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Lichtenberg M, Jakobsen TH, Kühl M, Kolpen M, Jensen PØ, Bjarnsholt T. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6574409. [PMID: 35472245 PMCID: PMC9438473 DOI: 10.1093/femsre/fuac018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/04/2022] [Accepted: 04/24/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2200, København, Denmark
| | - Peter Østrup Jensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital, Ole Maaløes vej 26, 2200, København, Denmark
| | - Thomas Bjarnsholt
- Corresponding author: Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark. Tel: +45 20659888; E-mail:
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2
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Boyle KK, Marzullo BJ, Yergeau DA, Nodzo SR, Crane JK, Duquin TR. Pathogenic genetic variations of C. acnes are associated with clinically relevant orthopedic shoulder infections. J Orthop Res 2020; 38:2731-2739. [PMID: 32644213 DOI: 10.1002/jor.24798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/22/2020] [Accepted: 06/24/2020] [Indexed: 02/04/2023]
Abstract
Many surgeons continue to face the clinical dilemma of interpreting a positive aspiration or unexpected positive Cutibacterium acnes (C. acnes) culture. There are factors that complicate the interpretation of positive cultures including variations in both frequency of false positive cultures and virulence properties. As indices of virulence, hemolytic strains, from previously confirmed clinically infected shoulders, were compared with non-hemolytic isolates determined to be contaminants, by RNA-sequencing (RNA-Seq). Six C. acnes isolates from patients who underwent revision total shoulder arthroplasty (TSA) were identified based on previously described infection criteria. Three C. acnes isolates from each group underwent RNA-Seq. Differential gene expression analysis, principal component analysis (PCA), and heatmap analysis were used to determine the gene variation and patterning between the definite infection and probable contaminant isolates. Differential gene expression analysis identified genes that were differentially expressed between the isolates classified as definite infection and isolates classified as probable contaminants. PCA using a 500 gene subset of identified genes was able to find combinations of these genes that separated out the definite infection and probable contaminants isolates. The heatmap demonstrated similar gene expression in the three Definite Infections isolates, and significantly different expression when compared with the probable contaminant isolates. Clinical significance: C. acnes revision TSA isolates classified as definite infection and probable contaminant demonstrated a similar gene expression pattern to each respective group and different gene expression pattern when compared between groups. These findings indicate distinct differences in C. acnes strains associated with clinically relevant orthopedic TSA infections.
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Affiliation(s)
- K Keely Boyle
- Department of Orthopaedics, State University of New York, Buffalo, New York
| | - Brandon J Marzullo
- Genomics and Bioinformatics Core, NYS Center of Excellence in Bioinformatics and Life Sciences (CBLS), State University of New York, Buffalo, New York
| | - Donald A Yergeau
- Genomics and Bioinformatics Core, NYS Center of Excellence in Bioinformatics and Life Sciences (CBLS), State University of New York, Buffalo, New York
| | - Scott R Nodzo
- Department of Orthopaedics, State University of New York, Buffalo, New York
| | - John K Crane
- Department of Infectious Disease, State University of New York, Buffalo, New York
| | - Thomas R Duquin
- Department of Orthopaedics, State University of New York, Buffalo, New York
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3
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Cao Q, Yang N, Wang Y, Xu C, Zhang X, Fan K, Chen F, Liang H, Zhang Y, Deng X, Feng Y, Yang CG, Wu M, Bae T, Lan L. Mutation-induced remodeling of the BfmRS two-component system in Pseudomonas aeruginosa clinical isolates. Sci Signal 2020; 13:13/656/eaaz1529. [PMID: 33144518 DOI: 10.1126/scisignal.aaz1529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genetic mutations are a primary driving force behind the adaptive evolution of bacterial pathogens. Multiple clinical isolates of Pseudomonas aeruginosa, an important human pathogen, have naturally evolved one or more missense mutations in bfmS, which encodes the sensor histidine kinase of the BfmRS two-component system (TCS). A mutant BfmS protein containing both the L181P and E376Q substitutions increased the phosphorylation and thus the transcriptional regulatory activity of its cognate downstream response regulator, BfmR. This reduced acute virulence and enhanced biofilm formation, both of which are phenotypic changes associated with a chronic infection state. The increased phosphorylation of BfmR was due, at least in part, to the cross-phosphorylation of BfmR by GtrS, a noncognate sensor kinase. Other spontaneous missense mutations in bfmS, such as A42E/G347D, T242R, and R393H, also caused a similar remodeling of the BfmRS TCS in P. aeruginosa This study highlights the plasticity of TCSs mediated by spontaneous mutations and suggests that mutation-induced activation of BfmRS may contribute to host adaptation by P. aeruginosa during chronic infections.
