1
|
Guillaume O, Butnarasu C, Visentin S, Reimhult E. Interplay between biofilm microenvironment and pathogenicity of Pseudomonas aeruginosa in cystic fibrosis lung chronic infection. Biofilm 2022; 4:100089. [PMID: 36324525 PMCID: PMC9618985 DOI: 10.1016/j.bioflm.2022.100089] [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: 08/02/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
Pseudomonas aeruginosa (PA) is a highly, if not the most, versatile microorganism capable of colonizing diverse environments. One of the niches in which PA is able to thrive is the lung of cystic fibrosis (CF) patients. Due to a genetic aberration, the lungs of CF-affected patients exhibit impaired functions, rendering them highly susceptible to bacterial colonization. Once PA attaches to the epithelial surface and transitions to a mucoid phenotype, the infection becomes chronic, and antibiotic treatments become inefficient. Due to the high number of affected people and the severity of this infection, CF-chronic infection is a well-documented disease. Still, numerous aspects of PA CF infection remain unclear. The scientific reports published over the last decades have stressed how PA can adapt to CF microenvironmental conditions and how its surrounding matrix of extracellular polymeric substances (EPS) plays a key role in its pathogenicity. In this context, it is of paramount interest to present the nature of the EPS together with the local CF-biofilm microenvironment. We review how the PA biofilm microenvironment interacts with drugs to contribute to the pathogenicity of CF-lung infection. Understanding why so many drugs are inefficient in treating CF chronic infection while effectively treating planktonic PA is essential to devising better therapeutic targets and drug formulations.
Collapse
Affiliation(s)
- Olivier Guillaume
- 3D Printing and Biofabrication Group, Institute of Materials Science and Technology, TU Wien (Technische Universität Wien), Getreidemarkt 9/308, 1060, Vienna, Austria,Austrian Cluster for Tissue Regeneration, Austria,Corresponding author. 3D Printing and Biofabrication Group, Institute of Materials Science and Technology, TU Wien (Technische Universität Wien), Getreidemarkt 9/308, 1060, Vienna, Austria.
| | - Cosmin Butnarasu
- Department of Molecular Biotechnology and Health Science, University of Turin, Turin, 10135, Italy
| | - Sonja Visentin
- Department of Molecular Biotechnology and Health Science, University of Turin, Turin, 10135, Italy
| | - Erik Reimhult
- Institute of Biologically Inspired Materials, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 11, 1190, Vienna, Austria
| |
Collapse
|
2
|
Afridi MS, Javed MA, Ali S, De Medeiros FHV, Ali B, Salam A, Sumaira, Marc RA, Alkhalifah DHM, Selim S, Santoyo G. New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:899464. [PMID: 36186071 PMCID: PMC9524194 DOI: 10.3389/fpls.2022.899464] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 07/30/2023]
Abstract
Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.
Collapse
Affiliation(s)
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), São Paulo, Brazil
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sumaira
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| |
Collapse
|
3
|
Rojas-Gätjens D, Valverde-Madrigal KS, Rojas-Jimenez K, Pereira R, Avey-Arroyo J, Chavarría M. Antibiotic-producing Micrococcales govern the microbiome that inhabits the fur of two- and three-toed sloths. Environ Microbiol 2022; 24:3148-3163. [PMID: 35621042 DOI: 10.1111/1462-2920.16082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022]
Abstract
Sloths have a dense coat on which insects, algae, and fungi coexist in a symbiotic relationship. This complex ecosystem requires different levels of control, however, most of these mechanisms remain unknown. We investigated the bacterial communities inhabiting the hair of two- (Choloepus Hoffmani) and three-toed (Bradypus variegatus) sloths and evaluated their potential for producing antibiotic molecules capable of exerting control over the hair microbiota. The analysis of 16S rRNA amplicon sequence variants (ASVs) revealed that the communities in both host species are dominated by Actinobacteriota and Firmicutes. The most abundant genera were Brevibacterium, Kocuria/Rothia, Staphylococcus, Rubrobacter, Nesterenkonia, and Janibacter. Furthermore, we isolated nine strains of Brevibacterium and Rothia capable of producing substances that inhibited the growth of common mammalian pathogens. The analysis of the biosynthetic gene clusters (BCGs) of these nine isolates suggests that the pathogen-inhibitory activity could be mediated by the presence of siderophores, terpenes, beta-lactones, Type III polyketide synthases (T3PKS), ribosomally synthesized, and post-translationally modified peptides (RiPPs), non-alpha poly-amino acids (NAPAA) like e-Polylysin, ectoine or nonribosomal peptides (NRPs). Our data suggest that Micrococcales that inhabit sloth hair could have a role in controlling microbial populations in that habitat, improving our understanding of this highly complex ecosystem. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Reinaldo Pereira
- Laboratorio Nacional de Nanotecnología (LANOTEC), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| |
Collapse
|
4
|
Ambreetha S, Marimuthu P, Mathee K, Balachandar D. Rhizospheric and endophytic Pseudomonas aeruginosa in edible vegetable plants share molecular and metabolic traits with clinical isolates. J Appl Microbiol 2021; 132:3226-3248. [PMID: 34608722 DOI: 10.1111/jam.15317] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/28/2021] [Accepted: 09/21/2021] [Indexed: 01/02/2023]
Abstract
