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Behringer MG, Ho WC, Miller SF, Worthan SB, Cen Z, Stikeleather R, Lynch M. Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine. Curr Biol 2024; 34:1403-1413.e5. [PMID: 38460514 PMCID: PMC11066936 DOI: 10.1016/j.cub.2024.02.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/12/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
Microbes are evolutionarily robust organisms capable of rapid adaptation to complex stress, which enables them to colonize harsh environments. In nature, microbes are regularly challenged by starvation, which is a particularly complex stress because resource limitation often co-occurs with changes in pH, osmolarity, and toxin accumulation created by metabolic waste. Often overlooked are the additional complications introduced by eventual resource replenishment, as successful microbes must withstand rapid environmental shifts before swiftly capitalizing on replenished resources to avoid invasion by competing species. To understand how microbes navigate trade-offs between growth and survival, ultimately adapting to thrive in environments with extreme fluctuations, we experimentally evolved 16 Escherichia coli populations for 900 days in repeated feast/famine conditions with cycles of 100-day starvation before resource replenishment. Using longitudinal population-genomic analysis, we found that evolution in response to extreme feast/famine is characterized by narrow adaptive trajectories with high mutational parallelism and notable mutational order. Genetic reconstructions reveal that early mutations result in trade-offs for biofilm and motility but trade-ups for growth and survival, as these mutations conferred positively correlated advantages during both short-term and long-term culture. Our results demonstrate how microbes can navigate the adaptive landscapes of regularly fluctuating conditions and ultimately follow mutational trajectories that confer benefits across diverse environments.
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Affiliation(s)
- Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA; Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, 21st Avenue S, Nashville, TN 37232, USA.
| | - Wei-Chin Ho
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA; Department of Biology, University of Texas at Tyler, University Blvd., Tyler, TX 75799, USA.
| | - Samuel F Miller
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Zeer Cen
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Ryan Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
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2
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Marmont LS, Orta AK, Baileeves BWA, Sychantha D, Fernández-Galliano A, Li YE, Greene NG, Corey RA, Stansfeld PJ, Clemons WM, Bernhardt TG. Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa. Nat Microbiol 2024; 9:763-775. [PMID: 38336881 PMCID: PMC10914600 DOI: 10.1038/s41564-024-01603-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Many bacterial surface glycans such as the peptidoglycan (PG) cell wall are built from monomeric units linked to a polyprenyl lipid carrier. How this limiting carrier is distributed among competing pathways has remained unclear. Here we describe the isolation of hyperactive variants of Pseudomonas aeruginosa MraY, the enzyme that forms the first lipid-linked PG precursor. These variants result in the elevated production of the final PG precursor lipid II in cells and are hyperactive in vitro. The activated MraY variants have substitutions that map to a cavity on the extracellular side of the dimer interface, far from the active site. Our structural and molecular dynamics results suggest that this cavity is a binding site for externalized lipid II. Overall, our results support a model in which excess externalized lipid II allosterically inhibits MraY, providing a feedback mechanism that prevents the sequestration of lipid carrier in the PG biogenesis pathway.
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Affiliation(s)
- Lindsey S Marmont
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Michael DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Anna K Orta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Becca W A Baileeves
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - David Sychantha
- Michael DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Ana Fernández-Galliano
- Michael DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Yancheng E Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Neil G Greene
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, USA
| | - Robin A Corey
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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3
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Tang M, Yang R, Zhuang Z, Han S, Sun Y, Li P, Fan K, Cai Z, Yang Q, Yu Z, Yang L, Li S. Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation. THE ISME JOURNAL 2024; 18:wrae135. [PMID: 39052320 PMCID: PMC11307329 DOI: 10.1093/ismejo/wrae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/09/2024] [Accepted: 07/24/2024] [Indexed: 07/27/2024]
Abstract
Biofilm is a group of heterogeneously structured and densely packed bacteria with limited access to nutrients and oxygen. These intrinsic features can allow a mono-species biofilm to diversify into polymorphic subpopulations, determining the overall community's adaptive capability to changing ecological niches. However, the specific biological functions underlying biofilm diversification and fitness adaptation are poorly demonstrated. Here, we launched and monitored the experimental evolution of Pseudomonas aeruginosa biofilms, finding that two divergent molecular trajectories were adopted for adaptation to higher competitive fitness in biofilm formation: one involved hijacking bacteriophage superinfection to aggressively inhibit kin competitors, whereas the other induced a subtle change in cyclic dimeric guanosine monophosphate signaling to gain a positional advantage via enhanced early biofilm adhesion. Bioinformatics analyses implicated that similar evolutionary strategies were prevalent among clinical P. aeruginosa strains, indicative of parallelism between natural and experimental evolution. Divergence in the molecular bases illustrated the adaptive values of genomic plasticity for gaining competitive fitness in biofilm formation. Finally, we demonstrated that these fitness-adaptive mutations reduced bacterial virulence. Our findings revealed how the mutations intrinsically generated from the biofilm environment influence the evolution of P. aeruginosa.
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Affiliation(s)
- Mingxing Tang
- Department of Otorhinolaryngology, Shenzhen Nanshan People’s Hospital, Shenzhen 518052, China
| | - Ruixue Yang
- Community Health Service Center of Southern University of Science and Technology, Nanshan Medical Group Headquarters, Shenzhen 518055, China
| | - Zilin Zhuang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shuhong Han
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yunke Sun
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Peiyu Li
- Department of Infectious Diseases, Shenzhen Nanshan People’s Hospital, Shenzhen University School of Medicine, Shenzhen 518052, China
| | - Kewei Fan
- Department of Infectious Diseases, Shenzhen Nanshan People’s Hospital, Shenzhen University School of Medicine, Shenzhen 518052, China
| | - Zhao Cai
- Department of Research and Development, Shenzhen Mindray Bio-Medical Electronics Co, Ltd, Shenzhen 518057, China
| | - Qiong Yang
- Department of Otorhinolaryngology, Shenzhen Nanshan People’s Hospital, Shenzhen 518052, China
| | - Zhijian Yu
- Department of Infectious Diseases, Shenzhen Nanshan People’s Hospital, Shenzhen University School of Medicine, Shenzhen 518052, China
| | - Liang Yang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shuo Li
- Department of Otorhinolaryngology, Shenzhen Nanshan People’s Hospital, Shenzhen 518052, China
- Allergy Prevention and Control Center, Nanshan People’s Hospital, Shenzhen 518052, China
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4
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Trikha R, Greig D, Sekimura T, Geiger EJ, Wessel L, Eckardt JJ, Bernthal NM. The microbial profile of infected endoprosthetic reconstructions after wide excision for patients with musculoskeletal tumors: A call for pathogen-based practices. J Surg Oncol 2023; 128:1437-1445. [PMID: 37610049 DOI: 10.1002/jso.27428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/25/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023]
Abstract
BACKGROUND AND OBJECTIVES Periprosthetic infection is a devastating complication following endoprosthetic reconstruction. This study utilized a large database of endoprostheses to describe the incidence, risk factors, and microbial profile of such infections to better catalogue and understand these catastrophic events. METHODS A retrospective review of endoprosthetic reconstructions for an oncologic indication from January 1, 1981 to December 31, 2020 was performed. Demographic, oncologic, procedural and outcome data was analyzed. Multivariable logistic regression was used to identify potential risk factors for infection with significance defined as p < 0.05. RESULTS Forty four out of 712 (6.2%) reconstructions resulted in infection at a mean time of 39.9 ± 44.5 months. Revision surgery (odds ratio [OR] 6.14, p < 0.001) or having a postoperative wound complication (OR 7.67, p < 0.001) were significantly associated with infection. Staphylococcus aureus and Staphylococcus epidermidis were the most commonly cultured organisms at a rate of 34.1% (15/44) and 22.7% (10/44), respectively. Ten infections resulted in amputation; five due to antimicrobial-resistant infections and three due to polymicrobial infections. CONCLUSION Understanding the microbial profile of patients undergoing endoprosthetic reconstruction is paramount. This study demonstrates a relatively high rate of polymicrobial and antibiotic-resistant infections that portend worse outcomes, thus suggesting that pathogen-specific infectious practices may be warranted. LEVEL OF EVIDENCE Retrospective cohort study, level III.
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Affiliation(s)
- Rishi Trikha
- Department of Orthopaedic Surgery at the University of California, Santa Monica, California, USA
| | - Danielle Greig
- Department of Orthopaedic Surgery at the University of California, Santa Monica, California, USA
| | - Troy Sekimura
- Department of Orthopaedic Surgery at the University of California, Santa Monica, California, USA
| | - Erik J Geiger
- Department of Orthopaedic Surgery at the University of California, Santa Monica, California, USA
| | - Lauren Wessel
- Department of Orthopaedic Surgery at the University of California, Santa Monica, California, USA
| | - Jeffrey J Eckardt
- Department of Orthopaedic Surgery at the University of California, Santa Monica, California, USA
| | - Nicholas M Bernthal
- Department of Orthopaedic Surgery at the University of California, Santa Monica, California, USA
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5
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Heiman CM, Vacheron J, Keel C. Evolutionary and ecological role of extracellular contractile injection systems: from threat to weapon. Front Microbiol 2023; 14:1264877. [PMID: 37886057 PMCID: PMC10598620 DOI: 10.3389/fmicb.2023.1264877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Contractile injection systems (CISs) are phage tail-related structures that are encoded in many bacterial genomes. These devices encompass the cell-based type VI secretion systems (T6SSs) as well as extracellular CISs (eCISs). The eCISs comprise the R-tailocins produced by various bacterial species as well as related phage tail-like structures such as the antifeeding prophages (Afps) of Serratia entomophila, the Photorhabdus virulence cassettes (PVCs), and the metamorphosis-associated contractile structures (MACs) of Pseudoalteromonas luteoviolacea. These contractile structures are released into the extracellular environment upon suicidal lysis of the producer cell and play important roles in bacterial ecology and evolution. In this review, we specifically portray the eCISs with a focus on the R-tailocins, sketch the history of their discovery and provide insights into their evolution within the bacterial host, their structures and how they are assembled and released. We then highlight ecological and evolutionary roles of eCISs and conceptualize how they can influence and shape bacterial communities. Finally, we point to their potential for biotechnological applications in medicine and agriculture.
