1
|
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.
Collapse
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
| |
Collapse
|
2
|
Elsayed MM, Elkenany RM, Zakari AI, Badawy BM. Isolation and characterization of bacteriophages for combating multidrug-resistant Listeria monocytogenes from dairy cattle farms in conjugation with silver nanoparticles. BMC Microbiol 2023; 23:146. [PMID: 37217869 DOI: 10.1186/s12866-023-02893-y] [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: 07/28/2022] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND This study aims to achieve biocontrol of multidrug-resistant Listeria monocytogenes in dairy cattle farms which poses a severe threat to our socio-economic balance and healthcare systems. METHODS Naturally occurring phages from dairy cattle environments were isolated and characterized, and the antimicrobial effect of isolated L. monocytogenes phages (LMPs) against multidrug-resistant L. monocytogenes strains were assessed alone and in conjugation with silver nanoparticles (AgNPs). RESULTS Six different phenotypic LMPs (LMP1-LMP6) were isolated from silage (n = 4; one by direct phage isolation and three by enrichment method) and manure (n = 2; both by enrichment method) from dairy cattle farms. The isolated phages were categorized into three different families by transmission electron microscopy (TEM): Siphoviridae (LMP1 and LMP5), Myoviridae (LMP2, LMP4, and LMP6), and Podoviridae (LMP3). The host range of the isolated LMPs was determined by the spot method using 22 multidrug-resistant L. monocytogenes strains. All 22 (100%) strains were susceptible to phage infection; 50% (3 out of 6) of the isolated phages showed narrow host ranges, while the other 50% showed moderate host ranges. We found that LMP3 (the phage with the shortest tail) had the ability to infect the widest range of L. monocytogenes strains. Eclipse and latent periods of LMP3 were 5 and 45 min, respectively. The burst size of LMP3 was 25 PFU per infected cell. LMP3 was stable with wide range of pH and temperature. In addition, time-kill curves of LMP3 alone at MOI of 10, 1 and 0.1, AgNPs alone, and LMP3 in combination with AgNPs against the most phage-resistant L. monocytogenes strain (ERIC A) were constructed. Among the five treatments, AgNPs alone had the lowest inhibition activity compared to LMP3 at a multiplicity of infection (MOI) of 0.1, 1, and 10. LMP3 at MOI of 0.1 in conjugation with AgNPs (10 µg/mL) exhibited complete inhibition activity after just 2 h, and the inhibition activity lasted for 24 h treatment. In contrast, the inhibition activity of AgNPs alone and phages alone, even at MOI of 10, stopped. Therefore, the combination of LMP3 and AgNPs enhanced the antimicrobial action and its stability and reduced the required concentrations of LMP3 and AgNPs, which would minimize the development of future resistance. CONCLUSIONS The results suggested that the combination of LMP3 and AgNPs could be used as a powerful and ecofriendly antibacterial agent in the dairy cattle farm environment to overcome multidrug-resistant L. monocytogenes.
Collapse
Affiliation(s)
- Mona M Elsayed
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt.
| | - Rasha M Elkenany
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Amira I Zakari
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Basma M Badawy
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| |
Collapse
|
3
|
Gomez M, Szewczyk A, Szamosi J, Leung V, Filipe C, Hosseinidoust Z. Stress Exposure of Evolved Bacteriophages under Laboratory versus Food Processing Conditions Highlights Challenges in Translatability. Viruses 2022; 15:113. [PMID: 36680153 PMCID: PMC9865000 DOI: 10.3390/v15010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/15/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Bacterial viruses, or bacteriophages, are highly potent, target-specific antimicrobials. Bacteriophages can be safely applied along the food production chain to aid control of foodborne pathogens. However, bacteriophages are often sensitive to the environments encountered in food matrices and under processing conditions, thus limiting their applicability. We sought to address this challenge by exposing commercially available Listeria monocytogenes bacteriophage, P100, to three stress conditions: desiccation, elevated temperature, and low pH, to select for stress-resistant bacteriophages. The stressed bacteriophage populations lost up to 5.1 log10 in infectivity; however, the surviving subpopulation retained their stress-resistant phenotype through five passages with a maximum of 2.0 log10 loss in infectivity when exposed to the same stressor. Sequencing identified key mutation regions but did not reveal a clear mechanism of resistance. The stress-selected bacteriophage populations effectively suppressed L. monocytogenes growth at a modest multiplicity of infection of 0.35-0.43, indicating no trade-off in lytic ability in return for improved survivability. The stressed subpopulations were tested for survival on food grade stainless steel, during milk pasteurization, and within acidic beverages. Interestingly, air drying on stainless steel and pasteurization in milk led to significantly less stress and titer loss in bacteriophage compared to similar stress under model lab conditions. This led to a diminished benefit for stress-selection, thus highlighting a major challenge in real-life translatability of bacteriophage adaptational evolution.
Collapse
Affiliation(s)
- Mellissa Gomez
- Department of Chemical Engineering, McMaster University, Hamilton, ON L8S 4L7, Canada
| | - Alexandra Szewczyk
- Department of Chemical Engineering, McMaster University, Hamilton, ON L8S 4L7, Canada
| | - Jake Szamosi
- Department of Medicine, McMaster University, Hamilton, ON L8P 1H6, Canada
| | - Vincent Leung
- Department of Chemical Engineering, McMaster University, Hamilton, ON L8S 4L7, Canada
| | - Carlos Filipe
- Department of Chemical Engineering, McMaster University, Hamilton, ON L8S 4L7, Canada
| | - Zeinab Hosseinidoust
- Department of Chemical Engineering, McMaster University, Hamilton, ON L8S 4L7, Canada
- School of Biomedical Engineering, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| |
Collapse
|
4
|
Buttimer C, Sutton T, Colom J, Murray E, Bettio PH, Smith L, Bolocan AS, Shkoporov A, Oka A, Liu B, Herzog JW, Sartor RB, Draper LA, Ross RP, Hill C. Impact of a phage cocktail targeting Escherichia coli and Enterococcus faecalis as members of a gut bacterial consortium in vitro and in vivo. Front Microbiol 2022; 13:936083. [PMID: 35935217 PMCID: PMC9355613 DOI: 10.3389/fmicb.2022.936083] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/01/2022] [Indexed: 01/14/2023] Open
Abstract
Escherichia coli and Enterococcus faecalis have been implicated as important players in human gut health that have been associated with the onset of inflammatory bowel disease (IBD). Bacteriophage (phage) therapy has been used for decades to target pathogens as an alternative to antibiotics, but the ability of phage to shape complex bacterial consortia in the lower gastrointestinal tract is not clearly understood. We administered a cocktail of six phages (either viable or heat-inactivated) targeting pro-inflammatory Escherichia coli LF82 and Enterococcus faecalis OG1RF as members of a defined community in both a continuous fermenter and a murine colitis model. The two target strains were members of a six species simplified human microbiome consortium (SIHUMI-6). In a 72-h continuous fermentation, the phage cocktail caused a 1.1 and 1.5 log (log10 genome copies/mL) reduction in E. faecalis and E. coli numbers, respectively. This interaction was accompanied by changes in the numbers of other SIHUMI-6 members, with an increase of Lactiplantibacillus plantarum (1.7 log) and Faecalibacterium prausnitzii (1.8 log). However, in germ-free mice colonized by the same bacterial consortium, the same phage cocktail administered twice a week over nine weeks did not cause a significant reduction of the target strains. Mice treated with active or inactive phage had similar levels of pro-inflammatory cytokines (IFN-y/IL12p40) in unstimulated colorectal colonic strip cultures. However, histology scores of the murine lower GIT (cecum and distal colon) were lower in the viable phage-treated mice, suggesting that the phage cocktail did influence the functionality of the SIHUMI-6 consortium. For this study, we conclude that the observed potential of phages to reduce host populations in in vitro models did not translate to a similar outcome in an in vivo setting, with this effect likely brought about by the reduction of phage numbers during transit of the mouse GIT.