AIM Pseudomonas aeruginosa, a leading opportunistic pathogen causing hospital-acquired infections, is also commonly found in agricultural settings. However, there are minimal attempts to examine the molecular and functional attributes shared by agricultural and clinical strains of P. aeruginosa. This study investigates the presence of P. aeruginosa in edible vegetable plants (including salad vegetables) and analyses the evolutionary and metabolic relatedness of the agricultural and clinical strains. METHODS AND RESULTS Eighteen rhizospheric and endophytic P. aeruginosa strains were isolated from cucumber, tomato, eggplant, and chili directly from the farms. The identity of these strains was confirmed using biochemical and molecular assays. The genetic and metabolic traits of these plant-associated P. aeruginosa isolates were compared with clinical strains. DNA fingerprinting and 16S rDNA-based phylogenetic analyses revealed that the plant- and human-associated strains are evolutionarily related. Both agricultural and clinical isolates possessed plant-beneficial properties, including mineral solubilization to release essential nutrients (phosphorous, potassium, and zinc), ammonification, and the ability to release extracellular pyocyanin, siderophore, and indole-3 acetic acid. CONCLUSION These findings suggest that rhizospheric and endophytic P. aeruginosa strains are genetically and functionally analogous to the clinical isolates. In addition, the genotypic and phenotypic traits do not correlate with plant sources or ecosystems. SIGNIFICANCE AND IMPACT OF THE STUDY This study reconfirms that edible plants are the potential source for human and animal transmission of P. aeruginosa.
Collapse
Affiliation(s)
- Sakthivel Ambreetha
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.,Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
| | - Ponnusamy Marimuthu
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA.,Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Dananjeyan Balachandar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| |
Collapse
|
5
|
Soto W, Nishiguchi MK. Environmental Stress Selects for Innovations That Drive Vibrio Symbiont Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.616973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Symbiotic bacteria in the Vibrionaceae are a dynamic group of γ-Proteobacteria that are commonly found throughout the world. Although they primarily are free-living in the environment, they can be commonly found associated with various Eukarya, either as beneficial or pathogenic symbionts. Interestingly, this dual lifestyle (free-living or in symbiosis) enables the bacteria to have enormous ecological breadth, where they can accommodate a variety of stresses in both stages. Here, we discuss some of the most common stressors that Vibrio bacteria encounter when in their free-living state or associated with an animal host, and how some of the mechanisms that are used to cope with these stressors can be used as an evolutionary advantage that increases their diversity both in the environment and within their specific hosts.
Collapse
|
6
|
Camus L, Vandenesch F, Moreau K. From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment. Microb Genom 2021; 7:mgen000513. [PMID: 33529147 PMCID: PMC8190622 DOI: 10.1099/mgen.0.000513] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile pulmonary environment, P. aeruginosa is able to establish chronic infections thanks to its strong adaptive capacity. Various longitudinal studies have attempted to compare the strains of early infection with the adapted strains of chronic infection. Thanks to new '-omics' techniques, convergent genetic mutations, as well as transcriptomic and proteomic dysregulations have been identified. As a consequence of this evolution, the adapted strains of P. aeruginosa have particular phenotypes that promote persistent infection.
Collapse
Affiliation(s)
- Laura Camus
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
| | - François Vandenesch
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Karen Moreau
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
| |
Collapse
|
7
|
Seers CA, Mahmud ASM, Huq NL, Cross KJ, Reynolds EC. Porphyromonas gingivalis laboratory strains and clinical isolates exhibit different distribution of cell surface and secreted gingipains. J Oral Microbiol 2020; 13:1858001. [PMID: 33391630 PMCID: PMC7733959 DOI: 10.1080/20002297.2020.1858001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: The cell-surface cysteine proteinases RgpA, RgpB (Arg-gingipain), and Kgp (Lys-gingipain) are major virulence factors of P. gingivalis, a keystone pathogen in the development of destructive periodontal disease. The gingipains function as proteinases and transpeptidases utilising small peptides such as glycylglycine as acceptor molecules. However, the characteristics of the gingipains from most P. gingivalis strains have not been determined. Methods: We determined the phenotypes of a panel of P. gingivalis laboratory strains and global clinical isolates with respect to growth on blood agar plus whole-cell and vesicle-free culture supernatant (VFSN) Arg- and Lys-specific proteinase activities. Results: The P. gingivalis isolates exhibited different growth characteristics and hydrolysis of haemoglobin in solid media. Whole-cell Arg-gingipain Vmax varied 5.8-fold and the whole cell Lys-gingipain Vmax varied 2.1-fold across the strains. Furthermore, the P. gingivalis strains showed more than 107-fold variance in soluble Arg-gingipain activity in VFSN and more than 371-fold variance in soluble Lys-gingipain activity in VFSN. Glycylglycine and cysteine stimulated Arg- and Lys-specific cleavage activities of all strains. The stimulation by cysteine was in addition to its redox effect consistent with both glycylglycine and cysteine promoting transpeptidation.