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Affiliation(s)
- Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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6
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Marmont LS, Orta AK, Corey RA, Sychantha D, Galliano AF, Li YE, Baileeves BW, Greene NG, Stansfeld PJ, Clemons WM, Bernhardt TG. A feedback control mechanism governs the synthesis of lipid-linked precursors of the bacterial cell wall. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551478. [PMID: 37577621 PMCID: PMC10418202 DOI: 10.1101/2023.08.01.551478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Many bacterial surface glycans such as the peptidoglycan (PG) cell wall, O-antigens, and capsules are built from monomeric units linked to a polyprenyl lipid carrier. How this limiting lipid carrier is effectively distributed among competing pathways has remained unclear for some time. Here, we describe the isolation and characterization of hyperactive variants of Pseudomonas aeruginosa MraY, the essential and conserved enzyme catalyzing the formation of the first lipid-linked PG precursor called lipid I. These variants result in the elevated production of the final PG precursor lipid II in cells and are hyperactive in a purified system. Amino acid substitutions within the activated MraY variants unexpectedly map to a cavity on the extracellular side of the dimer interface, far from the active site. Our structural evidence and molecular dynamics simulations suggest that the cavity is a binding site for lipid II molecules that have been transported to the outer leaflet of the membrane. Overall, our results support a model in which excess externalized lipid II allosterically inhibits MraY, providing a feedback mechanism to prevent the sequestration of lipid carrier in the PG biogenesis pathway. MraY belongs to the broadly distributed polyprenyl-phosphate N-acetylhexosamine 1-phosphate transferase (PNPT) superfamily of enzymes. We therefore propose that similar feedback mechanisms may be widely employed to coordinate precursor supply with demand by polymerases, thereby optimizing the partitioning of lipid carriers between competing glycan biogenesis pathways.
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Affiliation(s)
- Lindsey S. Marmont
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Anna K. Orta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Robin A. Corey
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
| | - David Sychantha
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ana Fernández Galliano
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Yancheng E. Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Becca W.A. Baileeves
- School of Life Sciences and Department of Chemistry, University of Warwick, Warwick, UK
| | - Neil G. Greene
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Phillip J. Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Warwick, UK
| | - William M. Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Boston, United States
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7
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Chan DK, Dykema K, Fatima M, Harvey H, Qaderi I, Burrows LL. Nutrient Limitation Sensitizes Pseudomonas aeruginosa to Vancomycin. ACS Infect Dis 2023; 9:1408-1423. [PMID: 37279282 PMCID: PMC10353551 DOI: 10.1021/acsinfecdis.3c00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Indexed: 06/08/2023]
Abstract
Traditional antibacterial screens rely on growing bacteria in nutrient-replete conditions which are not representative of the natural environment or sites of infection. Instead, screening in more physiologically relevant conditions may reveal novel activity for existing antibiotics. Here, we screened a panel of antibiotics reported to lack activity against the opportunistic Gram-negative bacterium, Pseudomonas aeruginosa, under low-nutrient and low-iron conditions, and discovered that the glycopeptide vancomycin inhibited the growth of P. aeruginosa at low micromolar concentrations through its canonical mechanism of action, disruption of peptidoglycan crosslinking. Spontaneous vancomycin-resistant mutants underwent activating mutations in the sensor kinase of the two-component CpxSR system, which induced cross-resistance to almost all classes of β-lactams, including the siderophore antibiotic cefiderocol. Other mutations that conferred vancomycin resistance mapped to WapR, an α-1,3-rhamnosyltransferase involved in lipopolysaccharide core biosynthesis. A WapR P164T mutant had a modified LPS profile compared to wild type that was accompanied by increased susceptibility to select bacteriophages. We conclude that screening in nutrient-limited conditions can reveal novel activity for existing antibiotics and lead to discovery of new and impactful resistance mechanisms.
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Affiliation(s)
- Derek
C. K. Chan
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Katherine Dykema
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Mahrukh Fatima
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Hanjeong Harvey
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Ikram Qaderi
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Lori L. Burrows
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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8
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Blasco L, de Aledo MG, Ortiz-Cartagena C, Blériot I, Pacios O, López M, Fernández-García L, Barrio-Pujante A, Hernández-Garcia M, Cantón R, Tomás M. Study of 32 new phage tail-like bacteriocins (pyocins) from a clinical collection of Pseudomonas aeruginosa and of their potential use as typing markers and antimicrobial agents. Sci Rep 2023; 13:117. [PMID: 36596850 PMCID: PMC9810705 DOI: 10.1038/s41598-022-27341-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Phage tail-like bacteriocins (PTLBs) are large proteomic structures similar to the tail phages. These structures function in bacterial competition by making pores in the membrane of their competitors. The PTLBs identified in Pseudomonas aeruginosa are known as R-type and F-type pyocins, which have a narrow spectrum of action. Their specificity is determined by the tail fiber and is closely related to the lipopolysaccharide type of the target competitor strain. In this study, the genome sequences of 32 clinical of P. aeruginosa clinical isolates were analysed to investigate the presence of R-type and F-type pyocins, and one was detected in all strains tested. The pyocins were classified into 4 groups on the basis of the tail fiber and also the homology, phylogeny and structure of the cluster components. A relationship was established between these groups and the sequence type and serotype of the strain of origin and finally the killing spectrum of the representative pyocins was determined showing a variable range of activity between 0 and 37.5%. The findings showed that these pyocins could potentially be used for typing of P. aeruginosa clinical isolates, on the basis of their genomic sequence and cluster structure, and also as antimicrobial agents.
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Affiliation(s)
- Lucía Blasco
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Manuel González de Aledo
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Concha Ortiz-Cartagena
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Inés Blériot
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Olga Pacios
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - María López
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Laura Fernández-García
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Antonio Barrio-Pujante
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Marta Hernández-Garcia
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain ,Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain ,Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- grid.8073.c0000 0001 2176 8535Microbiología Traslacional y Multidisciplinar (MicroTM)-Instituto de Investigación Biomédica (INIBIC), Servicio de Microbiología, Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain ,Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
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9
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Holban AM, Gregoire CM, Gestal MC. Conquering the host: Bordetella spp. and Pseudomonas aeruginosa molecular regulators in lung infection. Front Microbiol 2022; 13:983149. [PMID: 36225372 PMCID: PMC9549215 DOI: 10.3389/fmicb.2022.983149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 11/27/2022] Open
Abstract
When bacteria sense cues from the host environment, stress responses are activated. Two component systems, sigma factors, small RNAs, ppGpp stringent response, and chaperones start coordinate the expression of virulence factors or immunomodulators to allow bacteria to respond. Although, some of these are well studied, such as the two-component systems, the contribution of other regulators, such as sigma factors or ppGpp, is increasingly gaining attention. Pseudomonas aeruginosa is the gold standard pathogen for studying the molecular mechanisms to sense and respond to environmental cues. Bordetella spp., on the other hand, is a microbial model for studying host-pathogen interactions at the molecular level. These two pathogens have the ability to colonize the lungs of patients with chronic diseases, suggesting that they have the potential to share a niche and interact. However, the molecular networks that facilitate adaptation of Bordetella spp. to cues are unclear. Here, we offer a side-by-side comparison of what is known about these diverse molecular mechanisms that bacteria utilize to counteract host immune responses, while highlighting the relatively unexplored interactions between them.
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Affiliation(s)
- Alina M. Holban
- Research Institute of the University of Bucharest (ICUB), Bucharest, Romania
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Courtney M. Gregoire
- Department of Microbiology and Immunology, Louisiana State University Health Science Center, Shreveport, LA, United States
| | - Monica C. Gestal
- Department of Microbiology and Immunology, Louisiana State University Health Science Center, Shreveport, LA, United States
- *Correspondence: Monica C. Gestal, ;
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10
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Lin Y, Xu X, Maróti G, Strube ML, Kovács ÁT. Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes. NPJ Biofilms Microbiomes 2022; 8:27. [PMID: 35418164 PMCID: PMC9007996 DOI: 10.1038/s41522-022-00292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/19/2022] [Indexed: 11/12/2022] Open
Abstract
Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that produce biofilms on abiotic and biotic surfaces. While genetic and morphological diversification enables the adaptation of multicellular communities, this area remains largely unknown in the Bacillus cereus group. In this work, we dissected the experimental evolution of Bacillus thuringiensis 407 Cry- during continuous recolonization of plastic beads. We observed the evolution of a distinct colony morphotype that we named fuzzy spreader (FS) variant. Most multicellular traits of the FS variant displayed higher competitive ability versus the ancestral strain, suggesting an important role for diversification in the adaptation of B. thuringiensis to the biofilm lifestyle. Further genetic characterization of FS variant revealed the disruption of a guanylyltransferase gene by an insertion sequence (IS) element, which could be similarly observed in the genome of a natural isolate. The evolved FS and the deletion mutant in the guanylyltransferase gene (Bt407ΔrfbM) displayed similarly altered aggregation and hydrophobicity compared to the ancestor strain, suggesting that the adaptation process highly depends on the physical adhesive forces.