Collapse
Affiliation(s)
- Colin Buttimer
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Tom Sutton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Joan Colom
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ellen Murray
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Pedro H. Bettio
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Linda Smith
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | | | - Akihiko Oka
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Internal Medicine II, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Bo Liu
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeremy W. Herzog
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - R. Balfour Sartor
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
5
|
Erickson S, Paulson J, Brown M, Hahn W, Gil J, Barron-Montenegro R, Moreno-Switt AI, Eisenberg M, Nguyen MM. Isolation and engineering of a Listeria grayi bacteriophage. Sci Rep 2021; 11:18947. [PMID: 34556683 PMCID: PMC8460666 DOI: 10.1038/s41598-021-98134-1] [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] [Received: 03/10/2021] [Accepted: 09/03/2021] [Indexed: 01/02/2023] Open
Abstract
The lack of bacteriophages capable of infecting the Listeria species, Listeria grayi, is academically intriguing and presents an obstacle to the development of bacteriophage-based technologies for Listeria. We describe the isolation and engineering of a novel L. grayi bacteriophage, LPJP1, isolated from farm silage. With a genome over 200,000 base pairs, LPJP1 is the first and only reported jumbo bacteriophage infecting the Listeria genus. Similar to other Gram-positive jumbo phages, LPJP1 appeared to contain modified base pairs, which complicated initial attempts to obtain genomic sequence using standard methods. Following successful sequencing with a modified approach, a recombinant of LPJP1 encoding the NanoLuc luciferase was engineered using homologous recombination. This luciferase reporter bacteriophage successfully detected 100 stationary phase colony forming units of both subspecies of L. grayi in four hours. A single log phase colony forming unit was also sufficient for positive detection in the same time period. The recombinant demonstrated complete specificity for this particular Listeria species and did not infect 150 non-L. grayi Listeria strains nor any other bacterial genus. LPJP1 is believed to be the first reported lytic bacteriophage of L. grayi as well as the only jumbo bacteriophage to be successfully engineered into a luciferase reporter.
Collapse
Affiliation(s)
- Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA.
| | - John Paulson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Wendy Hahn
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA, 90062, USA
| | - Rocío Barron-Montenegro
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Marcia Eisenberg
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Minh M Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| |
Collapse
|
6
|
Ramos-Vivas J, Elexpuru-Zabaleta M, Samano ML, Barrera AP, Forbes-Hernández TY, Giampieri F, Battino M. Phages and Enzybiotics in Food Biopreservation. Molecules 2021; 26:molecules26175138. [PMID: 34500572 PMCID: PMC8433972 DOI: 10.3390/molecules26175138] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/27/2022] Open
Abstract
Presently, biopreservation through protective bacterial cultures and their antimicrobial products or using antibacterial compounds derived from plants are proposed as feasible strategies to maintain the long shelf-life of products. Another emerging category of food biopreservatives are bacteriophages or their antibacterial enzymes called "phage lysins" or "enzybiotics", which can be used directly as antibacterial agents due to their ability to act on the membranes of bacteria and destroy them. Bacteriophages are an alternative to antimicrobials in the fight against bacteria, mainly because they have a practically unique host range that gives them great specificity. In addition to their potential ability to specifically control strains of pathogenic bacteria, their use does not generate a negative environmental impact as in the case of antibiotics. Both phages and their enzymes can favor a reduction in antibiotic use, which is desirable given the alarming increase in resistance to antibiotics used not only in human medicine but also in veterinary medicine, agriculture, and in general all processes of manufacturing, preservation, and distribution of food. We present here an overview of the scientific background of phages and enzybiotics in the food industry, as well as food applications of these biopreservatives.
Collapse
Affiliation(s)
- José Ramos-Vivas
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | - María Elexpuru-Zabaleta
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
| | - María Luisa Samano
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | - Alina Pascual Barrera
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | | | - Francesca Giampieri
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (F.G.); (M.B.); Tel.: +339-071-220-4136 (F.G.); +339-071-220-4646 (M.B.)
| | - Maurizio Battino
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Correspondence: (F.G.); (M.B.); Tel.: +339-071-220-4136 (F.G.); +339-071-220-4646 (M.B.)
| |
Collapse
|
7
|
Song Y, Peters TL, Bryan DW, Hudson LK, Denes TG. Characterization of a Novel Group of Listeria Phages That Target Serotype 4b Listeria monocytogenes. Viruses 2021; 13:v13040671. [PMID: 33919793 PMCID: PMC8070769 DOI: 10.3390/v13040671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/26/2021] [Accepted: 04/10/2021] [Indexed: 12/19/2022] Open
Abstract
Listeria monocytogenes serotype 4b strains are the most prevalent clinical isolates and are widely found in food processing environments. Bacteriophages are natural viral predators of bacteria and are a promising biocontrol agent for L. monocytogenes. The aims of this study were to characterize phages that specifically infect serotype 4b strains and to assess their ability to inhibit the growth of serotype 4b strains. Out of 120 wild Listeria phages, nine phages were selected based on their strong lytic activity against the model serotype 4b strain F2365. These nine phages can be divided into two groups based on their morphological characteristics and host range. Comparison to previously characterized phage genomes revealed one of these groups qualifies to be defined as a novel species. Phages LP-020, LP-027, and LP-094 were selected as representatives of these two groups of phages for further characterization through one-step growth curve and inhibition of serotype 4b L. monocytogenes experiments. Listeria phages that target serotype 4b showed an inhibitory effect on the growth of F2365 and other serotype 4 strains and may be useful for biocontrol of L.monocytogenes in food processing environments.
