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Neve RL, Giedraitis E, Akbari MS, Cohen S, Phelan VV. Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits. mSystems 2024; 9:e0033924. [PMID: 38619244 PMCID: PMC11097636 DOI: 10.1128/msystems.00339-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/20/2024] [Indexed: 04/16/2024] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous Gram-negative opportunistic pathogen with remarkable phylogenetic and phenotypic variabilities. In this work, we applied classical molecular networking analysis to secondary metabolite profiling data from seven Pseudomonas aeruginosa strains, including five clinical isolates from the lung secretions of people with cystic fibrosis (CF). We provide three vignettes illustrating how secondary metabolite profiling aids in the identification of rare genomics traits in P. aeruginosa. First, we describe the identification of a previously unreported class of acyl putrescines produced by isolate mFLRO1. Secondary analysis of publicly available metabolomics data revealed that acyl putrescines are produced by <5% of P. aeruginosa strains. Second, we show that isolate SH3A does not produce di-rhamnolipids. Whole-genome sequencing and comparative genomics revealed that SH3A cannot produce di-rhamnolipids because its genome belongs to clade 5 of the P. aeruginosa phylogenetic tree. Previous phylogenetic analysis of thousands of P. aeruginosa strains concluded that <1% of publicly available genome sequences contribute to this clade. Last, we show that isolate SH1B does not produce the phenazine pyocyanin or rhamnolipids because it has a one-base insertion frameshift mutation (678insC) in the gene rhlR, which disrupts rhl-driven quorum sensing. Secondary analysis of the tens of thousands of publicly available genomes in the National Center for Biotechnology Information (NCBI) and the Pseudomonas Genome Database revealed that this mutation was present in only four P. aeruginosa genomes. Taken together, this study highlights that secondary metabolite profiling combined with genomic analysis can identify rare genetic traits of P. aeruginosa isolates.IMPORTANCESecondary metabolite profiling of five Pseudomonas aeruginosa isolates from cystic fibrosis sputum captured three traits present in <1%-5% of publicly available data, pointing to how our current library of P. aeruginosa strains may not represent the diversity within this species or the genetic variance that occurs in the CF lung.
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Affiliation(s)
- Rachel L. Neve
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Emily Giedraitis
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Madeline S. Akbari
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Shirli Cohen
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Vanessa V. Phelan
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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2
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Ungor I, Apidianakis Y. Bacterial synergies and antagonisms affecting Pseudomonas aeruginosa virulence in the human lung, skin and intestine. Future Microbiol 2024; 19:141-155. [PMID: 37843410 DOI: 10.2217/fmb-2022-0155] [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: 07/07/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Pseudomonas aeruginosa requires a significant breach in the host defense to cause an infection. While its virulence factors are well studied, its tropism cannot be explained only by studying its interaction with the host. Why are P. aeruginosa infections so rare in the intestine compared with the lung and skin? There is not enough evidence to claim specificity in virulence factors deployed by P. aeruginosa in each anatomical site, and host physiology differences between the lung and the intestine cannot easily explain the observed differences in virulence. This perspective highlights a relatively overlooked parameter in P. aeruginosa virulence, namely, potential synergies with bacteria found in the human skin and lung, as well as antagonisms with bacteria of the human intestine.
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Affiliation(s)
- Izel Ungor
- Department of Biological Sciences, University of Cyprus, Nicosia, 2109, Cyprus
| | - Yiorgos Apidianakis
- Department of Biological Sciences, University of Cyprus, Nicosia, 2109, Cyprus
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3
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El Fakhouri K, Ramdani C, Aasfar A, Boulamtat R, Sijilmassi B, El Bouhssini M, Kadmiri IM. Isolation, identification and pathogenicity of local entomopathogenic bacteria as biological control agents against the wild cochineal Dactylopius opuntiae (Cockerell) on cactus pear in Morocco. Sci Rep 2023; 13:21647. [PMID: 38062128 PMCID: PMC10703873 DOI: 10.1038/s41598-023-48976-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
The Opuntia ficus-indica (L.) cactus, a crucial crop in Morocco, is threatened by the wild cochineal, Dactylopius opuntiae (Cockerell). The aim of this research was to investigate the efficacy of nine bacterial strains against both D. opuntiae nymphs and adults females applied individually or after black soap in the laboratory, greenhouse, and field conditions. Using the partial 16S ribosomal DNA, the bacterial isolates were identified as Pseudomonas koreensis, Pseudomonas sp., Burkholderia sp. and Bacillus sp. Under laboratory conditions, the insecticidal activity of P. koreensis strain 66Ms.04 showed the level mortality (88%) of adult females' at 108 CFU/mL, 7 days after application. At a concentration of 108 CFU/mL, P. koreensis strain 66Ms.04 and Pseudomonas sp. (strains 37 and 5) caused 100% nymphs mortality rate three days after application. Under greenhouse conditions, the use of P. koreensis strain 66Ms.04 at 108 CFU/mL following the application of black soap (60 g/L) demonstrated the maximum levels of females and nymphs' mortalities with 80 and 91.25%, respectively, after 8 days of treatment. In field conditions, the combined application of the P. koreensis strain 66Ms.04 at 108 CFU/mL with black soap at 60 g/L, for an interval of 7 days, significantly increased the mortality of adult females to 93.33% at 7 days after the second application. These findings showed that the combined treatment of P. koreensis strain 66Ms.04 with black soap can be a potent and eco-friendly pesticide against D. opuntiae.