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Affiliation(s)
- Yicen Lin
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, 6726, Szeged, Hungary
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark.
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11
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Wangoye K, Mwesigye J, Tungotyo M, Twinomujuni Samba S. Chronic wound isolates and their minimum inhibitory concentrations against third generation cephalosporins at a tertiary hospital in Uganda. Sci Rep 2022; 12:1195. [PMID: 35075152 PMCID: PMC8786920 DOI: 10.1038/s41598-021-04722-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/30/2021] [Indexed: 02/04/2023] Open
Abstract
Globally, the burden of chronic wound infections is likely to increase due to the rising levels of bacterial resistance to antibiotics. In the United States of America alone, more than 6.5 million chronic wounds with evidence of bacterial infection are diagnosed every year. In addition, the polymicrobial environment in chronic wound infections has been observed from several studies as a risk factor for development of resistance to many antibiotics including the third generation cephalosporins currently used in Mbarara Regional Referral Hospital for treatment of chronic wound infections. Therefore the main objective of this study was to determine the prevalence of chronic wound isolates and their minimum inhibitory concentrations (MIC) against third generation cephalosporins. This study was a cross-sectional descriptive and analytical survey of bacterial isolates from chronic wound infection among 75 study participants admitted in the surgical ward of Mbarara Regional Referral Hospital (MRRH), a tertiary Hospital in Western Uganda. Standard laboratory bacterial culture and identification techniques as well as broth microdilution method were used to isolate, identify pathogens and test for MIC respectively. We found that 69/75 study participants had samples with bacterial growth and the most prevalent pathogens isolated were staphylococcus aureus (40.6%) and Klebsiella spp. (29%). Generally, most isolates were susceptible to cefoperazone + sulbactum 2 g (Sulcef) and ceftriaxone 1 g (Epicephin). The overall prevalence of isolates in chronic wound infection among patients admitted in the surgical ward of MRRH was 92% and the most prevalent isolates were Staphylococcus aureus, Klebsiella species and proteus species respectively. The observed MIC values were higher than the CLSI clinical breakpoint, implying a decreasing trend in susceptibility of chronic wound isolates to third generation cephalosporins.
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Affiliation(s)
- Khalim Wangoye
- Department of Pharmacy and Pharmacology, Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda.
| | - James Mwesigye
- Department of Medical Laboratory Science, Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda
| | - Martin Tungotyo
- Department of Surgery, Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda
| | - Silvano Twinomujuni Samba
- Department of Pharmacy and Pharmacology, Mbarara University of Science and Technology, P.O Box 1410, Mbarara, Uganda
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12
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Jørgensen E, Bjarnsholt T, Jacobsen S. Biofilm and Equine Limb Wounds. Animals (Basel) 2021; 11:2825. [PMID: 34679846 PMCID: PMC8532864 DOI: 10.3390/ani11102825] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/14/2021] [Accepted: 09/23/2021] [Indexed: 01/01/2023] Open
Abstract
In chronic wounds in humans, biofilm formation and wound chronicity are linked, as biofilms contribute to chronic inflammation and delayed healing. Biofilms are aggregates of bacteria, and living as biofilms is the default mode of bacterial life; within these aggregates, the bacteria are protected from both antimicrobial substances and the immune response of the host. In horses, delayed healing is more commonly seen in limb wounds than body wounds. Chronic inflammation and hypoxia are the main characteristics of delayed wound healing in equine limbs, and biofilms might also contribute to this healing pattern in horses. However, biofilm formation in equine wounds has been studied to a very limited degree. Biofilms have been detected in equine traumatic wounds, and recent experimental models have shown that biofilms protract the healing of equine limb wounds. Detection of biofilms within wounds necessitates advanced techniques that are not available in routine diagnostic yet. However, infections with biofilm should be suspected in equine limb wounds not healing as expected, as they are in human wounds. Treatment should be based on repeated debridement and application of topical antimicrobial therapy.
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Affiliation(s)
- Elin Jørgensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark;
- Department of Clinical Microbiology, Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Stine Jacobsen
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2630 Taastrup, Denmark;
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13
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Carim S, Azadeh AL, Kazakov AE, Price MN, Walian PJ, Lui LM, Nielsen TN, Chakraborty R, Deutschbauer AM, Mutalik VK, Arkin AP. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. THE ISME JOURNAL 2021; 15:2289-2305. [PMID: 33649553 PMCID: PMC8319346 DOI: 10.1038/s41396-021-00921-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022]
Abstract
Tailocins are bactericidal protein complexes produced by a wide variety of bacteria that kill closely related strains and may play a role in microbial community structure. Thanks to their high specificity, tailocins have been proposed as precision antibacterial agents for therapeutic applications. Compared to tailed phages, with whom they share an evolutionary and morphological relationship, bacterially produced tailocins kill their host upon production but producing strains display resistance to self-intoxication. Though lipopolysaccharide (LPS) has been shown to act as a receptor for tailocins, the breadth of factors involved in tailocin sensitivity, and the mechanisms behind resistance to self-intoxication, remain unclear. Here, we employed genome-wide screens in four non-model pseudomonads to identify mutants with altered fitness in the presence of tailocins produced by closely related pseudomonads. Our mutant screens identified O-antigen composition and display as most important in defining sensitivity to our tailocins. In addition, the screens suggest LPS thinning as a mechanism by which resistant strains can become more sensitive to tailocins. We validate many of these novel findings, and extend these observations of tailocin sensitivity to 130 genome-sequenced pseudomonads. This work offers insights into tailocin-bacteria interactions, informing the potential use of tailocins in microbiome manipulation and antibacterial therapy.
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Affiliation(s)
- Sean Carim
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Ashley L Azadeh
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Morgan N Price
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peter J Walian
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lauren M Lui
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivek K Mutalik
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Adam P Arkin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
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14
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Duan X, Pan Y, Cai Z, Liu Y, Zhang Y, Liu M, Liu Y, Wang K, Zhang L, Yang L. rpoS-mutation variants are selected in Pseudomonas aeruginosa biofilms under imipenem pressure. Cell Biosci 2021; 11:138. [PMID: 34289907 PMCID: PMC8293535 DOI: 10.1186/s13578-021-00655-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/11/2021] [Indexed: 12/14/2022] Open
Abstract
Background Pseudomonas aeruginosa is a notorious opportunistic pathogen causing various types of biofilm-related infections. Biofilm formation is a unique microbial strategy that allows P. aeruginosa to survive adverse conditions such as antibiotic treatment and human immune clearance. Results In this study, we experimentally evolved P. aeruginosa PAO1 biofilms for cyclic treatment in the presence of high dose of imipenem, and enriched hyperbiofilm mutants within six cycles in two independent lineages. The competition assay showed that the evolved hyperbiofilm mutants can outcompete the ancestral strain within biofilms but not in planktonic cultures. Whole-genome sequencing analysis revealed the hyperbiofilm phenotype is caused by point mutations in rpoS gene in all independently evolved mutants and the same mutation was found in P. aeruginosa clinical isolates. We further showed that mutation in rpoS gene increased the intracellular c-di-GMP level by turning on the expression of the diguanylate cyclases. Mutation in rpoS increased pyocyanin production and virulence in hyperbiofilm variants. Conclusion Here, our study revealed that antibiotic treatment of biofilm-related P. aeruginosa infections might induce a hyperbiofilm phenotype via rpoS mutation, which might partially explain antimicrobial treatment failure of many P. aeruginosa biofilm-related infections. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00655-9.
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Affiliation(s)
- Xiangke Duan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.,School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Yanrong Pan
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Zhao Cai
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Yumei Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Yingdan Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Moxiao Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Yang Liu
- Southern University of Science and Technology Hospital, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Ke Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, People's Republic of China
| | - Lianhui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, People's Republic of China.,Shenzhen Key Laboratory for Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, People's Republic of China
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15
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Abstract
Pseudomonas aeruginosa causes life-threatening infections that are associated with antibiotic failure. Previously, we identified the antibiotic G2637, an analog of arylomycin, targeting bacterial type I signal peptidase, which has moderate potency against P. aeruginosa. We hypothesized that an antibody-antibiotic conjugate (AAC) could increase its activity by colocalizing P. aeruginosa bacteria with high local concentrations of G2637 antibiotic in the intracellular environment of phagocytes. Using a novel technology of screening for hybridomas recognizing intact bacteria, we identified monoclonal antibody 26F8, which binds to lipopolysaccharide O antigen on the surface of P. aeruginosa bacteria. This antibody was engineered to contain 6 cysteines and was conjugated to the G2637 antibiotic via a lysosomal cathepsin-cleavable linker, yielding a drug-to-antibody ratio of approximately 6. The resulting AAC delivered a high intracellular concentration of free G2637 upon phagocytosis of AAC-bound P. aeruginosa by macrophages, and potently cleared viable P. aeruginosa bacteria intracellularly. The molar concentration of AAC-associated G2637 antibiotic that resulted in elimination of bacteria inside macrophages was approximately 2 orders of magnitude lower than the concentration of free G2637 required to eliminate extracellular bacteria. This study demonstrates that an anti-P. aeruginosa AAC can locally concentrate antibiotic and kill P. aeruginosa inside phagocytes, providing additional therapeutic options for antibiotics that are moderately active or have an unfavorable pharmacokinetics or toxicity profile.
