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Vukovic D, Gostimirovic S, Cvetanovic J, Gavric D, Aleksic Sabo V, Todorovic D, Medic D, Knezevic P. Antibacterial Potential of Non-Tailed Icosahedral Phages Alone and in Combination with Antibiotics. Curr Microbiol 2024; 81:215. [PMID: 38849666 DOI: 10.1007/s00284-024-03705-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/13/2024] [Indexed: 06/09/2024]
Abstract
Non-tailed icosahedral phages belonging to families Fiersviridae (phages MS2 and Qbeta), Tectiviridae (PRD1) and Microviridae (phiX174) have not been considered in detail so far as potential antibacterial agents. The aim of the study was to examine various aspects of the applicability of these phages as antibacterial agents. Antibacterial potential of four phages was investigated via bacterial growth and biofilm formation inhibition, lytic spectra determination, and phage safety examination. The phage phiX174 was combined with different classes of antibiotics to evaluate potential synergistic interactions. In addition, the incidence of phiX174-insensitive mutants was analyzed. The results showed that only phiX174 out of four phages tested against their corresponding hosts inhibited bacterial growth for > 90% at different multiplicity of infection and that only this phage considerably prevented biofilm formation. Although all phages show the absence of potentially undesirable genes, they also have extremely narrow lytic spectra. The synergism was determined between phage phiX174 and ceftazidime, ceftriaxone, ciprofloxacin, macrolides, and chloramphenicol. It was shown that the simultaneous application of agents is more effective than successive treatment, where one agent is applied first. The analysis of the appearance of phiX174 bacteriophage-insensitive mutants showed that mutations occur with a frequency of 10-3. The examined non-tailed phages have a limited potential for use as antibacterial agents, primarily due to a very narrow lytic spectrum and the high frequency of resistant mutants appearance, but Microviridae can be considered in the future as biocontrol agents against susceptible strains of E. coli in combinations with conventional antimicrobial agents.
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Affiliation(s)
- Darija Vukovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Sonja Gostimirovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Jelena Cvetanovic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Verica Aleksic Sabo
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | | | - Deana Medic
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia.
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2
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Han P, Lin W, Fan H, Tong Y. Characterization of phage evolution and phage resistance in drug-resistant Stenotrophomonas maltophilia. J Virol 2024; 98:e0124923. [PMID: 38189285 PMCID: PMC10878236 DOI: 10.1128/jvi.01249-23] [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: 10/23/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Phage therapy has become a viable antimicrobial treatment as an alternative to antibiotic treatment, with an increase in antibiotic resistance. Phage resistance is a major limitation in the therapeutic application of phages, and the lack of understanding of the dynamic changes between bacteria and phages constrains our response strategies to phage resistance. In this study, we investigated the changing trends of mutual resistance between Stenotrophomonas maltophilia (S. maltophilia) and its lytic phage, BUCT603. Our results revealed that S. maltophilia resisted phage infection through mutations in the cell membrane proteins, while the evolved phage re-infected the resistant strain primarily through mutations in structure-related proteins. Compared with the wild-type strain (SMA118), the evolved phage-resistant strain (R118-2) showed reduced virulence, weakened biofilm formation ability, and reduced resistance to aminoglycosides. In addition, the evolved phage BUCT603B1 in combination with kanamycin could inhibit the development of phage-resistant S. maltophilia in vitro and significantly improve the survival rate of S. maltophilia-infected mice. Altogether, these results suggest that in vitro characterization of bacteria-phage co-evolutionary relationships is a useful research tool to optimize phages for the treatment of drug-resistant bacterial infections.IMPORTANCEPhage therapy is a promising approach to treat infections caused by drug-resistant Stenotrophomonas maltophilia (S. maltophilia). However, the rapid development of phage resistance has hindered the therapeutic application of phages. In vitro evolutionary studies of bacteria-phage co-cultures can elucidate the mechanism of resistance development between phage and its host. In this study, we investigated the resistance trends between S. maltophilia and its phage and found that inhibition of phage adsorption is the primary strategy by which bacteria resist phage infection in vitro, while phages can re-infect bacterial cells by identifying other adsorption receptors. Although the final bacterial mutants were no longer infected by phages, they incurred a fitness cost that resulted in a significant reduction in virulence. In addition, the combination treatment with phage and aminoglycoside antibiotics could prevent the development of phage resistance in S. maltophilia in vitro. These findings contribute to increasing the understanding of the co-evolutionary relationships between phages and S. maltophilia.
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Affiliation(s)
- Pengjun Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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3
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Romeyer Dherbey J, Bertels F. The untapped potential of phage model systems as therapeutic agents. Virus Evol 2024; 10:veae007. [PMID: 38361821 PMCID: PMC10868562 DOI: 10.1093/ve/veae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/18/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
With the emergence of widespread antibiotic resistance, phages are an appealing alternative to antibiotics in the fight against multidrug-resistant bacteria. Over the past few years, many phages have been isolated from various environments to treat bacterial pathogens. While isolating novel phages for treatment has had some success for compassionate use, developing novel phages into a general therapeutic will require considerable time and financial resource investments. These investments may be less significant for well-established phage model systems. The knowledge acquired from decades of research on their structure, life cycle, and evolution ensures safe application and efficient handling. However, one major downside of the established phage model systems is their inability to infect pathogenic bacteria. This problem is not insurmountable; phage host range can be extended through genetic engineering or evolution experiments. In the future, breeding model phages to infect pathogens could provide a new avenue to develop phage therapeutic agents.
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Affiliation(s)
- Jordan Romeyer Dherbey
- Microbial Population Biology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön, Schleswig-Holstein 24306, Germany
| | - Frederic Bertels
- Microbial Population Biology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön, Schleswig-Holstein 24306, Germany
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Abstract
Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.
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Affiliation(s)
- Paul C Kirchberger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA;
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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Abuelizz HA, Bakheit AH, Marzouk M, El-Senousy WM, Abdellatif MM, Ali EE, Mostafa GAE, Al-Salahi R. Biological Investigation of 2-Thioxo-benzo[g]quinazolines against Adenovirus Type 7 and Bacteriophage Phi X174: An In Vitro Study. Curr Issues Mol Biol 2023; 45:3787-3800. [PMID: 37232713 DOI: 10.3390/cimb45050244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/09/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Mortality and morbidity caused by viruses are a global health problems. Therefore, there is always a need to create novel therapeutic agents and refine existing ones to maximize their efficacy. Our lab has produced benzoquinazolines derivatives that have proven effective activity as antiviral compounds against herpes simplex (HSV 1 and 2), coxsackievirus B4 (CVB4), and hepatitis viruses (HAV and HCV). This in vitro study was aimed at investigating the effectiveness of benzoquinazoline derivatives 1-16 against adenovirus type 7 and bacteriophage phiX174 using a plaque assay. The cytotoxicity against adenovirus type 7 was also performed in vitro, using a MTT assay. Most of the compounds exhibited antiviral activity against bacteriophage phiX174. However, compounds 1, 3, 9, and 11 showed statistically significant reductions of 60-70% against bacteriophage phiX174. By contrast, compounds 3, 5, 7, 12, 13, and 15 were ineffective against adenovirus type 7, and compounds 6 and 16 had remarkable efficacy (50%). Using the MOE-Site Finder Module, a docking study was carried out in order to create a prediction regarding the orientation of the lead compounds (1, 9, and 11). This was performed in order to investigate the activity of the lead compounds 1, 9, and 11 against the bacteriophage phiX174 by locating the ligand-target protein binding interaction active sites.
