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Silva MD, Pinto G, França A, Azeredo J, Melo LDR. Phage SEP1 hijacks Staphylococcus epidermidis stationary cells' metabolism to replicate. mSystems 2024; 9:e0026324. [PMID: 38904376 PMCID: PMC11265418 DOI: 10.1128/msystems.00263-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
In nature, bacteria often survive in a stationary state with low metabolic activity. Phages use the metabolic machinery of the host cell to replicate, and, therefore, their efficacy against non-dividing cells is usually limited. Nevertheless, it was previously shown that the Staphylococcus epidermidis phage SEP1 has the remarkable capacity to actively replicate in stationary-phase cells, reducing their numbers. Here, we studied for the first time the transcriptomic profiles of both exponential and stationary cells infected with SEP1 phage using RNA-seq to gain a better understanding of this rare phenomenon. We showed that SEP1 successfully takes over the transcriptional apparatus of both exponential and stationary cells. Infection was, however, delayed in stationary cells, with genes within the gp142-gp154 module putatively implicated in host takeover. S. epidermidis responded to SEP1 infection by upregulating three genes involved in a DNA modification system, with this being observed already 5 min after infection in exponential cells and later in stationary cells. In stationary cells, a significant number of genes involved in translation and RNA metabolic and biosynthetic processes were upregulated after 15 and 30 min of SEP1 infection in comparison with the uninfected control, showing that SEP1 activates metabolic and biosynthetic pathways necessary to its successful replication.IMPORTANCEMost phage-host interaction studies are performed with exponentially growing cells. However, this cell state is not representative of what happens in natural environments. Additionally, most phages fail to replicate in stationary cells. The Staphylococcus epidermidis phage SEP1 is one of the few phages reported to date to be able to infect stationary cells. Here, we unveiled the interaction of SEP1 with its host in both exponential and stationary states of growth at the transcriptomic level. The findings of this study provide valuable insights for a better implementation of phage therapy since phages able to infect stationary cells could be more efficient in the treatment of recalcitrant infections.
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Affiliation(s)
- Maria Daniela Silva
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
| | - Graça Pinto
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
| | - Angela França
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana Azeredo
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
| | - Luís D. R. Melo
- CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS–Associate Laboratory, Braga/Guimarães, Portugal
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2
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Lousada MB, Edelkamp J, Lachnit T, Fehrholz M, Pastar I, Jimenez F, Erdmann H, Bosch TCG, Paus R. Spatial Distribution and Functional Impact of Human Scalp Hair Follicle Microbiota. J Invest Dermatol 2024; 144:1353-1367.e15. [PMID: 38070726 DOI: 10.1016/j.jid.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/17/2023] [Accepted: 11/01/2023] [Indexed: 02/26/2024]
Abstract
Human hair follicles (HFs) constitute a unique microbiota habitat that differs substantially from the skin surface. Traditional HF sampling methods fail to eliminate skin microbiota contaminants or assess the HF microbiota incompletely, and microbiota functions in human HF physiology remain ill explored. Therefore, we used laser-capture microdissection, metagenomic shotgun sequencing, and FISH to characterize the human scalp HF microbiota in defined anatomical compartments. This revealed significant compartment-, tissue lineage-, and donor age-dependent variations in microbiota composition. Greatest abundance variations between HF compartments were observed for viruses, archaea, Staphylococcus epidermidis, Cutibacterium acnes, and Malassezia restricta, with the latter 2 being the most abundant viable HF colonizers (as tested by propidium monoazide assay) and, surprisingly, most abundant in the HF mesenchyme. Transfection of organ-cultured human scalp HFs with S. epidermidis-specific lytic bacteriophages ex vivo downregulated transcription of genes known to regulate HF growth and development, metabolism, and melanogenesis, suggesting that selected microbial products may modulate HF functions. Indeed, HF treatment with butyrate, a metabolite of S. epidermidis and other HF microbiota, delayed catagen and promoted autophagy, mitochondrial activity, and gp100 and dermcidin expression ex vivo. Thus, human HF microbiota show spatial variations in abundance and modulate the physiology of their host, which invites therapeutic targeting.
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Affiliation(s)
- Marta B Lousada
- Monasterium Laboratory, Münster, Germany; Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Tim Lachnit
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | | | - Irena Pastar
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Francisco Jimenez
- Mediteknia Skin & Hair Lab, Las Palmas de Gran Canaria, Spain; Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University in Kiel, Kiel, Germany
| | - Ralf Paus
- Monasterium Laboratory, Münster, Germany; Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA; CUTANEON, Hamburg, Germany.
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3
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Abreu G, Garcia E, Oliveira A, Oliveira H. Genome sequence of Erwinia amylovora bacteriophage Omen. Microbiol Resour Announc 2024; 13:e0012224. [PMID: 38526096 PMCID: PMC11008144 DOI: 10.1128/mra.00122-24] [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: 02/07/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024] Open
Abstract
We report the genome of Erwinia amylovora phage Omen, isolated from a Portuguese orchard. Omen has a genome size of 85,304 bp, belongs to the genus Kolesnikvirus (myovirus morphotype), and shares over 80% nucleotide identity with various Erwinia phage genomes.
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Affiliation(s)
- Gabriel Abreu
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Edgar Garcia
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ana Oliveira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Hugo Oliveira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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4
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Pottker ES, Rodrigues LB, Borges KA, de Souza SO, Furian TQ, Pippi Salle CT, de Souza Moraes HL, do Nascimento VP. Bacteriophages as an alternative for biological control of biofilm-forming Salmonella enterica. FOOD SCI TECHNOL INT 2024; 30:197-206. [PMID: 36529875 DOI: 10.1177/10820132221144341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Salmonellosis is one of the most common foodborne diseases worldwide. Surface adherence and biofilm formation are among the main strategies evolved by Salmonella to survive under harsh conditions and are risk factors for its spread through the food chain. Owing to the increase in antimicrobial resistance, there is a growing need to develop other methods to control foodborne pathogens, and bacteriophages have been suggested as a potential alternative for this purpose. The aim of this study was to evaluate bacteriophages as a biological control of Salmonella enterica serotypes to inhibit and remove bacterial biofilms. A total of 12 S. enterica isolates were selected for this study, all of which were biofilm producers. Seven bacteriophages were tested, individually and in a cocktail, for their host range and efficiency of plating (EOP). The phage cocktail was evaluated for its antibiofilm effect against the Salmonella biofilms. Phages UPF_BP1, UPF_BP2, UPF_BP3, UPF_BP6, and 10:2 possessed a broad lytic spectrum and could infect all S. enterica strains. Phages 10:2, UPF_BP6, and UPF_BP3 had high EOP in 10, 9, and 9 out of the 12 S. enterica strains, respectively. The cocktail was able to infect all S. enterica strains and had a high EOP in 10 out of 12 S. enterica isolates, presenting a broader host range than any of the tested single phages. A wide variation of inhibition among strains was observed, ranging from 14.72% to 88.53%. Multidrug-resistant and strong biofilm producer strains showed high biofilm inhibition levels by phage cocktail. Our findings demonstrate the ability of the cocktail to prevent biofilm formation and remove formed biofilms of Salmonella. These results indicate that the phage cocktail is a promising candidate to be used as an alternative for the control of Salmonella biofilms through surface conditioning.
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Affiliation(s)
- Emanuele Serro Pottker
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Laura Beatriz Rodrigues
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, RS, Brazil
| | - Karen Apellanis Borges
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Thales Quedi Furian
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Carlos Tadeu Pippi Salle
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Hamilton Luiz de Souza Moraes
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Vladimir Pinheiro do Nascimento
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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5
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Beck C, Krusche J, Elsherbini AMA, Du X, Peschel A. Phage susceptibility determinants of the opportunistic pathogen Staphylococcus epidermidis. Curr Opin Microbiol 2024; 78:102434. [PMID: 38364502 DOI: 10.1016/j.mib.2024.102434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
Staphylococcus epidermidis is a common member of the human skin and nose microbiomes and a frequent cause of invasive infections. Transducing phages accomplish the horizontal transfer of resistance and virulence genes by mispackaging of mobile-genetic elements, contributing to severe, therapy-refractory S. epidermidis infections. Lytic phages on the other hand can be interesting candidates for new anti-S. epidermidis phage therapies. Despite the importance of phages, we are only beginning to unravel S. epidermidis phage interactions. Recent studies shed new light on S. epidermidis phage diversity, host range, and receptor specificities. Modulation of cell wall teichoic acids, the major phage receptor structures, along with other phage defense mechanisms, are crucial determinants for S. epidermidis susceptibility to different phage groups.
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Affiliation(s)
- Christian Beck
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Janes Krusche
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Ahmed M A Elsherbini
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Xin Du
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Andreas Peschel
- Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)", University of Tübingen, 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany.
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6
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Roehrig C, Huemer M, Lorgé D, Arn F, Heinrich N, Selvakumar L, Gasser L, Hauswirth P, Chang CC, Schweizer TA, Eichenseher F, Lehmann S, Zinkernagel AS, Schmelcher M. MEndoB, a chimeric lysin featuring a novel domain architecture and superior activity for the treatment of staphylococcal infections. mBio 2024; 15:e0254023. [PMID: 38275913 PMCID: PMC10865858 DOI: 10.1128/mbio.02540-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Bacterial infections are a growing global healthcare concern, as an estimated annual 4.95 million deaths are associated with antimicrobial resistance (AMR). Methicillin-resistant Staphylococcus aureus is one of the deadliest pathogens and a high-priority pathogen according to the World Health Organization. Peptidoglycan hydrolases (PGHs) of phage origin have been postulated as a new class of antimicrobials for the treatment of bacterial infections, with a novel mechanism of action and no known resistances. The modular architecture of PGHs permits the creation of chimeric PGH libraries. In this study, the chimeric enzyme MEndoB was selected from a library of staphylococcal PGHs based on its rapid and sustained activity against staphylococci in human serum. The benefit of the presented screening approach was illustrated by the superiority of MEndoB in a head-to-head comparison with other PGHs intended for use against staphylococcal bacteremia. MEndoB displayed synergy with antibiotics and rapid killing in human whole blood with complete inhibition of re-growth over 24 h at low doses. Successful treatment of S. aureus-infected zebrafish larvae with MEndoB provided evidence for its in vivo effectiveness. This was further confirmed in a lethal systemic mouse infection model in which MEndoB significantly reduced S. aureus loads and tumor necrosis factor alpha levels in blood in a dose-dependent manner, which led to increased survival of the animals. Thus, the thorough lead candidate selection of MEndoB resulted in an outstanding second-generation PGH with in vitro, ex vivo, and in vivo results supporting further development.IMPORTANCEOne of the most pressing challenges of our era is the rising occurrence of bacteria that are resistant to antibiotics. Staphylococci are prominent pathogens in humans, which have developed multiple strategies to evade the effects of antibiotics. Infections caused by these bacteria have resulted in a high burden on the health care system and a significant loss of lives. In this study, we have successfully engineered lytic enzymes that exhibit an extraordinary ability to eradicate staphylococci. Our findings substantiate the importance of meticulous lead candidate selection to identify therapeutically promising peptidoglycan hydrolases with unprecedented activity. Hence, they offer a promising new avenue for treating staphylococcal infections.