Conclusion: The global P. gingivalis clinical isolates exhibit different Arg- and Lys‑gingipain activities with substantial variability in the level of soluble proteinases released into the environment.
Collapse
Affiliation(s)
- Christine A Seers
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - A Sayeed M Mahmud
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - N Laila Huq
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Keith J Cross
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| |
Collapse
|
8
|
A Al-Kafaween M, Mohd Hilmi AB, A Nagi Al-Jamal H, A Elsahoryi N, Jaffar N, Khairi Zahri M. Pseudomonas Aeruginosa and Streptococcus Pyogenes Exposed to Malaysian Trigona Honey In Vitro Demonstrated Downregulation of Virulence Factor. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2542. [PMID: 34056021 PMCID: PMC8148639 DOI: 10.30498/ijb.2020.2542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Honey has been known as a traditional medicine for centuries with its antibacterial properties. It is considered one of the most enduring substances used in wound management. Objectives This study aimed to: (i) evaluate the effects of Malaysian Trigona honey on bacterial structure and (ii) assess the anti-virulence potential of this honey by examining their impacts on the expression of selected genes (involved in stress survival and biofilm formation) in a test organism. Materials and Methods Trigona honey's impacts on the bacterial structure (cell morphology) and the expression profiles of select Pseudomonas Aeruginosa and Streptococcus Pyogenes genes were examined using scanning electron microscopy (SEM) and real-time PCR (RT-qPCR) analysis, respectively. Results SEM showed that the decreased cell density deformed, disrupted, and damaged cells for both bacteria. RT-qPCR showed that the expression of fleN, fleQ, and fleR genes of P.aeruginosa were decreased, 4.26-fold, 3.80-fold and 2.66- fold respectively. In addition, scpA, ftsY, and emm13 of S.pyogenes were decreased, 2.87-fold, 3.24-fold, and 4.65-fold respectively. Conclusion Our results indicate that Trigona honey may be an effective inhibitor and virulence modulator of P. aeruginosa and S. pyogenes via multiple molecular targets. This deduction needs to be investigated in vivo.
Collapse
Affiliation(s)
| | - Abu Bakar Mohd Hilmi
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Terengganu, Malaysia
| | | | - Nour A Elsahoryi
- Department of Nutrition /Faculty of Pharmacy and Medical Sciences/University of Petra/Amman/Jordan
| | - Norzawani Jaffar
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Terengganu, Malaysia
| | - Mohd Khairi Zahri
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Terengganu, Malaysia
| |
Collapse
|
9
|
Redfern J, Enright MC. Further understanding of Pseudomonas aeruginosa’s ability to horizontally acquire virulence: possible intervention strategies. Expert Rev Anti Infect Ther 2020; 18:539-549. [DOI: 10.1080/14787210.2020.1751610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- James Redfern
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Mark C. Enright
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| |
Collapse
|
10
|
Booth SC, Turner RJ. Phylogenetic characterization of the energy taxis receptor Aer in Pseudomonas and phenotypic characterization in Pseudomonas pseudoalcaligenes KF707. MICROBIOLOGY-SGM 2020; 165:1331-1344. [PMID: 31639075 DOI: 10.1099/mic.0.000864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemotaxis allows bacteria to sense gradients in their environment and respond by directing their swimming. Aer is a receptor that, instead of responding to a specific chemoattractant, allows bacteria to sense cellular energy levels and move towards favourable environments. In Pseudomonas, the number of apparent Aer homologues differs between the only two species it has been characterized in, Pseudomonas aeruginosa and Pseudomonas putida. Here we combined bioinformatic approaches with deletional mutagenesis in Pseudomonas pseudoalcaligenes KF707 to further characterize Aer. It was determined that the number of Aer homologues varies between zero and four throughout the genus Pseudomonas, and they were phylogenetically classified into five subgroups. We also used sequence analysis to show that these homologous receptors differ in their HAMP signal transduction domains. Genetic analysis also indicated that some Aer homologues have likely been subject to horizontal transfer. P. pseudoalcaligenes KF707 was unique among strains for having three Aer homologues as well as the receptors CttP and McpB. Phenotypic characterization in this strain showed that the most prevalent homologue of Aer was key, but not essential, for energy taxis. This study demonstrates that energy taxis in Pseudomonas varies between species and provides a new naming convention and associated phylogenetic details for Aer chemoreceptors.