Collapse
|
8
|
Gradaschi V, Payaslian F, Dieterle ME, Rondón Salazar L, Urdániz E, Di Paola M, Peña Cárcamo J, Zon F, Allievi M, Sosa E, Fernandez Do Porto D, Dunne M, Goeller P, Klumpp J, Raya RR, Reyes A, Piuri M. Genome Sequence and Characterization of Lactobacillus casei Phage, vB_LcaM_Lbab1 Isolated from Raw Milk. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:57-63. [PMID: 36148441 PMCID: PMC9041484 DOI: 10.1089/phage.2020.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Introduction: Only a few Lactobacillus casei phages have so far been characterized. As several L. casei strains are part of probiotic formulations, bacteriophage outbreaks targeting these strains can lead to critical losses within the dairy industry. Materials and Methods: A new L. casei phage was isolated from raw milk obtained from a milking yard from the province of Buenos Aires. The phage genome was sequenced, annotated, and analyzed. Morphology was determined by electron microscopy and the host range was established. Results: Lactobacillus phage vB_LcaM_Lbab1 is a member of the Herelleviridae family and features a host range including L. casei/Lactobacillus paracasei and Lactobacillus kefiri strains. We further analyzed the baseplate proteins in silico and found putative carbohydrate binding modules that are responsible for host recognition in other Lactobacillus phages. Conclusions: A new Lactobacillus phage was isolated and characterized. The focus was made on its host recognition mechanism, pointing toward the development of future strategies to avoid deleterious infections in the dairy industry.
Collapse
Affiliation(s)
- Victoria Gradaschi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Florencia Payaslian
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Maria Eugenia Dieterle
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Liliana Rondón Salazar
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Estefanía Urdániz
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Matias Di Paola
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - José Peña Cárcamo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Fabio Zon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Mariana Allievi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Ezequiel Sosa
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Darío Fernandez Do Porto
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Pauline Goeller
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| |
Collapse
|
9
|
Blanco Fernandez MD, Klumpp J, Barrios ME, Mbayed VA. Gene gain and loss and recombination shape evolution of Listeria bacteriophages of the genus Pecentumvirus. Genomics 2020; 113:411-419. [PMID: 33301894 DOI: 10.1016/j.ygeno.2020.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 11/20/2020] [Accepted: 12/04/2020] [Indexed: 12/27/2022]
Abstract
Listeria monocytogenes is an important food-borne pathogen and its bacteriophages are promising tools for its control in food and surfaces. Listeria bacteriophages belonging to the genus Pecentumvirus of the family Herelleviridae are strictly lytic, have a contractile tail and a large double stranded DNA genome (mean of 135.4 kb). We report the isolation and genome sequences of two new Pecentumvirus bacteriophages: vB_Lino_VEfB7 and vB_Liva_VAfA18. Twenty-one bacteriophages of this genus have been described and their genomes were used for the study of Pecentumvirus evolution. Analyses showed collinear genomes and gene gain and loss propensity and recombination events were distinctly found in two regions. A large potential recombination event (≈20 kB) was detected in P100 and vB_Liva_VAfA18. Phylogenetic analyses of multi-gene alignments showed that diversification events formed two groups of species distantly related.
Collapse
Affiliation(s)
- María Dolores Blanco Fernandez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Melina E Barrios
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Viviana A Mbayed
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| |
Collapse
|
10
|
Huang L, Xiang Y. Structures of the tailed bacteriophages that infect Gram-positive bacteria. Curr Opin Virol 2020; 45:65-74. [DOI: 10.1016/j.coviro.2020.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/07/2020] [Accepted: 09/06/2020] [Indexed: 01/04/2023]
|
11
|
Stone E, Lhomet A, Neve H, Grant IR, Campbell K, McAuliffe O. Isolation and Characterization of Listeria monocytogenes Phage vB_LmoH_P61, a Phage With Biocontrol Potential on Different Food Matrices. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.521645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
12
|
Mutant and Recombinant Phages Selected from In Vitro Coevolution Conditions Overcome Phage-Resistant Listeria monocytogenes. Appl Environ Microbiol 2020; 86:AEM.02138-20. [PMID: 32887717 DOI: 10.1128/aem.02138-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Bacteriophages (phages) are currently available for use by the food industry to control the foodborne pathogen Listeria monocytogenes Although phage biocontrols are effective under specific conditions, their use can select for phage-resistant bacteria that repopulate phage-treated environments. Here, we performed short-term coevolution experiments to investigate the impact of single phages and a two-phage cocktail on the regrowth of phage-resistant L. monocytogenes and the adaptation of the phages to overcome this resistance. We used whole-genome sequencing to identify mutations in the target host that confer phage resistance and in the phages that alter host range. We found that infections with Listeria phages LP-048, LP-125, or a combination of both select for different populations of phage-resistant L. monocytogenes bacteria with different regrowth times. Phages isolated from the end of the coevolution experiments were found to have gained the ability to infect phage-resistant mutants of L. monocytogenes and L. monocytogenes strains previously found to be broadly resistant to phage infection. Phages isolated from coinfected cultures were identified as recombinants of LP-048 and LP-125. Interestingly, recombination events occurred twice independently in a locus encoding two proteins putatively involved in DNA binding. We show that short-term coevolution of phages and their hosts can be utilized to obtain mutant and recombinant phages with adapted host ranges. These laboratory-evolved phages may be useful for limiting the emergence of phage resistance and for targeting strains that show general resistance to wild-type (WT) phages.IMPORTANCE Listeria monocytogenes is a life-threatening bacterial foodborne pathogen that can persist in food processing facilities for years. Phages can be used to control L. monocytogenes in food production, but phage-resistant bacterial subpopulations can regrow in phage-treated environments. Coevolution experiments were conducted on a Listeria phage-host system to provide insight into the genetic variation that emerges in both the phage and bacterial host under reciprocal selective pressure. As expected, mutations were identified in both phage and host, but additionally, recombination events were shown to have repeatedly occurred between closely related phages that coinfected L. monocytogenes This study demonstrates that in vitro evolution of phages can be utilized to expand the host range and improve the long-term efficacy of phage-based control of L. monocytogenes This approach may also be applied to other phage-host systems for applications in biocontrol, detection, and phage therapy.
Collapse
|
13
|
Núñez-Sánchez MA, Colom J, Walsh L, Buttimer C, Bolocan AS, Pang R, Gahan CGM, Hill C. Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model. Microorganisms 2020; 8:E1374. [PMID: 32906839 PMCID: PMC7563437 DOI: 10.3390/microorganisms8091374] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 12/24/2022] Open
Abstract
An intestinal epithelium model able to produce mucus was developed to provide an environment suitable for testing the therapeutic activity of gut bacteriophages. We show that Enterococcus faecalis adheres more effectively in the presence of mucus, can invade the intestinal epithelia and is able to translocate after damaging tight junctions. Furthermore, Enterococcus phage vB_EfaM_A2 (a member of Herelleviridae that possesses virion associated immunoglobin domains) was found to translocate through the epithelium in the presence and absence of its host bacteria. Phage A2 protected eukaryotic cells by reducing mortality and maintaining the structure of the cell layer structure. We suggest the mammalian cell model utilized within this study as an adaptable in vitro model that can be employed to enable a better understanding of phage-bacteria interactions and the protective impact of phage therapy relating to the intestinal epithelium.