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Affiliation(s)
- Karim El Fakhouri
- AgroBioSciences Program, College of Agriculture and Environmental Science, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco.
| | - Chaimae Ramdani
- AgroBioSciences Program, College of Agriculture and Environmental Science, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Abderrahim Aasfar
- Plant and Microbial Biotechnology center, Moroccan Foundation for Advanced Science, Innovation and Rescarch (MAScIR), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Rachid Boulamtat
- Entomology Laboratory, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Institutes, P.O. Box 6299, Rabat, Morocco
| | - Badreddine Sijilmassi
- Rhizobium Laboratory, Genetic Resources Section, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Institutes, P.O. Box 6299, Rabat, Morocco
| | - Mustapha El Bouhssini
- AgroBioSciences Program, College of Agriculture and Environmental Science, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Issam Meftah Kadmiri
- Plant and Microbial Biotechnology center, Moroccan Foundation for Advanced Science, Innovation and Rescarch (MAScIR), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
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Díaz-Pérez AL, Díaz-Pérez C, Gaona-García RY, Hernández-Santoyo A, Lázaro-Mixteco PE, Reyes-De La Cruz H, Campos-García J. Study of peripheral domains in structure-function of isocitrate lyase (ICL) from Pseudomonas aeruginosa. World J Microbiol Biotechnol 2023; 39:339. [PMID: 37821748 DOI: 10.1007/s11274-023-03768-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/15/2023] [Indexed: 10/13/2023]
Abstract
The capacity of Pseudomonas aeruginosa to assimilate nutrients is essential for niche colonization and contributes to its pathogenicity. Isocitrate lyase (ICL), the first enzyme of the glyoxylate cycle, redirects isocitrate from the tricarboxylic acid cycle to render glyoxylate and succinate. P. aeruginosa ICL (PaICL) is regarded as a virulence factor due to its role in carbon assimilation during infection. The AceA/ICL protein family shares the catalytic domain I, triosephosphate isomerase barrel (TIM-barrel). The carboxyl terminus of domain I is essential for Escherichia coli ICL (EcICL) of subfamily 1. PaICL, which belongs to subfamily 3, has domain II inserted at the periphery of domain I, which is believed to participate in enzyme oligomerization. In addition, PaICL has the α13-loop-α14 (extended motif), which protrudes from the enzyme core, being of unknown function. This study investigates the role of domain II, the extended motif, and the carboxyl-terminus (C-ICL) and amino-terminus (N-ICL) regions in the function of the PaICL enzyme, also as their involvement in the virulence of P. aeruginosa PAO1. Deletion of domain II and the extended motif results in enzyme inactivation and structural instability of the enzyme. The His6-tag fusion at the C-ICL protein produced a less efficient enzyme than fusion at the N-ICL, but without affecting the acetate assimilation or virulence. The PaICL homotetrameric structure of the enzyme was more stable in the N-His6-ICL than in the C-His6-ICL, suggesting that the C-terminus is critical for the ICL quaternary conformation. The ICL-mutant A39 complemented with the recombinant proteins N-His6-ICL or C-His6-ICL were more virulent than the WT PAO1 strain. The findings indicate that the domain II and the extended motif are essential for the ICL structure/function, and the C-terminus is involved in its quaternary structure conformation, confirming that in P. aeruginosa, the ICL is essential for acetate assimilation and virulence.
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Affiliation(s)
- Alma Laura Díaz-Pérez
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - César Díaz-Pérez
- Facultad de Agrobiologia, Campus Celaya-Salvatierra, Universiad de Guanajuato, Guanajuato, Gto., Mexico
| | - Roxana Yughadi Gaona-García
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - Alejandra Hernández-Santoyo
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pedro E Lázaro-Mixteco
- Facultad de Ingeniería Química, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich., Mexico
| | - Homero Reyes-De La Cruz
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - Jesús Campos-García
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico.
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5
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Pal R, Athamneh AI, Deshpande R, Ramirez JAR, Adu KT, Muthuirulan P, Pawar S, Biazzo M, Apidianakis Y, Sundekilde UK, de la Fuente-Nunez C, Martens MG, Tegos GP, Seleem MN. Probiotics: insights and new opportunities for Clostridioides difficile intervention. Crit Rev Microbiol 2023; 49:414-434. [PMID: 35574602 PMCID: PMC9743071 DOI: 10.1080/1040841x.2022.2072705] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/17/2022] [Accepted: 04/28/2022] [Indexed: 02/08/2023]
Abstract
Clostridioides difficile infection (CDI) is a life-threatening disease caused by the Gram-positive, opportunistic intestinal pathogen C. difficile. Despite the availability of antimicrobial drugs to treat CDI, such as vancomycin, metronidazole, and fidaxomicin, recurrence of infection remains a significant clinical challenge. The use of live commensal microorganisms, or probiotics, is one of the most investigated non-antibiotic therapeutic options to balance gastrointestinal (GI) microbiota and subsequently tackle dysbiosis. In this review, we will discuss major commensal probiotic strains that have the potential to prevent and/or treat CDI and its recurrence, reassess the efficacy of probiotics supplementation as a CDI intervention, delve into lessons learned from probiotic modulation of the immune system, explore avenues like genome-scale metabolic network reconstructions, genome sequencing, and multi-omics to identify novel strains and understand their functionality, and discuss the current regulatory framework, challenges, and future directions.