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Affiliation(s)
- Qiao Cao
- College of Life Science, Northwest University, Xi'an 710127, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Nana Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanhui Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chenchen Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xue Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ke Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Feifei Chen
- College of Life Science, Northwest University, Xi'an 710127, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Haihua Liang
- College of Life Science, Northwest University, Xi'an 710127, China
| | - Yingchao Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong 999077, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong 999077, China
| | - Youjun Feng
- School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58203-9037, USA
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN 46408, USA
| | - Lefu Lan
- College of Life Science, Northwest University, Xi'an 710127, China. .,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.,NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
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4
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RNA-based qPCR as a tool to quantify and to characterize dual-species biofilms. Sci Rep 2019; 9:13639. [PMID: 31541147 PMCID: PMC6754382 DOI: 10.1038/s41598-019-50094-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022] Open
Abstract
While considerable research has focused on studying individual-species, we now face the challenge of determining how interspecies interactions alter bacterial behaviours and pathogenesis. Pseudomonas aeruginosa and Staphylococcus aureus are often found to co-infect cystic-fibrosis patients. Curiously, their interaction is reported as competitive under laboratory conditions. Selecting appropriate methodologies is therefore critical to analyse multi-species communities. Herein, we demonstrated the major biases associated with qPCR quantification of bacterial populations and optimized a RNA-based qPCR able not only to quantify but also to characterize microbial interactions within dual-species biofilms composed by P. aeruginosa and S. aureus, as assessed by gene expression quantification. qPCR quantification was compared with flow-cytometry and culture-based quantification. Discrepancies between culture independent and culture dependent methods could be the result of the presence of viable but not-cultivable bacteria within the biofilm. Fluorescence microscopy confirmed this. A higher sensitivity to detect viable cells further highlights the potentialities of qPCR approach to quantify biofilm communities. By using bacterial RNA and an exogenous mRNA control, it was also possible to characterize bacterial transcriptomic profile, being this a major advantage of this method.
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5
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Sommer LM, Alanin MC, Marvig RL, Nielsen KG, Høiby N, von Buchwald C, Molin S, Johansen HK. Bacterial evolution in PCD and CF patients follows the same mutational steps. Sci Rep 2016; 6:28732. [PMID: 27349973 PMCID: PMC4923847 DOI: 10.1038/srep28732] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/08/2016] [Indexed: 11/25/2022] Open
Abstract
Infections with Pseudomonas aeruginosa increase morbidity in primary ciliary dyskinesia (PCD) and cystic fibrosis (CF) patients. Both diseases are associated with a defect of the mucociliary clearance; in PCD caused by non-functional cilia, in CF by changed mucus. Whole genome sequencing of P. aeruginosa isolates from CF patients has shown that persistence of clonal lineages in the airways is facilitated by genetic adaptation. It is unknown whether this also applies to P. aeruginosa airway infections in PCD. We compared within-host evolution of P. aeruginosa in PCD and CF patients. P. aeruginosa isolates from 12 PCD patients were whole genome sequenced and phenotypically characterised. Ten out of 12 PCD patients were infected with persisting clone types. We identified convergent evolution in eight genes, which are also important for persistent infections in CF airways: genes related to antibiotic resistance, quorum sensing, motility, type III secretion and mucoidity. We document phenotypic and genotypic parallelism in the evolution of P. aeruginosa across infected patients with different genetic disorders. The parallel changes and convergent adaptation and evolution may be caused by similar selective forces such as the intensive antibiotic treatment and the inflammatory response, which drive the evolutionary processes.