Collapse
Affiliation(s)
- María A. Núñez-Sánchez
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Joan Colom
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Lauren Walsh
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Colin Buttimer
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Andrei Sorin Bolocan
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Rory Pang
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
- School of Pharmacy, University College Cork, T12 YN60 Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
| |
Collapse
|
14
|
Bacteriophage biocontrol to fight Listeria outbreaks in seafood. Food Chem Toxicol 2020; 145:111682. [PMID: 32805341 DOI: 10.1016/j.fct.2020.111682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022]
Abstract
Listeria monocytogenes is a well-known pathogen responsible for the severe foodborne disease listeriosis. The control of L. monocytogenes occurrence in seafood products and seafood processing environments is an important challenge for the seafood industry and the public health sector. However, bacteriophage biocontrol shows great potential to be used as safety control measure in seafood. This review provides an update on Listeria-specific bacteriophages, focusing on their application as a safe and natural strategy to prevent L. monocytogenes contamination and growth in seafood products and seafood processing environments. Furthermore, the main properties required from bacteriophages intended to be used as biocontrol tools are summarized and emerging strategies to overcome the current limitations are considered. Also, major aspects relevant for bacteriophage production at industrial scale, their access to the market, as well as the current regulatory status of bacteriophage-based solutions for Listeria biocontrol are discussed.
Collapse
|
15
|
Buttimer C, Lynch C, Hendrix H, Neve H, Noben JP, Lavigne R, Coffey A. Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. Antibiotics (Basel) 2020; 9:E352. [PMID: 32575906 PMCID: PMC7344957 DOI: 10.3390/antibiotics9060352] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the Escherichia coli sigma70 promoter, which was found to be shared with other genus members. A number of dissimilarities were observed, relating to DNA methylation and nucleotide metabolism. Some members do not have homologues of a cytosine methylase and anaerobic nucleotide reductase subunits NrdD and NrdG, respectively. Furthermore, the genome of CB7 contains one of the largest numbers of homing endonucleases described in a single phage genome in the literature to date, with a total of 23 belonging to the HNH and LAGLIDADG families. Analysis by RT-PCR of the HNH homing endonuclease residing within introns of genes for the large terminase, DNA polymerase, ribonucleotide reductase subunits NrdA and NrdB show that they are splicing competent. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was also performed on the virion of CB7, allowing the identification of 26 structural proteins-20 of which were found to be shared with the type phages of the genera of Vequintavirus and Seunavirus. The results of this study provide greater insights into the phages of the Certrevirus genus as well as the subfamily Vequintavirinae.
Collapse
Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland
| | - Caoimhe Lynch
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
| | - Hanne Hendrix
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (H.H.); (R.L.)
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany;
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, 3590 Hasselt, Belgium;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (H.H.); (R.L.)
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland
| |
Collapse
|
16
|
Glycotyping and Specific Separation of Listeria monocytogenes with a Novel Bacteriophage Protein Tool Kit. Appl Environ Microbiol 2020; 86:AEM.00612-20. [PMID: 32358009 PMCID: PMC7301860 DOI: 10.1128/aem.00612-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022] Open
Abstract
Listeria monocytogenes is a ubiquitous opportunistic pathogen that presents a major concern to the food industry due to its propensity to cause foodborne illness. The Listeria genus contains 15 different serovars, with most of the variance depending on the wall-associated teichoic acid glycopolymers, which confer somatic antigenicity. Strains belonging to serovars 1/2 and 4b cause the vast majority of listeriosis cases and outbreaks, meaning that regulators, as well as the food industry itself, have an interest in rapidly identifying isolates of these particular serovars in food processing environments. Current methods for phenotypic serovar differentiation are slow and lack accuracy, and the food industry could benefit from new technologies allowing serovar-specific isolation. Therefore, the novel method described here for rapid glycotype determination could present a valuable asset to detect and control this bacterium. The Gram-positive pathogen Listeria monocytogenes can be subdivided into at least 12 different serovars, based on the differential expression of a set of somatic and flagellar antigens. Of note, strains belonging to serovars 1/2a, 1/2b, and 4b cause the vast majority of foodborne listeriosis cases and outbreaks. The standard protocol for serovar determination involves an agglutination method using a set of sera containing cell surface-recognizing antibodies. However, this procedure is imperfect in both precision and practicality, due to discrepancies resulting from subjective interpretation. Furthermore, the exact antigenic epitopes remain unclear, due to the preparation of the absorbed sera and the complex nature of polyvalent antibody binding. Here, we present a novel method for quantitative somatic antigen differentiation using a set of recombinant affinity proteins (cell wall-binding domains and receptor-binding proteins) derived from a collection of Listeria bacteriophages. These proteins enable rapid, objective, and precise identification of the different teichoic acid glycopolymer structures, which represent the O-antigens, and allow a near-complete differentiation. This glycotyping approach confirmed serovar designations of over 60 previously characterized Listeria strains. Using select phage receptor-binding proteins coupled to paramagnetic beads, we also demonstrate the ability to specifically isolate serovar 1/2 or 4b cells from a mixed culture. In addition, glycotyping led to the discovery that strains designated serovar 4e actually possess an intermediate 4b-4d teichoic acid glycosylation pattern, underpinning the high discerning power and precision of this novel technique. IMPORTANCEListeria monocytogenes is a ubiquitous opportunistic pathogen that presents a major concern to the food industry due to its propensity to cause foodborne illness. The Listeria genus contains 15 different serovars, with most of the variance depending on the wall-associated teichoic acid glycopolymers, which confer somatic antigenicity. Strains belonging to serovars 1/2 and 4b cause the vast majority of listeriosis cases and outbreaks, meaning that regulators, as well as the food industry itself, have an interest in rapidly identifying isolates of these particular serovars in food processing environments. Current methods for phenotypic serovar differentiation are slow and lack accuracy, and the food industry could benefit from new technologies allowing serovar-specific isolation. Therefore, the novel method described here for rapid glycotype determination could present a valuable asset to detect and control this bacterium.