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Affiliation(s)
- Rusha Pal
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Ahmad I.M. Athamneh
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | | | - Jose A. R Ramirez
- ProbioWorld Consulting Group, James Cook University, 4811, Queensland, Australia
| | - Kayode T. Adu
- ProbioWorld Consulting Group, James Cook University, 4811, Queensland, Australia
- Cann Group, Walter and Eliza Hall Institute, La Trobe University, Victoria 3083, Australia
| | | | - Shrikant Pawar
- The Anlyan Center Yale Center for Genomic Analysis, Yale School of Medicine, New Haven CT USA
| | - Manuele Biazzo
- The Bioarte Ltd Laboratories at Life Science Park, San Gwann, Malta
| | | | | | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark G. Martens
- Reading Hospital, Tower Health, West Reading, PA 19611, USA
- Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - George P. Tegos
- Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Mohamed N. Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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6
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Synergistic Antibacterial Activity of Benzalkonium Bromide and Cu-Bearing Duplex Stainless Steel against Pseudomonas aeruginosa. Microorganisms 2023; 11:microorganisms11030711. [PMID: 36985283 PMCID: PMC10057093 DOI: 10.3390/microorganisms11030711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/17/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
The bactericide benzalkonium bromide is widely used to kill Pseudomonas aeruginosa, which causes microbiologically influenced corrosion (MIC). However, the extensive use of benzalkonium bromide will enhance bacterial drug resistance and cause environmental pollution. In this study, benzalkonium bromide combined with Cu-bearing 2205 duplex stainless steel (2205-Cu DSS) was used to kill Pseudomonas aeruginosa; the germicidal rate of the combination of benzalkonium bromide and 2205-Cu DSS was 24.2% higher than that of using benzalkonium bromide alone, after five days. The antibacterial efficacy was evaluated using an antibacterial test and biofilm observation. The results showed that, in the presence of P. aeruginosa, the combination of 23.44 ppm benzalkonium bromide and 2205-Cu DSS showed the best antibacterial efficacy.
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7
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Anziani P, Becker J, Mignon C, Arnaud-Barbe N, Courtois V, Izac M, Pizzato R, Abi-Ghanem J, Tran VD, Sarafian M, Bunescu A, Garnier D, Abachin E, Renauld-Mongénie G, Guyard C. Deep longitudinal multi-omics analysis of Bordetella pertussis cultivated in bioreactors highlights medium starvations and transitory metabolisms, associated to vaccine antigen biosynthesis variations and global virulence regulation. Front Microbiol 2023; 14:1036386. [PMID: 36876086 PMCID: PMC9976334 DOI: 10.3389/fmicb.2023.1036386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/05/2023] [Indexed: 02/16/2023] Open
Abstract
Bordetella pertussis is the bacterial causative agent of whooping cough, a serious respiratory illness. An extensive knowledge on its virulence regulation and metabolism is a key factor to ensure pertussis vaccine manufacturing process robustness. The aim of this study was to refine our comprehension of B. pertussis physiology during in vitro cultures in bioreactors. A longitudinal multi-omics analysis was carried out over 26 h small-scale cultures of B. pertussis. Cultures were performed in batch mode and under culture conditions intending to mimic industrial processes. Putative cysteine and proline starvations were, respectively, observed at the beginning of the exponential phase (from 4 to 8 h) and during the exponential phase (18 h 45 min). As revealed by multi-omics analyses, the proline starvation induced major molecular changes, including a transient metabolism with internal stock consumption. In the meantime, growth and specific total PT, PRN, and Fim2 antigen productions were negatively affected. Interestingly, the master virulence-regulating two-component system of B. pertussis (BvgASR) was not evidenced as the sole virulence regulator in this in vitro growth condition. Indeed, novel intermediate regulators were identified as putatively involved in the expression of some virulence-activated genes (vags). Such longitudinal multi-omics analysis applied to B. pertussis culture process emerges as a powerful tool for characterization and incremental optimization of vaccine antigen production.
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Affiliation(s)
- Paul Anziani
- Sanofi, Marcy-l'Étoile, France.,BIOASTER, Lyon, France
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Jenior ML, Dickenson ME, Papin JA. Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae. NPJ Syst Biol Appl 2022; 8:41. [PMID: 36307414 PMCID: PMC9616910 DOI: 10.1038/s41540-022-00252-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Infections due to carbapenem-resistant Enterobacteriaceae have recently emerged as one of the most urgent threats to hospitalized patients within the United States and Europe. By far the most common etiological agent of these infections is Klebsiella pneumoniae, frequently manifesting in hospital-acquired pneumonia with a mortality rate of ~50% even with antimicrobial intervention. We performed transcriptomic analysis of data collected previously from in vitro characterization of both laboratory and clinical isolates which revealed shifts in expression of multiple master metabolic regulators across isolate types. Metabolism has been previously shown to be an effective target for antibacterial therapy, and genome-scale metabolic network reconstructions (GENREs) have provided a powerful means to accelerate identification of potential targets in silico. Combining these techniques with the transcriptome meta-analysis, we generated context-specific models of metabolism utilizing a well-curated GENRE of K. pneumoniae (iYL1228) to identify novel therapeutic targets. Functional metabolic analyses revealed that both composition and metabolic activity of clinical isolate-associated context-specific models significantly differs from laboratory isolate-associated models of the bacterium. Additionally, we identified increased catabolism of L-valine in clinical isolate-specific growth simulations. These findings warrant future studies for potential efficacy of valine transaminase inhibition as a target against K. pneumoniae infection.