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Affiliation(s)
- Hatem A Abuelizz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed Marzouk
- Chemistry of Tanning Materials and Leather Technology Department, Organic Chemicals Industries Division, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Waled M El-Senousy
- Environmental Virology Laboratory, Water Pollution Research Department, Environment and Climate Change Research Institute and Food-Borne Viruses Group, Centre of Excellence for Advanced Sciences, National Research Centre (NRC), 33 El-Buhouth Street, Dokki, Giza 12622, Egypt
| | - Mohamed M Abdellatif
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Osawa, Tokyo 192-0397, Japan
| | - Essam E Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Gamal A E Mostafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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6
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Lee H, Baxter AJ, Bator CM, Fane BA, Hafenstein SL. Cryo-EM Structure of Gokushovirus ΦEC6098 Reveals a Novel Capsid Architecture for a Single-Scaffolding Protein, Microvirus Assembly System. J Virol 2022; 96:e0099022. [PMID: 36255280 PMCID: PMC9645218 DOI: 10.1128/jvi.00990-22] [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: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022] Open
Abstract
Ubiquitous and abundant in ecosystems and microbiomes, gokushoviruses constitute a Microviridae subfamily, distantly related to bacteriophages ΦX174, α3, and G4. A high-resolution cryo-EM structure of gokushovirus ΦEC6098 was determined, and the atomic model was built de novo. Although gokushoviruses lack external scaffolding and spike proteins, which extensively interact with the ΦX174 capsid protein, the core of the ΦEC6098 coat protein (VP1) displayed a similar structure. There are, however, key differences. At each ΦEC6098 icosahedral 3-fold axis, a long insertion loop formed mushroom-like protrusions, which have been noted in lower-resolution gokushovirus structures. Hydrophobic interfaces at the bottom of these protrusions may confer stability to the capsid shell. In ΦX174, the N-terminus of the capsid protein resides directly atop the 3-fold axes of symmetry; however, the ΦEC6098 N-terminus stretched across the inner surface of the capsid shell, reaching nearly to the 5-fold axis of the neighboring pentamer. Thus, this extended N-terminus interconnected pentamers on the inside of the capsid shell, presumably promoting capsid assembly, a function performed by the ΦX174 external scaffolding protein. There were also key differences between the ΦX174-like DNA-binding J proteins and its ΦEC6098 homologue VP8. As seen with the J proteins, C-terminal VP8 residues were bound into a pocket within the major capsid protein; however, its N-terminal residues were disordered, likely due to flexibility. We show that the combined location and interaction of VP8's C-terminus and a portion of VP1's N-terminus are reminiscent of those seen with the ΦX174 and α3 J proteins. IMPORTANCE There is a dramatic structural and morphogenetic divide within the Microviridae. The well-studied ΦX174-like viruses have prominent spikes at their icosahedral vertices, which are absent in gokushoviruses. Instead, gokushovirus major coat proteins form extensive mushroom-like protrusions at the 3-fold axes of symmetry. In addition, gokushoviruses lack an external scaffolding protein, the more critical of the two ΦX174 assembly proteins, but retain an internal scaffolding protein. The ΦEC6098 virion suggests that key external scaffolding functions are likely performed by coat protein domains unique to gokushoviruses. Thus, within one family, different assembly paths have been taken, demonstrating how a two-scaffolding protein system can evolve into a one-scaffolding protein system, or vice versa.
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Affiliation(s)
- Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Alexis J. Baxter
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carol M. Bator
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Bentley A. Fane
- The BIO5 Institute, Keating Building, University of Arizona, Tucson, Arizona, USA
| | - Susan L. Hafenstein
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
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7
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Peng M, Joo J, Alvarado-Martinez Z, Tabashsum Z, Aditya A, Biswas D. Intracellular autolytic whole cell Salmonella vaccine prevents colonization of pathogenic Salmonella Typhimurium in chicken. Vaccine 2022; 40:6880-6892. [PMID: 36272875 DOI: 10.1016/j.vaccine.2022.10.013] [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: 04/11/2022] [Revised: 09/16/2022] [Accepted: 10/09/2022] [Indexed: 11/08/2022]
Abstract
Salmonella enterica (SE) is a major foodborne bacterial pathogen in the United States, commonly found as the normal flora of various animals that is attributed to causing at least 1.2 million infections annually. Poultry plays a major role in disseminating SE through direct contact with live animals and consumption of contaminated products. Vaccinating poultry against SE is a sustainable approach that can reduce SE in the host, preventing future infections in humans. An intracellular autolytic SE serovar Typhimurium vaccine (STLT2+P13+19) was developed by integrating genes 13 (holin) and 19 (lysozyme) of bacteriophage P22 into the bacterial chromosome. These were inserted downstream of sseA, an SPI-2 chaperone in SE that expresses during the intracellular phase of SE. Intracellular viability of STLT2+P13+19 reduced by 94.42% at 24 hr compared to the wild type in chicken macrophage cells (HD-11), whereas growth rate and adhesion ability remained unchanged. Inoculating STLT2+P13+19 in HD-11 significantly enhanced the relative log fold expression of genes associated to production of pro-inflammatory cytokines (IL-1β, IL-6, IL-8, IL-10, IL-12 p40, IL-18, and GM-CSF) and Toll-like-receptors (TRL-3 and 7). Vaccination of an in vivo chicken model demonstrated significant changes in secretion of iNOS, IL-6, IL-8, IL-12, and TNF-α, as well as a reduction in the intestinal colonization of SE serovar Typhimurium. Microbiome analysis of cecal fluid using 16S rRNA gene sequencing also showed modulation of intestinal microbial composition, specifically a decrease in relative abundance of Proteobacteria and increasing Firmicutes. This study provides insight into a novel vaccine design that could make food products safer without the use of synthetic compounds.
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Affiliation(s)
- Mengfei Peng
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Jungsoo Joo
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Zabdiel Alvarado-Martinez
- Biological Sciences Program - Molecular and Cellular Biology, University of Maryland, College Park, MD, USA.
| | - Zajeba Tabashsum
- Biological Sciences Program - Molecular and Cellular Biology, University of Maryland, College Park, MD, USA.
| | - Arpita Aditya
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
| | - Debabrata Biswas
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA; Biological Sciences Program - Molecular and Cellular Biology, University of Maryland, College Park, MD, USA; Center for Food Safety and Security Systems, University of Maryland, College Park, MD, USA.
