimulus. Further, adaptive resistance is intrinsically linked to lifestyles such as swarming motility and biofilm formation, both of which are important in infections and lead to multi-drug adaptive resistance. Here, we demonstrated that NtrBC, the master of nitrogen control, had a selective role in host colonization and a substantial role in determining intrinsic resistance to ciprofloxacin. P. aeruginosa mutant strains (ΔntrB, ΔntrC and ΔntrBC) colonized the skin but not the respiratory tract of mice as well as WT and, unlike WT, could be reduced or eradicated from the skin by ciprofloxacin. We hypothesized that nutrient availability contributed to these phenomena and found that susceptibility to ciprofloxacin was impacted by nitrogen source in laboratory media. P. aeruginosa ΔntrB, ΔntrC and ΔntrBC also exhibited distinct host interactions, including modestly increased cytotoxicity toward human bronchial epithelial cells, reduced virulence factor production and 10-fold increased uptake by macrophages. These data might explain why NtrBC mutants were less adept at colonizing the upper respiratory tract of mice. Thus, NtrBC represents a link between nitrogen metabolism, adaptation and virulence of the pathogen P. aeruginosa, and could represent a target for eradication of recalcitrant infections in situ.
Collapse
Affiliation(s)
- Morgan A Alford
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Beverlie Baquir
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Andy An
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Ka-Yee G Choi
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
26
|
Yu Y, Singh H, Tsitrin T, Bekele S, Lin YH, Sikorski P, Moncera KJ, Torralba MG, Morrow L, Wolcott R, Nelson KE, Pieper R. Urethral Catheter Biofilms Reveal Plasticity in Bacterial Composition and Metabolism and Withstand Host Immune Defenses in Hypoxic Environment. Front Med (Lausanne) 2021; 8:667462. [PMID: 34249966 PMCID: PMC8260951 DOI: 10.3389/fmed.2021.667462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/06/2021] [Indexed: 11/18/2022] Open
Abstract
Biofilms composed of multiple microorganisms colonize the surfaces of indwelling urethral catheters that are used serially by neurogenic bladder patients and cause chronic infections. Well-adapted pathogens in this niche are Escherichia coli, Proteus, and Enterococcus spp., species that cycle through adhesion and multilayered cell growth, trigger host immune responses, are starved off nutrients, and then disperse. Viable microbial foci retained in the urinary tract recolonize catheter surfaces. The molecular adaptations of bacteria in catheter biofilms (CBs) are not well-understood, promising new insights into this pathology based on host and microbial meta-omics analyses from clinical specimens. We examined catheters from nine neurogenic bladder patients longitudinally over up to 6 months. Taxonomic analyses from 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics revealed that 95% of all catheter and corresponding urinary pellet (UP) samples contained bacteria. CB biomasses were dominated by Enterobacteriaceae spp. and often accompanied by lactic acid and anaerobic bacteria. Systemic antibiotic drug treatments of patients resulted in either transient or lasting microbial community perturbations. Neutrophil effector proteins were abundant not only in UP but also CB samples, indicating their penetration of biofilm surfaces. In the context of one patient who advanced to a kidney infection, Proteus mirabilis proteomic data suggested a combination of factors associated with this disease complication: CB biomasses were high; the bacteria produced urease alkalinizing the pH and triggering urinary salt deposition on luminal catheter surfaces; P. mirabilis utilized energy-producing respiratory systems more than in CBs from other patients. The NADH:quinone oxidoreductase II (Nqr), a Na+ translocating enzyme not operating as a proton pump, and the nitrate reductase A (Nar) equipped the pathogen with electron transport chains promoting growth under hypoxic conditions. Both P. mirabilis and E. coli featured repertoires of transition metal ion acquisition systems in response to human host-mediated iron and zinc sequestration. We discovered a new drug target, the Nqr respiratory system, whose deactivation may compromise P. mirabilis growth in a basic pH milieu. Animal models would not allow such molecular-level insights into polymicrobial biofilm metabolism and interactions because the complexity cannot be replicated.
Collapse
Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, Rockville, MD, United States
| | | | | | | | - Yi-Han Lin
- J. Craig Venter Institute, Rockville, MD, United States
| | | | | | | | - Lisa Morrow
- Southwest Regional Wound Care Center, Lubbock, TX, United States
| | - Randall Wolcott
- Southwest Regional Wound Care Center, Lubbock, TX, United States
| | - Karen E. Nelson
- J. Craig Venter Institute, Rockville, MD, United States
- J. Craig Venter Institute, La Jolla, CA, United States
| | | |
Collapse
|
27
|
Hedetoft M, Jensen PØ, Moser C, Vinkel J, Hyldegaard O. Hyperbaric oxygen treatment impacts oxidative stress markers in patients with necrotizing soft-tissue infection. J Investig Med 2021; 69:1330-1338. [PMID: 34006573 PMCID: PMC8485130 DOI: 10.1136/jim-2021-001837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 02/02/2023]
Abstract
Necrotizing soft-tissue infection (NSTI) is a rare, severe, and fast-progressing bacterial infection associated with a high risk of developing sepsis or septic shock. Increasing evidence indicates that oxidative stress is crucial in the development and progression of sepsis, but its role in NSTI specifically has not been investigated. Some patients with NSTI receive hyperbaric oxygen (HBO2) treatment as the restoration of oxidative stress balance is considered an important mechanism of action, which HBO2 facilitates. However, a gap in knowledge exists regarding the effect of HBO2 treatment on oxidative stress in patients with NSTI. In the present observational study, we aimed to investigate HBO2 treatment effects on known markers of oxidative stress in patients with NSTI. We measured plasma myeloperoxidase (MPO), superoxide dismutase (SOD), heme oxygenase-1 (HO-1) and nitrite+nitrate in 80 patients with NSTI immediately before and after their first HBO2 treatment, and on the following day. We found that HBO2 treatment was associated with a significant increase in MPO and SOD by a median of 3.4 and 8.8 ng/mL, respectively. Moreover, we observed an HBO2 treatment-associated increase in HO-1 in patients presenting with septic shock (n=39) by a median of 301.3 pg/mL. All markers were significantly higher in patients presenting with septic shock compared to patients without shock, and all markers correlated with disease severity. High baseline SOD was associated with 90-day mortality. In conclusion, HBO2 treatment was associated with an increase in MPO and SOD in patients with NSTI, and oxidative stress was more pronounced in patients with septic shock.