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Affiliation(s)
- Lea M Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Mikkel Christian Alanin
- Department of Otorhinolaryngology - Head and Neck Surgery and Audiology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Rasmus L Marvig
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Denmark.,Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Kim Gjerum Nielsen
- Danish PCD Centre, Paediatric Pulmonary Service, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Niels Høiby
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Denmark.,Institute of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology - Head and Neck Surgery and Audiology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.,Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Helle Krogh Johansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Denmark
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6
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Cai Z, Liu Y, Chen Y, Yam JKH, Chew SC, Chua SL, Wang K, Givskov M, Yang L. RpoN Regulates Virulence Factors of Pseudomonas aeruginosa via Modulating the PqsR Quorum Sensing Regulator. Int J Mol Sci 2015; 16:28311-9. [PMID: 26633362 PMCID: PMC4691050 DOI: 10.3390/ijms161226103] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/09/2015] [Accepted: 11/23/2015] [Indexed: 12/16/2022] Open
Abstract
The alternative sigma factor RpoN regulates many cell functions, such as motility, quorum sensing, and virulence in the opportunistic pathogen Pseudomonas aeruginosa (P. aeruginosa). P. aeruginosa often evolves rpoN-negative variants during the chronic infection in cystic fibrosis patients. It is unclear how RpoN interacts with other regulatory mechanisms to control virulence of P. aeruginosa. In this study, we show that RpoN modulates the function of PqsR, a quorum sensing receptor regulating production of virulence factors including the phenazine pyocyanin. The ∆rpoN mutant is able to synthesize 4-quinolone signal molecule HHQ but unable to activate PqsR and Pseudomonas quinolone signal (pqs) quorum sensing. The ∆rpoN mutant produces minimal level of pyocyanin and is unable to produce the anti-staphylococcal agents. Providing pqsR in trans in the ∆rpoN mutant restores its pqs quorum sensing and virulence factor production to the wild-type level. Our study provides evidence that RpoN has a regulatory effect on P. aeruginosa virulence through modulating the function of the PqsR quorum sensing regulator.
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Affiliation(s)
- Zhao Cai
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551.
| | - Yang Liu
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.
| | - Yicai Chen
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551.
| | - Su Chuen Chew
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551.
| | - Song Lin Chua
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.
| | - Ke Wang
- Department of Respiratory Disease, First Affiliated Hospital of Guangxi Medical University, Nanning 530000, China.
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.
- Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark.
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551.
- School of Biological Sciences, Nanyang Technological University, Singapore 637551.
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7
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Pompilio A, Crocetta V, De Nicola S, Verginelli F, Fiscarelli E, Di Bonaventura G. Cooperative pathogenicity in cystic fibrosis: Stenotrophomonas maltophilia modulates Pseudomonas aeruginosa virulence in mixed biofilm. Front Microbiol 2015; 6:951. [PMID: 26441885 PMCID: PMC4584994 DOI: 10.3389/fmicb.2015.00951] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/27/2015] [Indexed: 12/23/2022] Open
Abstract
The present study was undertaken in order to understand more about the interaction occurring between S. maltophilia and P. aeruginosa, which are frequently co-isolated from CF airways. For this purpose, S. maltophilia RR7 and P. aeruginosa RR8 strains, co-isolated from the lung of a chronically infected CF patient during a pulmonary exacerbation episode, were evaluated for reciprocal effect during planktonic growth, adhesion and biofilm formation onto both polystyrene and CF bronchial cell monolayer, motility, as well as for gene expression in mixed biofilms. P. aeruginosa significantly affected S. maltophilia growth in both planktonic and biofilm cultures, due to an inhibitory activity probably requiring direct contact. Conversely, no effect was observed on P. aeruginosa by S. maltophilia. Compared with monocultures, the adhesiveness of P. aeruginosa on CFBE41o- cells was significantly reduced by S. maltophilia, which probably acts by reducing P. aeruginosa's swimming motility. An opposite trend was observed for biofilm formation, confirming the findings obtained using polystyrene. When grown in mixed biofilm with S. maltophilia, P. aeruginosa significantly over-expressed aprA, and algD-codifying for protease and alginate, respectively-while the quorum sensing related rhlR and lasI genes were down-regulated. The induced alginate expression by P. aeruginosa might be responsible for the protection of S. maltophilia against tobramycin activity we observed in mixed biofilms. Taken together, our results suggest that the existence of reciprocal interference of S. maltophilia and P. aeruginosa in CF lung is plausible. In particular, S. maltophilia might confer some selective "fitness advantage" to P. aeruginosa under the specific conditions of chronic infection or, alternatively, increase the virulence of P. aeruginosa thus leading to pulmonary exacerbation.