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8
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Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses. mSystems 2021; 6:6/3/e00046-21. [PMID: 33975962 PMCID: PMC8125068 DOI: 10.1128/msystems.00046-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A major part of the healthy human gut microbiome is the Microviridae bacteriophage, exemplified by the model φX174 phage, and their E. coli hosts. Although much has been learned from studying φX174 over the last half-century, until this work, the E. coli host response to infection has never been investigated in detail. Measuring host-bacteriophage dynamics is an important approach to understanding bacterial survival functions and responses to infection. The model Microviridae bacteriophage φX174 is endemic to the human gut and has been studied for over 70 years, but the host response to infection has never been investigated in detail. To address this gap in our understanding of this important interaction within our microbiome, we have measured host Escherichia coli C proteomic and transcriptomic response to φX174 infection. We used mass spectrometry and RNA sequencing (RNA-seq) to identify and quantify all 11 φX174 proteins and over 1,700 E. coli proteins, enabling us to comprehensively map host pathways involved in φX174 infection. Most notably, we see significant host responses centered on membrane damage and remodeling, cellular chaperone and translocon activity, and lipoprotein processing, which we speculate is due to the peptidoglycan-disruptive effects of the φX174 lysis protein E on MraY activity. We also observe the massive upregulation of small heat shock proteins IbpA/B, along with other heat shock pathway chaperones, and speculate on how the specific characteristics of holdase protein activity may be beneficial for viral infections. Together, this study enables us to begin to understand the proteomic and transcriptomic host responses of E. coli to Microviridae infections and contributes insights to the activities of this important model host-phage interaction. IMPORTANCE A major part of the healthy human gut microbiome is the Microviridae bacteriophage, exemplified by the model φX174 phage, and their E. coli hosts. Although much has been learned from studying φX174 over the last half-century, until this work, the E. coli host response to infection has never been investigated in detail. We reveal the proteomic and transcriptomic pathways differentially regulated during the φX174 infection cycle and uncover the details of a coordinated cellular response to membrane damage that results in increased lipoprotein processing and membrane trafficking, likely due to the phage antibiotic-like lysis protein. We also reveal that small heat shock proteins IbpA/B are massively upregulated during infection and that these holdase chaperones are highly conserved across the domains of life, indicating that reliance on them is likely widespread across viruses.
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9
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Madoroba E, Magwedere K, Chaora NS, Matle I, Muchadeyi F, Mathole MA, Pierneef R. Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa. Microorganisms 2021; 9:507. [PMID: 33673660 PMCID: PMC7997435 DOI: 10.3390/microorganisms9030507] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms.
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Affiliation(s)
- Evelyn Madoroba
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Kudakwashe Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria 0001, South Africa;
| | - Nyaradzo Stella Chaora
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida 1710, South Africa;
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (F.M.); (R.P.)
| | - Itumeleng Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort 0110, South Africa; (I.M.); (M.A.M.)
| | - Farai Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (F.M.); (R.P.)
| | - Masenyabu Aletta Mathole
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort 0110, South Africa; (I.M.); (M.A.M.)
| | - Rian Pierneef
- Biotechnology Platform, Agricultural Research Council, Private Bag X 05, Onderstepoort, Pretoria 0110, South Africa; (F.M.); (R.P.)
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10
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Hantke K. Compilation of Escherichia coli K-12 outer membrane phage receptors - their function and some historical remarks. FEMS Microbiol Lett 2021; 367:5721240. [PMID: 32009155 DOI: 10.1093/femsle/fnaa013] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Many Escherichia coli phages have been sequenced, but in most cases their sequences alone do not suffice to predict their host specificity. Analysis of phage resistant E. coli K-12 mutants have uncovered a certain set of outer membrane proteins and polysaccharides as receptors. In this review, a compilation of E. coli K12 phage receptors is provided and their functional characterization, often driven by studies on phage resistant mutants, is discussed in the historical context. While great progress has been made in this field thus far, several proteins in the outer membrane still await characterization as phage receptors.
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Affiliation(s)
- Klaus Hantke
- IMIT, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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11
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Federici S, Nobs SP, Elinav E. Phages and their potential to modulate the microbiome and immunity. Cell Mol Immunol 2020; 18:889-904. [PMID: 32901128 DOI: 10.1038/s41423-020-00532-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (hence termed phages) are viruses that target bacteria and have long been considered as potential future treatments against antibiotic-resistant bacterial infection. However, the molecular nature of phage interactions with bacteria and the human host has remained elusive for decades, limiting their therapeutic application. While many phages and their functional repertoires remain unknown, the advent of next-generation sequencing has increasingly enabled researchers to decode new lytic and lysogenic mechanisms by which they attack and destroy bacteria. Furthermore, the last decade has witnessed a renewed interest in the utilization of phages as therapeutic vectors and as a means of targeting pathogenic or commensal bacteria or inducing immunomodulation. Importantly, the narrow host range, immense antibacterial repertoire, and ease of manipulating phages may potentially allow for their use as targeted modulators of pathogenic, commensal and pathobiont members of the microbiome, thereby impacting mammalian physiology and immunity along mucosal surfaces in health and in microbiome-associated diseases. In this review, we aim to highlight recent advances in phage biology and how a mechanistic understanding of phage-bacteria-host interactions may facilitate the development of novel phage-based therapeutics. We provide an overview of the challenges of the therapeutic use of phages and how these could be addressed for future use of phages as specific modulators of the human microbiome in a variety of infectious and noncommunicable human diseases.
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Affiliation(s)
- Sara Federici
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Samuel P Nobs
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel. .,Cancer-Microbiome Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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12
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A high-resolution map of bacteriophage ϕX174 transcription. Virology 2020; 547:47-56. [DOI: 10.1016/j.virol.2020.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/26/2022]
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13
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Kirchberger PC, Ochman H. Resurrection of a global, metagenomically defined gokushovirus. eLife 2020; 9:e51599. [PMID: 32101162 PMCID: PMC7062461 DOI: 10.7554/elife.51599] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
Gokushoviruses are single-stranded, circular DNA bacteriophages found in metagenomic datasets from diverse ecosystems worldwide, including human gut microbiomes. Despite their ubiquity and abundance, little is known about their biology or host range: Isolates are exceedingly rare, known only from three obligate intracellular bacterial genera. By synthesizing circularized phage genomes from prophages embedded in diverse enteric bacteria, we produced gokushoviruses in an experimentally tractable model system, allowing us to investigate their features and biology. We demonstrate that virions can reliably infect and lysogenize hosts by hijacking a conserved chromosome-dimer resolution system. Sequence motifs required for lysogeny are detectable in other metagenomically defined gokushoviruses; however, we show that even partial motifs enable phages to persist cytoplasmically without leading to collapse of their host culture. This ability to employ multiple, disparate survival strategies is likely key to the long-term persistence and global distribution of Gokushovirinae.
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Affiliation(s)
- Paul C Kirchberger
- Department of Integrative Biology University of TexasAustinUnited States
| | - Howard Ochman
- Department of Integrative Biology University of TexasAustinUnited States
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14
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Mathieu A, Dion M, Deng L, Tremblay D, Moncaut E, Shah SA, Stokholm J, Krogfelt KA, Schjørring S, Bisgaard H, Nielsen DS, Moineau S, Petit MA. Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages. Nat Commun 2020; 11:378. [PMID: 31953385 PMCID: PMC6969025 DOI: 10.1038/s41467-019-14042-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/10/2019] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 648 fecal samples from 1-year-old children and obtain coliphages directly from the viral fraction of the same fecal samples. We find that 63% of strains hosted phages, while 24% of the viromes contain phages targeting E. coli. 150 of these phages, half recovered from strain supernatants, half from virome (73% temperate and 27% virulent) were tested for their host range on 75 E. coli strains isolated from the same cohort. Temperate phages barely infected the gut strains, whereas virulent phages killed up to 68% of them. We conclude that in fecal samples from children, temperate coliphages dominate, while virulent ones have greater infectivity and broader host range, likely playing a role in gut microbiota dynamics. The impact of bacteriophages in the human gut microbiome remains poorly understood. Here, the authors characterize coliphages isolated from a large cohort of 1-year-old infants and show that temperate coliphages dominate, while virulent ones have greater infectivity and broader host range.