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Affiliation(s)
- Christian Roehrig
- Micreos Pharmaceuticals AG, Baar, Zug, Switzerland
- Micreos GmbH, Wädenswil, Zurich, Switzerland
| | | | | | | | | | | | - Lynn Gasser
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), Wädenswil, Zurich, Switzerland
| | - Patrick Hauswirth
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), Wädenswil, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Steffi Lehmann
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), Wädenswil, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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7
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Kulshrestha M, Tiwari M, Tiwari V. Bacteriophage therapy against ESKAPE bacterial pathogens: Current status, strategies, challenges, and future scope. Microb Pathog 2024; 186:106467. [PMID: 38036110 DOI: 10.1016/j.micpath.2023.106467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/19/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
The ESKAPE pathogens are the primary threat due to their constant spread of drug resistance worldwide. These pathogens are also regarded as opportunistic pathogens and could potentially cause nosocomial infections. Most of the ESKAPE pathogens have developed resistance to almost all the antibiotics that are used against them. Therefore, to deal with antimicrobial resistance, there is an urgent requirement for alternative non-antibiotic strategies to combat this rising issue of drug-resistant organisms. One of the promising alternatives to this scenario is implementing bacteriophage therapy. This under-explored mode of treatment in modern medicine has posed several concerns, such as preferable phages for the treatment, impact on the microbiome (or gut microflora), dose optimisation, safety, etc. The review will cover a rationale for phage therapy, clinical challenges, and propose phage therapy as an effective therapeutic against bacterial coinfections during pandemics. This review also addresses the expected uncertainties for administering the phage as a treatment against the ESKAPE pathogens and the advantages of using lytic phage over temperate, the immune response to phages, and phages in combinational therapies. The interaction between bacteria and bacteriophages in humans and countless animal models can also be used to design novel and futuristic therapeutics like personalised medicine or bacteriophages as anti-biofilm agents. Hence, this review explores different aspects of phage therapy and its potential to emerge as a frontline therapy against the ESKAPE bacterial pathogen.
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Affiliation(s)
- Mukta Kulshrestha
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India.
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8
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Silva EC, Rodrigues LMR, Vila MMDC, Balcão VM. Newly isolated phages preying on Pseudomonas syringae pv. garcae: In vitro and ex vivo inactivation studies in coffee plant leafs. Enzyme Microb Technol 2023; 171:110325. [PMID: 37716050 DOI: 10.1016/j.enzmictec.2023.110325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/18/2023] [Accepted: 09/10/2023] [Indexed: 09/18/2023]
Abstract
Coffee canker, or bacterial halo blight (BHB) of coffee, is a disease caused by the phytopathogenic bacterium Pseudomonas syringae pv. garcae (Psg), having been found for the first time in 1955, in the Garça region (State of São Paulo), and which has stood out in the Brazilian coffee plantations in recent years, leading to severe economic losses that seriously affect coffee trade. The treatments available are still scarce, involving frequent spraying of coffee plantations with either copper derivatives or the antibiotic kasugamycin. However, these compounds should be avoided due to environmental toxicity and the development of bacterial resistances. Herein we report the isolation and physical/biological characterisation of two novel lytic phages and their efficacy in the control of Psg. Phages ph002F and ph004F were isolated from coffee plant leaves in Brazil (Sorocaba/SP and Itu/SP cities), using Psg IBSBF-158 as the host. According to the transmission electron microscopy analyses, both phages belong to the class Caudoviricetes and present myovirus-like morphotypes. Phages ph002F and ph004F showed eclipse times of 5 min and 20 min, respectively, and a burst size of 123 PFU/host cell and 12 PFU/host cell, respectively, allowing to conclude they replicate well in Psg IBSBF-158 with latency periods of 50 min. Phage ph002F (reduction of 4.59 log CFU/mL, compared to uninfected culture) was more effective in inactivating Psg than phage ph004F (reduction of 3.85 log CFU/mL) after 10 h of incubation at a MOI of 10. As a cocktail, the two phages were highly effective in reducing the bacterial load (reduction of 5.26 log CFU/mL at a MOI of 0.1 or reduction of 5.03 log CFU/mL at a MOI of 10, relative to untreated culture), after 12 h of treatment. This study provides evidence that the isolated phages are promising candidates against the causative agent of BHB in coffee plants.
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Affiliation(s)
- Erica C Silva
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Lucas M R Rodrigues
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil; Agronomic Institute of Campinas (IAC), Centro de café Alcides Carvalho, Campinas, SP, Brazil
| | - Marta M D C Vila
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Victor M Balcão
- VBlab - Laboratory of Bacterial Viruses, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil; Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal.
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9
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Plumet L, Morsli M, Ahmad-Mansour N, Clavijo-Coppens F, Berry L, Sotto A, Lavigne JP, Costechareyre D, Molle V. Isolation and Characterization of New Bacteriophages against Staphylococcal Clinical Isolates from Diabetic Foot Ulcers. Viruses 2023; 15:2287. [PMID: 38140529 PMCID: PMC10747802 DOI: 10.3390/v15122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/09/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Staphylococcus sp. is the most common bacterial genus in infections related to diabetic foot ulcers (DFUs). The emergence of multidrug-resistant bacteria places a serious burden on public health systems. Phage therapy is an alternative treatment to antibiotics, overcoming the issue of antibiotic resistance. In this study, six phages (SAVM01 to SAVM06) were isolated from effluents and were used against a panel of staphylococcal clinical samples isolated from DFUs. A genomic analysis revealed that the phages belonged to the Herelleviridae family, with sequences similar to those of the Kayvirus genus. No lysogeny-associated genes, known virulence or drug resistance genes were identified in the phage genomes. The phages displayed a strong lytic and antibiofilm activity against DFU clinical isolates, as well as against opportunistic pathogenic coagulase-negative staphylococci. The results presented here suggest that these phages could be effective biocontrol agents against staphylococcal clinical isolates from DFUs.
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Affiliation(s)
- Lucile Plumet
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
| | - Madjid Morsli
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
| | - Nour Ahmad-Mansour
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
| | | | - Laurence Berry
- Laboratory of Pathogen and Host Immunity, CNRS UMR5294, University of Montpellier, 34095 Montpellier, France;
| | - Albert Sotto
- VBIC, INSERM U1047, Department of Infectious Diseases, University of de Montpellier, CHU Nîmes, 30908 Nîmes, France;
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
| | | | - Virginie Molle
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
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10
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Keller AP, Huemer M, Chang CC, Mairpady Shambat S, Bjurnemark C, Oberortner N, Santschi MV, Zinsli LV, Röhrig C, Sobieraj AM, Shen Y, Eichenseher F, Zinkernagel AS, Loessner MJ, Schmelcher M. Systemic application of bone-targeting peptidoglycan hydrolases as a novel treatment approach for staphylococcal bone infection. mBio 2023; 14:e0183023. [PMID: 37768041 PMCID: PMC10653945 DOI: 10.1128/mbio.01830-23] [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: 07/19/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE The rising prevalence of antimicrobial resistance in S. aureus has rendered treatment of staphylococcal infections increasingly difficult, making the discovery of alternative treatment options a high priority. Peptidoglycan hydrolases, a diverse group of bacteriolytic enzymes, show high promise as such alternatives due to their rapid and specific lysis of bacterial cells, independent of antibiotic resistance profiles. However, using these enzymes for the systemic treatment of local infections, such as osteomyelitis foci, needs improvement, as the therapeutic distributes throughout the whole host, resulting in low concentrations at the actual infection site. In addition, the occurrence of intracellularly persisting bacteria can lead to relapsing infections. Here, we describe an approach using tissue-targeting to increase the local concentration of therapeutic enzymes in the infected bone. The enzymes were modified with a short targeting moiety that mediated accumulation of the therapeutic in osteoblasts and additionally enables targeting of intracellularly surviving bacteria.
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Affiliation(s)
- Anja P. Keller
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Nicole Oberortner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Léa V. Zinsli
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christian Röhrig
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Anna M. Sobieraj
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Fritz Eichenseher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Martin J. Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Mathias Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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11
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Suchithra KV, Hameed A, Rekha PD, Arun AB. Description and host-range determination of phage PseuPha1, a new species of Pakpunavirus infecting multidrug-resistant clinical strains of Pseudomonas aeruginosa. Virology 2023; 585:222-231. [PMID: 37392714 DOI: 10.1016/j.virol.2023.06.009] [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: 03/12/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/03/2023]
Abstract
A new phage PseuPha1, infecting multiple multi-drug resistant strains of Pseudomonas aeruginosa with strong anti-biofilm activities, was isolated from wastewater in India. PseuPha1 showed optimal multiplicity of infection at 10-3, maintained the infectivity at wide ranges of pH (6-9) and temperature (4-37 ⁰C), and exhibited 50 minutes latent period and a burst size of 200 when tested against P. aeruginosa PAO1. PseuPha1 shared 86.1-89.5% pairwise intergenomic similarity with Pakpunavirus species (n = 11) listed by the International Committee on Taxonomy of Viruses and established distinct phyletic lineages during phylogenetic analyses of phage proteins. While genomic data validated the taxonomic novelty and lytic attributes of PseuPha1, BOX-PCR profiling asserted the genetic heterogeneity of susceptible clinical P. aeruginosa. Our data supported the affiliation of PseuPha1 as a new Pakpunavirus species and provided the first line of evidence for its virulence and infectivity that can be harnessed in wound therapeutics.
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Affiliation(s)
- Kokkarambath Vannadil Suchithra
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
| | - Punchappady Devasya Rekha
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Ananthapadmanabha Bhagwath Arun
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India; Yenepoya Institute of Arts, Science, Commerce and Management, Balmatta, Mangalore, 575002, India.
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12
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Pereira AO, Barros NMA, Guerrero BR, Emencheta SC, Baldo DÂ, Oliveira JM, Vila MMDC, Balcão VM. An Edible Biopolymeric Microcapsular Wrapping Integrating Lytic Bacteriophage Particles for Salmonella enterica: Potential for Integration into Poultry Feed. Antibiotics (Basel) 2023; 12:988. [PMID: 37370307 DOI: 10.3390/antibiotics12060988] [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: 04/28/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
This research work aimed at developing an edible biopolymeric microcapsular wrapping (EBMW) integrating lytic bacteriophage particles for Salmonella enterica, with potential application in poultry feed for biocontrol of that pathogen. This pathogen is known as one of the main microorganisms responsible for contamination in the food industry and in foodstuff. The current techniques for decontamination and pathogen control in the food industry can be very expensive, not very selective, and even outdated, such as the use of broad-spectrum antibiotics that end up selecting resistant bacteria. Hence, there is a need for new technologies for pathogen biocontrol. In this context, bacteriophage-based biocontrol appears as a potential alternative. As a cocktail, both phages were able to significantly reduce the bacterial load after 12 h of treatment, at either multiplicity of infection (MOI) 1 and 10, by 84.3% and 87.6%, respectively. Entrapment of the phage virions within the EBMW matrix did not exert any deleterious effect upon their lytic activity. The results obtained showed high promise for integration in poultry feed aiming at controlling Salmonella enterica, since the edible biopolymeric microcapsular wrapping integrating lytic bacteriophage particles developed was successful in maintaining lytic phage viability while fully stabilizing the phage particles.