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Affiliation(s)
- Arianna Pompilio
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara Chieti, Italy ; Aging Research Center (Ce.S.I.), "G. d'Annunzio" University Foundation Chieti, Italy
| | - Valentina Crocetta
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara Chieti, Italy ; Aging Research Center (Ce.S.I.), "G. d'Annunzio" University Foundation Chieti, Italy
| | - Serena De Nicola
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara Chieti, Italy ; Aging Research Center (Ce.S.I.), "G. d'Annunzio" University Foundation Chieti, Italy
| | - Fabio Verginelli
- Aging Research Center (Ce.S.I.), "G. d'Annunzio" University Foundation Chieti, Italy ; Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara Chieti, Italy
| | | | - Giovanni Di Bonaventura
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara Chieti, Italy ; Aging Research Center (Ce.S.I.), "G. d'Annunzio" University Foundation Chieti, Italy
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8
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Bacterial Adaptation during Chronic Respiratory Infections. Pathogens 2015; 4:66-89. [PMID: 25738646 PMCID: PMC4384073 DOI: 10.3390/pathogens4010066] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/15/2015] [Accepted: 02/25/2015] [Indexed: 01/22/2023] Open
Abstract
Chronic lung infections are associated with increased morbidity and mortality for individuals with underlying respiratory conditions such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD). The process of chronic colonisation allows pathogens to adapt over time to cope with changing selection pressures, co-infecting species and antimicrobial therapies. These adaptations can occur due to environmental pressures in the lung such as inflammatory responses, hypoxia, nutrient deficiency, osmolarity, low pH and antibiotic therapies. Phenotypic adaptations in bacterial pathogens from acute to chronic infection include, but are not limited to, antibiotic resistance, exopolysaccharide production (mucoidy), loss in motility, formation of small colony variants, increased mutation rate, quorum sensing and altered production of virulence factors associated with chronic infection. The evolution of Pseudomonas aeruginosa during chronic lung infection has been widely studied. More recently, the adaptations that other chronically colonising respiratory pathogens, including Staphylococcus aureus, Burkholderia cepacia complex and Haemophilus influenzae undergo during chronic infection have also been investigated. This review aims to examine the adaptations utilised by different bacterial pathogens to aid in their evolution from acute to chronic pathogens of the immunocompromised lung including CF and COPD.
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9
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Cao Q, Wang Y, Chen F, Xia Y, Lou J, Zhang X, Yang N, Sun X, Zhang Q, Zhuo C, Huang X, Deng X, Yang CG, Ye Y, Zhao J, Wu M, Lan L. A novel signal transduction pathway that modulates rhl quorum sensing and bacterial virulence in Pseudomonas aeruginosa. PLoS Pathog 2014; 10:e1004340. [PMID: 25166864 PMCID: PMC4148453 DOI: 10.1371/journal.ppat.1004340] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/15/2014] [Indexed: 01/10/2023] Open
Abstract
The rhl quorum-sensing (QS) system plays critical roles in the pathogenesis of P. aeruginosa. However, the regulatory effects that occur directly upstream of the rhl QS system are poorly understood. Here, we show that deletion of gene encoding for the two-component sensor BfmS leads to the activation of its cognate response regulator BfmR, which in turn directly binds to the promoter and decreases the expression of the rhlR gene that encodes the QS regulator RhlR, causing the inhibition of the rhl QS system. In the absence of bfmS, the Acka-Pta pathway can modulate the regulatory activity of BfmR. In addition, BfmS tunes the expression of 202 genes that comprise 3.6% of the P. aeruginosa genome. We further demonstrate that deletion of bfmS causes substantially reduced virulence in lettuce leaf, reduced cytotoxicity, enhanced invasion, and reduced bacterial survival during acute mouse lung infection. Intriguingly, specific missense mutations, which occur naturally in the bfmS gene in P. aeruginosa cystic fibrosis (CF) isolates such as DK2 strains and RP73 strain, can produce BfmS variants (BfmSL181P, BfmSL181P/E376Q, and BfmSR393H) that no longer repress, but instead activate BfmR. As a result, BfmS variants, but not the wild-type BfmS, inhibit the rhl QS system. This study thus uncovers a previously unexplored signal transduction pathway, BfmS/BfmR/RhlR, for the regulation of rhl QS in P. aeruginosa. We