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Affiliation(s)
- Aurélie Mathieu
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Moïra Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Denise Tremblay
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Elisabeth Moncaut
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej5, 2300S, Copenhagen, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej5, 2300S, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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15
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Optical Trapping, Sizing, and Probing Acoustic Modes of a Small Virus. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10010394] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prior opto-mechanical techniques to measure vibrational frequencies of viruses work on large ensembles of particles, whereas, in this work, individually trapped viral particles were studied. Double nanohole (DNH) apertures in a gold film were used to achieve optical trapping of one of the smallest virus particles yet reported, PhiX174, which has a diameter of 25 nm. When a laser was focused onto these DNH apertures, it created high local fields due to plasmonic enhancement, which allowed stable trapping of small particles for prolonged periods at low powers. Two techniques were performed to characterize the virus particles. The particles were sized via an established autocorrelation analysis technique, and the acoustic modes were probed using the extraordinary acoustic Raman (EAR) method. The size of the trapped particle was determined to be 25 ± 3.8 nm, which is in good agreement with the established diameter of PhiX174. A peak in the EAR signal was observed at 32 GHz, which fits well with the predicted value from elastic theory.
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Safari F, Sharifi M, Farajnia S, Akbari B, Karimi Baba Ahmadi M, Negahdaripour M, Ghasemi Y. The interaction of phages and bacteria: the co-evolutionary arms race. Crit Rev Biotechnol 2019; 40:119-137. [PMID: 31793351 DOI: 10.1080/07388551.2019.1674774] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the dawn of life, bacteria and phages are locked in a constant battle and both are perpetually changing their tactics to overcome each other. Bacteria use various strategies to overcome the invading phages, including adsorption inhibition, restriction-modification (R/E) systems, CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, abortive infection (Abi), etc. To counteract, phages employ intelligent tactics for the nullification of bacterial defense systems, such as accessing host receptors, evading R/E systems, and anti-CRISPR proteins. Intense knowledge about the details of these defense pathways is the basis for their broad utilities in various fields of research from microbiology to biotechnology. Hence, in this review, we discuss some strategies used by bacteria to inhibit phage infections as well as phage tactics to circumvent bacterial defense systems. In addition, the application of these strategies will be described as a lesson learned from bacteria and phage combats. The ecological factors that affect the evolution of bacterial immune systems is the other issue represented in this review.
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Affiliation(s)
- Fatemeh Safari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehrdad Sharifi
- Department of Emergency Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, School of Medical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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17
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Steering Phages to Combat Bacterial Pathogens. Trends Microbiol 2019; 28:85-94. [PMID: 31744662 DOI: 10.1016/j.tim.2019.10.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/10/2019] [Accepted: 10/17/2019] [Indexed: 12/21/2022]
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Ge H, Hu M, Zhao G, Du Y, Xu N, Chen X, Jiao X. The "fighting wisdom and bravery" of tailed phage and host in the process of adsorption. Microbiol Res 2019; 230:126344. [PMID: 31561173 DOI: 10.1016/j.micres.2019.126344] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/30/2019] [Accepted: 09/18/2019] [Indexed: 01/07/2023]
Abstract
In the process of bacteriophage and bacteria struggle, adsorption is the key factor to determine who is the winner. In this paper, the molecular mechanism of tailed bacteriophage recognition and adsorption to host and the strategy of "fighting wisdom and courage" between them are reviewed.
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Affiliation(s)
- Haojie Ge
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Maozhi Hu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Ge Zhao
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yi Du
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Nannan Xu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiang Chen
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xin'an Jiao
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China
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León M, Kokkari C, García K, Castillo D, Katharios P, Bastías R. Diversification of Vibrio anguillarum Driven by the Bacteriophage CHOED. Front Microbiol 2019; 10:1396. [PMID: 31281297 PMCID: PMC6596326 DOI: 10.3389/fmicb.2019.01396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/04/2019] [Indexed: 01/16/2023] Open
Abstract
Bacteriophages are an important factor in bacterial evolution. Some reports suggest that lytic bacteriophages can select for resistant mutant strains with reduced virulence. The present study explores the role of the CHOED bacteriophage in the diversification and virulence of its host Vibrio anguillarum. Nine phage-resistant strains were analyzed for their phenotype and different virulence factors, showing alterations in their fitness, motility, biofilm formation, lipopolysaccharide profiles and/or protease activity. Seven of the nine phage-resistant strains showed virulence reduction in a Sparus aurata larvae model. However, this is not generalized since two of the resistant strains show equal virulence compared with the parental strain. The genomic analysis of representative resistant strains displayed that the majority of the mutations are specific for each isolate, affecting genes related to lipopolysaccharide biosynthesis, quorum sensing, motility, toxin and membrane transport. The observed mutations were coherent with the phenotypic and virulence differences observed. These results suggest that the CHOED phage acts as a selective pressure on V. anguillarum, allowing proliferation of resistant strains with different genotypes, phenotypes and degrees of virulence, contributing to bacterial diversification.
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Affiliation(s)
- Marcela León
- Laboratorio de Microbiología, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Constantina Kokkari
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Katherine García
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, San Miguel, Chile
| | - Daniel Castillo
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Roberto Bastías
- Laboratorio de Microbiología, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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20
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Recessive Host Range Mutants and Unsusceptible Cells That Inactivate Virions without Genome Penetration: Ecological and Technical Implications. J Virol 2019; 93:JVI.01767-18. [PMID: 30429341 DOI: 10.1128/jvi.01767-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/05/2018] [Indexed: 12/20/2022] Open
Abstract
Although microviruses do not possess a visible tail structure, one vertex rearranges after interacting with host lipopolysaccharides. Most examinations of host range, eclipse, and penetration were conducted before this "host-induced" unique vertex was discovered and before DNA sequencing became routine. Consequently, structure-function relationships dictating host range remain undefined. Biochemical and genetic analyses were conducted with two closely related microviruses, α3 and ST-1. Despite ∼90% amino acid identity, the natural host of α3 is Escherichia coli C, whereas ST-1 is a K-12-specific phage. Virions attached and eclipsed to both native and unsusceptible hosts; however, they breached only the native host's cell wall. This suggests that unsusceptible host-phage interactions promote off-pathway reactions that can inactivate viruses without penetration. This phenomenon may have broader ecological implications. To determine which structural proteins conferred host range specificity, chimeric virions were generated by individually interchanging the coat, spike, or DNA pilot proteins. Interchanging the coat protein switched host range. However, host range expansion could be conferred by single point mutations in the coat protein. The expansion phenotype was recessive: genetically mutant progeny from coinfected cells did not display the phenotype. Thus, mutant isolation required populations generated in environments with low multiplicities of infection (MOI), a phenomenon that may have impacted past host range studies in both prokaryotic and eukaryotic systems. The resulting genetic and structural data were consistent enough that host range expansion could be predicted, broadening the classical definition of antireceptors to include interfaces between protein complexes within the capsid.IMPORTANCE To expand host range, viruses must interact with unsusceptible host cell surfaces, which could be detrimental. As observed in this study, virions were inactivated without genome penetration. This may be advantageous to potential new hosts, culling the viral population from which an expanded host range mutant could emerge. When identified, altered host range mutations were recessive. Accordingly, isolation required populations generated in low-MOI environments. However, in laboratory settings, viral propagation includes high-MOI conditions. Typically, infected cultures incubate until all cells produce progeny. Thus, coinfections dominate later replication cycles, masking recessive host range expansion phenotypes. This may have impacted similar studies with other viruses. Last, structural and genetic data could be used to predict site-directed mutant phenotypes, which may broaden the classic antireceptor definition to include interfaces between capsid complexes.