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Affiliation(s)
- Matthew L Jenior
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Mary E Dickenson
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. .,Department of Medicine, Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA. .,Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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9
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Taylor M, Janasky L, Vega N. Convergent structure with divergent adaptations in combinatorial microbiome communities. FEMS Microbiol Ecol 2022; 98:6726631. [PMID: 36170949 DOI: 10.1093/femsec/fiac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 01/21/2023] Open
Abstract
Adaptation of replicate microbial communities frequently produces shared trajectories of community composition and structure. However, divergent adaptation of individual community members can occur and is associated with community-level divergence. The extent to which community-based adaptation of microbes should be convergent when community members are similar but not identical is, therefore, not well-understood. In these experiments, adaptation of combinatorial minimal communities of bacteria with the model host Caenorhabditis elegans produces structurally similar communities over time, but with divergent adaptation of member taxa and differences in community-level resistance to invasion. These results indicate that community-based adaptation from taxonomically similar starting points can produce compositionally similar communities that differ in traits of member taxa and in ecological properties.
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Affiliation(s)
- Megan Taylor
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Lili Janasky
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Nic Vega
- Biology Department, Emory University, Atlanta, GA, 30322, United States.,Physics Department, Emory University, Atlanta, GA, 30322, United States
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Abstract
Pf4 is a filamentous bacteriophage integrated as a prophage into the genome of Pseudomonas aeruginosa PAO1. Pf4 virions can be produced without killing P. aeruginosa. However, cell lysis can occur during superinfection when Pf virions successfully infect a host lysogenized by a Pf superinfective variant. We have previously shown that infection of P. aeruginosa PAO1 with a superinfective Pf4 variant abolished twitching motility and altered biofilm architecture. More precisely, most of the cells embedded into the biofilm were showing a filamentous morphology, suggesting the activation of the cell envelope stress response involving both AlgU and SigX extracytoplasmic function sigma factors. Here, we show that Pf4 variant infection results in a drastic dysregulation of 3,360 genes representing about 58% of P. aeruginosa genome; of these, 70% of the virulence factors encoding genes show a dysregulation. Accordingly, Pf4 variant infection (termed Pf4*) causes in vivo reduction of P. aeruginosa virulence and decreased production of N-acyl-homoserine lactones and 2-alkyl-4-quinolones quorum-sensing molecules and related virulence factors, such as pyocyanin, elastase, and pyoverdine. In addition, the expression of genes involved in metabolism, including energy generation and iron homeostasis, was affected, suggesting further relationships between virulence and central metabolism. Altogether, these data show that Pf4 phage variant infection results in complex network dysregulation, leading to reducing acute virulence in P. aeruginosa. This study contributes to the comprehension of the bacterial response to filamentous phage infection. IMPORTANCE Filamentous bacteriophages can become superinfective and infect P. aeruginosa, even though they are inserted in the genome as lysogens. Despite this productive infection, growth of the host is only mildly affected, allowing the study of the interaction between the phage and the host, which is not possible in the case of lytic phages killing rapidly their host. Here, we demonstrate by transcriptome and phenotypic analysis that the infection by a superinfective filamentous phage variant causes a massive disruption in gene expression, including those coding for virulence factors and metabolic pathways.
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11
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Sinha DK, Gupta A, Padmakumari AP, Bentur JS, Nair S. Infestation of Rice by Gall Midge Influences Density and Diversity of Pseudomonas and Wolbachia in the Host Plant Microbiome. Curr Genomics 2022; 23:126-136. [PMID: 36778977 PMCID: PMC9878839 DOI: 10.2174/1389202923666220401101604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/16/2022] [Accepted: 02/28/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The virulence of phytophagous insects is predominantly determined by their ability to evade or suppress host defense for their survival. The rice gall midge (GM, Orseolia oryzae), a monophagous pest of rice, elicits a host defense similar to the one elicited upon pathogen attack. This could be due to the GM feeding behaviour, wherein the GM endosymbionts are transferred to the host plant via oral secretions, and as a result, the host mounts an appropriate defense response(s) (i.e., up-regulation of the salicylic acid pathway) against these endosymbionts. Methods: The current study aimed to analyze the microbiome present at the feeding site of GM maggots to determine the exchange of bacterial species between GM and its host and to elucidate their role in rice-GM interaction using a next-generation sequencing approach. Results: Our results revealed differential representation of the phylum Proteobacteria in the GM-infested and -uninfested rice tissues. Furthermore, analysis of the species diversity of Pseudomonas and Wolbachia supergroups at the feeding sites indicated the exchange of bacterial species between GM and its host upon infestation. Conclusion: As rice-GM microbial associations remain relatively unstudied, these findings not only add to our current understanding of microbe-assisted insect-plant interactions but also provide valuable insights into how these bacteria drive insect-plant coevolution. Moreover, to the best of our knowledge, this is the first report analyzing the microbiome of a host plant (rice) at the feeding site of its insect pest (GM).
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Affiliation(s)
| | - Ayushi Gupta
- These authors contributed equally in this manuscript.