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16
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Heterogenous Susceptibility to R-Pyocins in Populations of Pseudomonas aeruginosa Sourced from Cystic Fibrosis Lungs. mBio 2021; 12:mBio.00458-21. [PMID: 33947755 PMCID: PMC8262887 DOI: 10.1128/mbio.00458-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bacteriocins are proteinaceous antimicrobials produced by bacteria that are active against other strains of the same species. R-type pyocins are phage tail-like bacteriocins produced by Pseudomonas aeruginosa Due to their antipseudomonal activity, R-pyocins have potential as therapeutics in infection. P. aeruginosa is a Gram-negative opportunistic pathogen and is particularly problematic for individuals with cystic fibrosis (CF). P. aeruginosa organisms from CF lung infections develop increasing resistance to antibiotics, making new treatment approaches essential. P. aeruginosa populations become phenotypically and genotypically diverse during infection; however, little is known of the efficacy of R-pyocins against heterogeneous populations. R-pyocins vary by subtype (R1 to R5), distinguished by binding to different residues on the lipopolysaccharide (LPS). Each type varies in killing spectrum, and each strain produces only one R-type. To evaluate the prevalence of different R-types, we screened P. aeruginosa strains from the International Pseudomonas Consortium Database (IPCD) and from our biobank of CF strains. We found that (i) R1-types were the most prevalent R-type among strains from respiratory sources, (ii) a large number of strains lack R-pyocin genes, and (iii) isolates collected from the same patient have the same R-type. We then assessed the impact of intrastrain diversity on R-pyocin susceptibility and found a heterogenous response to R-pyocins within populations, likely due to differences in the LPS core. Our work reveals that heterogeneous populations of microbes exhibit variable susceptibility to R-pyocins and highlights that there is likely heterogeneity in response to other types of LPS-binding antimicrobials, including phage.IMPORTANCE R-pyocins have potential as alternative therapeutics against Pseudomonas aeruginosa in chronic infection; however, little is known about the efficacy of R-pyocins in heterogeneous bacterial populations. P. aeruginosa is known to become resistant to multiple antibiotics and to evolve phenotypic and genotypic diversity over time; thus, it is particularly difficult to eradicate in chronic cystic fibrosis (CF) lung infections. In this study, we found that P. aeruginosa populations from CF lungs maintain the same R-pyocin genotype but exhibit heterogeneity in susceptibility to R-pyocins from other strains. Our findings suggest there is heterogeneity in response to other types of LPS-binding antimicrobials, such as phage, highlighting the necessity of further studying the potential of LPS-binding antimicrobial particles as alternative therapies in chronic infections.
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17
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Wolter DJ, Scott A, Armbruster CR, Whittington D, Edgar JS, Qin X, Buccat AM, McNamara S, Blackledge M, Waalkes A, Salipante SJ, Ernst RK, Hoffman LR. Repeated isolation of an antibiotic-dependent and temperature-sensitive mutant of Pseudomonas aeruginosa from a cystic fibrosis patient. J Antimicrob Chemother 2021; 76:616-625. [PMID: 33259594 DOI: 10.1093/jac/dkaa482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/02/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Bacteria adapt to survive and grow in different environments. Genetic mutations that promote bacterial survival under harsh conditions can also restrict growth. The causes and consequences of these adaptations have important implications for diagnosis, pathogenesis, and therapy. OBJECTIVES We describe the isolation and characterization of an antibiotic-dependent, temperature-sensitive Pseudomonas aeruginosa mutant chronically infecting the respiratory tract of a cystic fibrosis (CF) patient, underscoring the clinical challenges bacterial adaptations can present. METHODS Respiratory samples collected from a CF patient during routine care were cultured for standard pathogens. P. aeruginosa isolates recovered from samples were analysed for in vitro growth characteristics, antibiotic susceptibility, clonality, and membrane phospholipid and lipid A composition. Genetic mutations were identified by whole genome sequencing. RESULTS P. aeruginosa isolates collected over 5 years from respiratory samples of a CF patient frequently harboured a mutation in phosphatidylserine decarboxylase (psd), encoding an enzyme responsible for phospholipid synthesis. This mutant could only grow at 37°C when in the presence of supplemented magnesium, glycerol, or, surprisingly, the antibiotic sulfamethoxazole, which the source patient had repeatedly received. Of concern, this mutant was not detectable on standard selective medium at 37°C. This growth defect correlated with alterations in membrane phospholipid and lipid A content. CONCLUSIONS A P. aeruginosa mutant chronically infecting a CF patient exhibited dependence on sulphonamides and would likely evade detection using standard clinical laboratory methods. The diagnostic and therapeutic challenges presented by this mutant highlight the complex interplay between bacterial adaptation, antibiotics, and laboratory practices, during chronic bacterial infections.
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Affiliation(s)
- Daniel J Wolter
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Seattle Children's Hospital, Seattle, WA, USA
| | - Alison Scott
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, USA
| | | | - Dale Whittington
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - John S Edgar
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Xuan Qin
- Seattle Children's Hospital, Seattle, WA, USA
| | | | | | | | - Adam Waalkes
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, USA
| | - Lucas R Hoffman
- Department of Pediatrics, University of Washington, Seattle, WA, USA.,Seattle Children's Hospital, Seattle, WA, USA.,Department of Microbiology, University of Washington, Seattle, WA, USA
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18
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Connolly JPR, Roe AJ, O'Boyle N. Prokaryotic life finds a way: insights from evolutionary experimentation in bacteria. Crit Rev Microbiol 2020; 47:126-140. [PMID: 33332206 DOI: 10.1080/1040841x.2020.1854172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
While evolution proceeds through the generation of random variant alleles, the application of selective pressures can select for subsets of mutations that confer fitness-improving physiological benefits. This, in essence, defines the process of adaptive evolution. The rapid replication rate of bacteria has allowed for the design of experiments to study these processes over a reasonable timeframe within a laboratory setting. This has been greatly assisted by advances in tractability of diverse microorganisms, next generation sequencing technologies and bioinformatic analysis pipelines. Examining the processes by which organisms adapt their genetic code to cope with sub-optimal growth conditions has yielded a wealth of molecular insight into diverse biological processes. Here we discuss how the study of adaptive evolutionary trajectories in bacteria has allowed for improved understanding of stress responses, revealed important insight into microbial physiology, allowed for the production of highly optimised strains for use in biotechnology and increased our knowledge of the role of genomic plasticity in chronic infections.
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Affiliation(s)
- James P R Connolly
- Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Nicky O'Boyle
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
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19
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Werneburg GT, Farber N, Gotwald P, Shoskes DA. Culture-independent Next Generation Sequencing of Urine and Expressed Prostatic Secretions in Men With Chronic Pelvic Pain Syndrome. Urology 2020; 147:230-234. [PMID: 33098861 DOI: 10.1016/j.urology.2020.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/26/2020] [Accepted: 10/08/2020] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To compare standard cultures and next-generation sequencing (NGS) in men with chronic prostatitis/chronic pelvic pain syndrome (CPPS). CPPS shares clinical features with urinary tract infections, but bacteria are seldom found. NGS is more sensitive than standard cultures. MATERIALS AND METHODS Men diagnosed with CPPS (National Institute of Health Category III) underwent traditional cultures and NGS of their urine and expressed prostatic secretions (EPS). Characteristics between groups were compared statistically. RESULTS Thirty-one men with CPPS were included (mean age 44.5). All standard urine cultures were negative, and 3 EPS cultures were positive. Seventy-eight unique microbes were detected with NGS, including uropathogens in 10 of the men. There were no bacteria identified by NGS in EPS that were not also found in the urine. Men with positive NGS did not differ from those without in age, symptom severity or phenotype. Men with typical urinary tract infection symptoms (eg, dysuria, chills) were more likely to have uropathogens detected on NGS relative to men without such symptoms. Nine patients were prescribed antibiotics based on their NGS findings, but only 1 exhibited symptom improvement (11%). CONCLUSION NGS commonly identified bacteria in CPPS patients, but these did not localize to the prostate. NGS positivity did not correlate with symptom severity and antibiotic therapy was seldom effective. NGS detected uropathogens more frequently in those with clinical symptoms suggestive of urinary tract infection. Clinical trials are needed to examine the utility of NGS-guided antibiotics in this subpopulation.
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Affiliation(s)
- Glenn T Werneburg
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH.
| | - Nicholas Farber
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH
| | - Paige Gotwald
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH
| | - Daniel A Shoskes
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH
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20
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Yin Q, Wu S, Wu L, Wang Z, Mu Y, Zhang R, Dong C, Zhou B, Zhao B, Zheng J, Sun Y, Cheng X, Yang L. A novel in silico antimicrobial peptide DP7 combats MDR Pseudomonas aeruginosa and related biofilm infections. J Antimicrob Chemother 2020; 75:3248-3259. [PMID: 32737484 DOI: 10.1093/jac/dkaa308] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Antimicrobial peptides are promising alternative antimicrobial agents to combat MDR. DP7, an antimicrobial peptide designed in silico, possesses broad-spectrum antimicrobial activities and immunomodulatory effects. However, the effects of DP7 against Pseudomonas aeruginosa and biofilm infection remain largely unexplored.
Objectives
To assess (i) the antimicrobial activity of DP7 against MDR P. aeruginosa; and (ii) the antibiofilm activity against biofilm infection. Also, to preliminarily investigate the possible antimicrobial mode of action.
Methods
The MICs of DP7 for 104 clinical P. aeruginosa strains (including 57 MDR strains) and the antibiofilm activity were determined. RNA-Seq, genome sequencing and cell morphology were conducted. Both acute and chronic biofilm infection mouse models were established. Two mutants, resulting from point mutations associated with LPS and biofilms, were constructed to investigate the potential mode of action.