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21
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Li G, Shen M, Yang Y, Le S, Li M, Wang J, Zhao Y, Tan Y, Hu F, Lu S. Adaptation of Pseudomonas aeruginosa to Phage PaP1 Predation via O-Antigen Polymerase Mutation. Front Microbiol 2018; 9:1170. [PMID: 29910791 PMCID: PMC5992289 DOI: 10.3389/fmicb.2018.01170] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/15/2018] [Indexed: 12/27/2022] Open
Abstract
Adaptation of bacteria to phage predation poses a major obstacle for phage therapy. Bacteria adopt multiple mechanisms, such as inhibition of phage adsorption and CRISPR/Cas systems, to resist phage infection. Here, a phage-resistant mutant of Pseudomonas aeruginosa strain PA1 under the infection of lytic phage PaP1 was selected for further study. The PaP1-resistant variant, termed PA1RG, showed decreased adsorption to PaP1 and was devoid of long chain O-antigen on its cell envelope. Whole genome sequencing and comparative analysis revealed a single nucleotide mutation in the gene PA1S_08510, which encodes the O-antigen polymerase Wzy that is involved in lipopolysaccharide (LPS) biosynthesis. PA1_Wzy was classified into the O6 serotype based on sequence homology analysis and adopts a transmembrane topology similar to that seem with P. aeruginosa strain PAO1. Complementation of gene wzy in trans enabled the mutant PA1RG to produce the normal LPS pattern with long chain O-antigen and restored the susceptibility of PA1RG to phage PaP1 infection. While wzy mutation did not affect bacterial growth, mutant PA1RG exhibited decreased biofilm production, suggesting a fitness cost of PA1 associated with resistance of phage PaP1 predation. This study uncovered the mechanism responsible for PA1RG resistance to phage PaP1 via wzy mutation and revealed the role of phages in regulating bacterial behavior.
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Affiliation(s)
- Gang Li
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Mengyu Shen
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Yuhui Yang
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Shuai Le
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Ming Li
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Jing Wang
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Yan Zhao
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Yinling Tan
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Fuquan Hu
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Shuguang Lu
- Department of Microbiology, Army Medical University, Chongqing, China
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Exploration of RNA Sequence Space in the Absence of a Replicase. J Mol Evol 2018; 86:264-276. [PMID: 29748740 DOI: 10.1007/s00239-018-9846-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/04/2018] [Indexed: 12/29/2022]
Abstract
It is generally considered that if an RNA World ever existed that it would be driven by an RNA capable of RNA replication. Whether such a catalytic RNA could emerge in an RNA World or not, there would need to be prior routes to increasing complexity in order to produce it. It is hypothesized here that increasing sequence variety, if not complexity, can in fact readily emerge in response to a dynamic equilibrium between synthesis and degradation. A model system in which T4 RNA ligase catalyzes synthesis and Benzonase catalyzes degradation was constructed. An initial 20-mer served as a seed and was subjected to 180 min of simultaneous ligation and degradation. The seed RNA rapidly disappeared and was replaced by an increasing number and variety of both larger and smaller variants. Variants of 40-80 residues were consistently seen, typically representing 2-4% of the unique sequences. In a second experiment with four individual 9-mers, numerous variants were again produced. These included variants of the individual 9-mers as well as sequences that contained sequence segments from two or more 9-mers. In both cases, the RNA products lack large numbers of point mutations but instead incorporate additions and subtractions of fragments of the original RNAs. The system demonstrates that if such equilibrium were established in a prebiotic world it would result in significant exploration of RNA sequence space and likely increased complexity. It remains to be seen if the variety of products produced is affected by the presence of small peptide oligomers.
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Associations among Antibiotic and Phage Resistance Phenotypes in Natural and Clinical Escherichia coli Isolates. mBio 2017; 8:mBio.01341-17. [PMID: 29089428 PMCID: PMC5666156 DOI: 10.1128/mbio.01341-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The spread of antibiotic resistance is driving interest in new approaches to control bacterial pathogens. This includes applying multiple antibiotics strategically, using bacteriophages against antibiotic-resistant bacteria, and combining both types of antibacterial agents. All these approaches rely on or are impacted by associations among resistance phenotypes (where bacteria resistant to one antibacterial agent are also relatively susceptible or resistant to others). Experiments with laboratory strains have shown strong associations between some resistance phenotypes, but we lack a quantitative understanding of associations among antibiotic and phage resistance phenotypes in natural and clinical populations. To address this, we measured resistance to various antibiotics and bacteriophages for 94 natural and clinical Escherichia coli isolates. We found several positive associations between resistance phenotypes across isolates. Associations were on average stronger for antibacterial agents of the same type (antibiotic-antibiotic or phage-phage) than different types (antibiotic-phage). Plasmid profiles and genetic knockouts suggested that such associations can result from both colocalization of resistance genes and pleiotropic effects of individual resistance mechanisms, including one case of antibiotic-phage cross-resistance. Antibiotic resistance was predicted by core genome phylogeny and plasmid profile, but phage resistance was predicted only by core genome phylogeny. Finally, we used observed associations to predict genes involved in a previously uncharacterized phage resistance mechanism, which we verified using experimental evolution. Our data suggest that susceptibility to phages and antibiotics are evolving largely independently, and unlike in experiments with lab strains, negative associations between antibiotic resistance phenotypes in nature are rare. This is relevant for treatment scenarios where bacteria encounter multiple antibacterial agents.IMPORTANCE Rising antibiotic resistance is making it harder to treat bacterial infections. Whether resistance to a given antibiotic spreads or declines is influenced by whether it is associated with altered susceptibility to other antibiotics or other stressors that bacteria encounter in nature, such as bacteriophages (viruses that infect bacteria). We used natural and clinical isolates of Escherichia coli, an abundant species and key pathogen, to characterize associations among resistance phenotypes to various antibiotics and bacteriophages. We found associations between some resistance phenotypes, and in contrast to past work with laboratory strains, they were exclusively positive. Analysis of bacterial genome sequences and horizontally transferred genetic elements (plasmids) helped to explain this, as well as our finding that there was no overall association between antibiotic resistance and bacteriophage resistance profiles across isolates. This improves our understanding of resistance evolution in nature, potentially informing new rational therapies that combine different antibacterials, including bacteriophages.
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Uyaguari-Diaz MI, Chan M, Chaban BL, Croxen MA, Finke JF, Hill JE, Peabody MA, Van Rossum T, Suttle CA, Brinkman FSL, Isaac-Renton J, Prystajecky NA, Tang P. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. MICROBIOME 2016; 4:20. [PMID: 27391119 PMCID: PMC5011856 DOI: 10.1186/s40168-016-0166-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/04/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary. RESULTS We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels. CONCLUSION This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.