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Affiliation(s)
- Arthur O Pereira
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Nicole M A Barros
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Bruna R Guerrero
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Stephen C Emencheta
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Enugu, Nigeria
| | - Denicezar  Baldo
- LaFiNAU-Laboratory of Applied Nuclear Physics, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - José M Oliveira
- LaFiNAU-Laboratory of Applied Nuclear Physics, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Marta M D C Vila
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
| | - Victor M Balcão
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, SP, Brazil
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
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13
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Štrancar V, Marušić M, Tušar J, Praček N, Kolenc M, Šuster K, Horvat S, Janež N, Peterka M. Isolation and in vitro characterization of novel S. epidermidis phages for therapeutic applications. Front Cell Infect Microbiol 2023; 13:1169135. [PMID: 37293203 PMCID: PMC10244729 DOI: 10.3389/fcimb.2023.1169135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
S. epidermidis is an important opportunistic pathogen causing chronic prosthetic joint infections associated with biofilm growth. Increased tolerance to antibiotic therapy often requires prolonged treatment or revision surgery. Phage therapy is currently used as compassionate use therapy and continues to be evaluated for its viability as adjunctive therapy to antibiotic treatment or as an alternative treatment for infections caused by S. epidermidis to prevent relapses. In the present study, we report the isolation and in vitro characterization of three novel lytic S. epidermidis phages. Their genome content analysis indicated the absence of antibiotic resistance genes and virulence factors. Detailed investigation of the phage preparation indicated the absence of any prophage-related contamination and demonstrated the importance of selecting appropriate hosts for phage development from the outset. The isolated phages infect a high proportion of clinically relevant S. epidermidis strains and several other coagulase-negative species growing both in planktonic culture and as a biofilm. Clinical strains differing in their biofilm phenotype and antibiotic resistance profile were selected to further identify possible mechanisms behind increased tolerance to isolated phages.
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Affiliation(s)
- Vida Štrancar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Monika Marušić
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Jasmina Tušar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Neža Praček
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Marko Kolenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Šuster
- Valdoltra Orthopaedic Hospital, Ankaran, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nika Janež
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Matjaž Peterka
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
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14
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Ferreira A, Silva D, Almeida C, Rodrigues ME, Silva S, Castro J, Mil-Homens D, García-Meniño I, Mora A, Henriques M, Oliveira A. Effect of phage vB_EcoM_FJ1 on the reduction of ETEC O9:H9 infection in a neonatal pig cell line. Vet Res 2023; 54:26. [PMID: 36949480 PMCID: PMC10035155 DOI: 10.1186/s13567-023-01157-x] [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: 12/12/2022] [Accepted: 03/02/2023] [Indexed: 03/24/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) colonizes the intestine of young pigs causing severe diarrhoea and consequently bringing high production costs. The rise of antibiotic selective pressure together with ongoing limitations on their use, demands new strategies to tackle this pathology. The pertinence of using bacteriophages as an alternative is being explored, and in this work, the efficacy of phage vB_EcoM_FJ1 (FJ1) in reducing the load of ETEC EC43-Ph (serotype O9:H9 expressing the enterotoxin STa and two adhesins F5 and F41) was assessed. Foreseeing the oral application on piglets, FJ1 was encapsulated on calcium carbonate and alginate microparticles, thus preventing phage release under adverse conditions of the simulated gastric fluid (pH 3.0) and allowing phage availability in simulated intestinal fluid (pH 6.5). A single dose of encapsulated FJ1, provided to IPEC-1 cultured cells (from intestinal epithelium of piglets) previously infected by EC43, provided bacterial reductions of about 99.9% after 6 h. Although bacteriophage-insensitive mutants (BIMs) have emerged from treatment, the consequent fitness costs associated with this new phenotype were demonstrated, comparatively to the originating strain. The higher competence of the pig complement system to decrease BIMs' viability, the lower level of colonization of IPEC-1 cells observed with these mutants, and the increased survival rates and health index recorded in infected Galleria mellonella larvae supported this observation. Most of all, FJ1 established a proof-of-concept of the efficiency of phages to fight against ETEC in piglet intestinal cells.
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Affiliation(s)
- Alice Ferreira
- ALS ControlVet, Zona Industrial de Tondela ZIMII, Lote 6, 3460-605, Tondela, Portugal
| | - Daniela Silva
- ALS ControlVet, Zona Industrial de Tondela ZIMII, Lote 6, 3460-605, Tondela, Portugal
| | - Carina Almeida
- ALS ControlVet, Zona Industrial de Tondela ZIMII, Lote 6, 3460-605, Tondela, Portugal
| | - Maria Elisa Rodrigues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS- Associate Laboratory, 4800-122, Guimarães, Portugal
| | - Sónia Silva
- I.P - National Institute for Agrarian and Veterinarian Research (INIAV), Rua Dos Lagidos, 4485-655, Vila Do Conde, Portugal
| | - Joana Castro
- I.P - National Institute for Agrarian and Veterinarian Research (INIAV), Rua Dos Lagidos, 4485-655, Vila Do Conde, Portugal
| | - Dalila Mil-Homens
- Institute for Bioengineering and Biosciences (IBB), Instituto Superior Técnico, 1049-001, Lisbon, Portugal
| | - Isidro García-Meniño
- Laboratorio de Referencia de Escherichia Coli (LREC), Departamento de Microbioloxía E Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002, Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706, Santiago de Compostela, Spain
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia Coli (LREC), Departamento de Microbioloxía E Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002, Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706, Santiago de Compostela, Spain
| | - Mariana Henriques
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
- LABBELS- Associate Laboratory, 4800-122, Guimarães, Portugal
| | - Ana Oliveira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
- LABBELS- Associate Laboratory, 4800-122, Guimarães, Portugal.
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15
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More's the Same-Multiple Hosts Do Not Select for Broader Host Range Phages. Viruses 2023; 15:v15020518. [PMID: 36851732 PMCID: PMC9960766 DOI: 10.3390/v15020518] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Bacteriophage host range is a result of the interactions between phages and their hosts. For phage therapy, phages with a broader host range are desired so that a phage can infect and kill the broadest range of pathogen strains or related species possible. A common, but not well-tested, belief is that using multiple hosts during the phage isolation will make the isolation of broader host range phage more likely. Using a Bacillus cereus group system, we compared the host ranges of phages isolated on one or four hosts and found that there was no difference in the breadth of host ranges of the isolated phages. Both narrow and broader host range phage were also equally likely to be isolated from either isolation procedure. While there are methods that reliably isolate broader host range phages, such as sequential host isolation, and there are other reasons to use multiple hosts during isolation, multiple hosts are not a consistent way to obtain broader host range phages.
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16
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Characterization of novel of temperate phages of Staphylococcus aureus isolated from bovine milk. Arch Microbiol 2022; 204:680. [DOI: 10.1007/s00203-022-03296-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 11/02/2022]
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17
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Balcão VM, Belline BG, Silva EC, Almeida PFFB, Baldo DÂ, Amorim LRP, Oliveira Júnior JM, Vila MMDC, Del Fiol FS. Isolation and Molecular Characterization of Two Novel Lytic Bacteriophages for the Biocontrol of Escherichia coli in Uterine Infections: In Vitro and Ex Vivo Preliminary Studies in Veterinary Medicine. Pharmaceutics 2022; 14:2344. [PMID: 36365162 PMCID: PMC9692438 DOI: 10.3390/pharmaceutics14112344] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 09/18/2023] Open
Abstract
E. coli is one of the etiological agents responsible for pyometra in female dogs, with conventional treatment involving ovariohysterectomy. Here, we report the isolation and full characterization of two novel lytic phages, viz. vB_EcoM_Uniso11 (ph0011) and vB_EcoM_Uniso21 (ph0021). Both phages belong to the order Caudovirales and present myovirus-like morphotypes, with phage ph0011 being classified as Myoviridae genus Asteriusvirus and phage ph0021 being classified as Myoviridae genus Tequatrovirus, based on their complete genome sequences. The 348,288 bp phage ph0011 and 165,222 bp phage ph0021 genomes do not encode toxins, integrases or antimicrobial resistance genes neither depolymerases related sequences. Both phages were shown to be effective against at least twelve E. coli clinical isolates in in vitro antibacterial activity assays. Based on their features, both phages have potential for controlling pyometra infections caused by E. coli. Phage ph0011 (reduction of 4.24 log CFU/mL) was more effective than phage ph0021 (reduction of 1.90 log CFU/mL) after 12 h of incubation at MOI 1000. As a cocktail, the two phages were highly effective in reducing the bacterial load (reduction of 5.57 log CFU/mL) at MOI 100, after 12 h of treatment. Both phages were structurally and functionally stabilized in vaginal egg formulations.
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Affiliation(s)
- Victor M. Balcão
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
- Department of Biology and CESAM, Campus Universitário de Santiago, University of Aveiro, P-3810-193 Aveiro, Portugal
| | - Bianca G. Belline
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Erica C. Silva
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Pablo F. F. B. Almeida
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Denicezar Â. Baldo
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Lara R. P. Amorim
- Department of Education, Faculty of Sciences, University of Porto, P-4169-007 Porto, Portugal
| | - José M. Oliveira Júnior
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Marta M. D. C. Vila
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Fernando S. Del Fiol
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
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18
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Tian F, Li J, Li L, Li F, Tong Y. Molecular dissection of the first Staphylococcus cohnii temperate phage IME1354_01. Virus Res 2022; 318:198812. [DOI: 10.1016/j.virusres.2022.198812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/06/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
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19
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Ferreira R, Sousa C, Gonçalves RFS, Pinheiro AC, Oleastro M, Wagemans J, Lavigne R, Figueiredo C, Azeredo J, Melo LDR. Characterization and Genomic Analysis of a New Phage Infecting Helicobacter pylori. Int J Mol Sci 2022; 23:ijms23147885. [PMID: 35887231 PMCID: PMC9319048 DOI: 10.3390/ijms23147885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
Helicobacter pylori, a significant human gastric pathogen, has been demonstrating increased antibiotic resistance, causing difficulties in infection treatment. It is therefore important to develop alternatives or complementary approaches to antibiotics to tackle H. pylori infections, and (bacterio)phages have proven to be effective antibacterial agents. In this work, prophage isolation was attempted using H. pylori strains and UV radiation. One phage was isolated and further characterized to assess potential phage-inspired therapeutic alternatives to H. pylori infections. HPy1R is a new podovirus prophage with a genome length of 31,162 bp, 37.1% GC, encoding 36 predicted proteins, of which 17 were identified as structural. Phage particles remained stable at 37 °C, from pH 3 to 11, for 24 h in standard assays. Moreover, when submitted to an in vitro gastric digestion model, only a small decrease was observed in the gastric phase, suggesting that it is adapted to the gastric tract environment. Together with its other characteristics, its capability to suppress H. pylori population levels for up to 24 h post-infection at multiplicities of infection of 0.01, 0.1, and 1 suggests that this newly isolated phage is a potential candidate for phage therapy in the absence of strictly lytic phages.
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Affiliation(s)
- Rute Ferreira
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal;
| | - Cláudia Sousa
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - Raquel F. S. Gonçalves
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - Ana Cristina Pinheiro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - Mónica Oleastro
- Department of Infectious Diseases, National Institute of Health Doctor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal;
| | - Jeroen Wagemans
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (J.W.); (R.L.)
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (J.W.); (R.L.)
| | - Ceu Figueiredo
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal;
- Ipatimup—Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Joana Azeredo
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - Luís D. R. Melo
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
- Correspondence:
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20
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Novel Bacteriophage Specific against Staphylococcus epidermidis and with Antibiofilm Activity. Viruses 2022; 14:v14061340. [PMID: 35746811 PMCID: PMC9230115 DOI: 10.3390/v14061340] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/15/2022] [Accepted: 06/18/2022] [Indexed: 01/19/2023] Open
Abstract
Staphylococcus epidermidis has emerged as the most important pathogen in infections related to indwelling medical devices, and although these infections are not life-threatening, their frequency and the fact that they are extremely difficult to treat represent a serious burden on the public health system. Treatment is complicated by specific antibiotic resistance genes and the formation of biofilms. Hence, novel therapeutic strategies are needed to fight these infections. A novel bacteriophage CUB-EPI_14 specific to the bacterial species S. epidermidis was isolated from sewage and characterized genomically and phenotypically. Its genome contains a total of 46,098 bp and 63 predicted genes, among which some have been associated with packaging and lysis-associated proteins, structural proteins, or DNA- and metabolism-associated proteins. No lysogeny-associated proteins or known virulence proteins were identified in the phage genome. CUB-EPI_14 showed stability over a wide range of temperatures (from −20 °C to 50 °C) and pH values (pH 3–pH 12) and a narrow host range against S. epidermidis. Potent antimicrobial and antibiofilm activities were observed when the phage was tested against a highly susceptible bacterial isolate. These encouraging results open the door to new therapeutic opportunities in the fight against resilient biofilm-associated infections caused by S. epidermidis.