Results
DP7, at 8–32 mg/L, inhibited the growth of clinical P. aeruginosa strains and, at 64 mg/L, reduced biofilm formation by 43% to 68% in vitro. In acute lung infection, 0.5 mg/kg DP7 exhibited a 70% protection rate and reduced bacterial colonization by 50% in chronic infection. DP7 mainly suppressed gene expression involving LPS and outer membrane proteins and disrupted cell wall structure. Genome sequencing of the DP7-resistant strain DP7R revealed four SNPs controlling LPS and biofilm production. gshA44 and wbpJ139 mutants displayed LPS reduction and motility deficiency, conferring the reduction of LPS and biofilm biomass of strain DP7R and indicating that LPS was a potential target of DP7.
Conclusions
These results demonstrate that DP7 may hold potential as an effective antimicrobial agent against MDR P. aeruginosa and related infections.
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Affiliation(s)
- Qi Yin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Avenue, Nanshan Section, Shenzhen 518060, People’s Republic of China
| | - Siwen Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Lei Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Zhenling Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Yandong Mu
- Stomatology Department, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 611731, People’s Republic of China
| | - Rui Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Chunyan Dong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Bailing Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Binyan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Jiajun Zheng
- Stomatology Department, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 611731, People’s Republic of China
| | - Ying Sun
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Xingjun Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
| | - Li Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No. 17, Section 3, South Renmin Road, Chengdu, Sichuan 610041, People’s Republic of China
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Bridier A, Piard JC, Briandet R, Bouchez T. Emergence of a Synergistic Diversity as a Response to Competition in Pseudomonas putida Biofilms. MICROBIAL ECOLOGY 2020; 80:47-59. [PMID: 31844910 DOI: 10.1007/s00248-019-01470-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Genetic diversification through the emergence of variants is one of the known mechanisms enabling the adaptation of bacterial communities. We focused in this work on the adaptation of the model strain Pseudomonas putida KT2440 in association with another P. putida strain (PCL1480) recently isolated from soil to investigate the potential role of bacterial interactions in the diversification process. On the basis of colony morphology, three variants of P. putida KT2440 were obtained from co-culture after 168 h of growth whereas no variant was identified from the axenic KT2440 biofilm. The variants exhibited distinct phenotypes and produced biofilms with specific architecture in comparison with the ancestor. The variants better competed with the P. putida PCL1480 strain in the dual-strain biofilms after 24 h of co-culture in comparison with the ancestor. Moreover, the synergistic interaction of KT2440 ancestor and the variants led to an improved biofilm production and to higher competitive ability versus the PCL1480 strain, highlighting the key role of diversification in the adaptation of P. putida KT2440 in the mixed community. Whole genome sequencing revealed mutations in polysaccharides biosynthesis protein, membrane transporter, or lipoprotein signal peptidase genes in variants.
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Affiliation(s)
- Arnaud Bridier
- ANSES, Fougères Laboratory, AB2R, 10B rue Claude Bourgelat, 35300, Fougères, France.
- IRSTEA, UR PROSE, 1 rue Pierre-Gilles de Gennes, 92761, Antony Cedex, France.
| | - J C Piard
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - R Briandet
- Institut Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - T Bouchez
- IRSTEA, UR PROSE, 1 rue Pierre-Gilles de Gennes, 92761, Antony Cedex, France
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The Role of Pseudomonas aeruginosa Lipopolysaccharide in Bacterial Pathogenesis and Physiology. Pathogens 2019; 9:pathogens9010006. [PMID: 31861540 PMCID: PMC7168646 DOI: 10.3390/pathogens9010006] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
The major constituent of the outer membrane of Gram-negative bacteria is lipopolysaccharide (LPS), which is comprised of lipid A, core oligosaccharide, and O antigen, which is a long polysaccharide chain extending into the extracellular environment. Due to the localization of LPS, it is a key molecule on the bacterial cell wall that is recognized by the host to deploy an immune defence in order to neutralize invading pathogens. However, LPS also promotes bacterial survival in a host environment by protecting the bacteria from these threats. This review explores the relationship between the different LPS glycoforms of the opportunistic pathogen Pseudomonas aeruginosa and the ability of this organism to cause persistent infections, especially in the genetic disease cystic fibrosis. We also discuss the role of LPS in facilitating biofilm formation, antibiotic resistance, and how LPS may be targeted by new antimicrobial therapies.
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Weaver AA, Hasan NA, Klaassen M, Karathia H, Colwell RR, Shrout JD. Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods. J Med Microbiol 2019; 68:1507-1516. [PMID: 31460858 DOI: 10.1099/jmm.0.001068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Introduction. Prosthetic joint infections (PJIs) are challenging to treat therapeutically because the infectious agents often are resistant to antibiotics and capable of abundant growth in surface-attached biofilms. Though infection rates are low, ca. 1-2 %, the overall increase in the sheer number of joint replacement surgeries results in an increase in patients at risk.Aims. This study investigates the consensus of microbial species comprising PJI ecology, which is currently lacking.Methodology. In this study, PJI populations from seven patients were analysed using combined culturing and whole-genome shotgun sequencing (WGSS) to establish population profiles and compare WGSS and culture methods for detection and identification of the PJI microbiome.Results. WGSS detected strains when culture did not, notably dormant, culture-resistant and rare microbes. The CosmosID algorithm was used to predict micro-organisms present in the PJI and discriminate contaminants. However, culturing indicated the presence of microbes falling below the WGSS algorithm threshold. In these instances, microbes cultured are believed to be minor species. The two strategies were combined to build a population profile.Conclusions. Variability between and among PJIs showed that most infections were distinct and unique. Comparative analysis of populations revealed PJIs to form clusters that were related to, but separate from, vaginal, skin and gut microbiomes. Fungi and protists were detected by WGSS, but the role of fungi is just beginning to be understood and for protists it is unknown. These micro-organisms and their novel and strain-specific microbial interactions remain to be determined in current clinical tests.
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Affiliation(s)
| | - Nur A Hasan
- Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, 20742, USA.,CosmosID Inc, Rockville, MD, 20850, USA
| | | | | | - Rita R Colwell
- Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD, 21205, USA.,CosmosID Inc, Rockville, MD, 20850, USA.,Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, 20742, USA
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Baltrus DA, Clark M, Smith C, Hockett KL. Localized recombination drives diversification of killing spectra for phage-derived syringacins. THE ISME JOURNAL 2019; 13:237-249. [PMID: 30171255 PMCID: PMC6331570 DOI: 10.1038/s41396-018-0261-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/16/2018] [Accepted: 07/06/2018] [Indexed: 02/07/2023]
Abstract
To better understand the potential for antagonistic interactions between members of the same bacterial species, we have surveyed bacteriocin killing activity across a diverse suite of strains of the phytopathogen Pseudomonas syringae. Our data demonstrate that killing activity from phage-derived bacteriocins of P. syringae (R-type syringacins) is widespread. Despite a high overall diversity of bacteriocin activity, strains can broadly be classified into five main killing types and two main sensitivity types. Furthermore, we show that killing activity switches frequently between strains and that switches correlate with localized recombination of two genes that together encode the proteins that specify bacteriocin targeting. Lastly, we demonstrate that phage-derived bacteriocin killing activity can be swapped between strains simply through expression of these two genes in trans. Overall, our study characterizes extensive diversity of killing activity for phage-derived bacteriocins of P. syringae across strains and highlights the power of localized recombination to alter phenotypes that mediate strain interactions during evolution of natural populations and communities.
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Affiliation(s)
- David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA.
| | - Meara Clark
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Caitlin Smith
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Kevin L Hockett
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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25
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Bara JJ, Matson Z, Remold SK. Life in the cystic fibrosis upper respiratory tract influences competitive ability of the opportunistic pathogen Pseudomonas aeruginosa. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180623. [PMID: 30839703 PMCID: PMC6170537 DOI: 10.1098/rsos.180623] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/17/2018] [Indexed: 06/09/2023]
Abstract
Understanding characteristic differences between host-associated and free-living opportunistic pathogens can provide insight into the fundamental requirements for success after dispersal to the host environment, and more generally into the ecological and evolutionary processes by which populations respond to simultaneous selection on complex interacting traits. We examined how cystic fibrosis (CF)-associated and environmental isolates of the opportunistic pathogen Pseudomonas aeruginosa differ in the production of an ecologically important class of proteinaceous toxins known as bacteriocins, and how overall competitive ability depends on the production of and resistance to these bacteriocins. We determined bacteriocin gene content in a diverse collection of environmental and CF isolates and measured bacteriocin-mediated inhibition, resistance and the outcome of competition in a shared environment between all possible pairs of these isolates at 25°C and 37°C. Although CF isolates encoded significantly more bacteriocin genes, our phenotypic assays suggest that they have diminished bacteriocin-mediated killing and resistance capabilities relative to environmental isolates, regardless of incubation temperature. Notably, however, although bacteriocin killing and resistance profiles significantly predicted head-to-head competitive outcomes, CF and environmental isolates did not differ significantly in their competitive ability. This suggests that the contribution of bacteriocins to competitive ability involves selection on other traits that may be pleiotropically linked to interference competition mediated by bacteriocins.