propose that BfmRS TCS may have an important role in the regulation and evolution of P. aeruginosa virulence during chronic infection in CF lungs. The rhl quorum-sensing (QS) system allows P. aeruginosa to regulate diverse metabolic adaptations and virulence. However, how rhl QS system is regulated remains largely unknown. Here, we report that two-component sensor BfmS controls rhl QS system by repressing its cognate response regulator BfmR, which directly suppresses the expression of rhl QS regulator RhlR gene and reduces the production of QS signal molecule N-butanoyl-L-homoserine lactone (C4-HSL). We find that BfmS is critical to the ability of P. aeruginosa to modulate the expression of virulence-associated traits and adapt to the host. Intriguingly, although wild-type BfmS is a repressor of BfmR, naturally occurring missense mutation (L181P, L181P/E376Q, or R393H) can convert its function from a repressor to an activator of BfmR, leading to BfmR activation, which in turn reduces the level of rhl QS signal C4-HSL. These results, therefore, provide important and novel insight into the regulation and evolution of P. aeruginosa virulence.
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Affiliation(s)
- Qiao Cao
- Hainan University, Haikou, Hainan, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yue Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Institute of Chemistry and BioMedical Sciences, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Feifei Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yongjie Xia
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jingyu Lou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xue Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Nana Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxu Sun
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qin Zhang
- State Key Laboratory of Respiratory Diseases and the First Affiliated Hospital of Guangzhou Medical College, Guangzhou, China
| | - Chao Zhuo
- State Key Laboratory of Respiratory Diseases and the First Affiliated Hospital of Guangzhou Medical College, Guangzhou, China
| | - Xi Huang
- Hainan University, Haikou, Hainan, China
| | - Xin Deng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, United States of America
| | - Cai-Guang Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yan Ye
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota, United States of America
| | - Jing Zhao
- Institute of Chemistry and BioMedical Sciences, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- * E-mail: (JZ); (MW); (LL)
| | - Min Wu
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota, United States of America
- * E-mail: (JZ); (MW); (LL)
| | - Lefu Lan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (JZ); (MW); (LL)
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10
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Population dynamics of an Acinetobacter baumannii clonal complex during colonization of patients. J Clin Microbiol 2014; 52:3200-8. [PMID: 24951812 DOI: 10.1128/jcm.00921-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Acinetobacter baumannii has emerged as one of the leading pathogens causing hospital-acquired infection. The success of A. baumannii as a pathogen has to a large extent been attributed to its capacity to remodel its genome. Several major epidemic clonal complexes of A. baumannii spread across different health care facilities around the world, each of which contains a subset of diversified strains. However, little is known about the population dynamics during colonization of A. baumannii within hosts. Here, whole-genome sequencing was used to analyze population dynamics of A. baumannii strains isolated from a group of patients at different time points as well as from different sites of a particular patient. Seven out of nine of the sampled A. baumannii strains belonged to the international clone II (CC92 clonal complex). While the A. baumannii strains were found to be stable in three patients, there was a change of A. baumannii strains in one patient. Comparative genomic analysis revealed that the accessory genome of these strains contained a large set of virulence-encoding genes and these virulence factors might play a role in determining population dynamics. Microscale genome modification has been revealed by analysis of single nucleotide polymorphisms (SNPs) between A. baumannii strains isolated from the same patient. Parallel evolutionary traits have been observed during genome diversification when A. baumannii colonize in different patients. Our study suggested that both antibiotic usage and host environment might impose selective forces that drive the rapid adaptive evolution in colonizing A. baumannii.