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21
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Hernandez Santos H, Clark J, Terwilliger A, Maresso A. Discovery of the First Lytic Staphylococcus pseudintermedius/ Staphylococcus aureus Polyvalent Bacteriophages. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:116-124. [PMID: 36157281 PMCID: PMC9248872 DOI: 10.1089/phage.2022.0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Background There are no verified lytic Staphylococcus pseudintermedius phages in the literature and few temperate phage genomes in databases. S. pseudintermedius is an opportunistic zoonotic pathogen of great importance in veterinary and human medicine. Materials and Methods We discovered phages against canine-derived S. pseudintermedius isolates by screening dog feces, hair, and skin swabs. Fourteen new phages were isolated and characterized by genomic analysis, transmission electron microscopy, and host range determination. Results Three phages-DH2, DH5, and DS10, a phage K variant-were predicted lytic by sequencing, a designation supported by mitomycin C induction. All three are S. pseudintermedius and Staphylococcus aureus polyvalent phages, with DH2 and DS10 being strong killers of both species. Conclusions We report discovery of the first verified lytic S. pseudintermedius phages and suggest dog hair as a novel reservoir. DH2, DH5, and DS10 are promising candidates toward developing an anti-Staphylococcal phage cocktail.
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Affiliation(s)
- Haroldo Hernandez Santos
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Justin Clark
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Austen Terwilliger
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Anthony Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, Texas, USA
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22
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Milho C, Sillankorva S. Implication of a gene deletion on a Salmonella Enteritidis phage growth parameters. Virus Res 2022; 308:198654. [PMID: 34902446 DOI: 10.1016/j.virusres.2021.198654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 01/21/2023]
Abstract
Synthetic biology has been applied countless times for the modification and improvement of bacterial strains and for the synthesis of products that do not exist in nature. Phages are natural predators of bacteria controlling their population levels; however, their genomes carry several genes with unknown functions. In this work, Bacteriophage Recombineering of Electroporated DNA was used to assess the influence of deletion of a single gene with unknown function in the overall replication parameters of Salmonella phage PVP-SE2. Deletion of ORF_01, transcribed immediately after infection, reduced both the latent and rise periods by 5 min in PVP-SE2ΔORF_01 compared to the wild-type phage. A direct consequence of the deletion led to a smaller progeny release per infected cell by the mutant compared to the wild-type phage. Despite the difference in growth characteristics, the mutant phage remained infective towards exponentially growing cells. The mutation engineered endured for at least ten passages, showing that there is no reversion back to the wild-type sequence. This study provides proof of concept that methodologies used for phage engineering should always be complemented by phage growth characterization to assess whether a mutation can trigger undesirable characteristics.
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Affiliation(s)
- C Milho
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - S Sillankorva
- INL- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga, 4715-330 Braga, Portugal.
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23
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Harada LK, Silva EC, Rossi FP, Cieza B, Oliveira TJ, Pereira C, Tomazetto G, Silva BB, Squina FM, Vila MM, Setubal JC, Ha T, da Silva AM, Balcão VM. Characterization and in vitro testing of newly isolated lytic bacteriophages for the biocontrol of Pseudomonas aeruginosa. Future Microbiol 2022; 17:111-141. [PMID: 34989245 DOI: 10.2217/fmb-2021-0027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aim: Two lytic phages were isolated using P. aeruginosa DSM19880 as host and fully characterized. Materials & methods: Phages were characterized physicochemically, biologically and genomically. Results & conclusion: Host range analysis revealed that the phages also infect some multidrug-resistant (MDR) P. aeruginosa clinical isolates. Increasing MOI from 1 to 1000 significantly increased phage efficiency and retarded bacteria regrowth, but phage ph0034 (reduction of 7.5 log CFU/ml) was more effective than phage ph0031 (reduction of 5.1 log CFU/ml) after 24 h. Both phages belong to Myoviridae family. Genome sequencing of phages ph0031 and ph0034 showed that they do not carry toxin, virulence, antibiotic resistance and integrase genes. The results obtained are highly relevant in the actual context of bacterial resistance to antibiotics.
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Affiliation(s)
- Liliam K Harada
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Erica C Silva
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Fernando Pn Rossi
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Basilio Cieza
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Thais J Oliveira
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Carla Pereira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Geizecler Tomazetto
- Department of Engineering, Biological & Chemical Engineering Section (BCE), Aarhus University, Aarhus, Denmark
| | - Bianca B Silva
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Fabio M Squina
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Marta Mdc Vila
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - João C Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Taekjip Ha
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Victor M Balcão
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil.,Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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24
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Göller PC, Elsener T, Lorgé D, Radulovic N, Bernardi V, Naumann A, Amri N, Khatchatourova E, Coutinho FH, Loessner MJ, Gómez-Sanz E. Multi-species host range of staphylococcal phages isolated from wastewater. Nat Commun 2021; 12:6965. [PMID: 34845206 PMCID: PMC8629997 DOI: 10.1038/s41467-021-27037-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022] Open
Abstract
The host range of bacteriophages defines their impact on bacterial communities and genome diversity. Here, we characterize 94 novel staphylococcal phages from wastewater and establish their host range on a diversified panel of 117 staphylococci from 29 species. Using this high-resolution phage-bacteria interaction matrix, we unveil a multi-species host range as a dominant trait of the isolated staphylococcal phages. Phage genome sequencing shows this pattern to prevail irrespective of taxonomy. Network analysis between phage-infected bacteria reveals that hosts from multiple species, ecosystems, and drug-resistance phenotypes share numerous phages. Lastly, we show that phages throughout this network can package foreign genetic material enclosing an antibiotic resistance marker at various frequencies. Our findings indicate a weak host specialism of the tested phages, and therefore their potential to promote horizontal gene transfer in this environment.
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Affiliation(s)
- Pauline C. Göller
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Tabea Elsener
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Dominic Lorgé
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Natasa Radulovic
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Viona Bernardi
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Annika Naumann
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Nesrine Amri
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Ekaterina Khatchatourova
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Felipe Hernandes Coutinho
- grid.26811.3c0000 0001 0586 4893Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Martin J. Loessner
- grid.5801.c0000 0001 2156 2780Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland
| | - Elena Gómez-Sanz
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland. .,Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain.
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25
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Martinez-Soto CE, Cucić S, Lin JT, Kirst S, Mahmoud ES, Khursigara CM, Anany H. PHIDA: A High Throughput Turbidimetric Data Analytic Tool to Compare Host Range Profiles of Bacteriophages Isolated Using Different Enrichment Methods. Viruses 2021; 13:2120. [PMID: 34834927 PMCID: PMC8623551 DOI: 10.3390/v13112120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria and are present in niches where bacteria thrive. In recent years, the suggested application areas of lytic bacteriophage have been expanded to include therapy, biocontrol, detection, sanitation, and remediation. However, phage application is constrained by the phage's host range-the range of bacterial hosts sensitive to the phage and the degree of infection. Even though phage isolation and enrichment techniques are straightforward protocols, the correlation between the enrichment technique and host range profile has not been evaluated. Agar-based methods such as spotting assay and efficiency of plaquing (EOP) are the most used methods to determine the phage host range. These methods, aside from being labor intensive, can lead to subjective and incomplete results as they rely on qualitative observations of the lysis/plaques, do not reflect the lytic activity in liquid culture, and can overestimate the host range. In this study, phages against three bacterial genera were isolated using three different enrichment methods. Host range profiles of the isolated phages were quantitatively determined using a high throughput turbidimetric protocol and the data were analyzed with an accessible analytic tool "PHIDA". Using this tool, the host ranges of 9 Listeria, 14 Salmonella, and 20 Pseudomonas phages isolated with different enrichment methods were quantitatively compared. A high variability in the host range index (HRi) ranging from 0.86-0.63, 0.07-0.24, and 0.00-0.67 for Listeria, Salmonella, and Pseudomonas phages, respectively, was observed. Overall, no direct correlation was found between the phage host range breadth and the enrichment method in any of the three target bacterial genera. The high throughput method and analytics tool developed in this study can be easily adapted to any phage study and can provide a consensus for phage host range determination.
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Affiliation(s)
- Carlos E. Martinez-Soto
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (C.E.M.-S.); (S.C.); (J.T.L.); (S.K.); (C.M.K.)
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stevan Cucić
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (C.E.M.-S.); (S.C.); (J.T.L.); (S.K.); (C.M.K.)
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Janet T. Lin
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (C.E.M.-S.); (S.C.); (J.T.L.); (S.K.); (C.M.K.)
| | - Sarah Kirst
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (C.E.M.-S.); (S.C.); (J.T.L.); (S.K.); (C.M.K.)
| | - El Sayed Mahmoud
- Faculty of Applied Science and Technology, The Sheridan College Institute of Technology and Advanced Learning, Oakville, ON L6H 2L1, Canada;
| | - Cezar M. Khursigara
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (C.E.M.-S.); (S.C.); (J.T.L.); (S.K.); (C.M.K.)
| | - Hany Anany
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (C.E.M.-S.); (S.C.); (J.T.L.); (S.K.); (C.M.K.)
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada
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26
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Pinto G, Minnich SA, Hovde CJ, Oliveira H, Smidt H, Almeida C, Azeredo J. The interactions of bacteriophage Ace and Shiga toxin-producing Escherichia coli during biocontrol. FEMS Microbiol Ecol 2021; 97:fiab105. [PMID: 34329454 PMCID: PMC8492476 DOI: 10.1093/femsec/fiab105] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/28/2021] [Indexed: 11/15/2022] Open
Abstract
Strictly lytic phages are considered powerful tools for biocontrol of foodborne pathogens. Safety issues needed to be addressed for the biocontrol of Shiga toxin-producing Escherichia coli (STEC) include: lysogenic conversion, Shiga toxin production through phage induction, and emergence/proliferation of bacteriophage insensitive mutants (BIMs). To address these issues, two new lytic phages, vB_EcoS_Ace (Ace) and vB_EcoM_Shy (Shy), were isolated and characterized for life cycle, genome sequence and annotation, pH stability and efficacy at controlling STEC growth. Ace was efficient in controlling host planktonic cells and did not stimulate the production of the Stx prophage or Shiga toxin. A single dose of phage did not lead to the selection of BIMs. However, when reintroduced, BIMs were detected after 24 h of incubation. The gain of resistance was associated with lower virulence, as a subset of BIMs failed to agglutinate with O157-specific antibody and were more sensitive to human serum complement. BIM's biofilm formation capacity and susceptibility to disinfectants was equal to that of the wild-type strain. Overall, this work demonstrated that phage Ace is a safe biocontrol agent against STEC contamination and that the burden of BIM emergence did not represent a greater risk in environmental persistence and human pathogenicity.