Collapse
|
17
|
Ahmadi H, Barbut S, Lim LT, Balamurugan S. Examination of the Use of Bacteriophage as an Additive and Determining Its Best Application Method to Control Listeria monocytogenes in a Cooked-Meat Model System. Front Microbiol 2020; 11:779. [PMID: 32670205 PMCID: PMC7326079 DOI: 10.3389/fmicb.2020.00779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/01/2020] [Indexed: 11/13/2022] Open
Abstract
The study examined the efficacy of using bacteriophage as an additive in a cooked-meat model system to control growth of contaminating Listeria monocytogenes during subsequent storage. Studies were designed where Listeria bacteriophage A511 and L. monocytogenes introduced inside or on the surface of the cooked-meat to simulate different bacteriophage application and pathogen contamination scenarios. These scenarios include: (1) A511 and L. monocytogenes in meat; (2) A511 in meat, L. monocytogenes on surface; (3) L. monocytogenes in meat, A511 on surface; and (4) L. monocytogenes followed by A511 on meat surface. Real world bacteriophage application and pathogen contamination levels of 109 PFU/g and 103-4 CFU/g, respectively, were used. These meats were then vacuum packaged and stored at 4°C and changes in A511 titers and L. monocytogenes numbers were enumerated during the 28-day storage. Under the conditions tested, application of A511 directly on top of L. monocytogenes contaminating the surface of the meat was the only scenario where L. monocytogenes numbers were reduced to below detection limits and remained significantly lower than the controls for up to 20 days. Although A511 titers remained stable when applied as an additive in meat, they were not successful in controlling growth of the contaminating L. monocytogenes (present inside or on surface of meat). Similarly, application of A511 on the surface of the meat could not control growth of L. monocytogenes present inside the meat. L. monocytogenes numbers increased from the initial 3-log CFU/g to 9-log CFU/g similar to the controls by the end of the 28-day storage. These results suggest that bacteriophages are effective in controlling growth of surface contaminating bacteria only when applied directly onto the surface of the contaminated food product, and are ineffective as a biocontrol agent when used as an additive.
Collapse
Affiliation(s)
- Hanie Ahmadi
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada.,Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Shai Barbut
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Loong-Tak Lim
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - S Balamurugan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| |
Collapse
|
18
|
Engineered Reporter Phages for Rapid Bioluminescence-Based Detection and Differentiation of Viable Listeria Cells. Appl Environ Microbiol 2020; 86:AEM.00442-20. [PMID: 32245761 PMCID: PMC7237785 DOI: 10.1128/aem.00442-20] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/19/2020] [Indexed: 12/22/2022] Open
Abstract
The pathogen Listeria monocytogenes causes listeriosis, a severe foodborne disease associated with high mortality. Rapid and sensitive methods are required for specific detection of this pathogen during food production. Bioluminescence-based reporter bacteriophages are genetically engineered viruses that infect their host cells with high specificity and transduce a heterologous luciferase gene whose activity can be detected with high sensitivity to indicate the presence of viable target cells. Here, we use synthetic biology for de novo genome assembly and activation as well as CRISPR-Cas-assisted phage engineering to construct a set of reporter phages for the detection and differentiation of viable Listeria cells. Based on a single phage backbone, we compare the performance of four reporter phages that encode different crustacean, cnidarian, and bacterial luciferases. From this panel of reporter proteins, nanoluciferase (NLuc) was identified as a superior enzyme and was subsequently introduced into the genomes of a broad host range phage (A511) and two serovar 1/2- and serovar 4b/6a-specific Listeria phages (A006 and A500, respectively). The broad-range NLuc-based phage A511::nluc CPS detects one CFU of L. monocytogenes in 25 g of artificially contaminated milk, cold cuts, and lettuce within less than 24 h. In addition, this reporter phage successfully detected Listeria spp. in potentially contaminated natural food samples without producing false-positive or false-negative results. Finally, A006::nluc and A500::nluc enable serovar-specific Listeria diagnostics. In conclusion, these NLuc-based reporter phages enable rapid, ultrasensitive detection and differentiation of viable Listeria cells using a simple protocol that is 72 h faster than culture-dependent approaches.IMPORTANCE Culture-dependent methods are the gold standard for sensitive and specific detection of pathogenic bacteria within the food production chain. In contrast to molecular approaches, these methods detect viable cells, which is a key advantage for foods generated from heat-inactivated source material. However, culture-based diagnostics are typically much slower than molecular or proteomic strategies. Reporter phage assays combine the best of both worlds and allow for near online assessment of microbial safety because phage replication is extremely fast, highly target specific, and restricted to metabolically active host cells. In addition, reporter phage assays are inexpensive and do not require highly trained personnel, facilitating their on-site implementation. The reporter phages presented in this study not only allow for rapid detection but also enable an early estimation of the potential virulence of Listeria isolates from food production and processing sites.
Collapse
|
19
|
Hinkley TC, Garing S, Jain P, Williford J, Le Ny ALM, Nichols KP, Peters JE, Talbert JN, Nugen SR. A Syringe-Based Biosensor to Rapidly Detect Low Levels of Escherichia Coli (ECOR13) in Drinking Water Using Engineered Bacteriophages. SENSORS (BASEL, SWITZERLAND) 2020; 20:E1953. [PMID: 32244369 PMCID: PMC7181147 DOI: 10.3390/s20071953] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
A sanitized drinking water supply is an unconditional requirement for public health and the overall prosperity of humanity. Potential microbial and chemical contaminants of drinking water have been identified by a joint effort between the World Health Organization (WHO) and the United Nations Children's Fund (UNICEF), who together establish guidelines that define, in part, that the presence of Escherichia coli (E. coli) in drinking water is an indication of inadequate sanitation and a significant health risk. As E. coli is a nearly ubiquitous resident of mammalian gastrointestinal tracts, no detectable counts in 100 mL of drinking water is the standard used worldwide as an indicator of sanitation. The currently accepted EPA method relies on filtration, followed by growth on selective media, and requires 24-48 h from sample to results. In response, we developed a rapid bacteriophage-based detection assay with detection limit capabilities comparable to traditional methods in less than a quarter of the time. We coupled membrane filtration with selective enrichment using genetically engineered bacteriophages to identify less than 20 colony forming units (CFU) E. coli in 100 mL drinking water within 5 h. The combination of membrane filtration with phage infection produced a novel assay that demonstrated a rapid, selective, and sensitive detection of an indicator organism in large volumes of drinking water as recommended by the leading world regulatory authorities.
Collapse
Affiliation(s)
- Troy C. Hinkley
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Spencer Garing
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Paras Jain
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - John Williford
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Anne-Laure M. Le Ny
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Kevin P. Nichols
- Intellectual Ventures Laboratory/Global Good, Bellevue, WA 98007, USA; (S.G.); (P.J.); (J.W.); (A.-L.M.L.N.); (K.P.N.)