Collapse
Affiliation(s)
- Morten Hedetoft
- Department of Anaesthesia, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Peter Østrup Jensen
- Department of Clinical Microbiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Costerton Biofilm Center, Institute of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Moser
- Department of Clinical Microbiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Julie Vinkel
- Department of Anaesthesia, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Ole Hyldegaard
- Department of Anaesthesia, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
28
|
Denitrifying bacteria respond to and shape microscale gradients within particulate matrices. Commun Biol 2021; 4:570. [PMID: 33986448 PMCID: PMC8119678 DOI: 10.1038/s42003-021-02102-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/13/2021] [Indexed: 11/10/2022] Open
Abstract
Heterotrophic denitrification enables facultative anaerobes to continue growing even when limited by oxygen (O2) availability. Particles in particular provide physical matrices characterized by reduced O2 permeability even in well-oxygenated bulk conditions, creating microenvironments where microbial denitrifiers may proliferate. Whereas numerical particle models generally describe denitrification as a function of radius, here we provide evidence for heterogeneity of intraparticle denitrification activity due to local interactions within and among microcolonies. Pseudomonas aeruginosa cells and microcolonies act to metabolically shade each other, fostering anaerobic processes just microns from O2-saturated bulk water. Even within well-oxygenated fluid, suboxia and denitrification reproducibly developed and migrated along sharp 10 to 100 µm gradients, driven by the balance of oxidant diffusion and local respiration. Moreover, metabolic differentiation among densely packed cells is dictated by the diffusional supply of O2, leading to distinct bimodality in the distribution of nitrate and nitrite reductase expression. The initial seeding density controls the speed at which anoxia develops, and even particles seeded with few bacteria remain capable of becoming anoxic. Our empirical results capture the dynamics of denitrifier gene expression in direct association with O2 concentrations over microscale physical matrices, providing observations of the co-occurrence and spatial arrangement of aerobic and anaerobic processes. Smriga et al. investigate heterotrophic denitrification in particulate matrices. Their model shows that Pseudomonas aeruginosa cells and microcolonies metabolically shade each other, allowing denitrification to occur microns away from O2-saturated bulk water, and simulates microscale effects of a bulk system.
Collapse
|
29
|
Kolbeck S, Abele M, Hilgarth M, Vogel RF. Comparative Proteomics Reveals the Anaerobic Lifestyle of Meat-Spoiling Pseudomonas Species. Front Microbiol 2021; 12:664061. [PMID: 33889149 PMCID: PMC8055858 DOI: 10.3389/fmicb.2021.664061] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
The ability of certain Pseudomonas (P.) species to grow or persist in anoxic habitats by either denitrification, acetate fermentation, or arginine fermentation has been described in several studies as a special property. Previously, we had isolated strains belonging to the species P. lundensis, P. weihenstephanensis, and P. fragi from anoxic modified atmosphere packaged (MAP) minced beef and further proved their anaerobic growth in vitro on agar plates. This follow-up study investigated the anaerobic growth of two strains per respective species in situ on inoculated chicken breast filet under 100% N2 modified atmosphere. We were able to prove anaerobic growth of all six strains on chicken breast filet with cell division rates of 0.2–0.8/day. Furthermore, we characterized the anaerobic metabolic lifestyle of these Pseudomonas strains by comparative proteomics, upon their cultivation in meat simulation media, which were constantly gassed with either air or 100% N2 atmospheres. From these proteomic predictions, and respective complementation by physiological experiments, we conclude that the Pseudomonas strains P. fragi, P. weihenstephanensis, P. lundensis exhibit a similar anaerobic lifestyle and employ arginine fermentation via the arginine deiminase (ADI) pathway to grow anaerobically also on MAP meats. Furthermore, glucose fermentation to ethanol via the ED-pathway is predicted to enable long term survival but no true growth, while respiratory growth with nitrate as alternative electron acceptor or glucose fermentation to acetate could be excluded due to absence of essential genes. The citric acid cycle is partially bypassed by the glyoxylate shunt, functioning as the gluconeogenetic route without production of NADH2 under carbon limiting conditions as e.g., in packaged meats. Triggered by an altered redox balance, we also detected upregulation of enzymes involved in protein folding as well as disulfide bonds isomerization under anoxic conditions as a counteracting mechanism to reduce protein misfolding. Hence, this study reveals the mechanisms enabling anaerobic grow and persistence of common meat-spoiling Pseudomonas species, and further complements the hitherto limited knowledge of the anaerobic lifestyle of Pseudomonas species in general.
Collapse
Affiliation(s)
- Sandra Kolbeck
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Miriam Abele
- Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS), Freising, Germany
| | - Maik Hilgarth
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| |
Collapse
|
30
|
Moser C, Jensen PØ, Thomsen K, Kolpen M, Rybtke M, Lauland AS, Trøstrup H, Tolker-Nielsen T. Immune Responses to Pseudomonas aeruginosa Biofilm Infections. Front Immunol 2021; 12:625597. [PMID: 33692800 PMCID: PMC7937708 DOI: 10.3389/fimmu.2021.625597] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/20/2021] [Indexed: 12/17/2022] Open
Abstract
Pseudomonas aeruginosa is a key pathogen of chronic infections in the lungs of cystic fibrosis patients and in patients suffering from chronic wounds of diverse etiology. In these infections the bacteria congregate in biofilms and cannot be eradicated by standard antibiotic treatment or host immune responses. The persistent biofilms induce a hyper inflammatory state that results in collateral damage of the adjacent host tissue. The host fails to eradicate the biofilm infection, resulting in hindered remodeling and healing. In the present review we describe our current understanding of innate and adaptive immune responses elicited by P. aeruginosa biofilms in cystic fibrosis lung infections and chronic wounds. This includes the mechanisms that are involved in the activation of the immune responses, as well as the effector functions, the antimicrobial components and the associated tissue destruction. The mechanisms by which the biofilms evade immune responses, and potential treatment targets of the immune response are also discussed.