| | | | | | - Suresh Nair
- Address correspondence to this author at the Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India; Tel: 91-11-26741242; Fax: 91-11-26742316; E-mail:
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12
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Charalambous A, Grivogiannis E, Dieronitou I, Michael C, Rahme L, Apidianakis Y. Proteobacteria and Firmicutes Secreted Factors Exert Distinct Effects on Pseudomonas aeruginosa Infection under Normoxia or Mild Hypoxia. Metabolites 2022; 12:449. [PMID: 35629953 PMCID: PMC9146490 DOI: 10.3390/metabo12050449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023] Open
Abstract
Microbiota may alter a pathogen's virulence potential at polymicrobial infection sites. Here, we developed a multi-modal Drosophila assay, amenable to the assessment of human bacterial interactions using fly survival or midgut regeneration as a readout, under normoxia or mild hypoxia. Deploying a matrix of 12 by 33 one-to-one Drosophila co-infections via feeding, we classified bacterial interactions as neutral, synergistic, or antagonistic, based on fly survival. Twenty six percent of these interactions were antagonistic, mainly occurring between Proteobacteria. Specifically, Pseudomonas aeruginosa infection was antagonized by various Klebsiella strains, Acinetobacter baumannii, and Escherichia coli. We validated these interactions in a second screen of 7 by 34 one-to-one Drosophila co-infections based on assessments of midgut regeneration, and in bacterial co-culture test tube assays, where antagonistic interactions depended on secreted factors produced upon high sugar availability. Moreover, Enterococci interacted synergistically with P. aeruginosa in flies and in test tubes, enhancing the virulence and pyocyanin production by P. aeruginosa. However, neither lactic acid bacteria nor their severely hypoxic culture supernatants provided a survival benefit upon P. aeruginosa infection of flies or mice, respectively. We propose that at normoxic or mildly hypoxic sites, Firmicutes may exacerbate, whereas Proteobacteria secreted factors may ameliorate, P. aeruginosa infections.
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Affiliation(s)
- Anna Charalambous
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (A.C.); (E.G.); (I.D.); (C.M.)
| | - Evangelos Grivogiannis
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (A.C.); (E.G.); (I.D.); (C.M.)
| | - Irene Dieronitou
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (A.C.); (E.G.); (I.D.); (C.M.)
| | - Christina Michael
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (A.C.); (E.G.); (I.D.); (C.M.)
| | - Laurence Rahme
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA;
| | - Yiorgos Apidianakis
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (A.C.); (E.G.); (I.D.); (C.M.)
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13
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Tahmasebi H, Dehbashi S, Nasaj M, Arabestani MR. Molecular epidemiology and collaboration of siderophore-based iron acquisition with surface adhesion in hypervirulent Pseudomonas aeruginosa isolates from wound infections. Sci Rep 2022; 12:7791. [PMID: 35550578 PMCID: PMC9098452 DOI: 10.1038/s41598-022-11984-1] [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: 08/02/2021] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
Iron/siderophore uptake may play an important role in the biofilm formation and secretion of extracellular proteins in Pseudomonas aeruginosa isolates. In the present study, the role of siderophores, heme, and iron regulatory genes in the virulence of Pseudomonas aeruginosa isolates collected from wound infection was investigated. Three hundred eighty-four (384) swab samples were collected from wound infection and identified by phenotypic methods. The quantitative real-time PCR (qRT-PCR) method was evaluated for the gene expressions study. Multi-locus sequence typing (MLST) was used to screen unique sequence types (ST) and clonal complexes (CC). Fifty-five (55) P. aeruginosa isolates were detected in all swab samples. Also, 38 (69.1%) isolates formed biofilm. The prevalence of virulence factor genes was as follows: plcN (67.2%), exoY (70.9%), exoA (60.0%), phzM (58.1%), plcH (50.9%), lasB (36.3%), aprA (69.1%), lasA (34.5%), nanI (74.5%), exoU (70.9%), exoS (60.0%), exoT (63.6%) and algD (65.4%). According to qRT-PCR, genes regulating iron uptake were highly expressed in the toxigenic isolate. The highest expressions levels were observed for hemO, hasR, and pvdA genes in the biofilm-forming isolates. The MLST data confirmed a high prevalence of ST1, ST111, and ST235, with six, five, and 12 clusters, respectively. ST235 and ST1 were the most present among the biofilm-forming and toxigenic strains. Also, the nuoD gene with 54 and guaA with 19 showed the highest and lowest number of unique alleles. We demonstrated that iron/siderophore uptake is sufficient for biofilm formation and an increase in the pathogenesis of P. aeruginosa. These results suggest that the iron/siderophore uptake system may alter the MLST types of P. aeruginosa and predispose to bacterial pathogenesis in wound infections.
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Affiliation(s)
- Hamed Tahmasebi
- School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Sanaz Dehbashi
- Department of Laboratory Sciences, Varastegan Institute of Medical Sciences, Mashhad, Iran
| | - Mona Nasaj
- Microbiology Department, Faculty of Medicine, Hamadan University of Medical Sciences, Pajoohesh Junction, Hamadan, Iran
| | - Mohammad Reza Arabestani
- Microbiology Department, Faculty of Medicine, Hamadan University of Medical Sciences, Pajoohesh Junction, Hamadan, Iran. .,Nutrition Health Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
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14
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Bhowmik P, Rajagopal S, Hmar RV, Singh P, Saxena P, Amar P, Thomas T, Ravishankar R, Nagaraj S, Katagihallimath N, Sarangapani RK, Ramachandran V, Datta S. Validated In Silico Model for Biofilm Formation in Escherichia coli. ACS Synth Biol 2022; 11:713-731. [PMID: 35025506 DOI: 10.1021/acssynbio.1c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using Escherichia coli as the representative biofilm former, we report here the development of an in silico model built by simulating events that transform a free-living bacterial entity into self-encased multicellular biofilms. Published literature on ∼300 genes associated with pathways involved in biofilm formation was curated, static maps were created, and suitably interconnected with their respective metabolites using ordinary differential equations. Precise interplay of genetic networks that regulate the transitory switching of bacterial growth pattern in response to environmental changes and the resultant multicomponent synthesis of the extracellular matrix were appropriately represented. Subsequently, the in silico model was analyzed by simulating time-dependent changes in the concentration of components by using the R and python environment. The model was validated by simulating and verifying the impact of key gene knockouts (KOs) and systematic knockdowns on biofilm formation, thus ensuring the outcomes were comparable with the reported literature. Similarly, specific gene KOs in laboratory and pathogenic E. coli were constructed and assessed. MiaA, YdeO, and YgiV were found to be crucial in biofilm development. Furthermore, qRT-PCR confirmed the elevation of expression in biofilm-forming clinical isolates. Findings reported in this study offer opportunities for identifying biofilm inhibitors with applications in multiple industries. The application of this model can be extended to the health care sector specifically to develop novel adjunct therapies that prevent biofilms in medical implants and reduce emergence of biofilm-associated resistant polymicrobial-chronic infections. The in silico framework reported here is open source and accessible for further enhancements.