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Affiliation(s)
- Graça Pinto
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Scott A Minnich
- Animal Veterinary and Food Science, University of Idaho, Moscow, Idaho, 83844-3025 USA
| | - Carolyn J Hovde
- Animal Veterinary and Food Science, University of Idaho, Moscow, Idaho, 83844-3025 USA
| | - Hugo Oliveira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Carina Almeida
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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27
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Harada LK, Júnior WB, Silva EC, Oliveira TJ, Moreli FC, Júnior JMO, Tubino M, Vila MMDC, Balcão VM. Bacteriophage-Based Biosensing of Pseudomonas aeruginosa: An Integrated Approach for the Putative Real-Time Detection of Multi-Drug-Resistant Strains. BIOSENSORS-BASEL 2021; 11:bios11040124. [PMID: 33921071 PMCID: PMC8071457 DOI: 10.3390/bios11040124] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 12/19/2022]
Abstract
During the last decennium, it has become widely accepted that ubiquitous bacterial viruses, or bacteriophages, exert enormous influences on our planet’s biosphere, killing between 4–50% of the daily produced bacteria and constituting the largest genetic diversity pool on our planet. Currently, bacterial infections linked to healthcare services are widespread, which, when associated with the increasing surge of antibiotic-resistant microorganisms, play a major role in patient morbidity and mortality. In this scenario, Pseudomonas aeruginosa alone is responsible for ca. 13–15% of all hospital-acquired infections. The pathogen P. aeruginosa is an opportunistic one, being endowed with metabolic versatility and high (both intrinsic and acquired) resistance to antibiotics. Bacteriophages (or phages) have been recognized as a tool with high potential for the detection of bacterial infections since these metabolically inert entities specifically attach to, and lyse, bacterial host cells, thus, allowing confirmation of the presence of viable cells. In the research effort described herein, three different phages with broad lytic spectrum capable of infecting P. aeruginosa were isolated from environmental sources. The isolated phages were elected on the basis of their ability to form clear and distinctive plaques, which is a hallmark characteristic of virulent phages. Next, their structural and functional stabilization was achieved via entrapment within the matrix of porous alginate, biopolymeric, and bio-reactive, chromogenic hydrogels aiming at their use as sensitive matrices producing both color changes and/or light emissions evolving from a reaction with (released) cytoplasmic moieties, as a bio-detection kit for P. aeruginosa cells. Full physicochemical and biological characterization of the isolated bacteriophages was the subject of a previous research paper.
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Affiliation(s)
- Liliam K. Harada
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | | | - Erica C. Silva
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - Thais J. Oliveira
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - Fernanda C. Moreli
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - José M. Oliveira Júnior
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - Matthieu Tubino
- Institute of Chemistry, University of Campinas, Campinas, SP 13083-970, Brazil;
| | - Marta M. D. C. Vila
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
| | - Victor M. Balcão
- PhageLab—Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba, SP 18023-000, Brazil; (L.K.H.); (E.C.S.); (T.J.O.); (F.C.M.); (J.M.O.J.); (M.M.D.C.V.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
- Correspondence: ; Tel.: +55-(15)-2101-7029
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28
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Valente LG, Pitton M, Fürholz M, Oberhaensli S, Bruggmann R, Leib SL, Jakob SM, Resch G, Que YA, Cameron DR. Isolation and characterization of bacteriophages from the human skin microbiome that infect Staphylococcus epidermidis. FEMS MICROBES 2021; 2:xtab003. [PMID: 37334235 PMCID: PMC10117716 DOI: 10.1093/femsmc/xtab003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 07/20/2023] Open
Abstract
Phage therapy might be a useful approach for the treatment of nosocomial infections; however, only few lytic phages suitable for this application are available for the opportunistic pathogen, Staphylococcus epidermidis. In the current study, we developed an efficient method to isolate bacteriophages present within the human skin microbiome, by using niche-specific S. epidermidis as the host for phage propagation. Staphylococcus epidermidis was identified on the forehead of 92% of human subjects tested. These isolates were then used to propagate phages present in the same skin sample. Plaques were observable on bacterial lawns in 46% of the cases where S. epidermidis was isolated. A total of eight phage genomes were genetically characterized, including the previously described phage 456. A total of six phage sequences were unique, and spanned each of the major staphylococcal phage families; Siphoviridae (n = 3), Podoviridae (n = 1) and Myoviridae (n = 2). One of the myoviruses (vB_SepM_BE06) was identified on the skin of three different humans. Comparative analysis identified novel genes including a putative N-acetylmuramoyl-L-alanine amidase gene. The host-range of each unique phage was characterized using a panel of diverse staphylococcal strains (n = 78). None of the newly isolated phages infected more than 52% of the S. epidermidis strains tested (n = 44), and non-S. epidermidis strains where rarely infected, highlighting the narrow host-range of the phages. One of the phages (vB_SepM_BE04) was capable of killing staphylococcal cells within biofilms formed on polyurethane catheters. Uncovering a richer diversity of available phages will likely improve our understanding of S. epidermidis-phage interactions, which will be important for future therapy.
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Affiliation(s)
| | | | - Monika Fürholz
- Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Simone Oberhaensli
- Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Stephen L Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Stephan M Jakob
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Grégory Resch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - David R Cameron
- Corresponding author: Department of Intensive Care Medicine, Inselspital; Bern University Hospital, 3010 Bern, Switzerland. Tel: +41 31 632 42 55; E-mail:
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29
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Pires DP, Monteiro R, Mil-Homens D, Fialho A, Lu TK, Azeredo J. Designing P. aeruginosa synthetic phages with reduced genomes. Sci Rep 2021; 11:2164. [PMID: 33495501 PMCID: PMC7835345 DOI: 10.1038/s41598-021-81580-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/29/2020] [Indexed: 12/18/2022] Open
Abstract
In the era where antibiotic resistance is considered one of the major worldwide concerns, bacteriophages have emerged as a promising therapeutic approach to deal with this problem. Genetically engineered bacteriophages can enable enhanced anti-bacterial functionalities, but require cloning additional genes into the phage genomes, which might be challenging due to the DNA encapsulation capacity of a phage. To tackle this issue, we designed and assembled for the first time synthetic phages with smaller genomes by knocking out up to 48% of the genes encoding hypothetical proteins from the genome of the newly isolated Pseudomonas aeruginosa phage vB_PaeP_PE3. The antibacterial efficacy of the wild-type and the synthetic phages was assessed in vitro as well as in vivo using a Galleria mellonella infection model. Overall, both in vitro and in vivo studies revealed that the knock-outs made in phage genome do not impair the antibacterial properties of the synthetic phages, indicating that this could be a good strategy to clear space from phage genomes in order to enable the introduction of other genes of interest that can potentiate the future treatment of P. aeruginosa infections.
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Affiliation(s)
- Diana P Pires
- CEB - Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, Braga, Portugal.
| | - Rodrigo Monteiro
- CEB - Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, Braga, Portugal
| | - Dalila Mil-Homens
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Lisboa, Portugal
| | - Arsénio Fialho
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Lisboa, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science and Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, Braga, Portugal.
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30
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Silva EC, Oliveira TJ, Moreli FC, Harada LK, Vila MMDC, Balcão VM. Newly isolated lytic bacteriophages for Staphylococcus intermedius, structurally and functionally stabilized in a hydroxyethylcellulose gel containing choline geranate: Potential for transdermal permeation in veterinary phage therapy. Res Vet Sci 2020; 135:42-58. [PMID: 33440244 DOI: 10.1016/j.rvsc.2020.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/06/2020] [Accepted: 12/22/2020] [Indexed: 12/25/2022]
Abstract
In the present research work, we propose a new antimicrobial treatment for pyoderma via cutaneous permeation of bacteriophage particles conveyed in a hydroxyethylcellulose (HEC) gel integrating ionic liquid as a permeation enhancer. Ionic liquids are highly viscous fluids constituted exclusively by ions, that are usually hydrolytically stable and promote solubilization of amphipathic molecules such as proteins, hence serving as green solvents and promoting the transdermal permeation of biomolecules. In the research effort entertained herein, the synthesis and use of choline geranate for integrating a HEC gel aiming at the structural and functional stabilization of a cocktail of isolated lytic bacteriophage particles was sought, aiming at transdermal permeation in the antimicrobial treatment of animal pyoderma. The results obtained showed a high ability of the ionic liquid in enhancing transdermal permeation of the bacteriophage particles, with concomitant high potential of the HEC gel formulation in the antimicrobial treatment of animal skin infections.
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Affiliation(s)
- Erica C Silva
- PhageLab - Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Thais J Oliveira
- PhageLab - Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Fernanda C Moreli
- PhageLab - Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Liliam K Harada
- PhageLab - Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Marta M D C Vila
- PhageLab - Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Victor M Balcão
- PhageLab - Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, SP, Brazil; Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal.
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Urban-Chmiel R, Balicki I, Świąder K, Nowaczek A, Pyzik E, Stępień-Pyśniak D, Marek A, Puchalski A, Wernicki A, Poleszak E, Dec M. The in vitro efficacy of eye drops containing a bacteriophage solution specific for Staphylococcus spp. isolated from dogs with bacterial conjunctivitis. Ir Vet J 2020; 73:21. [PMID: 33319700 PMCID: PMC7643432 DOI: 10.1186/s13620-020-00175-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/22/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The purpose of the study was to evaluate the in vitro antibacterial effect of experimental eye drops with bacteriophages in elimination of Staphylococcus spp. isolated from dogs with bacterial conjunctivitis.. The bacterial material was collected from dogs with independent clinical signs of bacterial conjunctivitis. Staphylococcus spp. were identified by phenotypic and genotypic methods (MALDI-TOF MS mass spectrometry). Antibiotic resistance was determined by the disc-diffusion method. Phage activity (Plaque forming units, PFU) was determined on double-layer agar plates. Phages with lytic titres > 108 PFU were used to prepare eye drops. The stability of the antibacterial titre was evaluated for preparations stored in sealed bottles as well as after opening and reclosing. RESULTS The tests confirmed the occurrence of Staphylococcus spp. strains as etiological agents of bacterial conjunctivitis in dogs. A high percentage of strains were resistant to more than three antibiotics. The experimental phage eye drops used in the study exhibited 100% efficacy in vitro against the tested Staphylococcus isolates. Particularly noteworthy is the long duration of activity and constant antibacterial lytic titre of ≥108 PFU/mL of two eye drop solutions, nos. 7 and 12, after the bottle had been opened (21 days) and after hermetically sealed packaging (28 days) at 4-8 °C. CONCLUSIONS The results represent the first stage of research and require continuation in vivo. If positive effects are obtained in animals, the results can be used in applied research in humans and animals.
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Affiliation(s)
- Renata Urban-Chmiel
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Ireneusz Balicki
- Department and Clinic of Animal Surgery, Faculty of Veterinary Medicine, Lublin, Poland
| | - Katarzyna Świąder
- Department of Applied Pharmacy, Medical University of Lublin, Lublin, Poland
| | - Anna Nowaczek
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Ewelina Pyzik
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Dagmara Stępień-Pyśniak
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Agnieszka Marek
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Andrzej Puchalski
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Andrzej Wernicki
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland
| | - Ewa Poleszak
- Department of Applied Pharmacy, Medical University of Lublin, Lublin, Poland
| | - Marta Dec
- SubDepartment of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences Lublin, Lublin, Poland.