Collapse
Affiliation(s)
- Claus Moser
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peter Østrup Jensen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kim Thomsen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Sofie Lauland
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hannah Trøstrup
- Department of Plastic Surgery and Breast Surgery, Zealand University Hospital, Roskilde, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
31
|
Kim BO, Jang HJ, Chung IY, Bae HW, Kim ES, Cho YH. Nitrate Respiration Promotes Polymyxin B Resistance in Pseudomonas aeruginosa. Antioxid Redox Signal 2021; 34:442-451. [PMID: 32370551 DOI: 10.1089/ars.2019.7924] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aims: Polymyxin B (PMB) is known to require reactive oxygen species (ROS) for its bactericidal activity, but the mechanism of PMB resistance in various Pseudomonas aeruginosa strains has been poorly understood. This study examined the role of nitrate respiration (NR) of some P. aeruginosa strains in the PMB resistance. Results: We observed that the minimum inhibitory concentration (MIC) value of PMB against P. aeruginosa PA14 was eightfold reduced (from 2.0 to 0.25 μg/mL) by agitation, but not against P. aeruginosa PAO1 (from 2.0 to 1.0 μg/mL). Transcriptomic and phenotypic analyses using both strains and their NR mutants revealed that the higher NR in PAO1 than in PA14 accounted for the higher MIC value (i.e., PMB resistance) of PAO1, which was sufficient to compromise the antibacterial activity of PMB in Drosophila infections. We also confirmed the contribution of the NR to the PMB resistance is independent of the major catalase (KatA), suggesting that the NR might affect the ROS generation rather than the ROS disintegration. Furthermore, this PMB resistance was relatively common among clinical P. aeruginosa isolates and correlated with higher NR in those strains. Innovation and Conclusion: These results suggest P. aeruginosa strains could display intrinsic resistance to antibiotics in clinical settings and that NR is a crucial factor in the intrinsic antibiotic resistance, and also provide an insight into another key target for successful antibiotic treatment of P. aeruginosa infections. Antioxid. Redox Signal. 34, 442-451.
Collapse
Affiliation(s)
- Bi-O Kim
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do, Korea
| | - Hye-Jeong Jang
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do, Korea
| | - In-Young Chung
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do, Korea
| | - Hee-Won Bae
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do, Korea
| | - Eun Sook Kim
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do, Korea
| | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do, Korea
| |
Collapse
|
32
|
Mapping of the Denitrification Pathway in Burkholderia thailandensis by Genome-Wide Mutant Profiling. J Bacteriol 2020; 202:JB.00304-20. [PMID: 32900830 DOI: 10.1128/jb.00304-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Burkholderia thailandensis is a soil saprophyte that is closely related to the pathogen Burkholderia pseudomallei, the etiological agent of melioidosis in humans. The environmental niches and infection sites occupied by these bacteria are thought to contain only limited concentrations of oxygen, where they can generate energy via denitrification. However, knowledge of the underlying molecular basis of the denitrification pathway in these bacteria is scarce. In this study, we employed a transposon sequencing (Tn-Seq) approach to identify genes conferring a fitness benefit for anaerobic growth of B. thailandensis Of the 180 determinants identified, several genes were shown to be required for growth under denitrifying conditions: the nitrate reductase operon narIJHGK2K1, the aniA gene encoding a previously unknown nitrite reductase, and the petABC genes encoding a cytochrome bc 1, as well as three novel regulators that control denitrification. Our Tn-Seq data allowed us to reconstruct the entire denitrification pathway of B. thailandensis and shed light on its regulation. Analyses of growth behaviors combined with measurements of denitrification metabolites of various mutants revealed that nitrate reduction provides sufficient energy for anaerobic growth, an important finding in light of the fact that some pathogenic Burkholderia species can use nitrate as a terminal electron acceptor but are unable to complete denitrification. Finally, we demonstrated that a nitrous oxide reductase mutant is not affected for anaerobic growth but is defective in biofilm formation and accumulates N2O, which may play a role in the dispersal of B. thailandensis biofilms.IMPORTANCE Burkholderia thailandensis is a soil-dwelling saprophyte that is often used as surrogate of the closely related pathogen Burkholderia pseudomallei, the causative agent of melioidosis and a classified biowarfare agent. Both organisms are adapted to grow under oxygen-limited conditions in rice fields by generating energy through denitrification. Microoxic growth of B. pseudomallei is also considered essential for human infections. Here, we have used a Tn-Seq approach to identify the genes encoding the enzymes and regulators required for growth under denitrifying conditions. We show that a mutant that is defective in the conversion of N2O to N2, the last step in the denitrification process, is unaffected in microoxic growth but is severely impaired in biofilm formation, suggesting that N2O may play a role in biofilm dispersal. Our study identified novel targets for the development of therapeutic agents to treat meliodiosis.
Collapse
|
33
|
Walsh BJC, Giedroc DP. H 2S and reactive sulfur signaling at the host-bacterial pathogen interface. J Biol Chem 2020; 295:13150-13168. [PMID: 32699012 PMCID: PMC7504917 DOI: 10.1074/jbc.rev120.011304] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial pathogens that cause invasive disease in the vertebrate host must adapt to host efforts to cripple their viability. Major host insults are reactive oxygen and reactive nitrogen species as well as cellular stress induced by antibiotics. Hydrogen sulfide (H2S) is emerging as an important player in cytoprotection against these stressors, which may well be attributed to downstream more oxidized sulfur species termed reactive sulfur species (RSS). In this review, we summarize recent work that suggests that H2S/RSS impacts bacterial survival in infected cells and animals. We discuss the mechanisms of biogenesis and clearance of RSS in the context of a bacterial H2S/RSS homeostasis model and the bacterial transcriptional regulatory proteins that act as "sensors" of cellular RSS that maintain H2S/RSS homeostasis. In addition, we cover fluorescence imaging- and MS-based approaches used to detect and quantify RSS in bacterial cells. Last, we discuss proteome persulfidation (S-sulfuration) as a potential mediator of H2S/RSS signaling in bacteria in the context of the writer-reader-eraser paradigm, and progress toward ascribing regulatory significance to this widespread post-translational modification.
Collapse
Affiliation(s)
- Brenna J C Walsh
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA.