Collapse
Affiliation(s)
- Sean C Booth
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Present address: Department of Zoology, University of Oxford, Oxford, UK
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
11
|
Shaw E, Wuest WM. Virulence attenuating combination therapy: a potential multi-target synergy approach to treat Pseudomonas aeruginosa infections in cystic fibrosis patients. RSC Med Chem 2020; 11:358-369. [PMID: 33479641 PMCID: PMC7580779 DOI: 10.1039/c9md00566h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/06/2020] [Indexed: 12/15/2022] Open
Abstract
The World Health Organization considers the discovery of new treatments for P. aeruginosa a top priority. Virulence attenuating combination therapy (VACT) is a pragmatic strategy to improve bacterial clearance, repurpose outmoded antibiotics, improve drug efficacy at lower doses, and reduce the evolution of resistance. In vitro and in vivo studies have shown that adding a quorum sensing inhibitor or an extracellular polymeric substance repressor to classical antibiotics synergistically improves antipseudomonal activity. This review highlights why VACT could specifically benefit cystic fibrosis patients harboring chronic P. aeruginosa infections, outlines the current landscape of synergistic combinations between virulence-targeting small-molecules and anti-pseudomonal drugs, and suggests future directions for VACT research.
Collapse
Affiliation(s)
- Elana Shaw
- Department of Chemistry , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , USA .
| | - William M Wuest
- Department of Chemistry , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , USA .
- Emory Antibiotic Resistance Center , Emory University School of Medicine , 201 Dowman Drive , Atlanta , Georgia 30322 , USA
| |
Collapse
|
12
|
Diversity of Contact-Dependent Growth Inhibition Systems of Pseudomonas aeruginosa. J Bacteriol 2019; 201:JB.00776-18. [PMID: 31036723 DOI: 10.1128/jb.00776-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) systems are used in bacterial competition to hinder the growth of neighboring microbes. These systems utilize a two-partner secretion mechanism to display the CdiA exoprotein at the bacterial cell surface. CdiA forms a long filamentous stalk that facilitates binding to a target cell and delivery of a C-terminal toxin (CT) domain. This CT domain is processed and delivered into the cytoplasm of a target cell upon contact. CDI systems also encode a cognate immunity protein (CdiI) that protects siblings and resistant targeted cells from intoxication by high-affinity binding to the CT. CdiA CT domains vary among strains within a species, and many alleles encode enzymatic functions that target nucleic acids. This variation is thought to help drive diversity and adaptation within a species. CdiA diversity is well studied in Escherichia coli and several other bacteria, but little is known about the extent of this diversity in Pseudomonas aeruginosa. The purpose of this review is to highlight the variability that exists in CDI systems of P. aeruginosa. We show that this diversity is apparent even among strains isolated from a single geographical region, suggesting that CDI systems play an important role in the ecology of P. aeruginosa.
Collapse
|
13
|
Holbrook SY, Garneau-Tsodikova S. Evaluation of Aminoglycoside and Carbapenem Resistance in a Collection of Drug-Resistant Pseudomonas aeruginosa Clinical Isolates. Microb Drug Resist 2018; 24:1020-1030. [PMID: 29261405 PMCID: PMC6154764 DOI: 10.1089/mdr.2017.0101] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium, is a member of the ESKAPE pathogens and one of the leading causes of healthcare-associated infections worldwide. Aminoglycosides (AGs) are recognized for their efficacy against P. aeruginosa. The most common resistance mechanism against AGs is the acquisition of AG-modifying enzymes (AMEs) by the bacteria, including AG N-acetyltransferases (AACs), AG O-phosphotransferases (APHs), and AG O-nucleotidyltransferases (ANTs). In this study, we obtained 122 multidrug-resistant P. aeruginosa clinical isolates and evaluated the antibacterial effects of six AGs and two carbapenems alone against all clinical isolates, and in combination against eight selected strains. We further probed for four representatives of the most common AME genes [aac(6')-Ib, aac(3)-IV, ant(2")-Ia, and aph(3')-Ia] by polymerase chain reaction (PCR) and compared the AME patterns of these 122 clinical isolates to their antibiotic resistance profile. Among the diverse antibiotics resistance profile displayed by these clinical isolates, we found correlations between the resistance to various AGs as well as between the resistance to one AG and the resistance to carbapenems. PCR results revealed that the presence of aac(6')-Ib renders these isolates more resistant to a variety of antibiotics. The correlation between resistance to various AGs and carbapenems partially reflects the complex resistance strategies adapted in these pathogens and encourages the development of strategic treatment for each P. aeruginosa infection by considering the genetic information of each isolated bacteria.
Collapse
Affiliation(s)
- Selina Y.L. Holbrook
- College of Pharmacy, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky
| | - Sylvie Garneau-Tsodikova
- College of Pharmacy, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky
| |
Collapse
|
14
|
Sergaki C, Lagunas B, Lidbury I, Gifford ML, Schäfer P. Challenges and Approaches in Microbiome Research: From Fundamental to Applied. FRONTIERS IN PLANT SCIENCE 2018; 9:1205. [PMID: 30174681 PMCID: PMC6107787 DOI: 10.3389/fpls.2018.01205] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/26/2018] [Indexed: 05/07/2023]
Abstract
We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).