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Affiliation(s)
- Purnendu Bhowmik
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Sreenath Rajagopal
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Rothangamawi Victoria Hmar
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Purnima Singh
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Pragya Saxena
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Prakruthi Amar
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Teby Thomas
- St. John’s Research Institute, Bengaluru, Karnataka 560034, India
| | - Rajani Ravishankar
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Savitha Nagaraj
- St. John’s Medical College, Bengaluru, Karnataka 560034, India
| | - Nainesh Katagihallimath
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Ramanujan Kadambi Sarangapani
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
| | - Vasanthi Ramachandran
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka 560064, India
| | - Santanu Datta
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, GKVK, Bellary Road, Bengaluru, Karnataka 560065, India
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15
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Ducret V, Perron K, Valentini M. Role of Two-Component System Networks in Pseudomonas aeruginosa Pathogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:371-395. [PMID: 36258080 DOI: 10.1007/978-3-031-08491-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Two-component systems (TCS) are the largest family of signaling systems in the bacterial kingdom. They enable bacteria to cope with a wide range of environmental conditions via the sensing of stimuli and the transduction of the signal into an appropriate cellular adaptation response. Pseudomonas aeruginosa possesses one of the richest arrays of TCSs in bacteria and they have been the subject of intense investigation for more than 20 years. Most of the P. aeruginosa TCSs characterized to date affect its pathogenesis, via the regulation of virulence factors expression, modulation of the synthesis of antibiotic/antimicrobial resistance mechanisms, and/or via linking virulence to energy metabolism. Here, we give an overview of the current knowledge on P. aeruginosa TCSs, citing key examples for each of the above-mentioned regulatory actions. We then conclude by mentioning few small molecule inhibitors of P. aeruginosa TCSs that have shown an antimicrobial action in vitro.
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Affiliation(s)
- Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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16
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Martínez-Alcantar L, Orozco G, Díaz-Pérez AL, Villegas J, Reyes-De la Cruz H, García-Pineda E, Campos-García J. Participation of Acyl-Coenzyme A Synthetase FadD4 of Pseudomonas aeruginosa PAO1 in Acyclic Terpene/Fatty Acid Assimilation and Virulence by Lipid A Modification. Front Microbiol 2021; 12:785112. [PMID: 34867927 PMCID: PMC8637051 DOI: 10.3389/fmicb.2021.785112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
The pathogenic bacterium Pseudomonas aeruginosa possesses high metabolic versatility, with its effectiveness to cause infections likely due to its well-regulated genetic content. P. aeruginosa PAO1 has at least six fadD paralogous genes, which have been implicated in fatty acid (FA) degradation and pathogenicity. In this study, we used mutagenesis and a functional approach in P. aeruginosa PAO1 to determine the roles of the fadD4 gene in acyclic terpene (AT) and FA assimilation and on pathogenicity. The results indicate that fadD4 encodes a terpenoyl-CoA synthetase utilized for AT and FA assimilation. Additionally, mutations in fadD paralogs led to the modification of the quorum-sensing las/rhl systems, as well as the content of virulence factors pyocyanin, biofilm, rhamnolipids, lipopolysaccharides (LPS), and polyhydroxyalkanoates. In a Caenorhabditis elegans in vivo pathogenicity model, culture supernatants from the 24-h-grown fadD4 single mutant increased lethality compared to the PAO1 wild-type (WT) strain; however, the double mutants fadD1/fadD2, fadD1/fadD4, and fadD2/fadD4 and single mutant fadD2 increased worm survival. A correlation analysis indicated an interaction between worm death by the PAO1 strain, the fadD4 mutation, and the virulence factor LPS. Fatty acid methyl ester (FAME) analysis of LPS revealed that a proportion of the LPS and FA on lipid A were modified by the fadD4 mutation, suggesting that FadD4 is also involved in the synthesis/degradation and modification of the lipid A component of LPS. LPS isolated from the fadD4 mutant and double mutants fadD1/fadD4 and fadD2/fadD4 showed a differential behavior to induce an increase in body temperature in rats injected with LPS compared to the WT strain or from the fadD1 and fadD2 mutants. In agreement, LPS isolated from the fadD4 mutant and double mutants fadD1/fadD2 and fadD2/fadD4 increased the induction of IL-8 in rat sera, but IL1-β cytokine levels decreased in the double mutants fadD1/fadD2 and fadD1/fadD4. The results indicate that the fadD genes are implicated in the degree of pathogenicity of P. aeruginosa PAO1 induced by LPS-lipid A, suggesting that FadD4 contributes to the removal of acyl-linked FA from LPS, rendering modification in its immunogenic response associated to Toll-like receptor TLR4. The genetic redundancy of fadD is important for bacterial adaptability and pathogenicity over the host.