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Affiliation(s)
- Jeffrey J. Bara
- Department of Biology, University of Louisville, Louisville, KY, USA
- Department of Biology, Shenandoah University, Winchester, VA, USA
| | - Zachary Matson
- Department of Biology, University of Louisville, Louisville, KY, USA
| | - Susanna K. Remold
- Department of Biology, University of Louisville, Louisville, KY, USA
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26
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Abstract
Biofilms are often described as protective shelters that preserve bacteria from hostile surroundings. However, biofilm bacteria are also exposed to various stresses and need to adjust to the heterogeneous physicochemical conditions prevailing within biofilms. In Gram-negative bacteria, such adaptations can result in modifications of the lipopolysaccharide, a major component of the outer membrane characterized by a highly dynamic structure responding to environmental changes. We previously showed that Gram-negative biofilm bacteria undergo an increase in lipid A palmitoylation mediated by the PagP enzyme, contributing to increased resistance to host defenses. Here we describe a regulatory pathway leading to transcriptional induction of pagP in response to specific conditions created in the biofilm environment. We show that pagP expression is induced via the Rcs envelope stress system independently of the Rcs phosphorelay cascade and that it requires the GadE auxiliary regulator. Moreover, we identify an increase in osmolarity (i.e., ionic stress) as a signal able to induce pagP expression in an RcsB-dependent manner. Consistently, we show that the biofilm is a hyperosmolar environment and that RcsB-dependent pagP induction can be dampened in the presence of an osmoprotectant. These results provide new insights into the adaptive mechanisms of bacterial differentiation in biofilm.IMPORTANCE The development of the dense bacterial communities called biofilms creates a highly heterogeneous environment in which bacteria are subjected to a variety of physicochemical stresses. We investigated the mechanisms of a widespread and biofilm-associated chemical modification of the lipopolysaccharide (LPS), a major component of all Gram-negative bacterial outer membranes. This modification corresponds to the incorporation, mediated by the enzyme PagP, of a palmitate chain into lipid A (palmitoylation) that reduces bacterial recognition by host immune responses. Using biochemical and genetic approaches, we demonstrate that a significant part of biofilm-associated lipid A palmitoylation is triggered upon induction of pagP transcription by the hyperosmolar biofilm environment. pagP induction is regulated by RcsB, the response regulator of the Rcs stress response pathway, and is not observed under planktonic conditions. Our report provides new insights into how physiological adaptations to local biofilm microenvironments can contribute to decreases in susceptibility to antimicrobial agents and host immune defenses.
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27
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Xia H, Tang Q, Song J, Ye J, Wu H, Zhang H. A yigP mutant strain is a small colony variant of E. coli and shows pleiotropic antibiotic resistance. Can J Microbiol 2017; 63:961-969. [PMID: 28915357 DOI: 10.1139/cjm-2017-0347] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Small colony variants (SCVs) are a commonly observed subpopulation of bacteria that have a small colony size and distinctive biochemical characteristics. SCVs are more resistant than the wild type to some antibiotics and usually cause persistent infections in the clinic. SCV studies have been very active during the past 2 decades, especially Staphylococcus aureus SCVs. However, fewer studies on Escherichia coli SCVs exist, so we studied an E. coli SCV during an experiment involving the deletion of the yigP locus. PCR and DNA sequencing revealed that the SCV was attributable to a defect in the yigP function. Furthermore, we investigated the antibiotic resistance profile of the E. coli SCV and it showed increased erythromycin, kanamycin, and d-cycloserine resistance, but collateral sensitivity to ampicillin, polymyxin, chloramphenicol, tetracycline, rifampin, and nalidixic acid. We tried to determine the association between yigP and the pleiotropic antibiotic resistance of the SCV by analyzing biofilm formation, cellular morphology, and coenzyme Q (Q8) production. Our results indicated that impaired Q8 biosynthesis was the primary factor that contributed to the increased resistance and collateral sensitivity of the SCV. This study offers a novel genetic basis for E. coli SCVs and an insight into the development of alternative antimicrobial strategies for clinical therapy.
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Affiliation(s)
- Hui Xia
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Qiongwei Tang
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jie Song
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jiang Ye
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Haizhen Wu
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.,b Department of Applied Biology, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Huizhan Zhang
- a State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.,b Department of Applied Biology, East China University of Science and Technology, Shanghai, People's Republic of China
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Swearingen MC, DiBartola AC, Dusane D, Granger J, Stoodley P. 16S rRNA analysis provides evidence of biofilms on all components of three infected periprosthetic knees including permanent braided suture. Pathog Dis 2016; 74:ftw083. [PMID: 27549423 PMCID: PMC5985479 DOI: 10.1093/femspd/ftw083] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/01/2015] [Accepted: 08/16/2016] [Indexed: 01/19/2023] Open
Abstract
Bacterial biofilms are the main etiological agent of periprosthetic joint infections (PJI); however, it is unclear if biofilms colonize one or multiple components. Because biofilms can colonize a variety of surfaces, we hypothesized that biofilms would be present on all components. 16S ribosomal RNA (rRNA) gene sequencing analysis was used to identify bacteria recovered from individual components and non-absorbable suture material recovered from three PJI total knee revision cases. Bray-Curtis non-metric multidimensional scaling analysis revealed no significant differences in similarity when factoring component, material type, or suture versus non-suture material, but did reveal significant differences in organism profile between patients (P < 0.001) and negative controls (P < 0.001). Confocal microscopy and a novel agar encasement culturing method also confirmed biofilm growth on a subset of components. While 16S sequencing suggested that the microbiology was more complex than revealed by culture contaminating, bacterial DNA generates a risk of false positives. This report highlights that biofilm bacteria may colonize all infected prosthetic components including braided suture material, and provides further evidence that clinical culture can fail to sufficiently identify the full pathogen profile in PJI cases.
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Affiliation(s)
- Matthew C Swearingen
- Center for Microbial Interface Biology, Department of Microbial Infection and Immunity, The Ohio State University, Biomedical Research Tower, 460 West 12th Avenue, Room 760, Columbus, OH 43210, USA
| | - Alex C DiBartola
- School of Medicine, The Ohio State University, Mailing Hall, 370 West 9th Avenue, Columbus, OH 43210, USA
| | - Devendra Dusane
- Center for Microbial Interface Biology, Department of Microbial Infection and Immunity, The Ohio State University, Biomedical Research Tower, 460 West 12th Avenue, Room 760, Columbus, OH 43210, USA
| | - Jeffrey Granger
- Department of Orthopaedics, The Ohio State University, 543 Taylor Avenue, Columbus, OH 43203, USA
| | - Paul Stoodley
- Center for Microbial Interface Biology, Department of Microbial Infection and Immunity, The Ohio State University, Biomedical Research Tower, 460 West 12th Avenue, Room 760, Columbus, OH 43210, USA Department of Orthopaedics, The Ohio State University, 543 Taylor Avenue, Columbus, OH 43203, USA Engineering Sciences Unit, National Center for Advanced Tribology, University of Southampton, UK
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Evolution of Ecological Diversity in Biofilms of Pseudomonas aeruginosa by Altered Cyclic Diguanylate Signaling. J Bacteriol 2016; 198:2608-18. [PMID: 27021563 PMCID: PMC5019052 DOI: 10.1128/jb.00048-16] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
The ecological and evolutionary forces that promote and maintain diversity in biofilms are not well understood. To quantify these forces, three Pseudomonas aeruginosa populations were experimentally evolved from strain PA14 in a daily cycle of attachment, assembly, and dispersal for 600 generations. Each biofilm population evolved diverse colony morphologies and mutator genotypes defective in DNA mismatch repair. This diversity enhanced population fitness and biofilm output, owing partly to rare, early colonizing mutants that enhanced attachment of others. Evolved mutants exhibited various levels of the intracellular signal cyclic-di-GMP, which associated with their timing of adherence. Manipulating cyclic-di-GMP levels within individual mutants revealed a network of interactions in the population that depended on various attachment strategies related to this signal. Diversification in biofilms may therefore arise and be reinforced by initial colonists that enable community assembly.
IMPORTANCE How biofilm diversity assembles, evolves, and contributes to community function is largely unknown. This presents a major challenge for understanding evolution during chronic infections and during the growth of all surface-associated microbes. We used experimental evolution to probe these dynamics and found that diversity, partly related to altered cyclic-di-GMP levels, arose and persisted due to the emergence of ecological interdependencies related to attachment patterns. Clonal isolates failed to capture population attributes, which points to the need to account for diversity in infections. More broadly, this study offers an experimental framework for linking phenotypic variation to distinct ecological strategies in biofilms and for studying eco-evolutionary interactions.
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30
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Ramiro RS, Costa H, Gordo I. Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity. Evol Appl 2016; 9:994-1004. [PMID: 27606007 PMCID: PMC4999529 DOI: 10.1111/eva.12397] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 05/18/2016] [Indexed: 12/20/2022] Open
Abstract
Small-colony variants (SCVs) are commonly observed in evolution experiments and clinical isolates, being associated with antibiotic resistance and persistent infections. We recently observed the repeated emergence of Escherichia coli SCVs during adaptation to the interaction with macrophages. To identify the genetic targets underlying the emergence of this clinically relevant morphotype, we performed whole-genome sequencing of independently evolved SCV clones. We uncovered novel mutational targets, not previously associated with SCVs (e.g. cydA, pepP) and observed widespread functional parallelism. All SCV clones had mutations in genes related to the electron-transport chain. As SCVs emerged during adaptation to macrophages, and often show increased antibiotic resistance, we measured SCV fitness inside macrophages and measured their antibiotic resistance profiles. SCVs had a fitness advantage inside macrophages and showed increased aminoglycoside resistance in vitro, but had collateral sensitivity to other antibiotics (e.g. tetracycline). Importantly, we observed similar results in vivo. SCVs had a fitness advantage upon colonization of the mouse gut, which could be tuned by antibiotic treatment: kanamycin (aminoglycoside) increased SCV fitness, but tetracycline strongly reduced it. Our results highlight the power of using experimental evolution as the basis for identifying the causes and consequences of adaptation during host-microbe interactions.