| | - Joseph E. Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA;
| | - Joey N. Talbert
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA;
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| |
Collapse
|
20
|
Sumrall ET, Schefer CRE, Rismondo J, Schneider SR, Boulos S, Gründling A, Loessner MJ, Shen Y. Galactosylated wall teichoic acid, but not lipoteichoic acid, retains InlB on the surface of serovar 4b Listeria monocytogenes. Mol Microbiol 2020; 113:638-649. [PMID: 32185836 PMCID: PMC7155027 DOI: 10.1111/mmi.14455] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 11/20/2022]
Abstract
Listeria monocytogenes is a Gram-positive, intracellular pathogen harboring the surface-associated virulence factor InlB, which enables entry into certain host cells. Structurally diverse wall teichoic acids (WTAs), which can also be differentially glycosylated, determine the antigenic basis of the various Listeria serovars. WTAs have many physiological functions; they can serve as receptors for bacteriophages, and provide a substrate for binding of surface proteins such as InlB. In contrast, the membrane-anchored lipoteichoic acids (LTAs) do not show significant variation and do not contribute to serovar determination. It was previously demonstrated that surface-associated InlB non-covalently adheres to both WTA and LTA, mediating its retention on the cell wall. Here, we demonstrate that in a highly virulent serovar 4b strain, two genes gtlB and gttB are responsible for galactosylation of LTA and WTA respectively. We evaluated the InlB surface retention in mutants lacking each of these two genes, and found that only galactosylated WTA is required for InlB surface presentation and function, cellular invasiveness and phage adsorption, while galactosylated LTA plays no role thereof. Our findings demonstrate that a simple pathogen-defining serovar antigen, that mediates bacteriophage susceptibility, is necessary and sufficient to sustain the function of an important virulence factor.
Collapse
Affiliation(s)
- Eric T Sumrall
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Jeanine Rismondo
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | | | - Samy Boulos
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
21
|
Kiani AK, Anpilogov K, Dautaj A, Marceddu G, Sonna WN, Percio M, Dundar M, Beccari T, Bertelli M. Bacteriophages in food supplements obtained from natural sources. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:e2020025. [PMID: 33170168 PMCID: PMC8023131 DOI: 10.23750/abm.v91i13-s.10834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 11/09/2022]
Abstract
Human gastrointestinal tract is colonized by bacteria that constitute the interstinal microbiota. Changes in the microbiota may lead to several chronic disorders. Bacteriophages are viruses that specifically target bacteria. Several food components contain bacteriophages and probiotics. Bacteriophages have a great specificity for harmful bacteria, helping the growth of good bacteria. Because of their qualities, bacteriophages are considered beneficial component of probiotics that target the pathogenic bacteria and support the natural human microbiota.
Collapse
Affiliation(s)
- Aysha Karim Kiani
- Allama Iqbal Open University, Islamabad, Pakistan, MAGI EUREGIO, Bolzano, Italy
| | | | | | | | | | | | - Munis Dundar
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Tommaso Beccari
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Matteo Bertelli
- MAGI EUREGIO, Bolzano, Italy, EBTNA-LAB, Rovereto (TN), Italy, MAGI’S LAB, Rovereto (TN), Italy
| |
Collapse
|
22
|
Double Tubular Contractile Structure of the Type VI Secretion System Displays Striking Flexibility and Elasticity. J Bacteriol 2019; 202:JB.00425-19. [PMID: 31636107 DOI: 10.1128/jb.00425-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial treatment can induce many bacterial pathogens to enter a cell wall-deficient state that contributes to persistent infections. The effect of this physiological state on the assembly of transenvelope-anchored organelles is not well understood. The type VI secretion system (T6SS) is a widespread molecular weapon for interspecies interactions and virulence, comprising a long double tubular structure and a transenvelope/baseplate complex. Here, we report that cell wall-deficient spheroplasts assembled highly flexible and elastic T6SS structures forming U, O, or S shapes. Upon contacting the inner membrane, the T6SS tubes did not contract but rather continued to grow along the membrane. Such deformation likely results from continual addition of sheath/tube subunits at the distal end. Induction of TagA repressed curved sheath formation. Curved sheaths could also contract and deliver T6SS substrates and were readily disassembled by the ClpV ATPase after contraction. Our data highlight the dramatic effect of cell wall deficiency on the shape of the T6SS structures and reveal the elastic nature of this double tubular contractile injection nanomachine.IMPORTANCE The cell wall is a physical scaffold that all transenvelope complexes have to cross for assembly. However, the cell wall-deficient state has been described as a common condition found in both Gram-negative and Gram-positive pathogens during persistent infections. Loss of cell wall is known to have pleiotropic physiological effects, but how membrane-anchored large cellular organelles adapt to this unique state is less completely understood. Our study examined the assembly of the T6SS in cell wall-deficient spheroplast cells. We report the elastic nature of contractile T6SS tubules under such conditions, providing key insights for understanding how large intracellular structures such as the T6SS accommodate the multifaceted changes in cell wall-deficient cells.
Collapse
|
23
|
Complete Genome Sequences of Two Listeria Phages of the Genus Pecentumvirus. Microbiol Resour Announc 2019; 8:8/46/e01229-19. [PMID: 31727716 PMCID: PMC6856282 DOI: 10.1128/mra.01229-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages isolated from environmental sources can be used as a biocontrol against the foodborne pathogen Listeria monocytogenes Here, we present the complete genomes of LP-039 and LP-066, two Pecentumvirus bacteriophages that infect L. monocytogenes The genome sizes of LP-039 and LP-066 are 136.2 kb and 139.0 kb, respectively.
Collapse
|
24
|
Sumrall ET, Shen Y, Keller AP, Rismondo J, Pavlou M, Eugster MR, Boulos S, Disson O, Thouvenot P, Kilcher S, Wollscheid B, Cabanes D, Lecuit M, Gründling A, Loessner MJ. Phage resistance at the cost of virulence: Listeria monocytogenes serovar 4b requires galactosylated teichoic acids for InlB-mediated invasion. PLoS Pathog 2019; 15:e1008032. [PMID: 31589660 PMCID: PMC6779246 DOI: 10.1371/journal.ppat.1008032] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/15/2019] [Indexed: 01/13/2023] Open
Abstract
The intracellular pathogen Listeria monocytogenes is distinguished by its ability to invade and replicate within mammalian cells. Remarkably, of the 15 serovars within the genus, strains belonging to serovar 4b cause the majority of listeriosis clinical cases and outbreaks. The Listeria O-antigens are defined by subtle structural differences amongst the peptidoglycan-associated wall-teichoic acids (WTAs), and their specific glycosylation patterns. Here, we outline the genetic determinants required for WTA decoration in serovar 4b L. monocytogenes, and demonstrate the exact nature of the 4b-specific antigen. We show that challenge by bacteriophages selects for surviving clones that feature mutations in genes involved in teichoic acid glycosylation, leading to a loss of galactose from both wall teichoic acid and lipoteichoic acid molecules, and a switch from serovar 4b to 4d. Surprisingly, loss of this galactose decoration not only prevents phage adsorption, but leads to a complete loss of surface-associated Internalin B (InlB),the inability to form actin tails, and a virulence attenuation in vivo. We show that InlB specifically recognizes and attaches to galactosylated teichoic acid polymers, and is secreted upon loss of this modification, leading to a drastically reduced cellular invasiveness. Consequently, these phage-insensitive bacteria are unable to interact with cMet and gC1q-R host cell receptors, which normally trigger cellular uptake upon interaction with InlB. Collectively, we provide detailed mechanistic insight into the dual role of a surface antigen crucial for both phage adsorption and cellular invasiveness, demonstrating a trade-off between phage resistance and virulence in this opportunistic pathogen. L. monocytogenes is a Gram-positive, food-borne, intracellular pathogen that causes severe infection in susceptible individuals. Interestingly, almost all infections are caused by a subset of strains belonging to certain serovars featuring a complex glycosylation pattern on their cell surface. Using an engineered bacteriophage that specifically recognizes these modifications we selected for mutants that lost these sugars. We found that the resulting strains are severely deficient in invading host cells as we observed that a major virulence factor mediating host cell entry requires galactose decoration of the cell surface for its function. Without this galactose decoration, the strain represents a serovar not associated with disease. Altogether, we show a complex interplay between bacteriophages, bacteria, and the host, demonstrating that cellular invasiveness is dependent upon a serovar-defining structure, which also serves as a phage receptor.
