1
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Silva MD, Pinto G, França A, Azeredo J, Melo LDR. Phage SEP1 hijacks Staphylococcus epidermidis stationary cells' metabolism to replicate. mSystems 2024; 9:e0026324. [PMID: 38904376 PMCID: PMC11265418 DOI: 10.1128/msystems.00263-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
In nature, bacteria often survive in a stationary state with low metabolic activity. Phages use the metabolic machinery of the host cell to replicate, and, therefore, their efficacy against non-dividing cells is usually limited. Nevertheless, it was previously shown that the Staphylococcus epidermidis phage SEP1 has the remarkable capacity to actively replicate in stationary-phase cells, reducing their numbers. Here, we studied for the first time the transcriptomic profiles of both exponential and stationary cells infected with SEP1 phage using RNA-seq to gain a better understanding of this rare phenomenon. We showed that SEP1 successfully takes over the transcriptional apparatus of both exponential and stationary cells. Infection was, however, delayed in stationary cells, with genes within the gp142-gp154 module putatively implicated in host takeover. S. epidermidis responded to SEP1 infection by upregulating three genes involved in a DNA modification system, with this being observed already 5 min after infection in exponential cells and later in stationary cells. In stationary cells, a significant number of genes involved in translation and RNA metabolic and biosynthetic processes were upregulated after 15 and 30 min of SEP1 infection in comparison with the uninfected control, showing that SEP1 activates metabolic and biosynthetic pathways necessary to its successful replication.IMPORTANCEMost phage-host interaction studies are performed with exponentially growing cells. However, this cell state is not representative of what happens in natural environments. Additionally, most phages fail to replicate in stationary cells. The Staphylococcus epidermidis phage SEP1 is one of the few phages reported to date to be able to infect stationary cells. Here, we unveiled the interaction of SEP1 with its host in both exponential and stationary states of growth at the transcriptomic level. The findings of this study provide valuable insights for a better implementation of phage therapy since phages able to infect stationary cells could be more efficient in the treatment of recalcitrant infections.
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Affiliation(s)
- Maria Daniela Silva
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
| | - Graça Pinto
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
| | - Angela França
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana Azeredo
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
| | - Luís D. R. Melo
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
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2
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Wang X, Leptihn S. Defense and anti-defense mechanisms of bacteria and bacteriophages. J Zhejiang Univ Sci B 2024; 25:181-196. [PMID: 38453634 PMCID: PMC10918411 DOI: 10.1631/jzus.b2300101] [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: 02/14/2023] [Accepted: 06/24/2023] [Indexed: 03/09/2024]
Abstract
In the post-antibiotic era, the overuse of antimicrobials has led to a massive increase in antimicrobial resistance, leaving medical doctors few or no treatment options to fight infections caused by superbugs. The use of bacteriophages is a promising alternative to treat infections, supplementing or possibly even replacing antibiotics. Using phages for therapy is possible, since these bacterial viruses can kill bacteria specifically, causing no harm to the normal flora. However, bacteria have developed a multitude of sophisticated and complex ways to resist infection by phages, including abortive infection and the clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system. Phages also can evolve and acquire new anti-defense strategies to continue predation. An in-depth exploration of both defense and anti-defense mechanisms would contribute to optimizing phage therapy, while we would also gain novel insights into the microbial world. In this paper, we summarize recent research on bacterial phage resistance and phage anti-defense mechanisms, as well as collaborative win-win systems involving both virus and host.
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Affiliation(s)
- Xiaoqing Wang
- School of Medicine, Lishui University, Lishui 323000, China.
| | - Sebastian Leptihn
- University of Edinburgh Medical School, Biomedical Sciences, College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh EH8 9JZ, UK.
- HMU Health and Medical University, Am Anger 64/73- 99084 Erfurt, Germany.
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3
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Moryl M, Różalski A, de Figueiredo JAP, Palatyńska-Ulatowska A. How Do Phages Disrupt the Structure of Enterococcus faecalis Biofilm? Int J Mol Sci 2023; 24:17260. [PMID: 38139094 PMCID: PMC10744153 DOI: 10.3390/ijms242417260] [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: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Biofilms are composed of multicellular communities of microbial cells and their self-secreted extracellular polymeric substances (EPS). The viruses named bacteriophages can infect and lyze bacterial cells, leading to efficient biofilm eradication. The aim of this study was to analyze how bacteriophages disrupt the biofilm structure by killing bacterial cells and/or by damaging extracellular polysaccharides, proteins, and DNA. The use of colorimetric and spectrofluorimetric methods and confocal laser scanning microscopy (CLSM) enabled a comprehensive assessment of phage activity against E. faecalis biofilms. The impact of the phages vB_Efa29212_2e and vB_Efa29212_3e was investigated. They were applied separately or in combination on 1-day and 7-day-old biofilms. Phages 2e effectively inhibited the growth of planktonic cells with a limited effect on the biofilm. They did not notably affect extracellular polysaccharides and proteins; however, they increased DNA levels. Phages 3e demonstrated a potent and dispersing impact on E. faecalis biofilms, despite being slightly less effective than bacteriophages 2e against planktonic cells. Phages 3e reduced the amount of extracellular polysaccharides and increased eDNA levels in both 1-day-old and 7-day-old biofilm cultures. Phage cocktails had a strong antimicrobial effect on both planktonic and biofilm-associated bacteria. A significant reduction in the levels of polysaccharides, proteins, and eDNA in 1-day-old biofilm samples was noted, which confirms that phages interfere with the structure of E. faecalis biofilm by killing bacterial cells and affecting extracellular polymer levels.
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Affiliation(s)
- Magdalena Moryl
- Department of Biology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland;
| | - Antoni Różalski
- Department of Biology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland;
| | | | - Aleksandra Palatyńska-Ulatowska
- Department of Endodontics, Chair of Conservative Dentistry and Endodontics, Medical University of Lodz, 92-213 Lodz, Poland;
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4
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Štrancar V, Marušić M, Tušar J, Praček N, Kolenc M, Šuster K, Horvat S, Janež N, Peterka M. Isolation and in vitro characterization of novel S. epidermidis phages for therapeutic applications. Front Cell Infect Microbiol 2023; 13:1169135. [PMID: 37293203 PMCID: PMC10244729 DOI: 10.3389/fcimb.2023.1169135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
S. epidermidis is an important opportunistic pathogen causing chronic prosthetic joint infections associated with biofilm growth. Increased tolerance to antibiotic therapy often requires prolonged treatment or revision surgery. Phage therapy is currently used as compassionate use therapy and continues to be evaluated for its viability as adjunctive therapy to antibiotic treatment or as an alternative treatment for infections caused by S. epidermidis to prevent relapses. In the present study, we report the isolation and in vitro characterization of three novel lytic S. epidermidis phages. Their genome content analysis indicated the absence of antibiotic resistance genes and virulence factors. Detailed investigation of the phage preparation indicated the absence of any prophage-related contamination and demonstrated the importance of selecting appropriate hosts for phage development from the outset. The isolated phages infect a high proportion of clinically relevant S. epidermidis strains and several other coagulase-negative species growing both in planktonic culture and as a biofilm. Clinical strains differing in their biofilm phenotype and antibiotic resistance profile were selected to further identify possible mechanisms behind increased tolerance to isolated phages.
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Affiliation(s)
- Vida Štrancar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Monika Marušić
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Jasmina Tušar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Neža Praček
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Marko Kolenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Šuster
- Valdoltra Orthopaedic Hospital, Ankaran, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nika Janež
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Matjaž Peterka
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
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5
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França A. The Role of Coagulase-Negative Staphylococci Biofilms on Late-Onset Sepsis: Current Challenges and Emerging Diagnostics and Therapies. Antibiotics (Basel) 2023; 12:antibiotics12030554. [PMID: 36978421 PMCID: PMC10044083 DOI: 10.3390/antibiotics12030554] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Infections are one of the most significant complications of neonates, especially those born preterm, with sepsis as one of the principal causes of mortality. Coagulase-negative staphylococci (CoNS), a group of staphylococcal species that naturally inhabit healthy human skin and mucosa, are the most common cause of late-onset sepsis, especially in preterms. One of the risk factors for the development of CoNS infections is the presence of implanted biomedical devices, which are frequently used for medications and/or nutrient delivery, as they serve as a scaffold for biofilm formation. The major concerns related to CoNS infections have to do with the increasing resistance to multiple antibiotics observed among this bacterial group and biofilm cells’ increased tolerance to antibiotics. As such, the treatment of CoNS biofilm-associated infections with antibiotics is increasingly challenging and considering that antibiotics remain the primary form of treatment, this issue will likely persist in upcoming years. For that reason, the development of innovative and efficient therapeutic measures is of utmost importance. This narrative review assesses the current challenges and emerging diagnostic tools and therapies for the treatment of CoNS biofilm-associated infections, with a special focus on late-onset sepsis.