Collapse
Affiliation(s)
- Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Chrysi Sergaki,
| | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
| |
Collapse
|
15
|
Yu Y, Qian Y, Du D, Li Q, Xu C, Liu H, Chen M, Yao H, Lu C, Zhang W. Infection and adaption-based proteomic changes of Streptococcus suis serotype 2 in a pig model. J Proteomics 2017; 180:41-52. [PMID: 29247804 DOI: 10.1016/j.jprot.2017.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 11/10/2017] [Accepted: 12/01/2017] [Indexed: 12/28/2022]
Abstract
Streptococcus suis (S. suis) is an emerging zoonotic agent that is responsible for significant economic losses to the porcine industry worldwide. However, most research regarding the pathogenic mechanisms has used in vitro cultures of S. suis, which may not provide an accurate representation of the in vivo biological activities. In this study, 188 differential abundance S. suis proteins were identified in in vivo samples obtained from the blood of the infected pigs. These were compared with in vitro samples by a Tandem Mass Tags (TMT) experiment. Thus, a virulence associated network was established using the enriched differential abundance proteins (obtained via bioinformatics analysis in this study) and the previously reported putative virulence factors associated with in vivo infection. One of the most important up-regulated hubs in this network, adhE (an acetaldehyde-CoA/alcohol dehydrogenase) was found. Furthermore, knocking out adhE in S. suis serotype 2 strain ZY05719 decreased virulence. Cell culture experiments and far-western blot analysis showed that adhE is involved in adhesion to Caco-2 cells; Hsp60 could be one of the receptors for this protein. SIGNIFICANCE This study is a systematical research to identify in vivo regulated virulence associated proteins of S. suis in pigs. It constructs a network consisting of in vivo infection related factors for the first time to get to know the coordinated actions of a multitude of factors that lead to host pathogenicity and filter the most important hubs. The individual factors that contribute to infection is also identified. A novel differential protein adhE which is one of the most important hubs of this network and is up-regulated in abundance in vivo is found to moonlight as an important adhesion by binding Hsp60 and finally contributes to virulence.
Collapse
Affiliation(s)
- Yanfei Yu
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China; Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, National Center for Engineering Research of Veterinary Bio-products, Nanjing 210014, China
| | - Yunyun Qian
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dechao Du
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Quan Li
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chenyang Xu
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hanze Liu
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Mianmian Chen
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Huochun Yao
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chengping Lu
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wei Zhang
- Key Lab of Animal Bacteriology of Ministry of Agriculture, College of Veterinary Medicine & OIE Swine Streptococcosis Diagnostic Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
16
|
Molina L, Udaondo Z, Duque E, Fernández M, Bernal P, Roca A, de la Torre J, Ramos JL. Specific Gene Loci of Clinical Pseudomonas putida Isolates. PLoS One 2016; 11:e0147478. [PMID: 26820467 PMCID: PMC4731212 DOI: 10.1371/journal.pone.0147478] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/05/2016] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas putida are ubiquitous inhabitants of soils and clinical isolates of this species have been seldom described. Clinical isolates show significant variability in their ability to cause damage to hosts because some of them are able to modulate the host’s immune response. In the current study, comparisons between the genomes of different clinical and environmental strains of P. putida were done to identify genetic clusters shared by clinical isolates that are not present in environmental isolates. We show that in clinical strains specific genes are mostly present on transposons, and that this set of genes exhibit high identity with genes found in pathogens and opportunistic pathogens. The set of genes prevalent in P. putida clinical isolates, and absent in environmental isolates, are related with survival under oxidative stress conditions, resistance against biocides, amino acid metabolism and toxin/antitoxin (TA) systems. This set of functions have influence in colonization and survival within human tissues, since they avoid host immune response or enhance stress resistance. An in depth bioinformatic analysis was also carried out to identify genetic clusters that are exclusive to each of the clinical isolates and that correlate with phenotypical differences between them, a secretion system type III-like was found in one of these clinical strains, a determinant of pathogenicity in Gram-negative bacteria.
Collapse
Affiliation(s)
- Lázaro Molina
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- * E-mail:
| | - Zulema Udaondo
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- Abengoa Research, Campus de las Palmas Altas, Sevilla, Spain
| | - Estrella Duque
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- Abengoa Research, Campus de las Palmas Altas, Sevilla, Spain
| | - Matilde Fernández
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
| | - Patricia Bernal
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- Imperial College London, South Kensington Campus, London, United Kingdom
| | - Amalia Roca
- Bio-Iliberis R&D, C/ Capileira 7, 18210 Peligros, Granada, Spain
| | - Jesús de la Torre
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
| | - Juan Luis Ramos
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- Abengoa Research, Campus de las Palmas Altas, Sevilla, Spain
| |
Collapse
|
17
|
Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes. Appl Environ Microbiol 2015; 81:7668-79. [PMID: 26296728 DOI: 10.1128/aem.01367-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/09/2015] [Indexed: 01/23/2023] Open
Abstract
Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (P < 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of Flavobacteriaceae spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family Ruminococcaceae, class Bacilli, or phylum Proteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems.