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11
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Loss of social behaviours in populations of Pseudomonas aeruginosa infecting lungs of patients with cystic fibrosis. PLoS One 2014; 9:e83124. [PMID: 24454693 PMCID: PMC3891558 DOI: 10.1371/journal.pone.0083124] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/31/2013] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa, is an opportunistic, bacterial pathogen causing persistent and frequently fatal infections of the lung in patients with cystic fibrosis. Isolates from chronic infections differ from laboratory and environmental strains in a range of traits and this is widely interpreted as the result of adaptation to the lung environment. Typically, chronic strains carry mutations in global regulation factors that could effect reduced expression of social traits, raising the possibility that competitive dynamics between cooperative and selfish, cheating strains could also drive changes in P. aeruginosa infections. We compared the expression of cooperative traits - biofilm formation, secretion of exo-products and quorum sensing (QS) - in P. aeruginosa isolates that were estimated to have spent different lengths of time in the lung based on clinical information. All three exo-products involved in nutrient acquisition were produced in significantly smaller quantities with increased duration of infection, and patterns across four QS signal molecules were consistent with accumulation over time of mutations in lasR, which are known to disrupt the ability of cells to respond to QS signal. Pyocyanin production, and the proportion of cells in biofilm relative to motile, free-living cells in liquid culture, did not change. Overall, our results confirm that the loss of social behaviour is a consistent trend with time spent in the lung and suggest that social dynamics are potentially relevant to understanding the behaviour of P. aeruginosa in lung infections.
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Thøgersen JC, Mørup M, Damkiær S, Molin S, Jelsbak L. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways. BMC Bioinformatics 2013; 14:279. [PMID: 24059747 PMCID: PMC3870984 DOI: 10.1186/1471-2105-14-279] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 09/03/2013] [Indexed: 01/13/2023] Open
Abstract
Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data.
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Tielen P, Rosin N, Meyer AK, Dohnt K, Haddad I, Jänsch L, Klein J, Narten M, Pommerenke C, Scheer M, Schobert M, Schomburg D, Thielen B, Jahn D. Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions. PLoS One 2013; 8:e71845. [PMID: 23967252 PMCID: PMC3742457 DOI: 10.1371/journal.pone.0071845] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 07/04/2013] [Indexed: 11/19/2022] Open
Abstract
Biofilms of the Gram-negative bacterium Pseudomonas aeruginosa are one of the major causes of complicated urinary tract infections with detrimental outcome. To develop novel therapeutic strategies the molecular adaption strategies of P. aeruginosa biofilms to the conditions of the urinary tract were investigated thoroughly at the systems level using transcriptome, proteome, metabolome and enzyme activity analyses. For this purpose biofilms were grown anaerobically in artificial urine medium (AUM). Obtained data were integrated bioinformatically into gene regulatory and metabolic networks. The dominating response at the transcriptome and proteome level was the adaptation to iron limitation via the broad Fur regulon including 19 sigma factors and up to 80 regulated target genes or operons. In agreement, reduction of the iron cofactor-dependent nitrate respiratory metabolism was detected. An adaptation of the central metabolism to lactate, citrate and amino acid as carbon sources with the induction of the glyoxylate bypass was observed, while other components of AUM like urea and creatinine were not used. Amino acid utilization pathways were found induced, while fatty acid biosynthesis was reduced. The high amounts of phosphate found in AUM explain the reduction of phosphate assimilation systems. Increased quorum sensing activity with the parallel reduction of chemotaxis and flagellum assembly underscored the importance of the biofilm life style. However, reduced formation of the extracellular polysaccharide alginate, typical for P. aeruginosa biofilms in lungs, indicated a different biofilm type for urinary tract infections. Furthermore, the obtained quorum sensing response results in an increased production of virulence factors like the extracellular lipase LipA and protease LasB and AprA explaining the harmful cause of these infections.
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Affiliation(s)
- Petra Tielen
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.