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Affiliation(s)
- Angela França
- Centre of Biological Engineering, LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
- LABBELS—Associate Laboratory in Biotechnology and Bioengineering and Microelectromechanical Systems, Braga and Guimarães, Portugal
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6
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The Burden of Survivors: How Can Phage Infection Impact Non-Infected Bacteria? Int J Mol Sci 2023; 24:ijms24032733. [PMID: 36769055 PMCID: PMC9917116 DOI: 10.3390/ijms24032733] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
The contemporary understanding of complex interactions in natural microbial communities and the numerous mechanisms of bacterial communication challenge the classical concept of bacteria as unicellular organisms. Microbial populations, especially those in densely populated habitats, appear to behave cooperatively, coordinating their reactions in response to different stimuli and behaving as a quasi-tissue. The reaction of such systems to viral infection is likely to go beyond each cell or species tackling the phage attack independently. Bacteriophage infection of a fraction of the microbial community may also exert an influence on the physiological state and/or phenotypic features of those cells that have not yet had direct contact with the virus or are even intrinsically unable to become infected by the particular virus. These effects may be mediated by sensing the chemical signals released by lysing or by infected cells as well as by more indirect mechanisms.
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7
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Yu Z, Chen J, Tan Y, Shen Y, Zhu L, Yu P. Phage Predation Promotes Filamentous Bacterium Piscinibacter Colonization and Improves Structural and Hydraulic Stability of Microbial Aggregates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16230-16239. [PMID: 36173693 DOI: 10.1021/acs.est.2c04745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Although bacteria-phage interactions have broad environmental applications and ecological implications, the influence of phage predation on bacterial aggregation and structural stability remains largely unexplored. Herein, we demonstrate that inefficient lytic phage predation can promote host filamentous bacterium Piscinibacter colonization onto non-host Thauera aggregates, improving the structural and hydraulic stability of the dual-species aggregates. Specifically, phage predation at 103-104 PFU/mL (i.e., multiplication of infection at 0.01-0.1) promoted initial Piscinibacter colonization by 10-15 folds and resulted in 29-31% higher abundance of Piscinibacter in the stabilized aggregates than that in the control aggregates without phage predation. Transcriptomic analysis revealed upregulated genes related to quorum sensing (by 15-92 folds) and polysaccharide secretion (by 10-90 folds) within the treated aggregates, which was consistent with 120-172% higher content of polysaccharides for the treated dual-species aggregates. Confocal laser scanning microscopic images further confirmed the increase of filamentous bacteria and polysaccharides (both with wider distribution) within the dual-species aggregates. Accordlingly, the aggregates' structural strength (via atomic force microscopes) and shear resistance (via hydraulic stress tests) increased by 77 and 42%, respectively, relative to the control group. In the long-term experiments, the enhanced hydraulic stability of the treated aggregates could facilitate dwelling bacteria propagation in flow-through conditions. Overall, our study demonstrates that phage predation can promote bacterial aggregation and enhance aggregate structural stability, revealing the beneficial role of lytic phage predation on bacterial symbiosis and environmental adaptivity.
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Affiliation(s)
- Zhuodong Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yixiao Tan
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yun Shen
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Liang Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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8
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Transcriptome Analyses of Prophage in Mediating Persistent Methicillin-Resistant Staphylococcus aureus Endovascular Infection. Genes (Basel) 2022; 13:genes13091527. [PMID: 36140695 PMCID: PMC9498598 DOI: 10.3390/genes13091527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections represent a significant subset of S. aureus infections and correlate with exceptionally high mortality. We have recently demonstrated that the lysogenization of prophage ϕSA169 from a clinical persistent MRSA bacteremia isolate (300-169) into a clinical resolving bacteremia MRSA isolate (301-188) resulted in the acquisition of well-defined in vitro and in vivo phenotypic and genotypic profiles related to persistent outcome. However, the underlying mechanism(s) of this impact is unknown. In the current study, we explored the genetic mechanism that may contribute to the ϕSA169-correlated persistence using RNA sequencing. Transcriptomic analyses revealed that the most significant impacts of ϕSA169 were: (i) the enhancement of fatty acid biosynthesis and purine and pyrimidine metabolic pathways; (ii) the repression of galactose metabolism and phosphotransferase system (PTS); and (iii) the down-regulation of the mutual prophage genes in both 300-169 and 301-188 strains. In addition, the influence of different genetic backgrounds between 300-169 and 301-188 might also be involved in the persistent outcome. These findings may provide targets for future studies on the persistence of MRSA.
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9
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Understanding the Mechanisms That Drive Phage Resistance in Staphylococci to Prevent Phage Therapy Failure. Viruses 2022; 14:v14051061. [PMID: 35632803 PMCID: PMC9146914 DOI: 10.3390/v14051061] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 02/07/2023] Open
Abstract
Despite occurring at the microscopic scale, the armed race between phages and their bacterial hosts involves multiple mechanisms, some of which are just starting to be understood. On the one hand, bacteria have evolved strategies that can stop the viral infection at different stages (adsorption, DNA injection and replication, biosynthesis and assembly of the viral progeny and/or release of the newly formed virions); on the other, phages have gradually evolved counterattack strategies that allow them to continue infecting their prey. This co-evolutionary process has played a major role in the development of microbial populations in both natural and man-made environments. Notably, understanding the parameters of this microscopic war will be paramount to fully benefit from the application of phage therapy against dangerous, antibiotic-resistant human pathogens. This review gathers the current knowledge regarding the mechanisms of phage resistance in the Staphylococcus genus, which includes Staphylococcus aureus, one of the most concerning microorganisms in terms of antibiotic resistance acquisition. Some of these strategies involve permanent changes to the bacterial cell via mutations, while others are transient, adaptive changes whose expression depends on certain environmental cues or the growth phase. Finally, we discuss the most plausible strategies to limit the impact of phage resistance on therapy, with a special emphasis on the importance of a rational design of phage cocktails in order to thwart therapeutic failure.
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10
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Molina F, Menor-Flores M, Fernández L, Vega-Rodríguez MA, García P. Systematic analysis of putative phage-phage interactions on minimum-sized phage cocktails. Sci Rep 2022; 12:2458. [PMID: 35165352 PMCID: PMC8844382 DOI: 10.1038/s41598-022-06422-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022] Open
Abstract
The application of bacteriophages as antibacterial agents has many benefits in the “post-antibiotic age”. To increase the number of successfully targeted bacterial strains, phage cocktails, instead of a single phage, are commonly formulated. Nevertheless, there is currently no consensus pipeline for phage cocktail development. Thus, although large cocktails increase the spectrum of activity, they could produce side effects such as the mobilization of virulence or antibiotic resistance genes. On the other hand, coinfection (simultaneous infection of one host cell by several phages) might reduce the potential for bacteria to evolve phage resistance, but some antagonistic interactions amongst phages might be detrimental for the outcome of phage cocktail application. With this in mind, we introduce here a new method, which considers the host range and each individual phage-host interaction, to design the phage mixtures that best suppress the target bacteria while minimizing the number of phages to restrict manufacturing costs. Additionally, putative phage-phage interactions in cocktails and phage-bacteria networks are compared as the understanding of the complex interactions amongst bacteriophages could be critical in the development of realistic phage therapy models in the future.
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11
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Totten KMC, Patel R. Phage Activity against Planktonic and Biofilm Staphylococcus aureus Periprosthetic Joint Infection Isolates. Antimicrob Agents Chemother 2022; 66:e0187921. [PMID: 34662191 PMCID: PMC8765226 DOI: 10.1128/aac.01879-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023] Open
Abstract
We recently reported the successful treatment of a case of periprosthetic joint infection (PJI) with phage. Phage activity against bacteria causing PJI has not been systematically evaluated. Here, we examined the in vitro activity of seven phages against 122 clinical isolates of Staphylococcus aureus recovered between April 1999 and February 2018 from subjects with PJI. Phages were assessed against planktonic and biofilm phenotypes. Activity of individual phages was demonstrated against up to 73% of bacterial isolates in the planktonic state and up to 100% of biofilms formed by isolates that were planktonically phage susceptible. Susceptibility to phage was not correlated with small-colony-variant phenotype for planktonic or biofilm bacteria; correlation between antibiotic susceptibility and planktonic phage susceptibility and between biofilm phage susceptibility and strength of biofilm formation were noted under select conditions. These results demonstrate that phages can infect S. aureus causing PJI in both planktonic and biofilm phenotypes, and thus are worthy of investigation as an alternative or addition to antibiotics in this setting.