Collapse
|
18
|
Genome sequence of Xanthomonas sacchari R1, a biocontrol bacterium isolated from the rice seed. J Biotechnol 2015; 206:77-8. [PMID: 25931193 DOI: 10.1016/j.jbiotec.2015.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 04/20/2015] [Indexed: 11/24/2022]
Abstract
Xanthomonas sacchari, was first identified as a pathogenic bacterium isolated from diseased sugarcane in Guadeloupe. In this study, R1 was first isolated from rice seed samples from Philippines in 2002. The antagonistic ability against several rice pathogens raises our attention. The genomic feature of this strain was described in this paper. The total genome size of X. sacchari R1 is 5,000,479 bp with 4315 coding sequences (CDS), 59 tRNAs, 2rRNAs and one plasmid.
Collapse
|
19
|
Subramoni S, Florez Salcedo DV, Suarez-Moreno ZR. A bioinformatic survey of distribution, conservation, and probable functions of LuxR solo regulators in bacteria. Front Cell Infect Microbiol 2015; 5:16. [PMID: 25759807 PMCID: PMC4338825 DOI: 10.3389/fcimb.2015.00016] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 02/02/2015] [Indexed: 12/25/2022] Open
Abstract
LuxR solo transcriptional regulators contain both an autoinducer binding domain (ABD; N-terminal) and a DNA binding Helix-Turn-Helix domain (HTH; C-terminal), but are not associated with a cognate N-acyl homoserine lactone (AHL) synthase coding gene in the same genome. Although a few LuxR solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. In this study we have carried out a systematic survey of distribution of all ABD containing LuxR transcriptional regulators (QS domain LuxRs) available in the InterPro database (IPR005143), and identified those lacking a cognate AHL synthase. These LuxR solos were then analyzed regarding their taxonomical distribution, predicted functions of neighboring genes and the presence of complete AHL-QS systems in the genomes that carry them. Our analyses reveal the presence of one or multiple predicted LuxR solos in many proteobacterial genomes carrying QS domain LuxRs, some of them harboring genes for one or more AHL-QS circuits. The presence of LuxR solos in bacteria occupying diverse environments suggests potential ecological functions for these proteins beyond AHL and interkingdom signaling. Based on gene context and the conservation levels of invariant amino acids of ABD, we have classified LuxR solos into functionally meaningful groups or putative orthologs. Surprisingly, putative LuxR solos were also found in a few non-proteobacterial genomes which are not known to carry AHL-QS systems. Multiple predicted LuxR solos in the same genome appeared to have different levels of conservation of invariant amino acid residues of ABD questioning their binding to AHLs. In summary, this study provides a detailed overview of distribution of LuxR solos and their probable roles in bacteria with genome sequence information.
Collapse
Affiliation(s)
- Sujatha Subramoni
- Grupo de Bioprospección, Facultad de Ingeniería, Universidad de La Sabana, Campus del Puente del Común Chía, Colombia
| | | | - Zulma R Suarez-Moreno
- Grupo de Bioprospección, Facultad de Ingeniería, Universidad de La Sabana, Campus del Puente del Común Chía, Colombia
| |
Collapse
|
20
|
Beier R, Foley S, Davidson M, White D, McDermott P, Bodeis-Jones S, Zhao S, Andrews K, Crippen T, Sheffield C, Poole T, Anderson R, Nisbet D. Characterization of antibiotic and disinfectant susceptibility profiles among Pseudomonas aeruginosa
veterinary isolates recovered during 1994-2003. J Appl Microbiol 2014; 118:326-42. [DOI: 10.1111/jam.12707] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/06/2014] [Accepted: 11/14/2014] [Indexed: 11/28/2022]
Affiliation(s)
- R.C. Beier
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - S.L. Foley
- Division of Microbiology, National Center for Toxicological Research; U.S. Food and Drug Administration; Jefferson AR USA
| | - M.K. Davidson
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - D.G. White
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - P.F. McDermott
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - S. Bodeis-Jones
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - S. Zhao
- Office of Research; Center for Veterinary Medicine; U.S. Food and Drug Administration; Laurel MD USA
| | - K. Andrews
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - T.L. Crippen
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - C.L. Sheffield
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - T.L. Poole
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - R.C. Anderson
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| | - D.J. Nisbet
- Southern Plains Agricultural Research Center; Agricultural Research Service; U.S. Department of Agriculture; College Station TX USA
| |
Collapse
|
21
|
Juhas M. Type IV secretion systems and genomic islands-mediated horizontal gene transfer in Pseudomonas and Haemophilus. Microbiol Res 2014; 170:10-7. [PMID: 25183653 DOI: 10.1016/j.micres.2014.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/28/2014] [Accepted: 06/30/2014] [Indexed: 11/16/2022]
Abstract
Bacterial secretion systems, such as type IV secretion systems (T4SSs) are multi-subunit machines transferring macromolecules across membranes. Besides proteins, T4SSs also transfer nucleoprotein complexes, thus having a significant impact on the evolution of bacterial species. By T4SS-mediated horizontal gene transfer bacteria can acquire a broad spectrum of fitness genes allowing them to thrive in the wide variety of environments. Furthermore, acquisition of antibiotic-resistance and virulence genes can lead to the emergence of novel 'superbugs'. This review provides an update on the investigation of T4SSs. It highlights the role T4SSs play in the horizontal gene transfer, particularly in the evolution of catabolic pathways, antibiotic-resistance and virulence in Haemophilus and Pseudomonas.