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32
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Mourenza Á, Gil JA, Mateos LM, Letek M. Alternative Anti-Infective Treatments to Traditional Antibiotherapy against Staphylococcal Veterinary Pathogens. Antibiotics (Basel) 2020; 9:antibiotics9100702. [PMID: 33076497 PMCID: PMC7602553 DOI: 10.3390/antibiotics9100702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/29/2022] Open
Abstract
The genus Staphylococcus encompasses many species that may be pathogenic to both humans and farm animals. These bacteria have the potential to acquire multiple resistant traits to the antimicrobials currently used in the veterinary or medical settings. These pathogens may commonly cause zoonoses, and the infections they cause are becoming difficult to treat due to antimicrobial resistance. Therefore, the development of novel alternative treatments to traditional antibiotherapy has gained interest in recent years. Here, we reviewed the most promising therapeutic strategies developed to control staphylococcal infections in the veterinary field to overcome antibiotic resistance.
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Affiliation(s)
- Álvaro Mourenza
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (J.A.G.)
| | - José A. Gil
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (J.A.G.)
- Instituto de Biología Molecular, Genómica y Proteómica (INBIOMIC), Universidad de León, 24071 León, Spain
| | - Luis M. Mateos
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (J.A.G.)
- Instituto de Biología Molecular, Genómica y Proteómica (INBIOMIC), Universidad de León, 24071 León, Spain
- Correspondence: (L.M.M.); (M.L.)
| | - Michal Letek
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (J.A.G.)
- Instituto de Desarrollo Ganadero y Sanidad Animal (INDEGSAL), Universidad de León, 24071 León, Spain
- Correspondence: (L.M.M.); (M.L.)
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33
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Oliveira VC, Bim FL, Monteiro RM, Macedo AP, Santos ES, Silva-Lovato CH, Paranhos HFO, Melo LDR, Santos SB, Watanabe E. Identification and Characterization of New Bacteriophages to Control Multidrug-Resistant Pseudomonas aeruginosa Biofilm on Endotracheal Tubes. Front Microbiol 2020; 11:580779. [PMID: 33123112 PMCID: PMC7573221 DOI: 10.3389/fmicb.2020.580779] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/08/2020] [Indexed: 12/28/2022] Open
Abstract
Studies involving antimicrobial-coated endotracheal tubes are scarce, and new approaches to control multidrug-resistant Pseudomonas aeruginosa biofilm on these devices should be investigated. In this study, five new P. aeruginosa bacteriophages from domestic sewage were isolated. All of them belong to the order Caudovirales, Myoviridae family. They are pH and heat stable and produce 27 to 46 particles after a latent period of 30 min at 37°C. Their dsDNA genome (ranging from ∼62 to ∼65 kb) encodes 65 to 89 different putative proteins. They exhibit a broad lytic spectrum and infect 69.7% of the P. aeruginosa strains tested. All the bacteriophages were able to reduce the growth of P. aeruginosa strains in planktonic form. The bacteriophages were also able to reduce the biofilm viability rates and the metabolic activity of P. aeruginosa strains in a model of biofilms associated with endotracheal tubes. In addition, scanning electron microscopy micrographs showed disrupted biofilms and cell debris after treatment of bacteriophages, revealing remarkable biofilm reduction. The lytic activity on multidrug-resistant P. aeruginosa biofilm indicates that the isolated bacteriophages might be considered as good candidates for therapeutic studies and for the application of bacteriophage-encoded products.
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Affiliation(s)
- Viviane C Oliveira
- Human Exposome and Infectious Diseases Network, School of Nursing of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,Department of Dental Materials and Prostheses, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Felipe L Bim
- Human Exposome and Infectious Diseases Network, School of Nursing of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Rachel M Monteiro
- Human Exposome and Infectious Diseases Network, School of Nursing of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Ana Paula Macedo
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Emerson S Santos
- Department of Clinical Toxicological and Bromatologic Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Cláudia H Silva-Lovato
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Helena F O Paranhos
- Department of Dental Materials and Prostheses, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Luís D R Melo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Sílvio B Santos
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Evandro Watanabe
- Human Exposome and Infectious Diseases Network, School of Nursing of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.,Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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34
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The Protective Effect of Staphylococcus epidermidis Biofilm Matrix against Phage Predation. Viruses 2020; 12:v12101076. [PMID: 32992766 PMCID: PMC7601396 DOI: 10.3390/v12101076] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/13/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus epidermidis is a major causative agent of nosocomial infections, mainly associated with the use of indwelling devices, on which this bacterium forms structures known as biofilms. Due to biofilms’ high tolerance to antibiotics, virulent bacteriophages were previously tested as novel therapeutic agents. However, several staphylococcal bacteriophages were shown to be inefficient against biofilms. In this study, the previously characterized S. epidermidis-specific Sepunavirus phiIBB-SEP1 (SEP1), which has a broad spectrum and high activity against planktonic cells, was evaluated concerning its efficacy against S. epidermidis biofilms. The in vitro biofilm killing assays demonstrated a reduced activity of the phage. To understand the underlying factors impairing SEP1 inefficacy against biofilms, this phage was tested against distinct planktonic and biofilm-derived bacterial populations. Interestingly, SEP1 was able to lyse planktonic cells in different physiological states, suggesting that the inefficacy for biofilm control resulted from the biofilm 3D structure and the protective effect of the matrix. To assess the impact of the biofilm architecture on phage predation, SEP1 was tested in disrupted biofilms resulting in a 2 orders-of-magnitude reduction in the number of viable cells after 6 h of infection. The interaction between SEP1 and the biofilm matrix was further assessed by the addition of matrix to phage particles. Results showed that the matrix did not inactivate phages nor affected phage adsorption. Moreover, confocal laser scanning microscopy data demonstrated that phage infected cells were less predominant in the biofilm regions where the matrix was more abundant. Our results provide compelling evidence indicating that the biofilm matrix can work as a barrier, allowing the bacteria to be hindered from phage infection.
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35
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Complete Genome Sequences of Eight Phages Infecting Enterotoxigenic Escherichia coli in Swine. Microbiol Resour Announc 2020; 9:9/36/e00858-20. [PMID: 32883794 PMCID: PMC7471389 DOI: 10.1128/mra.00858-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We report eight phages infecting enterotoxigenic Escherichia coli responsible for intestinal infections in piglets. Phages vB_EcoM_F1, vB_EcoM_FB, vB_EcoS_FP, vB_EcoM_FT, vB_EcoM_SP1, vB_EcoP_SP5M, vB_EcoP_SP7, and vB_EcoS_SP8 were isolated between 2007 and 2018 in the Iberian Peninsula. These viruses span the three tailed phage families, Podoviridae, Siphoviridae, and Myoviridae.
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36
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Röhrig C, Huemer M, Lorgé D, Luterbacher S, Phothaworn P, Schefer C, Sobieraj AM, Zinsli LV, Mairpady Shambat S, Leimer N, Keller AP, Eichenseher F, Shen Y, Korbsrisate S, Zinkernagel AS, Loessner MJ, Schmelcher M. Targeting Hidden Pathogens: Cell-Penetrating Enzybiotics Eradicate Intracellular Drug-Resistant Staphylococcus aureus. mBio 2020; 11:e00209-20. [PMID: 32291298 PMCID: PMC7157818 DOI: 10.1128/mbio.00209-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/17/2020] [Indexed: 01/21/2023] Open
Abstract
Staphylococcus aureus is a major concern in human health care, mostly due to the increasing prevalence of antibiotic resistance. Intracellular localization of S. aureus plays a key role in recurrent infections by protecting the pathogens from antibiotics and immune responses. Peptidoglycan hydrolases (PGHs) are highly specific bactericidal enzymes active against both drug-sensitive and -resistant bacteria. However, PGHs able to effectively target intracellular S. aureus are not yet available. To overcome this limitation, we first screened 322 recombineered PGHs for staphylolytic activity under conditions found inside eukaryotic intracellular compartments. The most active constructs were modified by fusion to different cell-penetrating peptides (CPPs), resulting in increased uptake and enhanced intracellular killing (reduction by up to 4.5 log units) of various S. aureus strains (including methicillin-resistant S. aureus [MRSA]) in different tissue culture infection models. The combined application of synergistic PGH-CPP constructs further enhanced their intracellular efficacy. Finally, synergistically active PGH-CPP cocktails reduced the total S. aureus by more than 2.2 log units in a murine abscess model after peripheral injection. Significantly more intracellular bacteria were killed by the PGH-CPPs than by the PGHs alone. Collectively, our findings show that CPP-fused PGHs are effective novel protein therapeutics against both intracellular and drug-resistant S. aureusIMPORTANCE The increasing prevalence of antibiotic-resistant bacteria is one of the most urgent problems of our time. Staphylococcus aureus is an important human pathogen that has acquired several mechanisms to evade antibiotic treatment. In addition, S. aureus is able to invade and persist within human cells, hiding from the immune response and antibiotic therapies. For these reasons, novel antibacterial strategies against these pathogens are needed. Here, we developed lytic enzymes which are able to effectively target drug-resistant and intracellular S. aureus Fusion of these so-called enzybiotics to cell-penetrating peptides enhanced their uptake and intracellular bactericidal activity in cell culture and in an abscess mouse model. Our results suggest that cell-penetrating enzybiotics are a promising new class of therapeutics against staphylococcal infections.
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Affiliation(s)
- Christian Röhrig
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Dominique Lorgé
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Samuel Luterbacher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Preeda Phothaworn
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Anna M Sobieraj
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Léa V Zinsli
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nadja Leimer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anja P Keller
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Fritz Eichenseher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Mathias Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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37
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Ribeiro HG, Melo LDR, Oliveira H, Boon M, Lavigne R, Noben JP, Azeredo J, Oliveira A. Characterization of a new podovirus infecting Paenibacillus larvae. Sci Rep 2019; 9:20355. [PMID: 31889094 PMCID: PMC6937236 DOI: 10.1038/s41598-019-56699-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/28/2019] [Indexed: 12/17/2022] Open
Abstract
The Paenibacillus larvae infecting phage API480 (vB_PlaP_API480) is the first reported podovirus for this bacterial species, with an 58 nm icosahedral capsid and a 12 × 8 nm short, non-contractile tail. API480 encodes 77 coding sequences (CDSs) on its 45,026 bp dsDNA genome, of which 47 were confirmed using mass spectrometry. This phage has got very limited genomic and proteomic similarity to any other known ones registered in public databases, including P. larvae phages. Comparative genomics indicates API480 is a new species as it's a singleton with 28 unique proteins. Interestingly, the lysis module is highly conserved among P. larvae phages, containing a predicted endolysin and two putative holins. The well kept overall genomic organisation (from the structural and morphogenetic modules to the host lysis, DNA replication and metabolism related proteins) confirms a common evolutionary ancestor among P. larvae infecting phages. API480 is able to infect 69% of the 61 field strains with an ERIC I genotype, as well as ERIC II strains. Furthermore, this phage is very stable when exposed to high glucose concentrations and to larval gastrointestinal conditions. This highly-specific phage, with its broad lytic activity and stability in hive conditions, might potentially be used in the biocontrol of American Foulbrood (AFB).
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Affiliation(s)
- Henrique G Ribeiro
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Hugo Oliveira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Maarten Boon
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Agoralaan D, 3590, Hasselt, Belgium
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Ana Oliveira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal.