| |
Collapse
|
34
|
Cai YM, Webb JS. Optimization of nitric oxide donors for investigating biofilm dispersal response in Pseudomonas aeruginosa clinical isolates. Appl Microbiol Biotechnol 2020; 104:8859-8869. [PMID: 32865612 PMCID: PMC7502453 DOI: 10.1007/s00253-020-10859-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/13/2020] [Accepted: 08/23/2020] [Indexed: 02/07/2023]
Abstract
Pseudomonas aeruginosa biofilms contribute heavily to chronic lung infection in cystic fibrosis patients, leading to morbidity and mortality. Nitric oxide (NO) has been shown to disperse P. aeruginosa biofilms in vitro, ex vivo and in clinical trials as a promising anti-biofilm agent. Traditional NO donors such as sodium nitroprusside (SNP) have been extensively employed in different studies. However, the dosage of SNP in different studies was not consistent, ranging from 500 nM to 500 μM. SNP is light sensitive and produces cyanide, which may lead to data misinterpretation and inaccurate predictions of dispersal responses in clinical settings. New NO donors and NO delivery methods have therefore been explored. Here we assessed 7 NO donors using P. aeruginosa PAO1 and determined that SNP and Spermine NONOate (S150) successfully reduced > 60% biomass within 24 and 2 h, respectively. While neither dosage posed toxicity towards bacterial cells, chemiluminescence assays showed that SNP only released NO upon light exposure in M9 media and S150 delivered much higher performance spontaneously. S150 was then tested on 13 different cystic fibrosis P. aeruginosa (CF-PA) isolates; most CF-PA biofilms were significantly dispersed by 250 μM S150. Our work therefore discovered a commercially available NO donor S150, which disperses CF-PA biofilms efficiently within a short period of time and without releasing cyanide, as an alternative of SNP in clinical trials in the future. KEY POINTS: • S150 performs the best in dispersing P. aeruginosa biofilms among 7 NO donors. • SNP only releases NO in the presence of light, while S150 releases NO spontaneously. • S150 successfully disperses biofilms formed by P. aeruginosa cystic fibrosis clinical isolates.
Collapse
Affiliation(s)
- Yu-Ming Cai
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Jeremy S Webb
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| |
Collapse
|
35
|
Current Knowledge and Future Directions in Developing Strategies to Combat Pseudomonas aeruginosa Infection. J Mol Biol 2020; 432:5509-5528. [PMID: 32750389 DOI: 10.1016/j.jmb.2020.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022]
Abstract
In the face of growing antimicrobial resistance, there is an urgent need for the development of effective strategies to target Pseudomonas aeruginosa. This metabolically versatile bacterium can cause a wide range of severe opportunistic infections in patients with serious underlying medical conditions, such as those with burns, surgical wounds or people with cystic fibrosis. Many of the key adaptations that arise in this organism during infection are centered on core metabolism and virulence factor synthesis. Interfering with these processes may provide a new strategy to combat infection which could be combined with conventional antibiotics. This review will provide an overview of the most recent work that has advanced our understanding of P. aeruginosa infection. Strategies that exploit this recent knowledge to combat infection will be highlighted alongside potential alternative therapeutic options and their limitations.
Collapse
|
36
|
Margalit A, Carolan JC, Sheehan D, Kavanagh K. The Aspergillus fumigatus Secretome Alters the Proteome of Pseudomonas aeruginosa to Stimulate Bacterial Growth: Implications for Co-infection. Mol Cell Proteomics 2020; 19:1346-1359. [PMID: 32447284 PMCID: PMC8015003 DOI: 10.1074/mcp.ra120.002059] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/07/2020] [Indexed: 12/30/2022] Open
Abstract
Individuals with cystic fibrosis are susceptible to co-infection by Aspergillus fumigatus and Pseudomonas aeruginosa Despite the persistence of A. fumigatus in the cystic fibrosis lung P. aeruginosa eventually predominates as the primary pathogen. Several factors are likely to facilitate P. aeruginosa colonization in the airways, including alterations to the microbial environment. The cystic fibrosis airways are hypoxic, nitrate-rich environments, and the sputum has higher amino acid concentrations than normal. In this study, significant growth proliferation was observed in P. aeruginosa when the bacteria were exposed to A. fumigatus culture filtrates (CuF) containing a high nitrate content. Proteomic analysis of the A. fumigatus CuF identified a significant number of environment-altering proteases and peptidases. The molecular mechanisms promoting bacterial growth were investigated using label-free quantitative (LFQ) proteomics to compare the proteome of P. aeruginosa grown in the A. fumigatus CuF and in CuF produced by a P. aeruginosa-A. fumigatus co-culture, to that cultured in P. aeruginosa CuF. LFQ proteomics revealed distinct changes in the proteome of P. aeruginosa when cultured in the different CuFs, including increases in the levels of proteins involved in denitrification, stress response, replication, amino acid metabolism and efflux pumps, and a down-regulation of pathways involving ABC transporters. These findings offer novel insights into the complex dynamics that exist between P. aeruginosa and A. fumigatus Understanding the molecular strategies that enable P. aeruginosa to predominate in an environment where A. fumigatus exists is important in the context of therapeutic development to target this pathogen.
Collapse
Affiliation(s)
- Anatte Margalit
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - James C Carolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - David Sheehan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Kevin Kavanagh
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
37
|
Contextual Flexibility in Pseudomonas aeruginosa Central Carbon Metabolism during Growth in Single Carbon Sources. mBio 2020; 11:mBio.02684-19. [PMID: 32184246 PMCID: PMC7078475 DOI: 10.1128/mbio.02684-19] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that is well known for causing infections in the airways of people with cystic fibrosis. Although it is clear that P. aeruginosa is metabolically well adapted to life in the CF lung, little is currently known about how the organism metabolizes the nutrients available in the airways. In this work, we used a combination of gene expression and isotope tracer (“fluxomic”) analyses to find out exactly where the input carbon goes during growth on two CF-relevant carbon sources, acetate and glycerol (derived from the breakdown of lung surfactant). We found that carbon is routed (“fluxed”) through very different pathways during growth on these substrates and that this is accompanied by an unexpected remodeling of the cell’s electron transfer pathways. Having access to this “blueprint” is important because the metabolism of P. aeruginosa is increasingly being recognized as a target for the development of much-needed antimicrobial agents. Pseudomonas aeruginosa is an opportunistic human pathogen, particularly noted for causing infections in the lungs of people with cystic fibrosis (CF). Previous studies have shown that the gene expression profile of P. aeruginosa appears to converge toward a common metabolic program as the organism adapts to the CF airway environment. However, we still have only a limited understanding of how these transcriptional changes impact metabolic flux at the systems level. To address this, we analyzed the transcriptome, proteome, and fluxome of P. aeruginosa grown on glycerol or acetate. These carbon sources were chosen because they are the primary breakdown products of an airway surfactant, phosphatidylcholine, which is known to be a major carbon source for P. aeruginosa in CF airways. We show that the fluxes of carbon throughout central metabolism are radically different among carbon sources. For example, the newly recognized “EDEMP cycle” (which incorporates elements of the Entner-Doudoroff [ED] pathway, the Embden-Meyerhof-Parnas [EMP] pathway, and the pentose phosphate [PP] pathway) plays an important role in supplying NADPH during growth on glycerol. In contrast, the EDEMP cycle is attenuated during growth on acetate, and instead, NADPH is primarily supplied by the reaction catalyzed by isocitrate dehydrogenase(s). Perhaps more importantly, our proteomic and transcriptomic analyses revealed a global remodeling of gene expression during growth on the different carbon sources, with unanticipated impacts on aerobic denitrification, electron transport chain architecture, and the redox economy of the cell. Collectively, these data highlight the remarkable metabolic plasticity of P. aeruginosa; that plasticity allows the organism to seamlessly segue between different carbon sources, maximizing the energetic yield from each.