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31
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Kumar V, Zozaya-Valdes E, Kjelleberg S, Thomas T, Egan S. Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra. Environ Microbiol 2016; 18:3962-3975. [PMID: 27337296 DOI: 10.1111/1462-2920.13403] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While macroalgae (or seaweeds) are increasingly recognized to suffer from disease, in most cases the causative agents are unknown. The model macroalga Delisea pulchra is susceptible to a bleaching disease and previous work has identified two epiphytic bacteria, belonging to the Roseobacter clade, that cause bleaching under laboratory conditions. However, recent environmental surveys have shown that these in vitro pathogens are not abundant in naturally bleached D. pulchra, suggesting the presence of other pathogens capable of causing this algal disease. To test this hypothesis, we cultured bacteria that were abundant on bleached tissue across multiple disease events and assessed their ability to cause bleaching disease. We identified the new pathogens Alteromonas sp. BL110, Aquimarina sp. AD1 and BL5 and Agarivorans sp BL7 that are phylogenetically diverse, distinct from the previous two pathogens and can also be found in low abundance in healthy individuals. Moreover, we found that bacterial communities of diseased individuals that were infected with these pathogens were less diverse and more divergent from each other than those of healthy algae. This study demonstrates that multiple and opportunistic pathogens can cause the same disease outcome for D. pulchra and we postulate that such pathogens are more common in marine systems than previously anticipated.
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Affiliation(s)
- Vipra Kumar
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia
| | - Enrique Zozaya-Valdes
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia
| | - Staffan Kjelleberg
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Torsten Thomas
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences. The University of New South Wales Sydney, NSW, 2052, Australia
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32
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Hathroubi S, Beaudry F, Provost C, Martelet L, Segura M, Gagnon CA, Jacques M. Impact of Actinobacillus pleuropneumoniae biofilm mode of growth on the lipid A structures and stimulation of immune cells. Innate Immun 2016; 22:353-62. [PMID: 27226465 DOI: 10.1177/1753425916649676] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/21/2016] [Indexed: 11/17/2022] Open
Abstract
Actinobacillus pleuropneumoniae (APP), the etiologic agent of porcine pleuropneumonia, forms biofilms on biotic and abiotic surfaces. APP biofilms confers resistance to antibiotics. To our knowledge, no studies have examined the role of APP biofilm in immune evasion and infection persistence. This study was undertaken to (i) investigate biofilm-associated LPS modifications occurring during the switch to biofilm mode of growth; and (ii) characterize pro-inflammatory cytokines expression in porcine pulmonary alveolar macrophages (PAMs) and proliferation in porcine PBMCs challenged with planktonic or biofilm APP cells. Extracted lipid A samples from biofilm and planktonic cultures were analyzed by HPLC high-resolution, accurate mass spectrometry. Biofilm cells displayed significant changes in lipid A profiles when compared with their planktonic counterparts. Furthermore, in vitro experiments were conducted to examine the inflammatory response of PAMs exposed to UV-inactivated APP grown in biofilm or in suspension. Relative mRNA expression of pro-inflammatory genes IL1, IL6, IL8 and MCP1 decreased in PAMs when exposed to biofilm cells compared to planktonic cells. Additionally, the biofilm state reduced PBMCs proliferation. Taken together, APP biofilm cells show a weaker ability to stimulate innate immune cells, which could be due, in part, to lipid A structure modifications.
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Affiliation(s)
- Skander Hathroubi
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Francis Beaudry
- Groupe de Recherche en Pharmacologie Animale du Québec, Faculté de Médecine Vétérinaire, Université de Montréal, Québec, Canada
| | - Chantale Provost
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Léa Martelet
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Mariela Segura
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Carl A Gagnon
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Mario Jacques
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
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Abstract
A trait-based approach focuses on attributes of taxa that influence the structure and function of communities. Biofilm production is a common trait among microorganisms in a wide range of environmental, engineered, and host-associated ecosystems. Here, we used Pseudomonas aeruginosa to link biofilm production to moisture availability, a common stressor for microorganisms in soil. First, we demonstrate that biofilm production is a response trait that influences the desiccation phenotype by increasing survivorship, shifting the niche space, and reducing the minimum water potential needed to sustain a net-positive growth rate (Ψ*). Although the allocation of resources to biofilms is thought to be costly, we found no evidence for a trade-off between fitness and biofilm production along a soil moisture gradient. Second, we demonstrated that biofilm production is an effect trait. Specifically, biofilm production increased water retention in soils that were exposed to a series of drying and rewetting cycles. Although this form of niche construction should affect species interactions, we found no evidence that the benefits of biofilm production were extended to another co-occurring soil bacterium. Together, our results support the view that biofilm production is an important trait that may contribute to the distribution, abundance, and functioning of microorganisms in soils.
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Affiliation(s)
- Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Brent K Lehmkuhl
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Trade-off Mechanisms Shaping the Diversity of Bacteria. Trends Microbiol 2016; 24:209-223. [DOI: 10.1016/j.tim.2015.11.009] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 11/21/2015] [Accepted: 11/25/2015] [Indexed: 01/20/2023]
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Understanding persistent bacterial lung infections: clinical implications informed by the biology of the microbiota and biofilms. ACTA ACUST UNITED AC 2016; 23:57-66. [PMID: 27004018 DOI: 10.1097/cpm.0000000000000108] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The infections found in chronic obstructive pulmonary disease, cystic fibrosis, and bronchiectasis share a number of clinical similarities, the most striking of which is bacterial persistence despite the use of antibiotics. These infections have been clinically described using culture-based methods usually performed on sputum samples, and treatment has been directed towards the bacteria found in this manner. Unfortunately the clinical response to antibiotics is frequently not predictable based on these cultures, and the role of these cultured organisms in disease progression has been debated. The past 20 years have seen a revolution in the techniques used to describe bacterial populations and their growth patterns. These techniques have revealed these persistent lung infections are vastly more complicated than described by traditional, and still widely relied upon, sputum cultures. A better understanding of the initiation and evolution of these infections, and better clinical tools to describe them, will dramatically alter the way patients are cared for. While clinical tests to more accurately describe these infections are not yet available, the better appreciation of these infections afforded by current science should enlighten practitioners as to the care of their patients with these diseases.
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Steenackers HP, Parijs I, Dubey A, Foster KR, Vanderleyden J. Experimental evolution in biofilm populations. FEMS Microbiol Rev 2016; 40:373-97. [PMID: 26895713 PMCID: PMC4852284 DOI: 10.1093/femsre/fuw002] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2016] [Indexed: 12/19/2022] Open
Abstract
Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. This review paper provides an overview of (i) the different experimental models used to study biofilm evolution, (ii) the vast amount of diversification observed during biofilm evolution (including potential causes and consequences) and (iii) recent insights in how growth in biofilms can lead to the evolution of cooperative phenotypes.
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Affiliation(s)
- Hans P Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
| | - Ilse Parijs
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
| | | | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3QU, UK
| | - Jozef Vanderleyden
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
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Reed TP, Thomas LA, Weeren FR, Ruth JD, Anders BB. A novel dextran polymer hydrogel local antimicrobial therapy in dogs: A pilot study. THE CANADIAN VETERINARY JOURNAL = LA REVUE VETERINAIRE CANADIENNE 2016; 57:189-195. [PMID: 26834272 PMCID: PMC4713000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Our purpose was to evaluate physical, laboratory, and/or radiographic abnormalities associated with a novel dextran polymer hydrogel local antimicrobial agent impregnated with amikacin and clindamycin in dogs having tibial plateau leveling osteotomy implants removed due to suspected surgical site infection. A total of 28 client-owned dogs were enrolled and 20 completed the study. Routine plate explantation and bacterial cultures were performed and the polymer hydrogel was applied to the surgery site. No systemic antimicrobials were used after surgery. Serum biochemistry, hematology, urinalysis, physical examinations, and radiographs were monitored before surgery and up to 12 wk after surgery. Sixteen of the 20 dogs (80%) had a positive bacterial culture, 44% of which were methicillin resistant. There were no significant alterations of laboratory values, physical examination, or radiographs to indicate adverse reactions to the polymer hydrogel. There were no signs of inflammation or infection in any patient at the 12-week postoperative recheck.
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Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y. COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2016; 21:557-567. [PMID: 26776218 PMCID: PMC4832978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Technological advances are making large-scale measurements of microbial communities commonplace. These newly acquired datasets are allowing researchers to ask and answer questions about the composition of microbial communities, the roles of members in these communities, and how genes and molecular pathways are regulated in individual community members and communities as a whole to effectively respond to diverse and changing environments. In addition to providing a more comprehensive survey of the microbial world, this new information allows for the development of computational approaches to model the processes underlying microbial systems. We anticipate that the field of computational microbiology will continue to grow rapidly in the coming years. In this manuscript we highlight both areas of particular interest in microbiology as well as computational approaches that begin to address these challenges.
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Affiliation(s)
| | - James A. Foster
- Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844 USA
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Yana Bromberg
- Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA, Institute for Advanced Study, Technische Universität München Garching, Germany
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Abstract
Allelic exchange is an efficient method of bacterial genome engineering. This protocol describes the use of this technique to make gene knockouts and knock-ins, as well as single-nucleotide insertions, deletions and substitutions, in Pseudomonas aeruginosa. Unlike other approaches to allelic exchange, this protocol does not require heterologous recombinases to insert or excise selective markers from the target chromosome. Rather, positive and negative selections are enabled solely by suicide vector-encoded functions and host cell proteins. Here, mutant alleles, which are flanked by regions of homology to the recipient chromosome, are synthesized in vitro and then cloned into allelic exchange vectors using standard procedures. These suicide vectors are then introduced into recipient cells by conjugation. Homologous recombination then results in antibiotic-resistant single-crossover mutants in which the plasmid has integrated site-specifically into the chromosome. Subsequently, unmarked double-crossover mutants are isolated directly using sucrose-mediated counter-selection. This two-step process yields seamless mutations that are precise to a single base pair of DNA. The entire procedure requires ∼2 weeks.