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Zhang L, Gao Q, Chen W, Qin H, Hengzhuang W, Chen Y, Yang L, Zhang G. Regulation of pqs quorum sensing via catabolite repression control in Pseudomonas aeruginosa. MICROBIOLOGY-SGM 2013; 159:1931-1936. [PMID: 23831999 DOI: 10.1099/mic.0.066266-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Bacteria have evolved a set of regulatory pathways to adapt to the dynamic nutritional environment during the course of infection. However, the underlying mechanism of the regulatory effects by nutritional cues on bacterial pathogenesis is unclear. In the present study, we showed that the Pseudomonas aeruginosa catabolite repression control protein regulates the Pseudomonas quinolone signal quorum sensing, which further controls synthesis of virulence factor pyocyanin, biofilm formation and survival during infection models. Our study suggests that deregulation of the catabolite repression by P. aeruginosa might enhance its fitness during cystic fibrosis infections.
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Affiliation(s)
- Lianbo Zhang
- China-Japan Union Hospital, Jilin University, Changchun 130033, People's Republic of China
| | - Qingguo Gao
- China-Japan Union Hospital, Jilin University, Changchun 130033, People's Republic of China
| | - Wanying Chen
- China-Japan Union Hospital, Jilin University, Changchun 130033, People's Republic of China
| | - Haiyan Qin
- China-Japan Union Hospital, Jilin University, Changchun 130033, People's Republic of China
| | - Wang Hengzhuang
- Department of Clinical Microbiology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen 2100, Denmark
| | - Yicai Chen
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University 637551, Republic of Singapore
| | - Liang Yang
- School of Biological Sciences (SBS), Nanyang Technological University 637551, Republic of Singapore
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University 637551, Republic of Singapore
| | - Guang Zhang
- China-Japan Union Hospital, Jilin University, Changchun 130033, People's Republic of China
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Nichols SE, Hernández CX, Wang Y, McCammon JA. Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface. Protein Sci 2013; 22:745-54. [PMID: 23553730 PMCID: PMC3690714 DOI: 10.1002/pro.2258] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/27/2013] [Accepted: 03/17/2013] [Indexed: 01/24/2023]
Abstract
Crystallographic structures and experimental assays of human CXC chemokine receptor type 4 (CXCR4) provide strong evidence for the capacity to homodimerize, potentially as a means of allosteric regulation. Even so, how this homodimer forms and its biological significance has yet to be fully characterized. By applying principles from network analysis, sequence-based approaches such as statistical coupling analysis to determine coevolutionary residues, can be used in conjunction with molecular dynamics simulations to identify residues relevant to dimerization. Here, the predominant coevolution sector lies along the observed dimer interface, suggesting functional relevance. Furthermore, coevolution scoring provides a basis for determining significant nodes, termed hubs, in the network formed by residues found along the interface of the homodimer. These node residues coincide with hotspots indicating potential druggability. Drug design efforts targeting such key residues could potentially result in modulation of binding and therapeutic benefits for disease states, such as lung cancers, lymphomas and latent HIV-1 infection. Furthermore, this method may be applied to any protein-protein interaction.
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Affiliation(s)
- Sara E Nichols
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, USA.
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Unique biofilm signature, drug susceptibility and decreased virulence in Drosophila through the Pseudomonas aeruginosa two-component system PprAB. PLoS Pathog 2012; 8:e1003052. [PMID: 23209420 PMCID: PMC3510237 DOI: 10.1371/journal.ppat.1003052] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 09/09/2012] [Indexed: 12/29/2022] Open
Abstract
Bacterial biofilm is considered as a particular lifestyle helping cells to survive hostile environments triggered by a variety of signals sensed and integrated through adequate regulatory pathways. Pseudomonas aeruginosa, a Gram-negative bacterium causing severe infections in humans, forms biofilms and is a fantastic example for fine-tuning of the transition between planktonic and community lifestyles through two-component systems (TCS). Here we decipher the regulon of the P. aeruginosa response regulator PprB of the TCS PprAB. We identified genes under the control of this TCS and once this pathway is activated, analyzed and dissected at the molecular level the PprB-dependent phenotypes in various models. The TCS PprAB triggers a hyper-biofilm phenotype with a unique adhesive signature made of BapA adhesin, a Type 1 secretion system (T1SS) substrate, CupE CU fimbriae, Flp Type IVb pili and eDNA without EPS involvement. This unique signature is associated with drug hyper-susceptibility, decreased virulence in acutely infected flies and cytotoxicity toward various cell types linked to decreased Type III secretion (T3SS). Moreover, once the PprB pathway is activated, decreased virulence in orally infected flies associated with enhanced biofilm formation and dissemination defect from the intestinal lumen toward the hemolymph compartment is reported. PprB may thus represent a key bacterial adaptation checkpoint of multicellular and aggregative behavior triggering the production of a unique matrix associated with peculiar antibiotic susceptibility and attenuated virulence, a particular interesting breach for therapeutic intervention to consider in view of possible eradication of P. aeruginosa biofilm-associated infections.