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Affiliation(s)
- Miguel I. Uyaguari-Diaz
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Michael Chan
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Bonnie L. Chaban
- South Kensington Campus, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ UK
| | - Matthew A. Croxen
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Jan F. Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Michael A. Peabody
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Thea Van Rossum
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8 Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Judith Isaac-Renton
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Natalie A. Prystajecky
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
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Endrullat C, Glökler J, Franke P, Frohme M. Standardization and quality management in next-generation sequencing. Appl Transl Genom 2016; 10:2-9. [PMID: 27668169 PMCID: PMC5025460 DOI: 10.1016/j.atg.2016.06.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/13/2016] [Accepted: 06/29/2016] [Indexed: 11/30/2022]
Abstract
DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.
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Key Words
- ABRF, Association of Biomolecular Resource Facilities
- BAM, binary alignment/map
- CAP, College of American Pathologist's
- CEN, European Committee for Standardization
- CLIA, Clinical Laboratory Improvement Amendments
- Data quality
- ERCC, External RNA Controls Consortium
- FDA, Food and Drug Administration
- FFPE, formalin-fixed, paraffin-embedded
- FMEA, failure mode and effects analysis
- GATK, genome analysis toolkit
- GSC, Genomic Standards Consortium
- Guideline
- HGP, Human Genome Project
- Indel, insertion or deletion
- MAQC, MicroArray Quality Control Project
- MIGS, minimum information about a genome sequence
- MOL, molecular pathology checklist
- NGS, next-generation sequencing
- NIST, National Institute of Standards and Technology
- NTC, no-template control
- Nex-StoCT, next generation sequencing — standardization of clinical testing
- Next-generation sequencing
- PT, proficiency testing
- QA, quality assurance
- QC, quality control
- QM, quality management
- QMS, quality management system
- Quality management
- RIN, RNA integrity number
- SAM, sequence alignment/map
- SEQC, sequencing quality control
- SNP, single nucleotide polymorphism
- SOP, standard operating procedure
- Standardization
- TN, technical note
- VCF, variant call format
- Validation
- ddPCR, digital droplet PCR
- mtDNA, mitochondrial DNA
- qPCR, quantitative PCR
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Affiliation(s)
- Christoph Endrullat
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Jörn Glökler
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Philipp Franke
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
| | - Marcus Frohme
- Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany
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Baker CW, Miller CR, Thaweethai T, Yuan J, Baker MH, Joyce P, Weinreich DM. Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174. G3 (BETHESDA, MD.) 2016; 6:939-55. [PMID: 26921293 PMCID: PMC4825663 DOI: 10.1534/g3.115.024075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 02/02/2016] [Indexed: 11/18/2022]
Abstract
Researchers in evolutionary genetics recently have recognized an exciting opportunity in decomposing beneficial mutations into their proximal, mechanistic determinants. The application of methods and concepts from molecular biology and life history theory to studies of lytic bacteriophages (phages) has allowed them to understand how natural selection sees mutations influencing life history. This work motivated the research presented here, in which we explored whether, under consistent experimental conditions, small differences in the genome of bacteriophage φX174 could lead to altered life history phenotypes among a panel of eight genetically distinct clones. We assessed the clones' phenotypes by applying a novel statistical framework to the results of a serially sampled parallel infection assay, in which we simultaneously inoculated each of a large number of replicate host volumes with ∼1 phage particle. We sequentially plated the volumes over the course of infection and counted the plaques that formed after incubation. These counts served as a proxy for the number of phage particles in a single volume as a function of time. From repeated assays, we inferred significant, genetically determined heterogeneity in lysis time and burst size, including lysis time variance. These findings are interesting in light of the genetic and phenotypic constraints on the single-protein lysis mechanism of φX174. We speculate briefly on the mechanisms underlying our results, and we discuss the potential importance of lysis time variance in viral evolution.
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Affiliation(s)
- Christopher W Baker
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Craig R Miller
- Department of Mathematics, University of Idaho, Moscow, Idaho 83844 Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho 83844
| | - Tanayott Thaweethai
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Jeffrey Yuan
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Meghan Hollibaugh Baker
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Paul Joyce
- Department of Mathematics, University of Idaho, Moscow, Idaho 83844
| | - Daniel M Weinreich
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912 Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912
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Incomplete LPS Core-Specific Felix01-Like Virus vB_EcoM_VpaE1. Viruses 2015; 7:6163-81. [PMID: 26633460 PMCID: PMC4690856 DOI: 10.3390/v7122932] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/10/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022] Open
Abstract
Bacteriophages represent a valuable source for studying the mechanisms underlying virus-host interactions. A better understanding of the host-specificity of viruses at the molecular level can promote various phage applications, including bacterial diagnostics, antimicrobial therapeutics, and improve methods in molecular biology. In this study, we describe the isolation and characterization of a novel coliphage, vB_EcoM_VpaE1, which has different host specificity than its relatives. Morphology studies, coupled with the results of genomic and proteomic analyses, indicate that vB_EcoM_VpaE1 belongs to the newly proposed genus Felix01likevirus in the family Myoviridae. The genus Felix01likevirus comprises a group of highly similar phages that infect O-antigen-expressing Salmonella and Escherichia coli (E. coli) strains. Phage vB_EcoM_VpaE1 differs from the rest of Felix01-like viruses, since it infects O-antigen-deficient E. coli strains with an incomplete core lipopolysaccharide (LPS). We show that vB_EcoM_VpaE1 can infect mutants of E. coli that contain various truncations in their LPS, and can even recognize LPS that is truncated down to the inner-core oligosaccharide, showing potential for the control of rough E. coli strains, which usually emerge as resistant mutants upon infection by O-Ag-specific phages. Furthermore, VpaE1 can replicate in a wide temperature range from 9 to 49 °C, suggesting that this virus is well adapted to harsh environmental conditions. Since the structural proteins of such phages tend to be rather robust, the receptor-recognizing proteins of VpaE1 are an attractive tool for application in glycan analysis, bacterial diagnostics and antimicrobial therapeutics.
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28
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Leung RKK, Wu YK. Circulating microbial RNA and health. Sci Rep 2015; 5:16814. [PMID: 26576508 PMCID: PMC4649493 DOI: 10.1038/srep16814] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/15/2015] [Indexed: 12/22/2022] Open
Abstract
Measurement of health indicators in the blood is a commonly performed diagnostic procedure. Two blood studies one involving extended observations on the health of an individual by integrative Personal Omics Profiling (iPOP), and the other tracking the impact of Left Ventricular Assist Device (LVAD) placement on nine heart failure patients were examined for the association of change in health status with change in microbial RNA species. Decrease in RNA expression ratios of human to bacteria and viruses accompanying deteriorated conditions was evident in both studies. Despite large between-subject variations in bacterial composition before LVAD implantation among all the patients, on day 180 after the implantation they manifested apparent between-subject bacterial similarity. In the iPOP study three periods, namely, pre-respiratory syncytial virus (RSV) infection with normal blood glucose level, RSV infection with normal blood glucose level, and post-RSV infection with high blood glucose level could be defined. The upsurge of Enterobacteria phage PhiX 174 sensu lato and Escherichia coli gene expression, in which membrane transporters, membrane receptors for environment signalling, carbohydrate catabolic genes and carbohydrate-active enzymes were enriched only throughout the second period, which suggests a potentially overlooked microbial response to or modulation of the host blood glucose level.