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Affiliation(s)
- Katherine M. C. Totten
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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12
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Hatoum-Aslan A. The phages of staphylococci: critical catalysts in health and disease. Trends Microbiol 2021; 29:1117-1129. [PMID: 34030968 PMCID: PMC8578144 DOI: 10.1016/j.tim.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/21/2023]
Abstract
The phages that infect Staphylococcus species are dominant residents of the skin microbiome that play critical roles in health and disease. While temperate phages, which can integrate into the host genome, have the potential to promote staphylococcal pathogenesis, the strictly lytic variety are powerful antimicrobials that are being exploited for therapeutic applications. This article reviews recent insights into the diversity of staphylococcal phages and newly described mechanisms by which they influence host pathogenicity. The latest efforts to harness these viruses to eradicate staphylococcal infections are also highlighted. Decades of research has focused on the temperate phages of Staphylococcus aureus as model systems, thus underscoring the need to broaden basic research efforts to include diverse phages that infect other clinically relevant Staphylococcus species.
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Affiliation(s)
- Asma Hatoum-Aslan
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL, 61801, USA.
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13
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Ding Y, Zhang D, Zhao X, Tan W, Zheng X, Zhang Q, Ji X, Wei Y. Autoinducer-2-mediated quorum-sensing system resists T4 phage infection in Escherichia coli. J Basic Microbiol 2021; 61:1113-1123. [PMID: 34783039 DOI: 10.1002/jobm.202100344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/26/2021] [Accepted: 10/31/2021] [Indexed: 11/12/2022]
Abstract
In response to the restriction of nutrients and predation by natural enemies, bacteria have evolved complex coping strategies to ensure the reproduction and survival of individual species. Quorum sensing (QS) is involved in the bacterial response to phage predation and regulation of cellular metabolism. However, to date, no clear evidence exists regarding the involvement of autoinducer-2 (AI-2)-mediated QS systems in Escherichia coli in response to the challenges of nutrient restriction and phage infection. In this study, the role of the AI-2-mediated QS system in resisting T4 phage infection and regulating cell mechanisms in E. coli was revealed for the first time. This effect of the AI-2-mediated QS was achieved by simultaneously downregulating the T4 absorption site and carbon and glucose metabolism. Additionally, we found that lsrB, a metabolic brake, participates in AI-2-mediated regulation and maintenance of the normal metabolic balance of cells. The novel phage defense strategy and regulation and maintenance of cellular metabolism effectively limited the expansion of the phage population.
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Affiliation(s)
- Yafang Ding
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Dongfang Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiaoman Zhao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Wenzhang Tan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiaodan Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiuling Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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14
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Amankwah S, Abdella K, Kassa T. Bacterial Biofilm Destruction: A Focused Review On The Recent Use of Phage-Based Strategies With Other Antibiofilm Agents. Nanotechnol Sci Appl 2021; 14:161-177. [PMID: 34548785 PMCID: PMC8449863 DOI: 10.2147/nsa.s325594] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Biofilms are bacterial communities that live in association with biotic or abiotic surfaces and enclosed in an extracellular polymeric substance. Their formation on both biotic and abiotic surfaces, including human tissue and medical device surfaces, pose a major threat causing chronic infections. In addition, current antibiotics and antiseptic agents have shown limited ability to completely remove biofilms. In this review, the authors provide an overview on the formation of bacterial biofilms and its characteristics, burden and evolution with phages. Moreover, the most recent possible use of phages and phage-derived enzymes to combat bacteria in biofilm structures is elucidated. From the emerging results, it can be concluded that despite successful use of phages and phage-derived products in destroying biofilms, they are mostly not adequate to eradicate all bacterial cells. Nevertheless, a combined therapy with the use of phages and/or phage-derived products with other antimicrobial agents including antibiotics, nanoparticles, and antimicrobial peptides may be effective approaches to remove biofilms from medical device surfaces and to treat their associated infections in humans.
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Affiliation(s)
- Stephen Amankwah
- School of Medical Laboratory Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
- Accra Medical Centre, Accra, Ghana
| | - Kedir Abdella
- School of Medical Laboratory Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Tesfaye Kassa
- School of Medical Laboratory Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
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15
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Abstract
Bacteriophages and bacterial biofilms are widely present in natural environments, a fact that has accelerated the evolution of phages and their bacterial hosts in these particular niches. Phage-host interactions in biofilm communities are rather complex, where phages are not always merely predators but also can establish symbiotic relationships that induce and strengthen biofilms. In this review we provide an overview of the main features affecting phage-biofilm interactions as well as the currently available methods of studying these interactions. In addition, we address the applications of phages for biofilm control in different contexts.
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Affiliation(s)
- Diana P Pires
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Luís D R Melo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
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16
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Pires DP, Costa AR, Pinto G, Meneses L, Azeredo J. Current challenges and future opportunities of phage therapy. FEMS Microbiol Rev 2021; 44:684-700. [PMID: 32472938 DOI: 10.1093/femsre/fuaa017] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Antibiotic resistance is a major public health challenge worldwide, whose implications for global health might be devastating if novel antibacterial strategies are not quickly developed. As natural predators of bacteria, (bacterio)phages may play an essential role in escaping such a dreadful future. The rising problem of antibiotic resistance has revived the interest in phage therapy and important developments have been achieved over the last years. But where do we stand today and what can we expect from phage therapy in the future? This is the question we set to answer in this review. Here, we scour the outcomes of human phage therapy clinical trials and case reports, and address the major barriers that stand in the way of using phages in clinical settings. We particularly address the potential of phage resistance to hinder phage therapy and discuss future avenues to explore the full capacity of phage therapy.
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Affiliation(s)
- Diana P Pires
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Graça Pinto
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Luciana Meneses
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Kranjec C, Morales Angeles D, Torrissen Mårli M, Fernández L, García P, Kjos M, Diep DB. Staphylococcal Biofilms: Challenges and Novel Therapeutic Perspectives. Antibiotics (Basel) 2021; 10:131. [PMID: 33573022 PMCID: PMC7911828 DOI: 10.3390/antibiotics10020131] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
Staphylococci, like Staphylococcus aureus and S. epidermidis, are common colonizers of the human microbiota. While being harmless in many cases, many virulence factors result in them being opportunistic pathogens and one of the major causes of hospital-acquired infections worldwide. One of these virulence factors is the ability to form biofilms-three-dimensional communities of microorganisms embedded in an extracellular polymeric matrix (EPS). The EPS is composed of polysaccharides, proteins and extracellular DNA, and is finely regulated in response to environmental conditions. This structured environment protects the embedded bacteria from the human immune system and decreases their susceptibility to antimicrobials, making infections caused by staphylococci particularly difficult to treat. With the rise of antibiotic-resistant staphylococci, together with difficulty in removing biofilms, there is a great need for new treatment strategies. The purpose of this review is to provide an overview of our current knowledge of the stages of biofilm development and what difficulties may arise when trying to eradicate staphylococcal biofilms. Furthermore, we look into promising targets and therapeutic methods, including bacteriocins and phage-derived antibiofilm approaches.
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Affiliation(s)
- Christian Kranjec
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Danae Morales Angeles
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Lucía Fernández
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute of Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (L.F.); (P.G.)
- DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Pilar García
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute of Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (L.F.); (P.G.)
- DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, 1432 Ås, Norway; (C.K.); (D.M.A.); (M.T.M.)
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18
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Moller AG, Winston K, Ji S, Wang J, Hargita Davis MN, Solís-Lemus CR, Read TD. Genes Influencing Phage Host Range in Staphylococcus aureus on a Species-Wide Scale. mSphere 2021; 6:e01263-20. [PMID: 33441407 PMCID: PMC7845607 DOI: 10.1128/msphere.01263-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is a human pathogen that causes serious diseases, ranging from skin infections to septic shock. Bacteriophages (phages) are both natural killers of S. aureus, offering therapeutic possibilities, and important vectors of horizontal gene transfer (HGT) in the species. Here, we used high-throughput approaches to understand the genetic basis of strain-to-strain variation in sensitivity to phages, which defines the host range. We screened 259 diverse S. aureus strains covering more than 40 sequence types for sensitivity to eight phages, which were representatives of the three phage classes that infect the species. The phages were variable in host range, each infecting between 73 and 257 strains. Using genome-wide association approaches, we identified putative loci that affect host range and validated their function using USA300 transposon knockouts. In addition to rediscovering known host range determinants, we found several previously unreported genes affecting bacterial growth during phage infection, including trpA, phoR, isdB, sodM, fmtC, and relA We used the data from our host range matrix to develop predictive models that achieved between 40% and 95% accuracy. This work illustrates the complexity of the genetic basis for phage susceptibility in S. aureus but also shows that with more data, we may be able to understand much of the variation. With a knowledge of host range determination, we can rationally design phage therapy cocktails that target the broadest host range of S. aureus strains and address basic questions regarding phage-host interactions, such as the impact of phage on S. aureus evolution.IMPORTANCEStaphylococcus aureus is a widespread, hospital- and community-acquired pathogen, many strains of which are antibiotic resistant. It causes diverse diseases, ranging from local to systemic infection, and affects both the skin and many internal organs, including the heart, lungs, bones, and brain. Its ubiquity, antibiotic resistance, and disease burden make new therapies urgent. One alternative therapy to antibiotics is phage therapy, in which viruses specific to infecting bacteria clear infection. In this work, we identified and validated S. aureus genes that influence phage host range-the number of strains a phage can infect and kill-by testing strains representative of the diversity of the S. aureus species for phage host range and associating the genome sequences of strains with host range. These findings together improved our understanding of how phage therapy works in the bacterium and improve prediction of phage therapy efficacy based on the predicted host range of the infecting strain.