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38
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Milho C, Silva MD, Alves D, Oliveira H, Sousa C, Pastrana LM, Azeredo J, Sillankorva S. Escherichia coli and Salmonella Enteritidis dual-species biofilms: interspecies interactions and antibiofilm efficacy of phages. Sci Rep 2019; 9:18183. [PMID: 31796870 PMCID: PMC6890764 DOI: 10.1038/s41598-019-54847-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/20/2019] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli and Salmonella Enteritidis are foodborne pathogens forming challenging biofilms that contribute to their virulence, antimicrobial resistance, and survival on surfaces. Interspecies interactions occur between species in mixed biofilms promoting different outcomes to each species. Here we describe the interactions between E. coli and S. Enteritidis strains, and their control using specific phages. Single-species biofilms presented more cells compared to dual-species biofilms. The spatial organization of strains, observed by confocal microscopy, revealed similar arrangements in both single- and dual-species biofilms. The EPS matrix composition, assessed by Fourier-transform infrared spectroscopy, disclosed that the spectra extracted from the different dual-species biofilms can either be a combination of both species EPS matrix components or that the EPS matrix of one species predominates. Phages damaged more the single-species biofilms than the mixed biofilms, showing also that the killing efficacy was greatly dependent on the phage growth characteristics, bacterial growth parameters, and bacterial spatial distribution in biofilms. This combination of methodologies provides new knowledge of species-species and phage-host interactions in biofilms of these two major foodborne pathogens.
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Affiliation(s)
- Catarina Milho
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Maria Daniela Silva
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Diana Alves
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Hugo Oliveira
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Clara Sousa
- LAQV/REQUIMTE, Chemical Science Department, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Lorenzo M Pastrana
- INL- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga, 4715-330, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Sanna Sillankorva
- INL- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga, 4715-330, Braga, Portugal.
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Pinheiro LAM, Pereira C, Frazão C, Balcão VM, Almeida A. Efficiency of Phage φ6 for Biocontrol of Pseudomonas syringae pv. syringae: An in Vitro Preliminary Study. Microorganisms 2019; 7:E286. [PMID: 31450735 PMCID: PMC6780397 DOI: 10.3390/microorganisms7090286] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 07/31/2019] [Accepted: 08/21/2019] [Indexed: 12/14/2022] Open
Abstract
Pseudomonas syringae is a plant-associated bacterial species that has been divided into more than 60 pathovars, with the Pseudomonas syringae pv. syringae being the main causative agent of diseases in a wide variety of fruit trees. The most common treatments for biocontrol of P. syringae pv. syringae infections has involved copper derivatives and/or antibiotics. However, these treatments should be avoided due to their high toxicity to the environment and promotion of bacterial resistance. Therefore, it is essential to search for new approaches for controlling P. syringae pv. syringae. Phage therapy can be a useful alternative tool to the conventional treatments to control P. syringae pv. syringae infections in plants. In the present study, the efficacy of bacteriophage (or phage) φ6 (a commercially available phage) was evaluated in the control of P. syringae pv. syringae. As the plants are exposed to the natural variability of physical and chemical parameters, the influence of pH, temperature, solar radiation and UV-B irradiation on phage φ6 viability was also evaluated in order to develop an effective phage therapy protocol. The host range analysis revealed that the phage, besides its host (P. syringae pv. syringae), also infects the Pseudomonas syringae pv. actinidiae CRA-FRU 12.54 and P. syringae pv. actinidiae CRA-FRU 14.10 strains, not infecting strains from the other tested species. Both multiplicities of infection (MOIs) tested, 1 and 100, were effective to inactivate the bacterium, but the MOI 1 (maximum reduction of 3.9 log CFU/mL) was more effective than MOI 100 (maximum reduction of 2.6 log CFU/mL). The viability of phage φ6 was mostly affected by exposure to UV-B irradiation (decrease of 7.3 log PFU/mL after 8 h), exposure to solar radiation (maximum reduction of 2.1 PFU/mL after 6 h), and high temperatures (decrease of 8.5 PFU/mL after 6 days at 37 °C, but a decrease of only 2.0 log PFU/mL after 67 days at 15 °C and 25 °C). The host range, high bacterial control and low rates of development of phage-resistant bacterial clones (1.20 × 10-3) suggest that this phage can be used to control P. syringae pv. syringae infections in plants, but also to control infections by P. syringae pv. actinidiae, the causal agent of bacterial canker of kiwifruit. Although the stability of phage φ6 was affected by UV-B and solar radiation, this can be overcome by the application of phage suspensions at the end of the day or at night.
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Affiliation(s)
- Larindja A M Pinheiro
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Carolina Frazão
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Victor M Balcão
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, São Paulo, Brazil
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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40
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Barros J, Melo LDR, Poeta P, Igrejas G, Ferraz MP, Azeredo J, Monteiro FJ. Lytic bacteriophages against multidrug-resistant Staphylococcus aureus, Enterococcus faecalis and Escherichia coli isolates from orthopaedic implant-associated infections. Int J Antimicrob Agents 2019; 54:329-337. [PMID: 31229670 DOI: 10.1016/j.ijantimicag.2019.06.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 06/05/2019] [Accepted: 06/10/2019] [Indexed: 11/19/2022]
Abstract
Orthopaedic implant-associated infections are a devastating complication of orthopaedic surgery with a significant impact on patients and healthcare systems. The aims of this work were to describe the patterns of antimicrobial resistance, pathogenicity and virulence of clinical bacterial isolates from orthopaedic implant-associated infections and to further isolate and characterise bacteriophages that are efficient in controlling these bacteria. Staphylococcus aureus, Enterococcus faecalis and Escherichia coli isolated from orthopaedic infections showed multiresistance patterns to the most frequently used antibiotics in clinical settings. The presence of mobile genetic elements (mecA, Tn916/Tn1545 and intl1) and virulence determinants (icaB, cna, hlb, cylLs, cylM, agg, gelE, fsr and fimA) highlighted the pathogenicity of these isolates. Moreover, the isolates belonged to clonal complexes associated with the acquisition of pathogenicity islands and antimicrobial resistance genes by recombination and horizontal gene transfer. Bacteriophages vB_SauM_LM12, vB_EfaS_LM99 and vB_EcoM_JB75 were characterised and their ability to infect clinical isolates of S. aureus, E. faecalis and E. coli, respectively, was assessed. Morphological and genomic analyses revealed that vB_EfaS_LM99 and vB_EcoM_JB75 belong to the Siphoviridae and Myoviridae families, respectively, and no genes associated with lysogeny were found. The bacteriophages showed low latent periods, high burst sizes, broad host ranges and tolerance to several environmental conditions. Moreover, they showed high efficiency and specificity to infect and reduce clinical bacteria, including methicillin-resistant S. aureus and vancomycin-resistant enterococci. Therefore, the results obtained suggest that the bacteriophages used in this work are a promising approach to control these pathogens involved in orthopaedic implant-associated infections.
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Affiliation(s)
- Joana Barros
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB-Instituto Nacional de Engenharia Biomédica, Porto, Portugal; FEUP-Faculdade de Engenharia, Universidade do Porto, Porto, Portugal.
| | - Luís D R Melo
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Patrícia Poeta
- Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; LAQV‑REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - Gilberto Igrejas
- LAQV‑REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Maria P Ferraz
- FP-ENAS/CEBIMED-University Fernando Pessoa Energy, Environment and Health Research Unit/Biomedical Research Center, Porto, Portugal
| | - Joana Azeredo
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Fernando J Monteiro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB-Instituto Nacional de Engenharia Biomédica, Porto, Portugal; FEUP-Faculdade de Engenharia, Universidade do Porto, Porto, Portugal
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41
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Efficacy and safety assessment of two enterococci phages in an in vitro biofilm wound model. Sci Rep 2019; 9:6643. [PMID: 31040333 PMCID: PMC6491613 DOI: 10.1038/s41598-019-43115-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/18/2019] [Indexed: 01/22/2023] Open
Abstract
Chronic wounds affect thousands of people worldwide, causing pain and discomfort to patients and represent significant economical burdens to health care systems. The treatment of chronic wounds is very difficult and complex, particularly when wounds are colonized by bacterial biofilms which are highly tolerant to antibiotics. Enterococcus faecium and Enterococcus faecalis are within the most frequent bacteria present in chronic wounds. Bacteriophages (phages) have been proposed as an efficient and alternative against antibiotic-resistant infections, as those found in chronic wounds. We have isolated and characterized two novel enterococci phages, the siphovirus vB_EfaS-Zip (Zip) and the podovirus vB_EfaP-Max (Max) to be applied during wound treatment. Both phages demonstrated lytic behavior against E. faecalis and E. faecium. Genome analysis of both phages suggests the absence of genes associated with lysogeny. A phage cocktail containing both phages was tested against biofilms formed in wound simulated conditions at a multiplicity of infection of 1.0 and a 2.5 log CFU.mL−1 reduction in the bacterial load after at 3 h of treatment was observed. Phages were also tested in epithelial cells colonized by these bacterial species and a 3 log CFU.mL−1 reduction was observed using both phages. The high efficacy of these new isolated phages against multi-species biofilms, their stability at different temperatures and pH ranges, short latent periods and non-cytotoxicity to epithelial cells suggest their therapeutic use to control infectious biofilms present in chronic wounds.
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Hyman P. Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth. Pharmaceuticals (Basel) 2019; 12:E35. [PMID: 30862020 PMCID: PMC6469166 DOI: 10.3390/ph12010035] [Citation(s) in RCA: 235] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/20/2019] [Accepted: 03/04/2019] [Indexed: 01/21/2023] Open
Abstract
For a bacteriophage to be useful for phage therapy it must be both isolated from the environment and shown to have certain characteristics beyond just killing strains of the target bacterial pathogen. These include desirable characteristics such as a relatively broad host range and a lack of other characteristics such as carrying toxin genes and the ability to form a lysogen. While phages are commonly isolated first and subsequently characterized, it is possible to alter isolation procedures to bias the isolation toward phages with desirable characteristics. Some of these variations are regularly used by some groups while others have only been shown in a few publications. In this review I will describe (1) isolation procedures and variations that are designed to isolate phages with broader host ranges, (2) characterization procedures used to show that a phage may have utility in phage therapy, including some of the limits of such characterization, and (3) results of a survey and discussion with phage researchers in industry and academia on the practice of characterization of phages.
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Affiliation(s)
- Paul Hyman
- Department of Biology/Toxicology, Ashland University, 401 College Ave., Ashland, OH 44805, USA.
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43
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van Zyl LJ, Abrahams Y, Stander EA, Kirby-McCollough B, Jourdain R, Clavaud C, Breton L, Trindade M. Novel phages of healthy skin metaviromes from South Africa. Sci Rep 2018; 8:12265. [PMID: 30115980 PMCID: PMC6095929 DOI: 10.1038/s41598-018-30705-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 07/27/2018] [Indexed: 12/15/2022] Open
Abstract
Recent skin metagenomic studies have investigated the harbored viral diversity and its possible influence on healthy skin microbial populations, and tried to establish global patterns of skin-phage evolution. However, the detail associated with the phages that potentially play a role in skin health has not been investigated. While skin metagenome and -metavirome studies have indicated that the skin virome is highly site specific and shows marked interpersonal variation, they have not assessed the presence/absence of individual phages. Here, we took a semi-culture independent approach (metaviromic) to better understand the composition of phage communities on skin from South African study participants. Our data set adds over 130 new phage species of the skin to existing databases. We demonstrated that identical phages were present on different individuals and in different body sites, and we conducted a detailed analysis of the structural organization of these phages. We further found that a bacteriophage related to the Staphylococcus capitis phage Stb20 may be a common skin commensal virus potentially regulating its host and its activities on the skin.