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Han X, Chen C, Hyun TK, Kumar R, Kim JY. Metabolic module mining based on Independent Component Analysis in Arabidopsis thaliana. Mol Cells 2012; 34:295-304. [PMID: 22960738 PMCID: PMC3887838 DOI: 10.1007/s10059-012-0117-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 01/02/2023] Open
Abstract
Independent Component Analysis (ICA) has been introduced as one of the useful tools for gene-functional discovery in animals. However, this approach has been poorly utilized in the plant sciences. In the present study, we have exploited ICA combined with pathway enrichment analysis to address the statistical challenges associated with genome-wide analysis in plant system. To generate an Arabidopsis metabolic platform, we collected 4,373 Affy-metrix ATH1 microarray datasets. Out of the 3,232 metabolic genes and transcription factors, 99.47% of these genes were identified in at least one component, indicating the coverage of most of the metabolic pathways by the components. During the metabolic pathway enrichment analysis, we found components that indicate an independent regulation between the isoprenoid biosynthesis pathways. We also utilized this analysis tool to investigate some transcription factors involved in secondary cell wall biogenesis. This approach has identified remarkably more transcription factors compared to previously reported analysis tools. A website providing user-friendly searching and downloading of the entire dataset analyzed by ICA is available at http://kimjy.gnu.ac.kr/ICA.files/slide0002.htm . ICA combined with pathway enrichment analysis might provide a powerful approach for the extraction of the components responsible for a biological process of interest in plant systems.
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Affiliation(s)
- Xiao Han
- Division of Applied Life Science (Brain Korea 21-World Class University Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Cong Chen
- Institute of Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi’an Jiaotong University School of Life Science and Technology, Xi’an,
China
| | - Tae Kyung Hyun
- Division of Applied Life Science (Brain Korea 21-World Class University Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Ritesh Kumar
- Division of Applied Life Science (Brain Korea 21-World Class University Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (Brain Korea 21-World Class University Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701,
Korea
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Rau MH, Marvig RL, Ehrlich GD, Molin S, Jelsbak L. Deletion and acquisition of genomic content during early stage adaptation of Pseudomonas aeruginosa to a human host environment. Environ Microbiol 2012; 14:2200-11. [PMID: 22672046 DOI: 10.1111/j.1462-2920.2012.02795.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Adaptation of bacterial pathogens to a permanently host-associated lifestyle by means of deletion or acquisition of genetic material is usually examined through comparison of present-day isolates to a distant theoretical ancestor. This limits the resolution of the adaptation process. We conducted a retrospective study of the dissemination of the P.aeruginosa DK2 clone type among patients suffering from cystic fibrosis, sequencing the genomes of 45 isolates collected from 16 individuals over 35 years. Analysis of the genomes provides a high-resolution examination of the dynamics and mechanisms of the change in genetic content during the early stage of host adaptation by this P.aeruginosa strain as it adapts to the cystic fibrosis (CF) lung of several patients. Considerable genome reduction is detected predominantly through the deletion of large genomic regions, and up to 8% of the genome is deleted in one isolate. Compared with in vitro estimates the resulting average deletion rates are 12- to 36-fold higher. Deletions occur through both illegitimate and homologous recombination, but they are not IS element mediated as previously reported for early stage host adaptation. Uptake of novel DNA sequences during infection is limited as only one prophage region was putatively inserted in one isolate, demonstrating that early host adaptation is characterized by the reduction of genomic repertoire rather than acquisition of novel functions. Finally, we also describe the complete genome of this highly adapted pathogenic strain of P.aeruginosa to strengthen the genetic basis, which serves to help our understanding of microbial evolution in a natural environment.
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Affiliation(s)
- Martin H Rau
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
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