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Affiliation(s)
- Abraham G Moller
- Microbiology and Molecular Genetics (MMG) Program, Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia, USA
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Kyle Winston
- Department of Epidemiology, Rollins School of Public Health (RSPH), Emory University, Atlanta, Georgia, USA
| | - Shiyu Ji
- Eugene Gangarosa Laboratory Research Fellowship, Emory College Online & Summer Programs, Emory College of Arts and Sciences, Atlanta, Georgia, USA
| | - Junting Wang
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michelle N Hargita Davis
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Claudia R Solís-Lemus
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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19
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Zhang B, Yu P, Wang Z, Alvarez PJJ. Hormetic Promotion of Biofilm Growth by Polyvalent Bacteriophages at Low Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:12358-12365. [PMID: 32886494 DOI: 10.1021/acs.est.0c03558] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Interactions between bacteriophages (phages) and biofilms are poorly understood despite their broad ecological and water quality implications. Here, we report that biofilm exposure to lytic polyvalent phages at low concentrations (i.e., 102-104 phages/mL) can counterintuitively promote biofilm growth and densification (corroborated by confocal laser scanning microscopy (CLSM)). Such exposure hormetically upregulated quorum sensing genes (by 4.1- to 24.9-fold), polysaccharide production genes (by 3.7- to 9.3-fold), and curli synthesis genes (by 4.5- to 6.5-fold) in the biofilm-dwelling bacterial hosts (i.e., Escherichia coli and Pseudomonas aeruginosa) relative to unexposed controls. Accordingly, the biofilm matrix increased its polysaccharide and extracellular DNA content relative to unexposed controls (by 41.8 ± 2.3 and 81.4 ± 2.2%, respectively), which decreased biofilm permeability and increased structural integrity. This contributed to enhanced resistance to disinfection with chlorine (bacteria half-lives were 6.08 ± 0.05 vs 3.91 ± 0.03 min for unexposed controls) and to subsequent phage infection (biomass removal was 18.2 ± 1.2 vs 32.3 ± 1.2% for unexposed controls), apparently by mitigating diffusion of these antibacterial agents through the biofilm. Overall, low concentrations of phages reaching a biofilm may result in unintended biofilm stimulation, which might accelerate biofouling, biocorrosion, or other biofilm-related water quality problems.
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Affiliation(s)
- Bo Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston 77005, United States
| | - Zijian Wang
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston 77005, United States
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20
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Fernández L, Gutiérrez D, García P, Rodríguez A. Environmental pH is a key modulator of Staphylococcus aureus biofilm development under predation by the virulent phage phiIPLA-RODI. ISME JOURNAL 2020; 15:245-259. [PMID: 32963343 DOI: 10.1038/s41396-020-00778-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 11/09/2022]
Abstract
Previous work had shown that, in some Staphylococcus aureus strains, low concentrations of the virulent phage vB_SauM_phiIPLA-RODI (phiIPLA-RODI) promoted the formation of DNA-rich biofilms, whose cells exhibited significant transcriptional differences compared to an uninfected control. This study aimed to dissect the sequence of events leading to these changes. Analysis of phage propagation throughout biofilm development revealed that the number of phage particles increased steadily up to a certain point and then declined. This partial phage inactivation seemed to be a consequence of medium acidification due to glucose fermentation by the bacterium. Computer simulation of phage-host dynamics during biofilm development showed how even small differences in pH evolution can affect the outcome of phage infection. An acidic pH, together with successful phage propagation, was also necessary to observe the phage-associated changes in biofilm architecture and in the transcriptional profile of the bacterial population. Altogether, this study shows how the dynamics between phage and host can be tightly coordinated through an environmental cue, even in the context of a complex biofilm population.
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Affiliation(s)
- Lucía Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain. .,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.
| | - Diana Gutiérrez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.,Laboratory of Applied Biotechnology, Department of Applied Biosciences, Faculty of Bioscience engineering, Ghent University, 9000, Ghent, Belgium
| | - Pilar García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Ana Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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21
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Kreienbaum M, Dörrich AK, Brandt D, Schmid NE, Leonhard T, Hager F, Brenzinger S, Hahn J, Glatter T, Ruwe M, Briegel A, Kalinowski J, Thormann KM. Isolation and Characterization of Shewanella Phage Thanatos Infecting and Lysing Shewanella oneidensis and Promoting Nascent Biofilm Formation. Front Microbiol 2020; 11:573260. [PMID: 33072035 PMCID: PMC7530303 DOI: 10.3389/fmicb.2020.573260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/27/2020] [Indexed: 01/21/2023] Open
Abstract
Species of the genus Shewanella are widespread in nature in various habitats, however, little is known about phages affecting Shewanella sp. Here, we report the isolation of phages from diverse freshwater environments that infect and lyse strains of Shewanella oneidensis and other Shewanella sp. Sequence analysis and microscopic imaging strongly indicate that these phages form a so far unclassified genus, now named Shewanella phage Thanatos, which can be positioned within the subfamily of Tevenvirinae (Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tevenvirinae). We characterized one member of this group in more detail using S. oneidensis MR-1 as a host. Shewanella phage Thanatos-1 possesses a prolate icosahedral capsule of about 110 nm in height and 70 nm in width and a tail of about 95 nm in length. The dsDNA genome exhibits a GC content of about 34.5%, has a size of 160.6 kbp and encodes about 206 proteins (92 with an annotated putative function) and two tRNAs. Out of those 206, MS analyses identified about 155 phage proteins in PEG-precipitated samples of infected cells. Phage attachment likely requires the outer lipopolysaccharide of S. oneidensis, narrowing the phage's host range. Under the applied conditions, about 20 novel phage particles per cell were produced after a latent period of approximately 40 min, which are stable at a pH range from 4 to 12 and resist temperatures up to 55°C for at least 24 h. Addition of Thanatos to S. oneidensis results in partial dissolution of established biofilms, however, early exposure of planktonic cells to Thanatos significantly enhances biofilm formation. Taken together, we identified a novel genus of Myophages affecting S. oneidensis communities in different ways.
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Affiliation(s)
- Maximilian Kreienbaum
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anja K Dörrich
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - David Brandt
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Nicole E Schmid
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Tabea Leonhard
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Fabian Hager
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Susanne Brenzinger
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Julia Hahn
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Timo Glatter
- Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Matthias Ruwe
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Ariane Briegel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
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22
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Wasfi R, Hamed SM, Amer MA, Fahmy LI. Proteus mirabilis Biofilm: Development and Therapeutic Strategies. Front Cell Infect Microbiol 2020; 10:414. [PMID: 32923408 PMCID: PMC7456845 DOI: 10.3389/fcimb.2020.00414] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/06/2020] [Indexed: 01/21/2023] Open
Abstract
Proteus mirabilis is a Gram negative bacterium that is a frequent cause of catheter-associated urinary tract infections (CAUTIs). Its ability to cause such infections is mostly related to the formation of biofilms on catheter surfaces. In order to form biofilms, P. mirabilis expresses a number of virulence factors. Such factors may include adhesion proteins, quorum sensing molecules, lipopolysaccharides, efflux pumps, and urease enzyme. A unique feature of P. mirabilis biofilms that build up on catheter surfaces is their crystalline nature owing to their ureolytic biomineralization. This leads to catheter encrustation and blockage and, in most cases, is accompanied by urine retention and ascending UTIs. Bacteria embedded in crystalline biofilms become highly resistant to conventional antimicrobials as well as the immune system. Being refractory to antimicrobial treatment, alternative approaches for eradicating P. mirabilis biofilms have been sought by many studies. The current review focuses on the mechanism by which P. mirabilis biofilms are formed, and a state of the art update on preventing biofilm formation and reduction of mature biofilms. These treatment approaches include natural, and synthetic compounds targeting virulence factors and quorum sensing, beside other strategies that include carrier-mediated diffusion of antimicrobials into biofilm matrix. Bacteriophage therapy has also shown successful results in vitro for combating P. mirabilis biofilms either merely through their lytic effect or by acting as facilitators for antimicrobials diffusion.