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Affiliation(s)
- Ross Ka-Kit Leung
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, The People's Republic of China.,Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong Shatin, N.T., Hong Kong, The People's Republic of China
| | - Ying-Kit Wu
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, The People's Republic of China.,Division of Genomics and Bioinformatics, CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong Shatin, N.T., Hong Kong, The People's Republic of China
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29
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León M, Bastías R. Virulence reduction in bacteriophage resistant bacteria. Front Microbiol 2015; 6:343. [PMID: 25954266 PMCID: PMC4407575 DOI: 10.3389/fmicb.2015.00343] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/07/2015] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages can influence the abundance, diversity, and evolution of bacterial communities. Several bacteriophages have been reported to add virulence factors to their host and to increase bacterial virulence. However, lytic bacteriophages can also exert a selective pressure allowing the proliferation of strains with reduced virulence. This reduction can be explained because bacteriophages use structures present on the bacterial surface as receptors, which can be virulence factors in different bacterial species. Therefore, strains with modifications in these receptors will be resistant to bacteriophage infection and may also exhibit reduced virulence. This mini-review summarizes the reports on bacteriophage-resistant strains with reductions in virulence, and it discusses the potential consequences in phage therapy and in the use of bacteriophages to select attenuated strains for vaccines.
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Affiliation(s)
- Marcela León
- Laboratory of Microbiology, Institute of Biology, Pontificia Universidad Católica de Valparaíso Valparaíso, Chile
| | - Roberto Bastías
- Laboratory of Microbiology, Institute of Biology, Pontificia Universidad Católica de Valparaíso Valparaíso, Chile
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30
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Bryson SJ, Thurber AR, Correa AMS, Orphan VJ, Vega Thurber R. A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments. Environ Microbiol 2015; 17:3708-21. [PMID: 25640518 DOI: 10.1111/1462-2920.12758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 12/15/2014] [Accepted: 12/15/2014] [Indexed: 12/14/2022]
Abstract
Methane seep microbial communities perform a key ecosystem service by consuming the greenhouse gas methane prior to its release into the hydrosphere, minimizing the impact of marine methane sources on our climate. Although previous studies have examined the ecology and biochemistry of these communities, none has examined viral assemblages associated with these habitats. We employed virus particle purification, genome amplification, pyrosequencing and gene/genome reconstruction and annotation on two metagenomic libraries, one prepared for ssDNA and the other for all DNA, to identify the viral community in a methane seep. Similarity analysis of these libraries (raw and assembled) revealed a community dominated by phages, with a significant proportion of similarities to the Microviridae family of ssDNA phages. We define these viruses as the Eel River Basin Microviridae (ERBM). Assembly and comparison of 21 ERBM closed circular genomes identified five as members of a novel sister clade to the Microvirus genus of Enterobacteria phages. Comparisons among other metagenomes and these Microviridae major-capsid sequences indicated that this clade of phages is currently unique to the Eel River Basin sediments. Given this ERBM clade's relationship to the Microviridae genus Microvirus, we define this sister clade as the candidate genus Pequeñovirus.
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Affiliation(s)
- Samuel Joseph Bryson
- Department of Microbiology, Oregon State University, 454 Nash Hall, Corvallis, OR, 97331, USA
| | - Andrew R Thurber
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, 454 Nash Hall, Corvallis, OR, 97331, USA
| | - Adrienne M S Correa
- Department of Microbiology, Oregon State University, 454 Nash Hall, Corvallis, OR, 97331, USA.,Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, 454 Nash Hall, Corvallis, OR, 97331, USA
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31
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Sun L, Rossmann MG, Fane BA. High-resolution structure of a virally encoded DNA-translocating conduit and the mechanism of DNA penetration. J Virol 2014; 88:10276-9. [PMID: 24990998 PMCID: PMC4178903 DOI: 10.1128/jvi.00291-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although ϕX174 DNA pilot protein H is monomeric during procapsid assembly, it forms an oligomeric tube on the host cell surface. Reminiscent of a double-stranded DNA phage tail in form and function, the H tube transports the single-stranded ϕX174 genome across the Escherichia coli cell wall. The 2.4-Å resolution H-tube crystal structure suggests functional and energetic mechanisms that may be common features of DNA transport through virally encoded conduits.
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Affiliation(s)
- Lei Sun
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Bentley A Fane
- The BIO5 Institute, University of Arizona, Tucson, Arizona, USA
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32
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Mutations in Ralstonia solanacearum loci involved in lipopolysaccharide biogenesis, phospholipid trafficking and peptidoglycan recycling render bacteriophage infection. Arch Microbiol 2014; 196:667-74. [DOI: 10.1007/s00203-014-1002-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 05/13/2014] [Accepted: 05/30/2014] [Indexed: 10/25/2022]
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33
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Li CH, Wang KC, Hong YH, Chu TH, Chu YJ, Chou IC, Lu DK, Chen CY, Yang WC, Lin YM, Cheng CP. Roles of different forms of lipopolysaccharides in Ralstonia solanacearum pathogenesis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:471-8. [PMID: 24580105 DOI: 10.1094/mpmi-08-13-0248-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Lipopolysaccharides (LPS) are critical components for the fitness of most gram-negative bacteria. Ralstonia solanacearum causes a deadly wilting disease in many crops; however, the pathogenic roles of different forms of LPS and their pathways of biogenesis remain unknown. By screening for phage-resistant mutants of R. solanacearum Pss4, whose genome sequence is unavailable, mutants with various types of structural defects in LPS were isolated. Pathogenesis assays of the mutants revealed that production of rough LPS (R-LPS), which does not contain O-polysaccharides, was sufficient to cause necrosis on Nicotiana benthamiana and induce the hypersensitive response on N. tabacum. However, biosynthesis of smooth LPS (S-LPS), which contains O-polysaccharides, was required for bacterial proliferation at infection sites on N. benthamiana leaves and for proliferation and causing wilt on tomato. Complementation tests confirmed the involvement of the previously unidentified cluster RSc2201 to RSc2204 in the formation of R. solanacearum S-LPS. With these data and the availability of the annotated genomic sequence of strain GMI1000, certain loci involved in key steps of R. solanacearum LPS biosynthesis were identified. The strategy of this work could be useful for similar studies in other bacteria without available genome sequences.