Collapse
|
38
|
Jensen P, Møller S, Lerche C, Moser C, Bjarnsholt T, Ciofu O, Faurholt-Jepsen D, Høiby N, Kolpen M. Improving antibiotic treatment of bacterial biofilm by hyperbaric oxygen therapy: Not just hot air. Biofilm 2019; 1:100008. [PMID: 33447795 PMCID: PMC7798444 DOI: 10.1016/j.bioflm.2019.100008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 10/26/2022] Open
Abstract
Bacteria and fungi show substantial increased recalcitrance when growing as infectious biofilms. Chronic infections caused by biofilm growing microorganisms is considered a major problem of modern medicine. New strategies are needed to improve antibiotic treatment of biofilms. We have improved antibiotic treatment of bacterial biofilms by reviving the dormant bacteria and thereby make them susceptible to antibiotics by means of reoxygenation. Here we review the rationale for associating lack of oxygen with low susceptibility in infectious biofilm, and how hyperbaric oxygen therapy may result in reoxygenation leading to enhanced bactericidal activity of antibiotics. We address issues of feasibility and potential adverse effects regarding patient safety and development of resistance. Finally, we propose means for supplying reoxygenation to antibiotic treatment of infectious biofilm with the potential to benefit large groups of patients.
Collapse
Affiliation(s)
- P.Ø. Jensen
- Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen, Denmark
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences University of Copenhagen, 2200, Copenhagen, Denmark
| | - S.A. Møller
- Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen, Denmark
| | - C.J. Lerche
- Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen, Denmark
| | - C. Moser
- Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen, Denmark
| | - T. Bjarnsholt
- Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen, Denmark
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences University of Copenhagen, 2200, Copenhagen, Denmark
| | - O. Ciofu
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences University of Copenhagen, 2200, Copenhagen, Denmark
| | - D. Faurholt-Jepsen
- Copenhagen Cystic Fibrosis Center, Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK2100, Copenhagen, Denmark
| | - N. Høiby
- Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen, Denmark
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences University of Copenhagen, 2200, Copenhagen, Denmark
| | - M. Kolpen
- Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen, Denmark
| |
Collapse
|
39
|
Conceptual Model of Biofilm Antibiotic Tolerance That Integrates Phenomena of Diffusion, Metabolism, Gene Expression, and Physiology. J Bacteriol 2019; 201:JB.00307-19. [PMID: 31501280 DOI: 10.1128/jb.00307-19] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/28/2019] [Indexed: 01/14/2023] Open
Abstract
Transcriptomic, metabolomic, physiological, and computational modeling approaches were integrated to gain insight into the mechanisms of antibiotic tolerance in an in vitro biofilm system. Pseudomonas aeruginosa biofilms were grown in drip flow reactors on a medium composed to mimic the exudate from a chronic wound. After 4 days, the biofilm was 114 μm thick with 9.45 log10 CFU cm-2 These biofilms exhibited tolerance, relative to exponential-phase planktonic cells, to subsequent treatment with ciprofloxacin. The specific growth rate of the biofilm was estimated via elemental balances to be approximately 0.37 h-1 and with a reaction-diffusion model to be 0.32 h-1, or one-third of the maximum specific growth rate for planktonic cells. Global analysis of gene expression indicated lower transcription of ribosomal genes and genes for other anabolic functions in biofilms than in exponential-phase planktonic cells and revealed the induction of multiple stress responses in biofilm cells, including those associated with growth arrest, zinc limitation, hypoxia, and acyl-homoserine lactone quorum sensing. Metabolic pathways for phenazine biosynthesis and denitrification were transcriptionally activated in biofilms. A customized reaction-diffusion model predicted that steep oxygen concentration gradients will form when these biofilms are thicker than about 40 μm. Mutant strains that were deficient in Psl polysaccharide synthesis, the stringent response, the stationary-phase response, and the membrane stress response exhibited increased ciprofloxacin susceptibility when cultured in biofilms. These results support a sequence of phenomena leading to biofilm antibiotic tolerance, involving oxygen limitation, electron acceptor starvation and growth arrest, induction of associated stress responses, and differentiation into protected cell states.IMPORTANCE Bacteria in biofilms are protected from killing by antibiotics, and this reduced susceptibility contributes to the persistence of infections such as those in the cystic fibrosis lung and chronic wounds. A generalized conceptual model of biofilm antimicrobial tolerance with the following mechanistic steps is proposed: (i) establishment of concentration gradients in metabolic substrates and products; (ii) active biological responses to these changes in the local chemical microenvironment; (iii) entry of biofilm cells into a spectrum of states involving alternative metabolisms, stress responses, slow growth, cessation of growth, or dormancy (all prior to antibiotic treatment); (iv) adaptive responses to antibiotic exposure; and (v) reduced susceptibility of microbial cells to antimicrobial challenges in some of the physiological states accessed through these changes.
Collapse
|
40
|
Lack of the Major Multifunctional Catalase KatA in Pseudomonas aeruginosa Accelerates Evolution of Antibiotic Resistance in Ciprofloxacin-Treated Biofilms. Antimicrob Agents Chemother 2019; 63:AAC.00766-19. [PMID: 31307984 DOI: 10.1128/aac.00766-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/30/2019] [Indexed: 01/20/2023] Open
Abstract
During chronic biofilm infections, Pseudomonas aeruginosa bacteria are exposed to increased oxidative stress as a result of the inflammatory response. As reactive oxygen species (ROS) are mutagenic, the evolution of resistance to ciprofloxacin (CIP) in biofilms under oxidative stress conditions was investigated. We experimentally evolved six replicate populations of P. aeruginosa lacking the major catalase KatA in colony biofilms and stationary-phase cultures for seven passages in the presence of subinhibitory levels (0.1 mg/liter) of CIP or without CIP (eight replicate lineages for controls) under aerobic conditions. In CIP-evolved biofilms, a larger CIP-resistant subpopulation was isolated in the ΔkatA strain than in the wild-type (WT) PAO1 population, suggesting oxidative stress as a promoter of the development of antibiotic resistance. A higher number of mutations identified by population sequencing were observed in evolved ΔkatA biofilm populations (CIP and control) than in WT PAO1 populations evolved under the same conditions. Genes involved in iron assimilation were found to be exclusively mutated in CIP-evolved ΔkatA biofilm populations, probably as a defense mechanism against ROS formation resulting from Fenton reactions. Furthermore, a hypermutable lineage due to mutL inactivation developed in one CIP-evolved ΔkatA biofilm lineage. In CIP-evolved biofilms of both the ΔkatA strain and WT PAO1, mutations in nfxB, the negative regulator of the MexCD-OprJ efflux pump, were observed while in CIP-evolved planktonic cultures of both the ΔkatA strain and WT PAO1, mutations in mexR and nalD, regulators of the MexAB-OprM efflux pump, were repeatedly found. In conclusion, these results emphasize the role of oxidative stress as an environmental factor that might increase the development of antibiotic resistance in in vivo biofilms.