Collapse
Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP Cambridge, UK.
| |
Collapse
|
22
|
Tümmler B, Wiehlmann L, Klockgether J, Cramer N. Advances in understanding Pseudomonas. F1000PRIME REPORTS 2014; 6:9. [PMID: 24592321 PMCID: PMC3913036 DOI: 10.12703/p6-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pseudomonas aeruginosa, the type species of pseudomonads, is an opportunistic pathogen that colonizes a wide range of niches. Current genome sequencing projects are producing previously inconceivable detail about the population biology and evolution of P. aeruginosa. Its pan-genome has a larger genetic repertoire than the human genome, which explains the broad metabolic capabilities of P. aeruginosa and its ubiquitous distribution in aquatic habitats. P. aeruginosa may persist in the airways of individuals with cystic fibrosis for decades. The ongoing whole-genome analyses of serial isolates from cystic fibrosis patients provide the so far singular opportunity to monitor the microevolution of a bacterial pathogen during chronic infection over thousands of generations. Although the evolution in cystic fibrosis lungs is neutral overall, some pathoadaptive mutations are selected during the within-host evolutionary process. Even a single mutation may be sufficient to generate novel complex traits provided that predisposing mutational events have previously occurred in the clonal lineage.
Collapse
|
23
|
Lim YW, Schmieder R, Haynes M, Willner D, Furlan M, Youle M, Abbott K, Edwards R, Evangelista J, Conrad D, Rohwer F. Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. J Cyst Fibros 2012; 12:154-64. [PMID: 22951208 DOI: 10.1016/j.jcf.2012.07.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/15/2012] [Accepted: 07/27/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND Samples collected from CF patient airways often contain large amounts of host-derived nucleic acids that interfere with recovery and purification of microbial and viral nucleic acids. This study describes metagenomic and metatranscriptomic methods that address these issues. METHODS Microbial and viral metagenomes, and microbial metatranscriptomes, were successfully prepared from sputum samples from five adult CF patients. RESULTS Contaminating host DNA was dramatically reduced in the metagenomes. Each CF patient presented a unique microbiome; in some Pseudomonas aeruginosa was replaced by other opportunistic bacteria. Even though the taxonomic composition of the microbiomes is very different, the metabolic potentials encoded by the community are very similar. The viral communities were dominated by phages that infect major CF pathogens. The metatranscriptomes reveal differential expression of encoded metabolic potential with changing health status. CONCLUSIONS Microbial and viral metagenomics combined with microbial transcriptomics characterize the dynamic polymicrobial communities found in CF airways, revealing both the taxa present and their current metabolic activities. These approaches can facilitate the development of individualized treatment plans and novel therapeutic approaches.
Collapse
Affiliation(s)
- Yan Wei Lim
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
| | - Robert Schmieder
- Computational Science Research Center, San Diego State University, San Diego, CA, 92182, USA
| | - Matthew Haynes
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA; DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Dana Willner
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Mike Furlan
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | | | - Katelynn Abbott
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Robert Edwards
- Computational Science Research Center, San Diego State University, San Diego, CA, 92182, USA; Mathematics and Computer Science Division, Argonne National, Laboratory, Argonne, IL 60439, USA
| | - Jose Evangelista
- Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Douglas Conrad
- Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| |
Collapse
|
24
|
Structural and functional consequences of mutating a proteobacteria-specific surface residue in the catalytic domain of Escherichia coli GluRS. FEBS Lett 2012; 586:1724-30. [PMID: 22584057 DOI: 10.1016/j.febslet.2012.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/02/2012] [Accepted: 05/02/2012] [Indexed: 11/22/2022]
Abstract
Nucleotides whose mutations seriously affect glutamylation efficiency are experimentally known for Escherichia coli tRNA(Glu). However, not much is known about functional hotspots on the complementary enzyme, glutamyl-tRNA synthetase (GluRS). From structural and functional studies on an Arg266Leu mutant of E. coli GluRS, we demonstrate that Arg266 is essential for efficient glutamylation of tRNA(Glu). Consistent with this result, we found that Arg266 is a conserved signature of proteobacterial GluRS. In contrast, most non-proteobacterial GluRS contain Leu, and never Arg, at this position. Our results imply a unique strategy of glutamylation of tRNA(Glu) in proteobacteria under phylum-specific evolutionary compulsions.