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Affiliation(s)
- Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa.
| | - Yoonus Abrahams
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
| | - Emily Amor Stander
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
| | - Bronwyn Kirby-McCollough
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
| | - Roland Jourdain
- L'Oréal Research and Innovation, 1 Avenue Eugène Schueller, 93600, Aulnay sous Bois, France
| | - Cécile Clavaud
- L'Oréal Research and Innovation, 1 Avenue Eugène Schueller, 93600, Aulnay sous Bois, France
| | - Lionel Breton
- L'Oréal Research and Innovation, 1 Avenue Eugène Schueller, 93600, Aulnay sous Bois, France
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
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44
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Milho C, Silva MD, Melo L, Santos S, Azeredo J, Sillankorva S. Control of Salmonella Enteritidis on food contact surfaces with bacteriophage PVP-SE2. BIOFOULING 2018; 34:753-768. [PMID: 30270665 DOI: 10.1080/08927014.2018.1501475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
Salmonella is one of the worldwide leading foodborne pathogens responsible for illnesses and hospitalizations, and its capacity to form biofilms is one of its many virulence factors. This work evaluated (bacterio)phage control of adhered and biofilm cells of Salmonella Enteritidis on three different substrata at refrigerated and room temperatures, and also a preventive approach in poultry skin. PVP-SE2 phage was efficient in reducing both 24- and 48-h old Salmonella biofilms from polystyrene and stainless steel causing 2 to 5 log CFU cm-2 reductions with a higher killing efficiency at room temperature. PVP-SE2 phage application on poultry skins reduced levels of Salmonella. Freezing phage-pretreated poultry skin samples had no influence on the viability of phage PVP-SE2 and their in vitro contamination with S. Enteritidis provided evidence that phages prevented their further growth. Although not all conditions favor phage treatment, this study endorses their use to prevent and control foodborne pathogen colonization of surfaces.
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Affiliation(s)
- Catarina Milho
- a Centre of Biological Engineering , LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho , Braga , Portugal
| | - Maria Daniela Silva
- a Centre of Biological Engineering , LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho , Braga , Portugal
| | - Luís Melo
- a Centre of Biological Engineering , LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho , Braga , Portugal
| | - Sílvio Santos
- a Centre of Biological Engineering , LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho , Braga , Portugal
| | - Joana Azeredo
- a Centre of Biological Engineering , LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho , Braga , Portugal
| | - Sanna Sillankorva
- a Centre of Biological Engineering , LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho , Braga , Portugal
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45
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Melo LDR, França A, Brandão A, Sillankorva S, Cerca N, Azeredo J. Assessment of Sep1virus interaction with stationary cultures by transcriptional and flow cytometry studies. FEMS Microbiol Ecol 2018; 94:5061119. [DOI: 10.1093/femsec/fiy143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/26/2018] [Indexed: 12/24/2022] Open
Affiliation(s)
- Luís D R Melo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - Angela França
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - Ana Brandão
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - Sanna Sillankorva
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - Nuno Cerca
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
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46
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Melo LDR, Brandão A, Akturk E, Santos SB, Azeredo J. Characterization of a New Staphylococcus aureus Kayvirus Harboring a Lysin Active against Biofilms. Viruses 2018; 10:v10040182. [PMID: 29642449 PMCID: PMC5923476 DOI: 10.3390/v10040182] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/29/2018] [Accepted: 04/04/2018] [Indexed: 12/15/2022] Open
Abstract
Staphylococcus aureus is one of the most relevant opportunistic pathogens involved in many biofilm-associated diseases, and is a major cause of nosocomial infections, mainly due to the increasing prevalence of multidrug-resistant strains. Consequently, alternative methods to eradicate the pathogen are urgent. It has been previously shown that polyvalent staphylococcal kayviruses and their derived endolysins are excellent candidates for therapy. Here we present the characterization of a new bacteriophage: vB_SauM-LM12 (LM12). LM12 has a broad host range (>90%; 56 strains tested), and is active against several MRSA strains. The genome of LM12 is composed of a dsDNA molecule with 143,625 bp, with average GC content of 30.25% and codes for 227 Coding Sequences (CDSs). Bioinformatics analysis did not identify any gene encoding virulence factors, toxins, or antibiotic resistance determinants. Antibiofilm assays have shown that this phage significantly reduced the number of viable cells (less than one order of magnitude). Moreover, the encoded endolysin also showed activity against biofilms, with a consistent biomass reduction during prolonged periods of treatment (of about one order of magnitude). Interestingly, the endolysin was shown to be much more active against stationary-phase cells and suspended biofilm cells than against intact and scraped biofilms, suggesting that cellular aggregates protected by the biofilm matrix reduced protein activity. Both phage LM12 and its endolysin seem to have a strong antimicrobial effect and broad host range against S. aureus, suggesting their potential to treat S. aureus biofilm infections.
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Affiliation(s)
- Luís D R Melo
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057, Braga, Portugal.
| | - Ana Brandão
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057, Braga, Portugal.
| | - Ergun Akturk
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057, Braga, Portugal.
| | - Silvio B Santos
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057, Braga, Portugal.
| | - Joana Azeredo
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057, Braga, Portugal.
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47
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Oliveira A, Ribeiro HG, Silva AC, Silva MD, Sousa JC, Rodrigues CF, Melo LDR, Henriques AF, Sillankorva S. Synergistic Antimicrobial Interaction between Honey and Phage against Escherichia coli Biofilms. Front Microbiol 2017; 8:2407. [PMID: 29276503 PMCID: PMC5727068 DOI: 10.3389/fmicb.2017.02407] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/20/2017] [Indexed: 01/21/2023] Open
Abstract
Chronic wounds afford a hostile environment of damaged tissues that allow bacterial proliferation and further wound colonization. Escherichia coli is among the most common colonizers of infected wounds and it is a prolific biofilm former. Living in biofilm communities, cells are protected, become more difficult to control and eradicate, and less susceptible to antibiotic therapy. This work presents insights into the proceedings triggering E. coli biofilm control with phage, honey, and their combination, achieved through standard antimicrobial activity assays, zeta potential and flow cytometry studies and further visual insights sought by scanning electron microscopy and transmission electron microscopy. Two Portuguese honeys (PF2 and U3) with different floral origin and an E. coli-specific phage (EC3a), possessing depolymerase activity, were tested against 24- and 48-h-old biofilms. Synergic and additive effects were perceived in some phage–honey experiments. Combined therapy prompted similar phenomena in biofilm cells, visualized by electron microscopy, as the individual treatments. Honey caused minor membrane perturbations to complete collapse and consequent discharge of cytoplasmic content, and phage completely destroyed cells leaving only vesicle-like structures and debris. Our experiments show that the addition of phage to low honey concentrations is advantageous, and that even fourfold diluted honey combined with phage, presents no loss of antibacterial activity toward E. coli. Portuguese honeys possess excellent antibiofilm activity and may be potential alternative therapeutic agents in biofilm-related wound infection. Furthermore, to our knowledge this is the first study that assessed the impacts of phage–honey combinations in bacterial cells. The synergistic effect obtained was shown to be promising, since the antiviral effect of honey limits the emergence of phage resistant phenotypes.
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Affiliation(s)
- Ana Oliveira
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Henrique G Ribeiro
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ana C Silva
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Maria D Silva
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Jessica C Sousa
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Célia F Rodrigues
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Luís D R Melo
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ana F Henriques
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Sanna Sillankorva
- LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
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48
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Phage mobility is a core determinant of phage-bacteria coexistence in biofilms. ISME JOURNAL 2017; 12:531-543. [PMID: 29125597 PMCID: PMC5776469 DOI: 10.1038/ismej.2017.190] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/17/2017] [Accepted: 09/26/2017] [Indexed: 12/12/2022]
Abstract
Many bacteria are adapted for attaching to surfaces and for building complex communities, termed biofilms. The biofilm mode of life is predominant in bacterial ecology. So too is the exposure of bacteria to ubiquitous viral pathogens, termed bacteriophages. Although biofilm-phage encounters are likely to be common in nature, little is known about how phages might interact with biofilm-dwelling bacteria. It is also unclear how the ecological dynamics of phages and their hosts depend on the biological and physical properties of the biofilm environment. To make headway in this area, we develop a biofilm simulation framework that captures key mechanistic features of biofilm growth and phage infection. Using these simulations, we find that the equilibrium state of interaction between biofilms and phages is governed largely by nutrient availability to biofilms, infection likelihood per host encounter and the ability of phages to diffuse through biofilm populations. Interactions between the biofilm matrix and phage particles are thus likely to be of fundamental importance, controlling the extent to which bacteria and phages can coexist in natural contexts. Our results open avenues to new questions of host-parasite coevolution and horizontal gene transfer in spatially structured biofilm contexts.
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49
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Melo LDR, Veiga P, Cerca N, Kropinski AM, Almeida C, Azeredo J, Sillankorva S. Development of a Phage Cocktail to Control Proteus mirabilis Catheter-associated Urinary Tract Infections. Front Microbiol 2016; 7:1024. [PMID: 27446059 PMCID: PMC4923195 DOI: 10.3389/fmicb.2016.01024] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/16/2016] [Indexed: 11/13/2022] Open
Abstract
Proteus mirabilis is an enterobacterium that causes catheter-associated urinary tract infections (CAUTIs) due to its ability to colonize and form crystalline biofilms on the catheters surface. CAUTIs are very difficult to treat, since biofilm structures are highly tolerant to antibiotics. Phages have been used widely to control a diversity of bacterial species, however, a limited number of phages for P. mirabilis have been isolated and studied. Here we report the isolation of two novel virulent phages, the podovirus vB_PmiP_5460 and the myovirus vB_PmiM_5461, which are able to target, respectively, 16 of the 26 and all the Proteus strains tested in this study. Both phages have been characterized thoroughly and sequencing data revealed no traces of genes associated with lysogeny. To further evaluate the phages’ ability to prevent catheter’s colonization by Proteus, the phages adherence to silicone surfaces was assessed. Further tests in phage-coated catheters using a dynamic biofilm model simulating CAUTIs, have shown a significant reduction of P. mirabilis biofilm formation up to 168 h of catheterization. These results highlight the potential usefulness of the two isolated phages for the prevention of surface colonization by this bacterium.
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Affiliation(s)
- Luís D R Melo
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga Braga, Portugal
| | - Patrícia Veiga
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga Braga, Portugal
| | - Nuno Cerca
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga Braga, Portugal
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biology, and Pathobiology, University of Guelph, Guelph ON, Canada
| | - Carina Almeida
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga Braga, Portugal
| | - Joana Azeredo
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga Braga, Portugal
| | - Sanna Sillankorva
- Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho Braga Braga, Portugal
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50
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Domingo-Calap P, Georgel P, Bahram S. Back to the future: bacteriophages as promising therapeutic tools. HLA 2016; 87:133-40. [PMID: 26891965 DOI: 10.1111/tan.12742] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 01/18/2016] [Indexed: 01/21/2023]
Abstract
Bacteriophages (phages), natural predators of bacteria, are becoming increasingly attractive in medical and pharmaceutical applications. After their discovery almost a century ago, they have been particularly instrumental in the comprehension of basic molecular biology and genetics processes. The more recent emergence of multi-drug-resistant bacteria requires novel therapeutic strategies, and phages are being (re)considered as promising potential antibacterial tools. Furthermore, phages are also used for other purposes, e.g. vaccine production, gene/drug carriers, bacterial detection and typing. These new alternative approaches using phages are of major interest and have allowed unexpected developments, from the decipherment of fundamental biological processes to potential clinical applications.
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Affiliation(s)
- P Domingo-Calap
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Fédération Hospitalo-Universitaire OMICARE, Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
| | - P Georgel
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Fédération Hospitalo-Universitaire OMICARE, Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
| | - S Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Fédération Hospitalo-Universitaire OMICARE, Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
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