Collapse
|
41
|
Ubiquinone Biosynthesis over the Entire O 2 Range: Characterization of a Conserved O 2-Independent Pathway. mBio 2019; 10:mBio.01319-19. [PMID: 31289180 PMCID: PMC6747719 DOI: 10.1128/mbio.01319-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In order to colonize environments with large O2 gradients or fluctuating O2 levels, bacteria have developed metabolic responses that remain incompletely understood. Such adaptations have been recently linked to antibiotic resistance, virulence, and the capacity to develop in complex ecosystems like the microbiota. Here, we identify a novel pathway for the biosynthesis of ubiquinone, a molecule with a key role in cellular bioenergetics. We link three uncharacterized genes of Escherichia coli to this pathway and show that the pathway functions independently from O2. In contrast, the long-described pathway for ubiquinone biosynthesis requires O2 as a substrate. In fact, we find that many proteobacteria are equipped with the O2-dependent and O2-independent pathways, supporting that they are able to synthesize ubiquinone over the entire O2 range. Overall, we propose that the novel O2-independent pathway is part of the metabolic plasticity developed by proteobacteria to face various environmental O2 levels. Most bacteria can generate ATP by respiratory metabolism, in which electrons are shuttled from reduced substrates to terminal electron acceptors, via quinone molecules like ubiquinone. Dioxygen (O2) is the terminal electron acceptor of aerobic respiration and serves as a co-substrate in the biosynthesis of ubiquinone. Here, we characterize a novel, O2-independent pathway for the biosynthesis of ubiquinone. This pathway relies on three proteins, UbiT (YhbT), UbiU (YhbU), and UbiV (YhbV). UbiT contains an SCP2 lipid-binding domain and is likely an accessory factor of the biosynthetic pathway, while UbiU and UbiV (UbiU-UbiV) are involved in hydroxylation reactions and represent a novel class of O2-independent hydroxylases. We demonstrate that UbiU-UbiV form a heterodimer, wherein each protein binds a 4Fe-4S cluster via conserved cysteines that are essential for activity. The UbiT, -U, and -V proteins are found in alpha-, beta-, and gammaproteobacterial clades, including several human pathogens, supporting the widespread distribution of a previously unrecognized capacity to synthesize ubiquinone in the absence of O2. Together, the O2-dependent and O2-independent ubiquinone biosynthesis pathways contribute to optimizing bacterial metabolism over the entire O2 range.
Collapse
|
42
|
Scott JE, O'Toole GA. The Yin and Yang of Streptococcus Lung Infections in Cystic Fibrosis: a Model for Studying Polymicrobial Interactions. J Bacteriol 2019; 201:e00115-19. [PMID: 30885933 PMCID: PMC6509657 DOI: 10.1128/jb.00115-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The streptococci are increasingly recognized as a core component of the cystic fibrosis (CF) lung microbiome, yet the role that they play in CF lung disease is unclear. The presence of the Streptococcus milleri group (SMG; also known as the anginosus group streptococci [AGS]) correlates with exacerbation when these microbes are the predominant species in the lung. In contrast, microbiome studies have indicated that an increased relative abundance of streptococci in the lung, including members of the oral microflora, correlates with impacts on lung disease less severe than those caused by other CF-associated microflora, indicating a complex role for this genus in the context of CF. Recent findings suggest that streptococci in the CF lung microenvironment may influence the growth and/or virulence of other CF pathogens, as evidenced by increased virulence factor production by Pseudomonas aeruginosa when grown in coculture with oral streptococci. Conversely, the presence of P. aeruginosa can enhance the growth of streptococci, including members of the SMG, a phenomenon that could be exacerbated by the fact that streptococci are not susceptible to some of the frontline antibiotics used to treat P. aeruginosa infections. Collectively, these studies indicate the necessity for further investigation into the role of streptococci in the CF airway to determine how these microbes, alone or via interactions with other CF-associated pathogens, might influence CF lung disease, for better or for worse. We also propose that the interactions of streptococci with other CF pathogens is an ideal model to study clinically relevant microbial interactions.
Collapse
Affiliation(s)
- Jessie E Scott
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| |
Collapse
|
43
|
Chlorate Specifically Targets Oxidant-Starved, Antibiotic-Tolerant Populations of Pseudomonas aeruginosa Biofilms. mBio 2018; 9:mBio.01400-18. [PMID: 30254119 PMCID: PMC6156191 DOI: 10.1128/mbio.01400-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The anaerobic growth and survival of bacteria are often correlated with physiological tolerance to conventional antibiotics, motivating the development of novel strategies targeting pathogens in anoxic environments. A key challenge is to identify drug targets that are specific to this metabolic state. Chlorate is a nontoxic compound that can be reduced to toxic chlorite by a widespread enzyme of anaerobic metabolism. We tested the antibacterial properties of chlorate against Pseudomonas aeruginosa, a pathogen that can inhabit hypoxic or anoxic microenvironments, including those that arise in human infection. Chlorate and the antibiotic tobramycin kill distinct metabolic populations in P. aeruginosa biofilms, where chlorate targets anaerobic cells that tolerate tobramycin. Chlorate is particularly effective against P. aeruginosalasR mutants, which are frequently isolated from human infections and more resistant to some antibiotics. This work suggests that chlorate may hold potential as an anaerobic prodrug. Nitrate respiration is a widespread mode of anaerobic energy generation used by many bacterial pathogens, and the respiratory nitrate reductase, Nar, has long been known to reduce chlorate to the toxic oxidizing agent chlorite. Here, we demonstrate the antibacterial activity of chlorate against Pseudomonas aeruginosa, a representative pathogen that can inhabit hypoxic or anoxic host microenvironments during infection. Aerobically grown P. aeruginosa cells are tobramycin sensitive but chlorate tolerant. In the absence of oxygen or an alternative electron acceptor, cells are tobramycin tolerant but chlorate sensitive via Nar-dependent reduction. The fact that chlorite, the product of chlorate reduction, is not detected in culture supernatants suggests that it may react rapidly and be retained intracellularly. Tobramycin and chlorate target distinct populations within metabolically stratified aggregate biofilms; tobramycin kills cells on the oxic periphery, whereas chlorate kills hypoxic and anoxic cells in the interior. In a matrix populated by multiple aggregates, tobramycin-mediated death of surface aggregates enables deeper oxygen penetration into the matrix, benefiting select aggregate populations by increasing survival and removing chlorate sensitivity. Finally, lasR mutants, which commonly arise in P. aeruginosa infections and are known to withstand conventional antibiotic treatment, are hypersensitive to chlorate. A lasR mutant shows a propensity to respire nitrate and reduce chlorate more rapidly than the wild type does, consistent with its heightened chlorate sensitivity. These findings illustrate chlorate’s potential to selectively target oxidant-starved pathogens, including physiological states and genotypes of P. aeruginosa that represent antibiotic-tolerant populations during infections.