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Affiliation(s)
- Lorena Martínez-Alcantar
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Gabriela Orozco
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Alma Laura Díaz-Pérez
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Javier Villegas
- Laboratorio de Interacción Suelo, Planta, Microorganismo, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Homero Reyes-De la Cruz
- Laboratorio de Control Traduccional, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Ernesto García-Pineda
- Laboratorio de Bioquímica y Biología Molecular, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Jesús Campos-García
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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17
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Laborda P, Sanz-García F, Hernando-Amado S, Martínez JL. Pseudomonas aeruginosa: an antibiotic resilient pathogen with environmental origin. Curr Opin Microbiol 2021; 64:125-132. [PMID: 34710741 DOI: 10.1016/j.mib.2021.09.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 12/24/2022]
Abstract
Pseudomonas aeruginosa, a bacterium characterized for its low antibiotics' susceptibility, is one of the most relevant opportunistic pathogens, causing infections at hospitals and in cystic fibrosis patients. Besides its relevance for human health, P. aeruginosa colonizes environmental ecosystems; therefore the elements driving its infectivity and antibiotic resistance must be analyzed from a One-Health perspective. Although some epidemic clones have been described, there are not specific lineages linked to infections, suggesting that P. aeruginosa virulence and antibiotic resistance determinants evolved in nature to play functions other than infecting the human host and avoiding antimicrobial treatment. Herein, we review current information on the population structure of P. aeruginosa and on the functional role that its resistance and virulence determinants have in non-clinical ecosystems.
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Affiliation(s)
- Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, 28049, Madrid, Spain
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18
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D'Arpa P, Karna SLR, Chen T, Leung KP. Pseudomonas aeruginosa transcriptome adaptations from colonization to biofilm infection of skin wounds. Sci Rep 2021; 11:20632. [PMID: 34667187 PMCID: PMC8526614 DOI: 10.1038/s41598-021-00073-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
In burn patients Pseudomonas aeruginosa infection is a major cause of morbidity. Analysis of the pathogen's gene expression as it transitions from colonization to acute and then biofilm wound infection may provide strategies for infection control. Toward this goal, we seeded log-phase P. aeruginosa (PAO1) into 3-day-old, full-thickness excision wounds (rabbit ear) and harvested the bacteria during colonization (Hrs 2 and 6), acute infection (Hr 24), and biofilm infection (Days 5 and 9) for transcriptome analysis (RNA-Seq). After 2-6 h in the wound, genes for metabolism and cell replication were down-regulated while wound-adaptation genes were up-regulated (vs. expression in log-phase culture). As the infection progressed from acute to biofilm infection, more genes became up-regulated than down-regulated, but the down-regulated genes enriched in more pathways, likely because the genes and pathways that bacteria already colonizing wounds up-regulate to establish biofilm infection are less known. Across the stages of infection, carbon-utilization pathways shifted. During acute infection, itaconate produced by myeloid cells appears to have been a carbon source because myeloid cell infiltration and the expression of the host gene, ACOD1, for itaconate production peaked coincidently with the expression of the PAO1 genes for itaconate transport and catabolism. Additionally, branched-chain amino acids are suggested to be a carbon source in acute infection and in biofilm infection. In biofilm infection, fatty acid degradation was also up-regulated. These carbon sources feed into the glyoxylate cycle that was coincidently up-regulated, suggesting it provided the precursors for P. aeruginosa to synthesize macromolecules in establishing wound infection.
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Affiliation(s)
- Peter D'Arpa
- Combat Wound Repair Group and Tissue Regeneration Department, US Army Institute of Surgical Research, JBSA Fort Sam Houston, San Antonio, TX, USA.,The Geneva Foundation, Tacoma, USA
| | - S L Rajasekhar Karna
- Combat Wound Repair Group and Tissue Regeneration Department, US Army Institute of Surgical Research, JBSA Fort Sam Houston, San Antonio, TX, USA
| | - Tsute Chen
- The Forsyth Institute, Cambridge, MA, USA
| | - Kai P Leung
- Combat Wound Repair Group and Tissue Regeneration Department, US Army Institute of Surgical Research, JBSA Fort Sam Houston, San Antonio, TX, USA.
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19
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Ijoma GN, Nkuna R, Mutungwazi A, Rashama C, Matambo TS. Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production. Sci Rep 2021; 11:19913. [PMID: 34620937 PMCID: PMC8497515 DOI: 10.1038/s41598-021-99389-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
An estimated 25 million tons of animal manure is produced globally every year, causing considerable impact to the environment. These impacts can be managed through the use of anaerobic digestion (AD) This process achieves waste degradation through enzymatic activity, the efficiency of the AD process is directly related to microorganisms that produce these enzymes. Biomethane potential (BMP) assays remain the standard theoretical framework to pre-determine biogas yield and have been used to determine the feasibility of substrates or their combination for biogas production. However, an integrated approach that combines substrate choice and co-digestion would provide an improvement to the current predictive models. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) addresses the limitations of assays in this regard. In this paper, the biochemical functions of horse, cow, and pig manures are predicted. A total of 135 predicted KEGG Orthologies (KOs) showed amino acids, carbohydrate, energy, lipid, and xenobiotic metabolisms in all the samples. Linear discriminant analysis (LDA) combined with the effect size measurements (LEfSe), showed that fructose, mannose, amino acid and nucleotide sugar, phosphotransferase (PST) as well as starch and sucrose metabolisms were significantly higher in horse manure samples. 36 of the KOs were related to the acidogenesis and/or acetogenesis AD stages. Extended bar plots showed that 11 significant predictions were observed for horse-cow, while 5 were predicted for horse-pig and for cow-pig manures. Based on these predictions, the AD process can be enhanced through co-digestion strategies that takes into account the predicted metabolic contributions of the manure samples. The results supported the BMP calculations for the samples in this study. Biogas yields can be improved if this combined approach is employed in routine analysis before co-digesting different substrates.