Collapse
|
25
|
Genotypic and phenotypic variation in Pseudomonas aeruginosa reveals signatures of secondary infection and mutator activity in certain cystic fibrosis patients with chronic lung infections. Infect Immun 2011; 79:4802-18. [PMID: 21930755 DOI: 10.1128/iai.05282-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Evolutionary adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung is limited by genetic variation, which depends on rates of horizontal gene transfer and mutation supply. Because each may increase following secondary infection or mutator emergence, we sought to ascertain the incidence of secondary infection and genetic variability in populations containing or lacking mutators. Forty-nine strains collected over 3 years from 16 patients were phenotyped for antibiotic resistance and mutator status and were genotyped by repetitive-sequence PCR (rep-PCR), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Though phenotypic and genetic polymorphisms were widespread and clustered more strongly within than between longitudinal series, their distribution revealed instances of secondary infection. Sequence data, however, indicated that interlineage recombination predated initial strain isolation. Mutator series were more likely to be multiply antibiotic resistant, but not necessarily more variable in their nucleotide sequences, than nonmutators. One mutator and one nonmutator series were sequenced at mismatch repair loci and analyzed for gene content using DNA microarrays. Both were wild type with respect to mutL, but mutators carried an 8-bp mutS deletion causing a frameshift mutation. Both series lacked 126 genes encoding pilins, siderophores, and virulence factors whose inactivation has been linked to adaptation during chronic infection. Mutators exhibited loss of severalfold more genes having functions related to mobile elements, motility, and attachment. A 105-kb, 86-gene deletion was observed in one nonmutator that resulted in loss of virulence factors related to pyoverdine synthesis and elements of the multidrug efflux regulon. Diminished DNA repair activity may facilitate but not be absolutely required for rapid evolutionary change.
Collapse
|
26
|
Abstract
Pseudomonas aeruginosa strains exhibit significant variability in pathogenicity and ecological flexibility. Such interstrain differences reflect the dynamic nature of the P. aeruginosa genome, which is composed of a relatively invariable "core genome" and a highly variable "accessory genome." Here we review the major classes of genetic elements comprising the P. aeruginosa accessory genome and highlight emerging themes in the acquisition and functional importance of these elements. Although the precise phenotypes endowed by the majority of the P. aeruginosa accessory genome have yet to be determined, rapid progress is being made, and a clearer understanding of the role of the P. aeruginosa accessory genome in ecology and infection is emerging.
Collapse
|
27
|
Jackson RW, Johnson LJ, Clarke SR, Arnold DL. Bacterial pathogen evolution: breaking news. Trends Genet 2010; 27:32-40. [PMID: 21047697 DOI: 10.1016/j.tig.2010.10.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 09/21/2010] [Accepted: 10/07/2010] [Indexed: 02/04/2023]
Abstract
The immense social and economic impact of bacterial pathogens, from drug-resistant infections in hospitals to the devastation of agricultural resources, has resulted in major investment to understand the causes and consequences of pathogen evolution. Recent genome sequencing projects have provided insight into the evolution of bacterial genome structures; revealing the impact of mobile DNA on genome restructuring and pathogenicity. Sequencing of multiple genomes of related strains has enabled the delineation of pathogen evolution and facilitated the tracking of bacterial pathogens globally. Other recent theoretical and empirical studies have shown that pathogen evolution is significantly influenced by ecological factors, such as the distribution of hosts within the environment and the effects of co-infection. We suggest that the time is ripe for experimentalists to use genomics in conjunction with evolutionary ecology experiments to further understanding of how bacterial pathogens evolve.
Collapse
Affiliation(s)
- Robert W Jackson
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AJ, UK.
| | | | | | | |
Collapse
|
28
|
Variation in Streptococcus pyogenes NAD+ glycohydrolase is associated with tissue tropism. J Bacteriol 2010; 192:3735-46. [PMID: 20494994 DOI: 10.1128/jb.00234-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Streptococcus pyogenes is an important pathogen that causes a variety of diseases. The most common infections involve the throat (pharyngitis) or skin (impetigo); however, the factors that determine tissue tropism and severity are incompletely understood. The S. pyogenes NAD(+) glycohydrolase (SPN) is a virulence factor that has been implicated in contributing to the pathogenesis of severe infections. However, the role of SPN in determining the bacterium's tissue tropism has not been evaluated. In this report, we examine the sequences of spn and its endogenous inhibitor ifs from a worldwide collection of S. pyogenes strains. Analysis of average pairwise nucleotide diversity, average number of nucleotide differences, and ratio of nonsynonymous to synonymous substitutions revealed significant diversity in spn and ifs. Application of established models of molecular evolution shows that SPN is evolving under positive selection and diverging into NAD(+) glycohydrolase (NADase)-active and -inactive subtypes. Additionally, the NADase-inactive SPN subtypes maintain the characteristics of a functional gene while ifs becomes a pseudogene. Thus, NADase-inactive SPN continues to evolve under functional constraint. Furthermore, NADase activity did not correlate with invasive disease in our collection but was associated with tissue tropism. The ability to cause infection at both the pharynx and the skin ("generalist" strains) is correlated with NADase-active SPN, while the preference for causing infection at either the throat or the skin ("specialist" strains) is associated with NADase-inactive SPN. These findings suggest that SPN has a NADase-independent function and prompt a reevaluation of the role of SPN in streptococcal pathogenesis.
Collapse
|