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Affiliation(s)
- Reham Wasfi
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Samira M Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Mai A Amer
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Lamiaa Ismail Fahmy
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
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23
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Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in Staphylococcus aureus. mSphere 2020; 5:5/4/e00439-20. [PMID: 32727859 PMCID: PMC7392542 DOI: 10.1128/msphere.00439-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Regulatory small RNAs (sRNAs) are known to play important roles in the Gram-positive bacterial pathogen Staphylococcus aureus; however, their existence is often overlooked, primarily because sRNA genes are absent from genome annotation files. Consequently, transcriptome sequencing (RNA-Seq)-based experimental approaches, performed using standard genome annotation files as a reference, have likely overlooked data for sRNAs. Previously, we created an updated S. aureus genome annotation file, which included annotations for 303 known sRNAs in USA300. Here, we utilized this updated reference file to reexamine publicly available RNA-Seq data sets in an attempt to recover lost information on sRNA expression, stability, and potential to encode peptides. First, we used transcriptomic data from 22 studies to identify how the expression of 303 sRNAs changed under 64 different experimental conditions. Next, we used RNA-Seq data from an RNA stability assay to identify highly stable/unstable sRNAs. We went on to reanalyze a ribosome profiling (Ribo-seq) data set to identify sRNAs that have the potential to encode peptides and to experimentally confirm the presence of three of these peptides in the USA300 background. Interestingly, one of these sRNAs/peptides, encoded at the tsr37 locus, influences the ability of S. aureus cells to autoaggregate. Finally, we reexamined two recently published in vivo RNA-Seq data sets, from the cystic fibrosis (CF) lung and a murine vaginal colonization study, and identified 29 sRNAs that may play a role in vivo Collectively, these results can help inform future studies of these important regulatory elements in S. aureus and highlight the need for ongoing curating and updating of genome annotation files.IMPORTANCE Regulatory small RNAs (sRNAs) are a class of RNA molecules that are produced in bacterial cells but that typically do not encode proteins. Instead, they perform a variety of critical functions within the cell as RNA. Most bacterial genomes do not include annotations for sRNA genes, and any type of analysis that is performed using a bacterial genome as a reference will therefore overlook data for sRNAs. In this study, we reexamined hundreds of previously generated S. aureus RNA-Seq data sets and reanalyzed them to generate data for sRNAs. To do so, we utilized an updated S. aureus genome annotation file, previously generated by our group, which contains annotations for 303 sRNAs. The data generated (which were previously discarded) shed new light on sRNAs in S. aureus, most of which are unstudied, and highlight certain sRNAs that are likely to play important roles in the cell.
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24
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Li L, Wang G, Li Y, Francois P, Bayer AS, Chen L, Seidl K, Cheung A, Xiong YQ. Impact of the Novel Prophage ϕSA169 on Persistent Methicillin-Resistant Staphylococcus aureus Endovascular Infection. mSystems 2020; 5:e00178-20. [PMID: 32606024 PMCID: PMC7329321 DOI: 10.1128/msystems.00178-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections are life-threatening syndromes with few therapeutic options. The potential impact of bacteriophages on the persistent outcome has not been well studied. In this study, we investigated the role of a novel prophage (ϕSA169) in MRSA persistence by using a lysogen-free clinically resolving bacteremia (RB) isolate and comparing it to a derivative which was obtained by infecting the RB strain with ϕSA169, which has been lysogenized in a clinical persistent MRSA bacteremia (PB) isolate. Similar to the PB isolate, the ϕSA169-lysogenized RB strain exhibited well-defined in vitro and in vivo phenotypic and genotypic signatures related to the persistent outcome, including earlier activation of global regulators (i.e., sigB, sarA, agr RNAIII, and sae); higher expression of a critical purine biosynthesis gene, purF; and higher growth rates accompanied by lower ATP levels and vancomycin (VAN) susceptibility and stronger δ-hemolysin and biofilm formation versus its isogenic parental RB isolate. Notably, the contribution of ϕSA169 in persistent outcome with VAN treatment was confirmed in an experimental infective endocarditis model. Taken together, these results indicate the critical role of the prophage ϕSA169 in persistent MRSA endovascular infections. Further studies are needed to identify the mechanisms of ϕSA169 in mediating the persistence, as well as establishing the scope of impact, of this prophage in other PB strains.IMPORTANCE Bacteriophages are viruses that invade the bacterial host, disrupt bacterial metabolism, and cause the bacterium to lyse. Because of its remarkable antibacterial activity and unique advantages over antibiotics, for instance, bacteriophage is specific for one species of bacteria and resistance to phage is less common than resistance to antibiotics. Indeed, bacteriophage therapy for treating infections due to multidrug-resistant pathogens in humans has become a research hot spot. However, it is also worth considering that bacteriophages are transferable and could cotransfer host chromosomal genes, e.g., virulence and antimicrobial resistance genes, while lysogenizing and integrating into the bacterial chromosome (prophage), thus playing a role in bacterial evolution and virulence. In the current study, we identified a novel prophage, ϕSA169, from a clinical persistent MRSA bacteremia isolate, and we determined that ϕSA169 mediated well-defined in vitro and in vivo phenotypic and genotypic signatures related to the persistent outcome, which may represent a unique and important persistent mechanism(s).
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Affiliation(s)
- Liang Li
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Genzhu Wang
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Yi Li
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | | | - Arnold S Bayer
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Liang Chen
- Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Kati Seidl
- University Hospital of Zurich, Zurich, Switzerland
| | | | - Yan Q Xiong
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Department of Medicine, Division of Infectious Diseases, Harbor-UCLA Medical Center, Torrance, California, USA
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25
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A widespread toxin-antitoxin system exploiting growth control via alarmone signaling. Proc Natl Acad Sci U S A 2020; 117:10500-10510. [PMID: 32345719 PMCID: PMC7229694 DOI: 10.1073/pnas.1916617117] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The alarmone (p)ppGpp is a central signaling nucleotide that is synthesized by RelA-SpoT Homologue (RSH) enzymes, and rewires bacterial physiology in response to stress. It is an unanswered question why bacteria often carry multiple (p)ppGpp-synthesising RSHs in the same genome. We have answered that question for five subfamilies of small alarmone synthetases (SASs) by discovering that they are toxins of a novel toxin−antitoxin system, and that they act by synthesizing ppGpp and its unusual analogue—ppApp. These distinct toxic SAS (toxSAS) subfamilies are neutralized by six neighboring antitoxin genes. The toxSAS system and its weaponizing of nucleotide second messengers gives a new angle to the hotly debated and controversial topic of cross-talk between TAs and the alarmone-mediated stringent response. Under stressful conditions, bacterial RelA-SpoT Homolog (RSH) enzymes synthesize the alarmone (p)ppGpp, a nucleotide second messenger. (p)ppGpp rewires bacterial transcription and metabolism to cope with stress, and, at high concentrations, inhibits the process of protein synthesis and bacterial growth to save and redirect resources until conditions improve. Single-domain small alarmone synthetases (SASs) are RSH family members that contain the (p)ppGpp synthesis (SYNTH) domain, but lack the hydrolysis (HD) domain and regulatory C-terminal domains of the long RSHs such as Rel, RelA, and SpoT. We asked whether analysis of the genomic context of SASs can indicate possible functional roles. Indeed, multiple SAS subfamilies are encoded in widespread conserved bicistronic operon architectures that are reminiscent of those typically seen in toxin−antitoxin (TA) operons. We have validated five of these SASs as being toxic (toxSASs), with neutralization by the protein products of six neighboring antitoxin genes. The toxicity of Cellulomonas marina toxSAS FaRel is mediated by the accumulation of alarmones ppGpp and ppApp, and an associated depletion of cellular guanosine triphosphate and adenosine triphosphate pools, and is counteracted by its HD domain-containing antitoxin. Thus, the ToxSAS–antiToxSAS system with its multiple different antitoxins exemplifies how ancient nucleotide-based signaling mechanisms can be repurposed as TA modules during evolution, potentially multiple times independently.
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Hernández I, Vecchi D. The Interactive Construction of Biological Individuality Through Biotic Entrenchment. Front Psychol 2019; 10:2578. [PMID: 31849738 PMCID: PMC6900962 DOI: 10.3389/fpsyg.2019.02578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/31/2019] [Indexed: 12/30/2022] Open
Abstract
In this article, we propose to critically evaluate whether a closure of constraints interpretation can make sense of biotic entrenchment, the process of assimilation and functional integration of environmental elements of biotic origin in development and, eventually, evolution. In order to achieve the aims of our analysis, we shall focus on multi-species partnerships, biological systems characterised by ontogenetic dependencies of various strengths between the partners. Our main research question is to tackle the foundational problem posed by the dynamics of biotic entrenchment characterising multi-species partnerships for the closure of constraints interpretation, namely, to understand for which biological system (i.e., the partners taken individually or the partnership as the encompassing system) closure of constraints is realised. Through the analysis of significant illustrative examples, we shall progressively refine the closure thesis and articulate an answer to our main research question. We shall also propose that biotic entrenchment provides a chief example of the phenomenon of interactive and horizontal construction of biological individuality and inter-identity.