Collapse
|
44
|
Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC. Niche partitioning of a pathogenic microbiome driven by chemical gradients. SCIENCE ADVANCES 2018; 4:eaau1908. [PMID: 30263961 PMCID: PMC6157970 DOI: 10.1126/sciadv.aau1908] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/10/2018] [Indexed: 05/25/2023]
Abstract
Environmental microbial communities are stratified by chemical gradients that shape the structure and function of these systems. Similar chemical gradients exist in the human body, but how they influence these microbial systems is more poorly understood. Understanding these effects can be particularly important for dysbiotic shifts in microbiome structure that are often associated with disease. We show that pH and oxygen strongly partition the microbial community from a diseased human lung into two mutually exclusive communities of pathogens and anaerobes. Antimicrobial treatment disrupted this chemical partitioning, causing complex death, survival, and resistance outcomes that were highly dependent on the individual microorganism and on community stratification. These effects were mathematically modeled, enabling a predictive understanding of this complex polymicrobial system. Harnessing the power of these chemical gradients could be a drug-free method of shaping microbial communities in the human body from undesirable dysbiotic states.
Collapse
Affiliation(s)
- Robert A. Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA 92093, USA
| | - William Comstock
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Tianyu Zhang
- Department of Mathematical Sciences, Montana State University, Bozeman, MT 59717, USA
| | - James T. Morton
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ricardo da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alda Tran
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexander Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA 92093, USA
| | - Louis-Felix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Daniel Wangpraseurt
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexey V. Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093, USA
| | - Douglas Conrad
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Isaac Klapper
- Department of Mathematics, Temple University, Philadelphia, PA 19122, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
45
|
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, designated by the World Health Organization as a critical priority for development of new therapeutics due to high levels of intrinsic and acquired antibiotic resistance. Other challenges include its versatility (it can persist in the environment and most strains are capable of causing disease in compromised hosts), robust efflux mechanisms that limit drug penetration, and the propensity to form antimicrobial-tolerant biofilms. Novel therapeutics in development to prevent or treat P. aeruginosa infections include vaccines, biologics such as antimicrobial peptides and therapeutic antibodies, virulence inhibitors, antimicrobials with novel targets, antibody-drug conjugates, resistance inhibitor-antibiotic or antibiotic-potentiator combinations, and bacteriophages or phage-derived lysins.
Collapse
Affiliation(s)
- Lori L. Burrows
- Department of Biochemistry & Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, 4H18 Health Sciences Centre, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| |
Collapse
|
46
|
Modelling of ciprofloxacin killing enhanced by hyperbaric oxygen treatment in Pseudomonas aeruginosa PAO1 biofilms. PLoS One 2018; 13:e0198909. [PMID: 29902223 PMCID: PMC6002088 DOI: 10.1371/journal.pone.0198909] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/29/2018] [Indexed: 01/12/2023] Open
Abstract
Outline In chronic lung infections by Pseudomonas aeruginosa (PA) the bacteria thrive in biofilm structures protected from the immune system of the host and from antibiotic treatment. Increasing evidence suggests that the susceptibility of the bacteria to antibiotic treatment can be significantly enhanced by hyperbaric oxygen treatment. The aim of this study is to simulate the effect of ciprofloxacin treatment in a PAO1 biofilm model with aggregates in agarose when combined with hyperbaric oxygen treatment. This is achieved in a reaction-diffusion model that describes the combined effect of ciprofloxacin diffusion, oxygen diffusion and depletion, bacterial growth and killing, and adaptation of the bacteria to ciprofloxacin. In the model, the oxygen diffusion and depletion use a set of parameters derived from experimental results presented in this work. The part of the model describing ciprofloxacin killing uses parameter values from the literature in combination with our estimates (Jacobs, et al., 2016; Grillon, et al., 2016). Micro-respirometry experiments were conducted to determine the oxygen consumption in the P. aeruginosa strain PAO1. The parameters were validated against existing data from an HBOT experiment by Kolpen et al. (2017). The complete oxygen model comprises a reaction-diffusion equation describing the oxygen consumption by using a Michaelis-Menten reaction term. The oxygen model performed well in predicting oxygen concentrations in both time and depth into the biofilm. At 2.8 bar pure oxygen pressure, HBOT increases the penetration depth of oxygen into the biofilm almost by a of factor 4 in agreement with the scaling that follows from the stationary balance between the consumption term and diffusion term. Conclusion In the full reaction-diffusion model we see that hyperbaric oxygen treatment significantly increases the killing by ciprofloxacin in a PAO1 biofilm in alignment with the experimental results from Kolpen et al. (Kolpen, et al., 2017; Kolpen, et al. 2016). The enhanced killing, in turn, lowers the oxygen consumption in the outer layers of the biofilm, and leads to even deeper penetration of oxygen into the biofilm.