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Affiliation(s)
- Grace N Ijoma
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa.
| | - Rosina Nkuna
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
| | - Asheal Mutungwazi
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
| | - Charles Rashama
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
| | - Tonderayi S Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
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20
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Impact of artificial sputum media formulation on Pseudomonas aeruginosa secondary metabolite production. J Bacteriol 2021; 203:e0025021. [PMID: 34398662 PMCID: PMC8508215 DOI: 10.1128/jb.00250-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In vitro culture media are being developed to understand how host site-specific nutrient profiles influence microbial pathogenicity and ecology. To mimic the cystic fibrosis (CF) lung environment, a variety of artificial sputum media (ASM) have been created. However, the composition of these ASM vary in the concentration of key nutrients, including amino acids, lipids, DNA, and mucin. In this work, we used feature-based molecular networking (FBMN) to perform comparative metabolomics of Pseudomonas aeruginosa, the predominant opportunistic pathogen infecting the lungs of people with CF, cultured in nine different ASM. We found that the concentration of aromatic amino acids and iron from mucin added to the media contributes to differences in the production of P. aeruginosa virulence-associated secondary metabolites. IMPORTANCE Different media formulations aiming to replicate in vivo infection environments contain different nutrients, which affects interpretation of experimental results. Inclusion of undefined components, such as commercial porcine gastric mucin (PGM), in an otherwise chemically defined medium can alter the nutrient content of the medium in unexpected ways and influence experimental outcomes.
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21
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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.
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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
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22
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Teoh MC, Furusawa G, Veera Singham G. Multifaceted interactions between the pseudomonads and insects: mechanisms and prospects. Arch Microbiol 2021; 203:1891-1915. [PMID: 33634321 DOI: 10.1007/s00203-021-02230-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/19/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023]
Abstract
Insects and bacteria are the most widespread groups of organisms found in nearly all habitats on earth, establishing diverse interactions that encompass the entire range of possible symbiotic associations from strict parasitism to obligate mutualism. The complexity of their interactions is instrumental in shaping the roles of insects in the environment, meanwhile ensuring the survival and persistence of the associated bacteria. This review aims to provide detailed insight on the multifaceted symbiosis between one of the most versatile bacterial genera, Pseudomonas (Gammaproteobacteria: Pseudomonadaceae) and a diverse group of insect species. The Pseudomonas engages with varied interactions with insects, being either a pathogen or beneficial endosymbiont, as well as using insects as vectors. In addition, this review also provides updates on existing and potential applications of Pseudomonas and their numerous insecticidal metabolites as biocontrol agents against pest insects for the improvement of integrated pest management strategies. Here, we have summarized several known modes of action and the virulence factors of entomopathogenic Pseudomonas strains essential for their pathogenicity against insects. Meanwhile, the beneficial interactions between pseudomonads and insects are currently limited to a few known insect taxa, despite numerous studies reporting identification of pseudomonads in the guts and haemocoel of various insect species. The vector-symbiont association between pseudomonads and insects can be diverse from strict phoresy to a role switch from commensalism to parasitism following a dose-dependent response. Overall, the pseudomonads appeared to have evolved independently to be either exclusively pathogenic or beneficial towards insects.
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Affiliation(s)
- Miao-Ching Teoh
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900, Bayan Lepas, Penang, Malaysia
| | - Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900, Bayan Lepas, Penang, Malaysia
| | - G Veera Singham
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900, Bayan Lepas, Penang, Malaysia.
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23
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Shao X, Xie Y, Zhang Y, Liu J, Ding Y, Wu M, Wang X, Deng X. Novel therapeutic strategies for treating Pseudomonas aeruginosa infection. Expert Opin Drug Discov 2020; 15:1403-1423. [PMID: 32880507 DOI: 10.1080/17460441.2020.1803274] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Persistent infections caused by the superbug Pseudomonas aeruginosa and its resistance to multiple antimicrobial agents are huge threats to patients with cystic fibrosis as well as those with compromised immune systems. Multidrug-resistant P. aeruginosa has posed a major challenge to conventional antibiotics and therapeutic approaches, which show limited efficacy and cause serious side effects. The public demand for new antibiotics is enormous; yet, drug development pipelines have started to run dry with limited targets available for inventing new antibacterial drugs. Consequently, it is important to uncover potential therapeutic targets. AREAS COVERED The authors review the current state of drug development strategies that are promising in terms of the development of novel and potent drugs to treat P. aeruginosa infection. EXPERT OPINION The prevention of P. aeruginosa infection is increasingly challenging. Furthermore, targeting key virulence regulators has great potential for developing novel anti-P. aeruginosa drugs. Additional promising strategies include bacteriophage therapy, immunotherapies, and antimicrobial peptides. Additionally, the authors believe that in the coming years, the overall network of molecular regulatory mechanism of P. aeruginosa virulence will be fully elucidated, which will provide more novel and promising drug targets for treating P. aeruginosa infections.
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Affiliation(s)
- Xiaolong Shao
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Yingpeng Xie
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Yingchao Zhang
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Jingui Liu
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Yiqing Ding
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota , Grand Forks, North Dakota, USA
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong , Hong Kong SAR, China.,Shenzhen Research Institute, City University of Hong Kong , Shenzhen, China
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