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Affiliation(s)
- Isaac Hernández
- Laboratoire de Recherche ERRAPHIS, Département de Philosophie, Université Toulouse Jean Jaurès, Toulouse, France
| | - Davide Vecchi
- Centro de Filosofia das Ciências, Departamento de História e Filosofia das Ciências, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Biofilm Formation by Staphylococcus aureus Clinical Isolates is Differentially Affected by Glucose and Sodium Chloride Supplemented Culture Media. J Clin Med 2019; 8:jcm8111853. [PMID: 31684101 PMCID: PMC6912320 DOI: 10.3390/jcm8111853] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus aureus (S. aureus) causes persistent biofilm-related infections. Biofilm formation by S. aureus is affected by the culture conditions and is associated with certain genotypic characteristics. Here, we show that glucose and sodium chloride (NaCl) supplementation of culture media, a common practice in studies of biofilms in vitro, influences both biofilm formation by 40 S. aureus clinical isolates (methicillin-resistant and methicillin-sensitive S. aureus) and causes variations in biofilm quantification. Methicillin-resistant strains formed more robust biofilms than methicillin-sensitive strains in tryptic soy broth (TSB). However, glucose supplementation in TSB greatly promoted and stabilized biofilm formation of all strains, while additional NaCl was less efficient in this respect and resulted in significant variation in biofilm measurements. In addition, we observed that the ST239-SCCmec (Staphylococcal Cassette Chromosome mec) type III lineage formed strong biofilms in TSB supplemented with glucose and NaCl. Links between biofilm formation and accessory gene regulator (agr) status, as assessed by δ-toxin production, and with mannitol fermentation were not found. Our results show that TSB supplemented with 1.0% glucose supports robust biofilm production and reproducible quantification of S. aureus biofilm formation in vitro, whereas additional NaCl results in major variations in measurements of biofilm formation.
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28
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Ingmer H, Gerlach D, Wolz C. Temperate Phages of Staphylococcus aureus. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0058-2018. [PMID: 31562736 PMCID: PMC10921950 DOI: 10.1128/microbiolspec.gpp3-0058-2018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 12/22/2022] Open
Abstract
Most Staphylococcus aureus isolates carry multiple bacteriophages in their genome, which provide the pathogen with traits important for niche adaptation. Such temperate S. aureus phages often encode a variety of accessory factors that influence virulence, immune evasion and host preference of the bacterial lysogen. Moreover, transducing phages are primary vehicles for horizontal gene transfer. Wall teichoic acid (WTA) acts as a common phage receptor for staphylococcal phages and structural variations of WTA govern phage-host specificity thereby shaping gene transfer across clonal lineages and even species. Thus, bacteriophages are central for the success of S. aureus as a human pathogen.
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Affiliation(s)
- Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Gerlach
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
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29
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Fernández L, Gutiérrez D, García P, Rodríguez A. The Perfect Bacteriophage for Therapeutic Applications-A Quick Guide. Antibiotics (Basel) 2019; 8:E126. [PMID: 31443585 PMCID: PMC6783975 DOI: 10.3390/antibiotics8030126] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 11/16/2022] Open
Abstract
The alarming spread of multiresistant infections has kick-started the quest for alternative antimicrobials. In a way, given the steady increase in untreatable infectious diseases, success in this endeavor has become a matter of life and death. Perhaps we should stop searching for an antibacterial panacea and explore a multifaceted strategy in which a wide range of compounds are available on demand depending on the specific situation. In the context of this novel tailor-made approach to combating bacterial pathogens, the once forgotten phage therapy is undergoing a revival. Indeed, the compassionate use of bacteriophages against seemingly incurable infections has been attracting a lot of media attention lately. However, in order to take full advantage of this strategy, bacteria's natural predators must be taken from their environment and then carefully selected to suit our needs. In this review, we have explored the vast literature regarding phage isolation and characterization for therapeutic purposes, paying special attention to the most recent studies, in search of findings that hint at the most efficient strategies to identify suitable candidates. From this information, we will list and discuss the traits that, at the moment, are considered particularly valuable in phages destined for antimicrobial therapy applications. Due to the growing importance given to biofilms in the context of bacterial infections, we will dedicate a specific section to those characteristics that indicate the suitability of a bacteriophage as an antibiofilm agent. Overall, the objective is not just to have a large collection of phages, but to have the best possible candidates to guarantee elimination of the target pathogens.
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Affiliation(s)
- Lucía Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), (DairySafe Group), Paseo Río Linares s/n -Villaviciosa, 33300 Asturias, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain.
| | - Diana Gutiérrez
- Laboratory of Applied Biotechnology, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Pilar García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), (DairySafe Group), Paseo Río Linares s/n -Villaviciosa, 33300 Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Ana Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), (DairySafe Group), Paseo Río Linares s/n -Villaviciosa, 33300 Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Fernández L, Allende-Prieto C, Peón J, Recondo C, Rodríguez-Gonzálvez P, Gutiérrez D, Martínez B, García P, Rodríguez A. Preliminary Assessment of Visible, Near-Infrared, and Short-Wavelength-Infrared Spectroscopy with a Portable Instrument for the Detection of Staphylococcus aureus Biofilms on Surfaces. J Food Prot 2019; 82:1314-1319. [PMID: 31310170 DOI: 10.4315/0362-028x.jfp-18-567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacterial biofilms constitute a major source of sanitary problems and economic losses in the food industry. Indeed, biofilm removal may require intense mechanical cleaning procedures or very high concentrations of disinfectants or both, which can be damaging to the environment and human health. This study assessed the efficacy of a technique based on spectroscopy in the visible, near-infrared, and short-wavelength infrared range for the quick detection of biofilms formed on polystyrene by the pathogenic bacterium Staphylococcus aureus. To do that, biofilms corresponding to three S. aureus strains, which differed in biofilm-forming ability and composition of the extracellular matrix, were allowed to develop for 5 or 24 h, representing an active formation stage and mature biofilms, respectively. Spectral analysis of the samples, corresponding to three biological replicates of each condition, was then performed by using a portable device. The results of these experiments showed that partial least-squares discriminant analysis of the spectral profile could discriminate between surfaces containing attached bacterial biomass and noninoculated ones. In this model, the two first principal components accounted for 39 and 19% of the variance and the estimated error rate stabilized after four components. Cross-validation accuracy of this assessment was 100%. This work lays the foundation for subsequent development of a spectroscopy-based protocol that allows biofilm detection on food industrial surfaces.
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Affiliation(s)
- Lucía Fernández
- 1 Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Cristina Allende-Prieto
- 2 Remote Sensing Applications (RSApps) Research Group, Area of Cartographic, Geodesic and Photogrammetric Engineering, Department of Mining Exploitation and Prospecting, University of Oviedo, Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Asturias, Spain
| | - Juanjo Peón
- 2 Remote Sensing Applications (RSApps) Research Group, Area of Cartographic, Geodesic and Photogrammetric Engineering, Department of Mining Exploitation and Prospecting, University of Oviedo, Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Asturias, Spain
| | - Carmen Recondo
- 2 Remote Sensing Applications (RSApps) Research Group, Area of Cartographic, Geodesic and Photogrammetric Engineering, Department of Mining Exploitation and Prospecting, University of Oviedo, Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Asturias, Spain.,3 Institute of Natural Resources and Spatial Planning (INDUROT), University of Oviedo, Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Asturias, Spain (ORCID: https://orcid.org/0000-0001-7551-2236 [J.P.])
| | - Pablo Rodríguez-Gonzálvez
- 4 Department of Mining Technology, Topography and Structures, Universidad de León, Avda. Astorga s/n, 24401 Ponferrada, León, Spain
| | - Diana Gutiérrez
- 1 Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Beatriz Martínez
- 1 Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Pilar García
- 1 Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Ana Rodríguez
- 1 Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
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Big Impact of the Tiny: Bacteriophage-Bacteria Interactions in Biofilms. Trends Microbiol 2019; 27:739-752. [PMID: 31128928 DOI: 10.1016/j.tim.2019.04.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/10/2019] [Accepted: 04/19/2019] [Indexed: 01/17/2023]
Abstract
Bacteriophages (phages) have been shaping bacterial ecology and evolution for millions of years, for example, by selecting for defence strategies. Evidence supports that bacterial biofilm formation is one such strategy and that biofilm-mediated protection against phage infection depends on maturation and composition of the extracellular matrix. Interestingly, studies have revealed that phages can induce and strengthen biofilms. Here we review interactions between bacteria and phages in biofilms, discuss the underlying mechanisms, the potential of phage therapy for biofilm control, and emphasize the importance of considering biofilms in future phage research. This is especially relevant as biofilms are associated with increased tolerance towards antibiotics and are implicated in the majority of chronic infections.