Collapse
|
47
|
Pinilla-Redondo R, Riber L, Sørensen SJ. Fluorescence Recovery Allows the Implementation of a Fluorescence Reporter Gene Platform Applicable for the Detection and Quantification of Horizontal Gene Transfer in Anoxic Environments. Appl Environ Microbiol 2018; 84:e02507-17. [PMID: 29330182 PMCID: PMC5835726 DOI: 10.1128/aem.02507-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 12/20/2017] [Indexed: 02/02/2023] Open
Abstract
The study of horizontal gene transfer (HGT) in microbial communities has been revolutionized by significant advances in cultivation-independent methods based on fluorescence reporter gene technologies. Recently, the combination of these novel approaches with flow cytometry has presented itself as one of the most powerful tools to study the spread of mobile genetic elements (MGEs) in the environment. However, the use of fluorescent markers, like green fluorescent protein (GFP) and mCherry, is limited by environmental constraints, such as oxygen availability and pH levels, that affect the correct maturation of their fluorophores. Few studies have characterized the effects of such environmental conditions in a systematic way, and the sheer amount of distinct protein variants requires each system to be examined in an individual fashion. The lack of efficient and reliable markers to monitor HGT in anaerobic environments, coupled to the abundance of ecologically and clinically relevant oxygen-deprived niches in which bacteria thrive, calls for the urgent development of suitable tools that permit its study. In an attempt to devise a process that allows the implementation of the mentioned dual-labeling system to anoxic milieus, the aerobic fluorescence recovery of mCherry and GFPmut3, as well as the effect of pH on their fluorescence intensities, was studied. The findings present a solution to an intrinsic problem that has long hampered the utilization of this system, highlight its pH limitations, and provide experimental tools that will help broaden its horizon of application to other fields.IMPORTANCE Many anaerobic environments, like the gastrointestinal tract, anaerobic digesters, and the interiors of dense biofilms, have been shown to be hotspots for horizontal gene transfer (HGT). Despite the increasing wealth of reports warning about the alarming spread of antibiotic resistance determinants, to date, HGT studies mainly rely on cultivation-based methods. Unfortunately, the relevance of these studies is often questionable, as only a minor fraction of bacteria can be cultivated. A recently developed approach to monitoring the fate of plasmids in microbial communities is based on a fluorescence dual-labeling system and allows the bypassing of cultivation. However, the fluorescent proteins on which it is founded are constrained by pH levels and by their strict dependence on oxygen for the maturation of their fluorophores. This study focused on the development and validation of an appropriate aerobic fluorescence recovery (AFR) method for this platform, as this embodies the missing technical link impeding its implementation in anoxic environments.
Collapse
Affiliation(s)
| | - Leise Riber
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
48
|
Kosuru RY, Aashique M, Fathima A, Roy A, Bera S. Revealing the dual role of gallic acid in modulating ampicillin sensitivity of Pseudomonas aeruginosa biofilms. Future Microbiol 2018; 13:297-312. [DOI: 10.2217/fmb-2017-0132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aim: To understand the effects of gallic acid (GA) on ampicillin (Amp) sensitive or resistant strain of Pseudomonas sp. and also in modulating the corresponding biofilms. Methodology: The cell viability was determined by broth dilution, dry weight and CFU assays. Biofilm formation was measured by crystal violet assay while oxygen consumption rate was measured to verify the metabolic status of the cells. The membrane damage and drug efflux/accumulation were studied by fluorimetric assays. Results: GA transformed the Amp resistant cells, both planktonic and biofilms, into highly sensitive one by inducing membrane damage and enhancing accumulation of drug, whereas the Amp sensitive cells gained resistance against Amp. Conclusion: Use of GA as an antimicrobial compound should be analyzed more critically depending on the drug dosages, drug sensitivity as well as types of bacterial strains being studied.
Collapse
Affiliation(s)
- Rekha Yamini Kosuru
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
| | - Md Aashique
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
| | - Aisha Fathima
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
| | - Amrita Roy
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
| | - Soumen Bera
- School of Life Sciences, BS Abdur Rahman University, Vandalur, Chennai, Tamil Nadu 600048, India
| |
Collapse
|
49
|
Sønderholm M, Koren K, Wangpraseurt D, Jensen PØ, Kolpen M, Kragh KN, Bjarnsholt T, Kühl M. Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate bead model. NPJ Biofilms Microbiomes 2018; 4:3. [PMID: 29479470 PMCID: PMC5818519 DOI: 10.1038/s41522-018-0047-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/07/2018] [Accepted: 01/24/2018] [Indexed: 12/31/2022] Open
Abstract
In chronic infections, bacterial pathogens typically grow as small dense cell aggregates embedded in a matrix consisting of, e.g., wound bed sludge or lung mucus. Such biofilm growth mode exhibits extreme tolerance towards antibiotics and the immune defence system. The bacterial aggregates are exposed to physiological heterogeneity and O2 limitation due to steep chemical gradients through the matrix, which is are hypothesised to contribute to antibiotic tolerance. Using a novel combination of microsensor and bioimaging analysis, we investigated growth patterns and chemical dynamics of the pathogen Pseudomonas aeruginosa in an alginate bead model, which mimics growth in chronic infections better than traditional biofilm experiments in flow chambers. Growth patterns were strongly affected by electron acceptor availability and the presence of chemical gradients, where the combined presence of O2 and nitrate yielded highest bacterial growth by combined aerobic respiration and denitrification.
Collapse
Affiliation(s)
- Majken Sønderholm
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Klaus Koren
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
| | - Daniel Wangpraseurt
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Peter Østrup Jensen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
- Department of Clinical Microbiology 9301, Copenhagen University Hospital, Rigshospitalet, Juliane Maries Vej 22, Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology 9301, Copenhagen University Hospital, Rigshospitalet, Juliane Maries Vej 22, Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
- Department of Clinical Microbiology 9301, Copenhagen University Hospital, Rigshospitalet, Juliane Maries Vej 22, Copenhagen, Denmark
| | - Michael Kühl
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW 2007 Australia
| |
Collapse
|
50
|
Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium, is characterized by its versatility that enables persistent survival under adverse conditions. It can grow on diverse energy sources and readily acquire resistance to antimicrobial agents. As an opportunistic human pathogen, it also causes chronic infections inside the anaerobic mucus airways of cystic fibrosis patients. As a strict respirer, P. aeruginosa can grow by anaerobic nitrate ( [Formula: see text] ) respiration. Nitric oxide (NO) produced as an intermediate during anaerobic respiration exerts many important effects on the biological characteristics of P. aeruginosa. This review provides information regarding (i) how P. aeruginosa grows by anaerobic respiration, (ii) mechanisms by which NO is produced under such growth, and (iii) bacterial adaptation to NO. We also review the clinical relevance of NO in the fitness of P. aeruginosa and the use of NO as a potential therapeutic for treating P. aeruginosa infection.
Collapse
|