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34
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35
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Adaptive divergence in experimental populations of Pseudomonas fluorescens. V. Insight into the niche specialist fuzzy spreader compels revision of the model Pseudomonas radiation. Genetics 2013; 195:1319-35. [PMID: 24077305 DOI: 10.1534/genetics.113.154948] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas fluorescens is a model for the study of adaptive radiation. When propagated in a spatially structured environment, the bacterium rapidly diversifies into a range of niche specialist genotypes. Here we present a genetic dissection and phenotypic characterization of the fuzzy spreader (FS) morphotype-a type that arises repeatedly during the course of the P. fluorescens radiation and appears to colonize the bottom of static broth microcosms. The causal mutation is located within gene fuzY (pflu0478)-the fourth gene of the five-gene fuzVWXYZ operon. fuzY encodes a β-glycosyltransferase that is predicted to modify lipopolysaccharide (LPS) O antigens. The effect of the mutation is to cause cell flocculation. Analysis of 92 independent FS genotypes showed each to have arisen as the result of a loss-of-function mutation in fuzY, although different mutations have subtly different phenotypic and fitness effects. Mutations within fuzY were previously shown to suppress the phenotype of mat-forming wrinkly spreader (WS) types. This prompted a reinvestigation of FS niche preference. Time-lapse photography showed that FS colonizes the meniscus of broth microcosms, forming cellular rafts that, being too flimsy to form a mat, collapse to the vial bottom and then repeatably reform only to collapse. This led to a reassessment of the ecology of the P. fluorescens radiation. Finally, we show that ecological interactions between the three dominant emergent types (smooth, WS, and FS), combined with the interdependence of FS and WS on fuzY, can, at least in part, underpin an evolutionary arms race with bacteriophage SBW25Φ2, to which mutation in fuzY confers resistance.
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36
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Abstract
Bacteria and their viral predators (bacteriophages) are locked in a constant battle. In order to proliferate in phage-rich environments, bacteria have an impressive arsenal of defence mechanisms, and in response, phages have evolved counter-strategies to evade these antiviral systems. In this Review, we describe the various tactics that are used by phages to overcome bacterial resistance mechanisms, including adsorption inhibition, restriction-modification, CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems and abortive infection. Furthermore, we consider how these observations have enhanced our knowledge of phage biology, evolution and phage-host interactions.
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37
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Browning DF, Wells TJ, França FLS, Morris FC, Sevastsyanovich YR, Bryant JA, Johnson MD, Lund PA, Cunningham AF, Hobman JL, May RC, Webber MA, Henderson IR. Laboratory adapted Escherichia coli K-12 becomes a pathogen of Caenorhabditis elegans upon restoration of O antigen biosynthesis. Mol Microbiol 2013; 87:939-50. [PMID: 23350972 DOI: 10.1111/mmi.12144] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2012] [Indexed: 01/13/2023]
Abstract
Escherichia coli has been the leading model organism for many decades. It is a fundamental player in modern biology, facilitating the molecular biology revolution of the last century. The acceptance of E. coli as model organism is predicated primarily on the study of one E. coli lineage; E. coli K-12. However, the antecedents of today's laboratory strains have undergone extensive mutagenesis to create genetically tractable offspring but which resulted in loss of several genetic traits such as O antigen expression. Here we have repaired the wbbL locus, restoring the ability of E. coli K-12 strain MG1655 to express the O antigen. We demonstrate that O antigen production results in drastic alterations of many phenotypes and the density of the O antigen is critical for the observed phenotypes. Importantly, O antigen production enables laboratory strains of E. coli to enter the gut of the Caenorhabditis elegans worm and to kill C. elegans at rates similar to pathogenic bacterial species. We demonstrate C. elegans killing is a feature of other commensal E. coli. We show killing is associated with bacterial resistance to mechanical shear and persistence in the C. elegans gut. These results suggest C. elegans is not an effective model of human-pathogenic E. coli infectious disease.
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Affiliation(s)
- Douglas F Browning
- School of Immunity and Infection, University of Birmingham, Birmingham, UK.
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38
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Scanlan PD, Hall AR, Burlinson P, Preston G, Buckling A. No effect of host-parasite co-evolution on host range expansion. J Evol Biol 2012; 26:205-9. [PMID: 23167752 DOI: 10.1111/jeb.12021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/20/2012] [Indexed: 01/21/2023]
Abstract
Antagonistic co-evolution between hosts and parasites (reciprocal selection for resistance and infectivity) is hypothesized to play an important role in host range expansion by selecting for novel infectivity alleles, but tests are lacking. Here, we determine whether experimental co-evolution between a bacterium (Pseudomonas fluorescens SBW25) and a phage (SBW25Φ2) affects interstrain host range: the ability to infect different strains of P. fluorescens other than SBW25. We identified and tested a genetically and phenotypically diverse suite of co-evolved phage variants of SBW25Φ2 against both sympatric and allopatric co-evolving hosts (P. fluorescens SBW25) and a large set of other P. fluorescens strains. Although all co-evolved phage had a greater host range than the ancestral phage and could differentially infect co-evolved variants of P. fluorescens SBW25, none could infect any of the alternative P. fluorescens strains. Thus, parasite generalism at one genetic scale does not appear to affect generalism at other scales, suggesting fundamental genetic constraints on parasite adaptation for this virus.
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Affiliation(s)
- P D Scanlan
- Department of Zoology, University of Oxford, Oxford, UK.
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39
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Shin J, Jardine P, Noireaux V. Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS Synth Biol 2012; 1:408-13. [PMID: 23651338 DOI: 10.1021/sb300049p] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of living entities in the laboratory is a standing challenge that calls for innovative approaches. Using a cell-free transcription-translation system as a molecular programming platform, we show that the bacteriophage T7, encoded by a 40 kbp DNA program composed of about 60 genes, can be entirely synthesized from its genomic DNA in a test tube reaction. More than a billion infectious bacteriophages T7 per milliliter of reaction are produced after a few hours of incubation. The replication of the genomic DNA occurs concurrently with phage gene expression, protein synthesis, and viral assembly. The demonstration that genome-sized viral DNA can be expressed in a test tube, recapitulating the entire chain of information processing including the replication of the DNA instructions, opens new possibilities to program and to study complex biochemical systems in vitro.
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Affiliation(s)
- Jonghyeon Shin
- School
of Physics and Astronomy and ‡Department of Diagnostic and Biological Sciences
and Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Paul Jardine
- School
of Physics and Astronomy and ‡Department of Diagnostic and Biological Sciences
and Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Vincent Noireaux
- School
of Physics and Astronomy and ‡Department of Diagnostic and Biological Sciences
and Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, United States
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40
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Roux S, Krupovic M, Poulet A, Debroas D, Enault F. Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads. PLoS One 2012; 7:e40418. [PMID: 22808158 PMCID: PMC3394797 DOI: 10.1371/journal.pone.0040418] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 06/07/2012] [Indexed: 01/21/2023] Open
Abstract
Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found in great number among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes highlights the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the microviruses. In addition, a peptidase gene was found in 10 Microviridae and its analysis indicates a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in Microviridae. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
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Affiliation(s)
- Simon Roux
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes : Génome et Environnement”, Clermont-Ferrand, France
- Laboratoire “Microorganismes : Génome et Environnement”, Aubière, France
| | - Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extremophiles, Paris, France
| | - Axel Poulet
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes : Génome et Environnement”, Clermont-Ferrand, France
- Laboratoire “Microorganismes : Génome et Environnement”, Aubière, France
| | - Didier Debroas
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes : Génome et Environnement”, Clermont-Ferrand, France
- Laboratoire “Microorganismes : Génome et Environnement”, Aubière, France
| | - François Enault
- Clermont Université, Université Blaise Pascal, Laboratoire “Microorganismes : Génome et Environnement”, Clermont-Ferrand, France
- Laboratoire “Microorganismes : Génome et Environnement”, Aubière, France
- * E-mail:
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41
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Pathogen detection using engineered bacteriophages. Anal Bioanal Chem 2011; 402:3127-46. [DOI: 10.1007/s00216-011-5555-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/29/2011] [Accepted: 11/02/2011] [Indexed: 12/19/2022]
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