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Kovács ÁT, Dragoš A. Evolved Biofilm: Review on the Experimental Evolution Studies of Bacillus subtilis Pellicles. J Mol Biol 2019; 431:4749-4759. [PMID: 30769118 DOI: 10.1016/j.jmb.2019.02.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 01/21/2019] [Accepted: 02/04/2019] [Indexed: 12/25/2022]
Abstract
For several decades, laboratory evolution has served as a powerful method to manipulate microorganisms and to explore long-term dynamics in microbial populations. Next to canonical Escherichia coli planktonic cultures, experimental evolution has expanded into alternative cultivation methods and species, opening the doors to new research questions. Bacillus subtilis, the spore-forming and root-colonizing bacterium, can easily develop in the laboratory as a liquid-air interface colonizing pellicle biofilm. Here, we summarize recent findings derived from this tractable experimental model. Clonal pellicle biofilms of B. subtilis can rapidly undergo morphological and genetic diversification creating new ecological interactions, for example, exploitation by biofilm non-producers. Moreover, long-term exposure to such matrix non-producers can modulate cooperation in biofilms, leading to different phenotypic heterogeneity pattern of matrix production with larger subpopulation of "ON" cells. Alternatively, complementary variants of biofilm non-producers, each lacking a distinct matrix component, can engage in a genetic division of labor, resulting in superior biofilm productivity compared to the "generalist" wild type. Nevertheless, inter-genetic cooperation appears to be evanescent and rapidly vanquished by individual biofilm formation strategies altering the amount or the properties of the remaining matrix component. Finally, fast-evolving mobile genetic elements can unpredictably shift intra-species interactions in B. subtilis biofilms. Understanding evolution in clonal biofilm populations will facilitate future studies in complex multispecies biofilms that are more representative of nature.
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Affiliation(s)
- Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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33
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Bárdy P, Hrebík D, Pantůček R, Plevka P. Future prospects of structural studies to advance our understanding of phage biology. MICROBIOLOGY AUSTRALIA 2019. [DOI: 10.1071/ma19009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacteriophages, being the most abundant biological entities on the Earth, play a major role in regulating populations of bacteria and thus influence the evolution and stability of ecosystems. Phage infections of pathogenic bacteria can both exacerbate and alleviate the severity of the disease. The structural characterisations of phage particles and individual proteins have enabled the understanding of many aspects of phage biology. Due to methodological limitations, most of the structures were determined from purified samples in vitro. However, studies performed outside the cellular context cannot capture the complex and dynamic interactions of the macromolecules that are required for their biological functions. Current developments in structural biology, in particular cryo-electron microscopy, allow in situ high-resolution studies of phage-infected cells. Here we discuss open questions in phage biology that could be addressed by structural biology techniques and their potential to enable the use of tailed phages in industrial applications and human therapy.
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González S, Fernández L, Gutiérrez D, Campelo AB, Rodríguez A, García P. Analysis of Different Parameters Affecting Diffusion, Propagation and Survival of Staphylophages in Bacterial Biofilms. Front Microbiol 2018; 9:2348. [PMID: 30323804 PMCID: PMC6172340 DOI: 10.3389/fmicb.2018.02348] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/12/2018] [Indexed: 02/04/2023] Open
Abstract
The elimination of bacterial biofilms remains a major challenge due to their recalcitrant nature. Bacteriophages, viruses that infect bacteria, have been gaining increasing attention as biofilm control agents. However, the development of a successful phage-based strategy requires in-depth analysis of different parameters. It is particularly important to determine the ability of a given phage to diffuse, propagate and remain viable within the complex biofilm structure. Here, we examine some of these properties for two staphylophages, vB_SauM_phiIPLA-RODI and vB_SepM_phiIPLA-C1C. Both Staphylococcus aureus and Staphylococcus epidermidis are important opportunistic pathogens that readily form biofilms on a wide array of biotic and abiotic surfaces. Our results confirmed that both phages could penetrate through biofilms formed by several bacterial strains with varying degrees of susceptibility to the viruses and biofilm-forming abilities. However, phage penetration differed depending on the specific bacterium or combination of bacteria. The data presented here suggest that the factors determining the diffusion rate of phages in biofilms include the amount of attached biomass, susceptibility of the strain, initial phage titer, phage entrapment in the extracellular matrix, and phage inactivation. This information will help to further characterize phage-bacteria interactions within biofilm communities and will be valuable for the development of antistaphylococcal products based on these phages.
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Affiliation(s)
- Silvia González
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Spain
| | - Lucía Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Spain
| | - Diana Gutiérrez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Spain
| | - Ana Belén Campelo
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Spain
| | - Ana Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Spain
| | - Pilar García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Spain
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35
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Fernández L, González S, Quiles-Puchalt N, Gutiérrez D, Penadés JR, García P, Rodríguez A. Lysogenization of Staphylococcus aureus RN450 by phages ϕ11 and ϕ80α leads to the activation of the SigB regulon. Sci Rep 2018; 8:12662. [PMID: 30139986 PMCID: PMC6107660 DOI: 10.1038/s41598-018-31107-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/10/2018] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus is a major opportunistic pathogen that commonly forms biofilms on various biotic and abiotic surfaces. Also, most isolates are known to carry prophages in their genomes. With this in mind, it seems that acquiring a better knowledge of the impact of prophages on the physiology of S. aureus biofilm cells would be useful for developing strategies to eliminate this pathogen. Here, we performed RNA-seq analysis of biofilm cells formed by S. aureus RN450 and two derived strains carrying prophages ϕ11 and ϕ80α. The lysogenic strains displayed increased biofilm formation and production of the carotenoid pigment staphyloxanthin. These phenotypes could be partly explained by the differences in gene expression displayed by prophage-harboring strains, namely an activation of the alternative sigma factor (SigB) regulon and downregulation of genes controlled by the Agr quorum-sensing system, especially the decreased transcription of genes encoding dispersion factors like proteases. Nonetheless, spontaneous lysis of part of the population could also contribute to the increased attached biomass. Interestingly, it appears that the phage CI protein plays a role in orchestrating these phage-host interactions, although more research is needed to confirm this possibility. Likewise, future studies should examine the impact of these two prophages during the infection.
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Affiliation(s)
- Lucía Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n 33300 -, Villaviciosa, Asturias, Spain.
| | - Silvia González
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n 33300 -, Villaviciosa, Asturias, Spain
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8TA, Glasgow, UK
| | - Diana Gutiérrez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n 33300 -, Villaviciosa, Asturias, Spain
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8TA, Glasgow, UK
| | - Pilar García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n 33300 -, Villaviciosa, Asturias, Spain
| | - Ana Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n 33300 -, Villaviciosa, Asturias, Spain
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36
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Mechanisms of Bacterial Tolerance and Persistence in the Gastrointestinal and Respiratory Environments. Clin Microbiol Rev 2018; 31:31/4/e00023-18. [PMID: 30068737 DOI: 10.1128/cmr.00023-18] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Pathogens that infect the gastrointestinal and respiratory tracts are subjected to intense pressure due to the environmental conditions of the surroundings. This pressure has led to the development of mechanisms of bacterial tolerance or persistence which enable microorganisms to survive in these locations. In this review, we analyze the general stress response (RpoS mediated), reactive oxygen species (ROS) tolerance, energy metabolism, drug efflux pumps, SOS response, quorum sensing (QS) bacterial communication, (p)ppGpp signaling, and toxin-antitoxin (TA) systems of pathogens, such as Escherichia coli, Salmonella spp., Vibrio spp., Helicobacter spp., Campylobacter jejuni, Enterococcus spp., Shigella spp., Yersinia spp., and Clostridium difficile, all of which inhabit the gastrointestinal tract. The following respiratory tract pathogens are also considered: Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Burkholderia cenocepacia, and Mycobacterium tuberculosis Knowledge of the molecular mechanisms regulating the bacterial tolerance and persistence phenotypes is essential in the fight against multiresistant pathogens, as it will enable the identification of new targets for developing innovative anti-infective treatments.