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Juhas M. Pseudomonas aeruginosa essentials: an update on investigation of essential genes. MICROBIOLOGY-SGM 2015; 161:2053-60. [PMID: 26311069 DOI: 10.1099/mic.0.000161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pseudomonas aeruginosa is the leading cause of nosocomial infections, particularly in immunocompromised, cancer, burn and cystic fibrosis patients. Development of novel antimicrobials against P. aeruginosa is therefore of the highest importance. Although the first reports on P. aeruginosa essential genes date back to the early 2000s, a number of more sensitive genomic approaches have been used recently to better define essential genes in this organism. These analyses highlight the evolution of the definition of an 'essential' gene from the traditional to the context-dependent. Essential genes, particularly those indispensable under the clinically relevant conditions, are considered to be promising targets of novel antibiotics against P. aeruginosa. This review provides an update on the investigation of P. aeruginosa essential genes. Special focus is on recently identified P. aeruginosa essential genes and their exploitation for the development of antimicrobials.
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Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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Oliveira NM, Martinez-Garcia E, Xavier J, Durham WM, Kolter R, Kim W, Foster KR. Biofilm Formation As a Response to Ecological Competition. PLoS Biol 2015; 13:e1002191. [PMID: 26158271 PMCID: PMC4497666 DOI: 10.1371/journal.pbio.1002191] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/29/2015] [Indexed: 12/28/2022] Open
Abstract
Bacteria form dense surface-associated communities known as biofilms that are central to their persistence and how they affect us. Biofilm formation is commonly viewed as a cooperative enterprise, where strains and species work together for a common goal. Here we explore an alternative model: biofilm formation is a response to ecological competition. We co-cultured a diverse collection of natural isolates of the opportunistic pathogen Pseudomonas aeruginosa and studied the effect on biofilm formation. We show that strain mixing reliably increases biofilm formation compared to unmixed conditions. Importantly, strain mixing leads to strong competition: one strain dominates and largely excludes the other from the biofilm. Furthermore, we show that pyocins, narrow-spectrum antibiotics made by other P. aeruginosa strains, can stimulate biofilm formation by increasing the attachment of cells. Side-by-side comparisons using microfluidic assays suggest that the increase in biofilm occurs due to a general response to cellular damage: a comparable biofilm response occurs for pyocins that disrupt membranes as for commercial antibiotics that damage DNA, inhibit protein synthesis or transcription. Our data show that bacteria increase biofilm formation in response to ecological competition that is detected by antibiotic stress. This is inconsistent with the idea that sub-lethal concentrations of antibiotics are cooperative signals that coordinate microbial communities, as is often concluded. Instead, our work is consistent with competition sensing where low-levels of antibiotics are used to detect and respond to the competing genotypes that produce them. Mixing natural isolates of the pathogenic bacterium Pseudomonas aeruginosa shows that the formation of biofilm is a response to antibiotic stress from competing genotypes. Bacteria often attach to each other and to surfaces and make biofilms. These dense communities occur everywhere, including on us and inside us, where they are central to both health and disease. Biofilm formation is often viewed as the coordinated action of multiple strains that work together in order to prosper and protect each other. In this study, we provide evidence for a very different view: biofilms are formed when bacterial strains compete with one another. We mixed together different strains of the widespread pathogen Pseudomonas aeruginosa and found that pairs often make bigger biofilms than either one alone. Rather than working together, however, we show that one strain normally kills the other off and that biofilm formation is actually a response to the damage of antibiotic warfare. Our work helps to explain the widespread observation that treating bacteria with clinical antibiotics can stimulate biofilm formation. When we treat bacteria, they respond as if the attack is coming from a foreign strain that must be outnumbered and outcompeted in a biofilm.
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Affiliation(s)
- Nuno M. Oliveira
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, United Kingdom
| | - Esteban Martinez-Garcia
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
- Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Joao Xavier
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
- Memorial Sloan-Kettering Cancer Center, Computational Biology Program, New York, New York, United States of America
| | | | - Roberto Kolter
- Harvard Medical School, Department of Microbiology and Immunobiology, Boston, Massachusetts, United States of America
| | - Wook Kim
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, United Kingdom
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
| | - Kevin R. Foster
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, United Kingdom
- FAS Center for Systems Biology, University of Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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Gallium Compounds Exhibit Potential as New Therapeutic Agents against Mycobacterium abscessus. Antimicrob Agents Chemother 2015; 59:4826-34. [PMID: 26033732 DOI: 10.1128/aac.00331-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/27/2015] [Indexed: 12/14/2022] Open
Abstract
The rapidly growing nontuberculous mycobacterial species Mycobacterium abscessus has recently emerged as an important pathogen in patients with cystic fibrosis (CF). Treatment options are limited because of the organism's innate resistance to standard antituberculous antibiotics, as well as other currently available antibiotics. New antibiotic approaches to the treatment of M. abscessus are urgently needed. The goal of the present study was to assess the growth-inhibitory activity of different Ga compounds against an American Type Culture Collection (ATCC) strain and clinical isolates of M. abscessus obtained from CF and other patients. In our results, using Ga(NO3)3 and all of the other Ga compounds tested inhibited the growth of ATCC 19977 and clinical isolates of M. abscessus. Inhibition was mediated by disrupting iron uptake, as the addition of exogenous iron (Fe) restored basal growth. There were modest differences in inhibition among the isolates for the same Ga chelates, and for most Ga chelates there was only a slight difference in potency from Ga(NO3)3. In contrast, Ga-protoporphyrin completely and significantly inhibited the ATCC strain and clinical isolates of M. abscessus at much lower concentrations than Ga(NO3)3. In in vitro broth culture, Ga-protoporphyrin was more potent than Ga(NO3)3. When M. abscessus growth inside the human macrophage THP-1 cell line was assessed, Ga-protoporphyrin was >20 times more active than Ga(NO3)3. The present work suggests that Ga exhibits potent growth-inhibitory capacity against the ATCC strain, as well as against antibiotic-resistant clinical isolates of M. abscessus, including the highly antibiotic-resistant strain MC2638. Ga-based therapy offers the potential for further development as a novel therapy against M. abscessus.
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Høiby N, Bjarnsholt T, Moser C, Bassi G, Coenye T, Donelli G, Hall-Stoodley L, Holá V, Imbert C, Kirketerp-Møller K, Lebeaux D, Oliver A, Ullmann A, Williams C. ESCMID∗ guideline for the diagnosis and treatment of biofilm infections 2014. Clin Microbiol Infect 2015; 21 Suppl 1:S1-25. [DOI: 10.1016/j.cmi.2014.10.024] [Citation(s) in RCA: 451] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/14/2014] [Accepted: 10/14/2014] [Indexed: 01/22/2023]
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General and condition-specific essential functions of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2015; 112:5189-94. [PMID: 25848053 DOI: 10.1073/pnas.1422186112] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The essential functions of a bacterial pathogen reflect the most basic processes required for its viability and growth, and represent potential therapeutic targets. Most screens for essential genes have assayed a single condition--growth in a rich undefined medium--and thus have not distinguished genes that are generally essential from those that are specific to this particular condition. To help define these classes for Pseudomonas aeruginosa, we identified genes required for growth on six different media, including a medium made from cystic fibrosis patient sputum. The analysis used the Tn-seq circle method to achieve high genome coverage and analyzed more than 1,000,000 unique insertion positions (an average of one insertion every 6.0 bp). We identified 352 general and 199 condition-specific essential genes. A subset of assignments was verified in individual strains with regulated expression alleles. The profile of essential genes revealed that, compared with Escherichia coli, P. aeruginosa is highly vulnerable to mutations disrupting central carbon-energy metabolism and reactive oxygen defenses. These vulnerabilities may arise from the stripped-down architecture of the organism's carbohydrate utilization pathways and its reliance on respiration for energy generation. The essential function profile thus provides fundamental insights into P. aeruginosa physiology as well as identifying candidate targets for new antibacterial agents.
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45
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Biological cost of pyocin production during the SOS response in Pseudomonas aeruginosa. J Bacteriol 2014; 196:3351-9. [PMID: 25022851 DOI: 10.1128/jb.01889-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
LexA and two structurally related regulators, PrtR and PA0906, coordinate the Pseudomonas aeruginosa SOS response. RecA-mediated autocleavage of LexA induces the expression of a protective set of genes that increase DNA damage repair and tolerance. In contrast, RecA-mediated autocleavage of PrtR induces antimicrobial pyocin production and a program that lyses cells to release the newly synthesized pyocin. Recently, PrtR-regulated genes were shown to sensitize P. aeruginosa to quinolones, antibiotics that elicit a strong SOS response. Here, we investigated the mechanisms by which PrtR-regulated genes determine antimicrobial resistance and genotoxic stress survival. We found that induction of PrtR-regulated genes lowers resistance to clinically important antibiotics and impairs the survival of bacteria exposed to one of several genotoxic agents. Two distinct mechanisms mediated these effects. Cell lysis genes that are induced following PrtR autocleavage reduced resistance to bactericidal levels of ciprofloxacin, and production of extracellular R2 pyocin was lethal to cells that initially survived UV light treatment. Although typically resistant to R2 pyocin, P. aeruginosa becomes transiently sensitive to R2 pyocin following UV light treatment, likely because of the strong downregulation of lipopolysaccharide synthesis genes that are required for resistance to R2 pyocin. Our results demonstrate that pyocin production during the P. aeruginosa SOS response carries both expected and unexpected costs.
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