Collapse
Affiliation(s)
- Eric T. Sumrall
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
- * E-mail: (YS); (MJL)
| | - Anja P. Keller
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Jeanine Rismondo
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Maria Pavlou
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Marcel R. Eugster
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Samy Boulos
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Olivier Disson
- Biology of Infection Unit, Institut Pasteur, Paris, France
- Inserm U1117, Paris, France
| | - Pierre Thouvenot
- Biology of Infection Unit, Institut Pasteur, Paris, France
- Inserm U1117, Paris, France
| | - Samuel Kilcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Didier Cabanes
- i3S - Instituto de Investigação e Inovação em Saúde; Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
| | - Marc Lecuit
- Biology of Infection Unit, Institut Pasteur, Paris, France
- Inserm U1117, Paris, France
- Paris Descartes University, Department of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, APHP, Institut Imagine, Paris, France
| | - Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Martin J. Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
- * E-mail: (YS); (MJL)
| |
Collapse
|
25
|
Meeske AJ, Nakandakari-Higa S, Marraffini LA. Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature 2019; 570:241-245. [PMID: 31142834 PMCID: PMC6570424 DOI: 10.1038/s41586-019-1257-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022]
Abstract
Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci of prokaryotes are composed of 30-40 bp repeats separated by equally short sequences of plasmid and bacteriophage origin known as spacers1–3. Spacers are transcribed and processed into short CRISPR RNAs (crRNAs) that are used as guides by CRISPR-associated (Cas) nucleases to recognize and destroy complementary sequences (known as protospacers) within invaders4,5. In contrast to most Cas nucleases which destroy the invader’s DNA4–7, the type VI effector nuclease Cas13 employs RNA guides to locate complementary transcripts and catalyze both sequence-specific cis-, and non-specific trans-RNA cleavage8. While it has been hypothesized that Cas13 naturally defends against RNA phages8, type VI spacer sequences have exclusively been found to match the genomes of double-stranded DNA (dsDNA) phages9,10, suggesting that Cas13 can provide immunity against these invaders. However, whether and how Cas13 utilizes the cis- and/or trans-RNA cleavage activities in defending against dsDNA phages is not understood. Here we show that trans-cleavage of transcripts halts the growth of the host cell and results in the abortion of the infectious cycle. This depletes the phage population and provides herd immunity to uninfected bacteria. Phages harboring target mutations, which easily evade DNA-targeting CRISPR systems11–13, are also depleted due to the activation of Cas13 by co-infecting wild type phages. Thus, by acting on the host rather than directly targeting the virus, type VI CRISPR systems not only provide robust defense against DNA phages but also prevent outbreaks of CRISPR-resistant phage.
Collapse
Affiliation(s)
- Alexander J Meeske
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
| | | | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
26
|
Born Y, Knecht LE, Eigenmann M, Bolliger M, Klumpp J, Fieseler L. A major-capsid-protein-based multiplex PCR assay for rapid identification of selected virulent bacteriophage types. Arch Virol 2019; 164:819-830. [PMID: 30673846 PMCID: PMC6394723 DOI: 10.1007/s00705-019-04148-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/14/2018] [Indexed: 12/17/2022]
Abstract
Bacteriophages represent a promising alternative for controlling pathogenic bacteria. They are ubiquitous in the environment, and their isolation is usually simple and fast. However, not every phage is suitable for biocontrol applications. It must be virulent (i.e., strictly lytic), non-transducing, and safe. We have developed a method for identifying selected types of virulent phages at an early stage of the isolation process to simplify the search for suitable candidates. Using the major capsid protein (MCP) as a phylogenetic marker, we designed degenerate primers for the identification of Felix O1-, GJ1-, N4-, SP6-, T4-, T7-, and Vi1-like phages in multiplex PCR setups with single phage plaques as templates. Performance of the MCP PCR assay was evaluated with a set of 26 well-characterized phages. Neither false-positive nor false-negative results were obtained. In addition, 154 phages from enrichment cultures from various environmental samples were subjected to MCP PCR analysis. Eight of them, specific for Salmonella enterica, Escherichia coli, or Erwinia amylovora, belonged to one of the selected phage types. Their PCR-based identification was successfully confirmed by pulsed-field gel electrophoresis of the phage genomes, electron microscopy, and sequencing of the amplified mcp gene fragment. The MCP PCR assay was shown to be a simple method for preliminary assignment of new phages to a certain group and thus to identify candidates for biocontrol immediately after their isolation. Given that sufficient sequence data are available, this method can be extended to any phage group of interest.
Collapse
Affiliation(s)
- Yannick Born
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
| | - Leandra E Knecht
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Mirjam Eigenmann
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
| | - Michel Bolliger
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Lars Fieseler
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland.
| |
Collapse
|
27
|
Guerrero-Ferreira RC, Hupfeld M, Nazarov S, Taylor NM, Shneider MM, Obbineni JM, Loessner MJ, Ishikawa T, Klumpp J, Leiman PG. Structure and transformation of bacteriophage A511 baseplate and tail upon infection of Listeria cells. EMBO J 2019; 38:embj.201899455. [PMID: 30606715 DOI: 10.15252/embj.201899455] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 11/09/2022] Open
Abstract
Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteriophages that infect Gram-positive bacteria represent the least understood members. Here, we describe the structure of Listeria bacteriophage A511 tail in its pre- and post-host attachment states (extended and contracted, respectively) using cryo-electron microscopy, cryo-electron tomography, and X-ray crystallography. We show that the structure of the tube-baseplate complex of A511 is similar to that of phage T4, but the A511 baseplate is decorated with different receptor-binding proteins, which undergo a large structural transformation upon host attachment and switch the symmetry of the baseplate-tail fiber assembly from threefold to sixfold. For the first time under native conditions, we show that contraction of the phage tail sheath assembly starts at the baseplate and propagates through the sheath in a domino-like motion.