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37
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Sacher JC, Flint A, Butcher J, Blasdel B, Reynolds HM, Lavigne R, Stintzi A, Szymanski CM. Transcriptomic Analysis of the Campylobacter jejuni Response to T4-Like Phage NCTC 12673 Infection. Viruses 2018; 10:E332. [PMID: 29914170 PMCID: PMC6024767 DOI: 10.3390/v10060332] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/13/2018] [Accepted: 06/13/2018] [Indexed: 12/14/2022] Open
Abstract
Campylobacter jejuni is a frequent foodborne pathogen of humans. As C. jejuni infections commonly arise from contaminated poultry, phage treatments have been proposed to reduce the C. jejuni load on farms to prevent human infections. While a prior report documented the transcriptome of C. jejuni phages during the carrier state life cycle, transcriptomic analysis of a lytic C. jejuni phage infection has not been reported. We used RNA-sequencing to profile the infection of C. jejuni NCTC 11168 by the lytic T4-like myovirus NCTC 12673. Interestingly, we found that the most highly upregulated host genes upon infection make up an uncharacterized operon (cj0423⁻cj0425), which includes genes with similarity to T4 superinfection exclusion and antitoxin genes. Other significantly upregulated genes include those involved in oxidative stress defense and the Campylobactermultidrug efflux pump (CmeABC). We found that phage infectivity is altered by mutagenesis of the oxidative stress defense genes catalase (katA), alkyl-hydroxyperoxidase (ahpC), and superoxide dismutase (sodB), and by mutagenesis of the efflux pump genes cmeA and cmeB. This suggests a role for these gene products in phage infection. Together, our results shed light on the phage-host dynamics of an important foodborne pathogen during lytic infection by a T4-like phage.
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Affiliation(s)
- Jessica C Sacher
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Annika Flint
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - James Butcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Bob Blasdel
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven 3001, Belgium.
| | - Hayley M Reynolds
- Department of Microbiology and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven 3001, Belgium.
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Christine M Szymanski
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
- Department of Microbiology and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
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38
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Fernández L, Rodríguez A, García P. Phage or foe: an insight into the impact of viral predation on microbial communities. THE ISME JOURNAL 2018; 12:1171-1179. [PMID: 29371652 PMCID: PMC5932045 DOI: 10.1038/s41396-018-0049-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/24/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022]
Abstract
Since their discovery, bacteriophages have been traditionally regarded as the natural enemies of bacteria. However, recent advances in molecular biology techniques, especially data from "omics" analyses, have revealed that the interplay between bacterial viruses and their hosts is far more intricate than initially thought. On the one hand, we have become more aware of the impact of viral predation on the composition and genetic makeup of microbial communities thanks to genomic and metagenomic approaches. Moreover, data obtained from transcriptomic, proteomic, and metabolomic studies have shown that responses to phage predation are complex and diverse, varying greatly depending on the bacterial host, phage, and multiplicity of infection. Interestingly, phage exposure may alter different phenotypes, including virulence and biofilm formation. The complexity of the interactions between microbes and their viral predators is also evidenced by the link between quorum-sensing signaling pathways and bacteriophage resistance. Overall, new data increasingly suggests that both temperate and virulent phages have a positive effect on the evolution and adaptation of microbial populations. From this perspective, further research is still necessary to fully understand the interactions between phage and host under conditions that allow co-existence of both populations, reflecting more accurately the dynamics in natural microbial communities.
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Affiliation(s)
- Lucía Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
| | - Ana Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Pilar García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
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39
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Bari SMN, Walker FC, Cater K, Aslan B, Hatoum-Aslan A. Strategies for Editing Virulent Staphylococcal Phages Using CRISPR-Cas10. ACS Synth Biol 2017; 6:2316-2325. [PMID: 28885820 DOI: 10.1021/acssynbio.7b00240] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Staphylococci are prevalent skin-dwelling bacteria that are also leading causes of antibiotic-resistant infections. Viruses that infect and lyse these organisms (virulent staphylococcal phages) can be used as alternatives to conventional antibiotics and represent promising tools to eliminate or manipulate specific species in the microbiome. However, since over half their genes have unknown functions, virulent staphylococcal phages carry inherent risk to cause unknown downstream side effects. Further, their swift and destructive reproductive cycle make them intractable by current genetic engineering techniques. CRISPR-Cas10 is an elaborate prokaryotic immune system that employs small RNAs and a multisubunit protein complex to detect and destroy phages and other foreign nucleic acids. Some staphylococci naturally possess CRISPR-Cas10 systems, thus providing an attractive tool already installed in the host chromosome to harness for phage genome engineering. However, the efficiency of CRISPR-Cas10 immunity against virulent staphylococcal phages and corresponding utility as a tool to facilitate their genome editing has not been explored. Here, we show that the CRISPR-Cas10 system native to Staphylococcus epidermidis exhibits robust immunity against diverse virulent staphylococcal phages. On the basis of this activity, a general two-step approach was developed to edit these phages that relies upon homologous recombination machinery encoded in the host. Variations of this approach to edit toxic phage genes and access phages that infect CRISPR-less staphylococci are also presented. This versatile set of genetic tools enables the systematic study of phage genes of unknown functions and the design of genetically defined phage-based antimicrobials that can eliminate or manipulate specific Staphylococcus species.
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Affiliation(s)
- S. M. Nayeemul Bari
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Forrest C. Walker
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Katie Cater
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Barbaros Aslan
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Asma Hatoum-Aslan
- Department of Biological
Sciences, University of Alabama, Tuscaloosa, Alabama 35487, United States
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Yu P, Mathieu J, Yang Y, Alvarez PJJ. Suppression of Enteric Bacteria by Bacteriophages: Importance of Phage Polyvalence in the Presence of Soil Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5270-5278. [PMID: 28414441 DOI: 10.1021/acs.est.7b00529] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Bacteriophages are widely recognized for their importance in microbial ecology and bacterial control. However, little is known about how phage polyvalence (i.e., broad host range) affects bacterial suppression and interspecies competition in environments harboring enteric pathogens and soil bacteria. Here we compare the efficacy of polyvalent phage PEf1 versus coliphage T4 in suppressing a model enteric bacterium (E. coli K-12) in mixtures with soil bacteria (Pseudomonas putida F1 and Bacillus subtilis 168). Although T4 was more effective than PEf1 in infecting E. coli K-12 in pure cultures, PEf1 was 20-fold more effective in suppressing E. coli under simulated multispecies biofilm conditions because polyvalence enhanced PEf1 propagation in P. putida. In contrast, soil bacteria do not propagate coliphages and hindered T4 diffusion through the biofilm. Similar tests were also conducted under planktonic conditions to discern how interspecies competition contributes to E. coli suppression without the confounding effects of restricted phage diffusion. Significant synergistic suppression was observed by the combined effects of phages plus competing bacteria. T4 was slightly more effective in suppressing E. coli in these planktonic mixed cultures, even though PEf1 reached higher concentrations by reproducing also in P. putida (7.2 ± 0.4 vs 6.0 ± 1.0 log10PFU/mL). Apparently, enhanced suppression by higher PEf1 propagation was offset by P. putida lysis, which decreased stress from interspecies competition relative to incubations with T4. In similar planktonic tests with more competing soil bacteria species, P. putida lysis was less critical in mitigating interspecies competition and PEf1 eliminated E. coli faster than T4 (36 vs 42 h). Overall, this study shows that polyvalent phages can propagate in soil bacteria and significantly enhance suppression of co-occurring enteric species.
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Affiliation(s)
- Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University , Houston, Texas 77005, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University , Houston, Texas 77005, United States
| | - Yu Yang
- Department of Civil and Environmental Engineering, Rice University , Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University , Houston, Texas 77005, United States
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41
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Downregulation of Autolysin-Encoding Genes by Phage-Derived Lytic Proteins Inhibits Biofilm Formation in Staphylococcus aureus. Antimicrob Agents Chemother 2017; 61:AAC.02724-16. [PMID: 28289031 DOI: 10.1128/aac.02724-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 03/06/2017] [Indexed: 12/27/2022] Open
Abstract
Phage-derived lytic proteins are a promising alternative to conventional antimicrobials. One of their most interesting properties is that they do not readily select for resistant strains, which is likely due to the fact that their targets are essential for the viability of the bacterial cell. Moreover, genetic engineering allows the design of new "tailor-made" proteins that may exhibit improved antibacterial properties. One example of this is the chimeric protein CHAPSH3b, which consists of a catalytic domain from the virion-associated peptidoglycan hydrolase of phage vB_SauS-phiIPLA88 (HydH5) and the cell wall binding domain of lysostaphin. CHAPSH3b had previously shown the ability to kill Staphylococcus aureus cells. Here, we demonstrate that this lytic protein also has potential for the control of biofilm-embedded S. aureus cells. Additionally, subinhibitory doses of CHAPSH3b can decrease biofilm formation by some S. aureus strains. Transcriptional analysis revealed that exposure of S. aureus cells to this enzyme leads to the downregulation of several genes coding for bacterial autolysins. One of these proteins, namely, the major autolysin AtlA, is known to participate in staphylococcal biofilm development. Interestingly, an atl mutant strain did not display inhibition of biofilm development when grown at subinhibitory concentrations of CHAPSH3b, contrary to the observations made for the parental and complemented strains. Also, deletion of atl led to low-level resistance to CHAPSH3b and the endolysin LysH5. Overall, our results reveal new aspects that should be considered when designing new phage-derived lytic proteins aimed for antimicrobial applications.
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