Collapse
Affiliation(s)
- Ricardo C Guerrero-Ferreira
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mario Hupfeld
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Sergey Nazarov
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicholas Mi Taylor
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mikhail M Shneider
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Bioengineering, Moscow, Russia
| | - Jagan M Obbineni
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.,Centre for Agricultural Innovations and Advanced Learning (VAIAL), Vellore Institute of Technology, Vellore, India
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Takashi Ishikawa
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Petr G Leiman
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| |
Collapse
|
28
|
Brownell D, King J, Caliando B, Sycheva L, Koeris M. Engineering Bacteriophage-Based Biosensors. Methods Mol Biol 2019; 1898:37-50. [PMID: 30570721 DOI: 10.1007/978-1-4939-8940-9_3] [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] [Indexed: 06/09/2023]
Abstract
Bacteriophages have been used for diagnostic purposes in the past, but a lack of parallelizable engineering methods had limited their applicability to a narrow subset of diagnostic settings. More recently, however, advances in DNA sequencing and the introduction of more sensitive reporter systems have enabled novel engineering methods, which in turn have broadened the scope of modern phage diagnostics. Here we describe advanced methods to engineer the genomes of bacteriophages in a modular and rapid fashion.
Collapse
Affiliation(s)
- Daniel Brownell
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA
| | - John King
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA
| | - Brian Caliando
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA
| | - Lada Sycheva
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA
| | - Michael Koeris
- Sample 6 Technologies, 15300 Bothell Way NE Lake Forest Park, WA, 98155, Woburn, MA, USA.
| |
Collapse
|
29
|
Hupfeld M, Trasanidou D, Ramazzini L, Klumpp J, Loessner MJ, Kilcher S. A functional type II-A CRISPR-Cas system from Listeria enables efficient genome editing of large non-integrating bacteriophage. Nucleic Acids Res 2018; 46:6920-6933. [PMID: 30053228 PMCID: PMC6061871 DOI: 10.1093/nar/gky544] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/31/2022] Open
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against invading DNA elements including bacteriophages and plasmids. While CRISPR technology has revolutionized eukaryotic genome engineering, its application to prokaryotes and their viruses remains less well established. Here we report the first functional CRISPR-Cas system from the genus Listeria and demonstrate its native role in phage defense. LivCRISPR-1 is a type II-A system from the genome of L. ivanovii subspecies londoniensis that uses a small, 1078 amino acid Cas9 variant and a unique NNACAC protospacer adjacent motif. We transferred LivCRISPR-1 cas9 and trans-activating crRNA into Listeria monocytogenes. Along with crRNA encoding plasmids, this programmable interference system enables efficient cleavage of bacterial DNA and incoming phage genomes. We used LivCRISPR-1 to develop an effective engineering platform for large, non-integrating Listeria phages based on allelic replacement and CRISPR-Cas-mediated counterselection. The broad host-range Listeria phage A511 was engineered to encode and express lysostaphin, a cell wall hydrolase that specifically targets Staphylococcus peptidoglycan. In bacterial co-culture, the armed phages not only killed Listeria hosts but also lysed Staphylococcus cells by enzymatic collateral damage. Simultaneous killing of unrelated bacteria by a single phage demonstrates the potential of CRISPR-Cas-assisted phage engineering, beyond single pathogen control.
Collapse
Affiliation(s)
- Mario Hupfeld
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Despoina Trasanidou
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Livia Ramazzini
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Samuel Kilcher
- Institute of Food, Nutrition, and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| |
Collapse
|
30
|
Komora N, Bruschi C, Ferreira V, Maciel C, Brandão TRS, Fernandes R, Saraiva JA, Castro SM, Teixeira P. The protective effect of food matrices on Listeria lytic bacteriophage P100 application towards high pressure processing. Food Microbiol 2018; 76:416-425. [PMID: 30166169 DOI: 10.1016/j.fm.2018.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 06/19/2018] [Accepted: 07/02/2018] [Indexed: 12/13/2022]
Abstract
The application of lytic phages as biocontrol agents is emerging as a promising strategy towards elimination or reduction of foodborne pathogens in a variety of food products. This technology is particularly advantageous for minimally processed and ready-to-eat (RTE) foods. In this study, the potential use of Listex™ P100 combined with high hydrostatic pressure (HPP), to enhance the control of Listeria monocytogenes in food was evaluated. For that, the effect of three pressures (200, 300 or 400 MPa; 5 min, 10 °C) on phage P100 stability was tested when inoculated in six different matrices: phosphate buffered saline (PBS, pH 7.4); apple juice (pH 3.41); orange/carrot nectar (pH 3.54); UHT whole milk (pH 6.73); and, two traditional Portuguese fermented products, "Serra da Estrela" cheese (pH 5.66) and "Alheira", a meat sausage (pH 6.07). The results showed that treatment at 400 MPa reduced phage titres to below the detection level in all matrices, whereas at milder pressures the survival of the phage was matrix dependent. "Alheira", "Serra da Estrela" cheese and UHT whole milk were shown to be baroprotective matrices that support phage P100 application in HHP up to 300 MPa; however, an accentuated phage inactivation was observed in apple and orange/carrot nectar, which may be related to the acidic pH values of these matrices. The initial phage load did not affect the inactivation rate during HHP processing (300 MPa, 5 min, 10 °C) in PBS, cheese, sausage or milk matrices, and the phage titres were stable in these matrices during storage at 4 °C for 28 days for milk and 60 days for "Alheira" and "Serra da Estrela" cheese. In addition, a baroprotective effect on phage stability was observed when PBS was supplemented with reducing sugars, dextrin, casein, and tween 80. In conclusion, at mild HHP treatment, phage P100 remained active in specific matrices and seems to present potential to be added in non-thermal inactivation of L. monocytogenes.
Collapse
Affiliation(s)
- Norton Komora
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital 172, 4200-374 Porto, Portugal
| | - Carolina Bruschi
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital 172, 4200-374 Porto, Portugal
| | - Vânia Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital 172, 4200-374 Porto, Portugal
| | - Cláudia Maciel
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital 172, 4200-374 Porto, Portugal
| | - Teresa R S Brandão
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital 172, 4200-374 Porto, Portugal
| | - Rui Fernandes
- HEMS - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200-135, Portugal
| | - Jorge A Saraiva
- QOPNA - Organic Chemistry, Natural Products and Food Stuffs, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Sónia Marília Castro
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital 172, 4200-374 Porto, Portugal; QOPNA - Organic Chemistry, Natural Products and Food Stuffs, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Paula Teixeira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital 172, 4200-374 Porto, Portugal.
| |
Collapse
|
31
|
Roy B, Philippe C, Loessner MJ, Goulet J, Moineau S. Production of Bacteriophages by Listeria Cells Entrapped in Organic Polymers. Viruses 2018; 10:E324. [PMID: 29899227 PMCID: PMC6024803 DOI: 10.3390/v10060324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/29/2022] Open
Abstract
Applications for bacteriophages as antimicrobial agents are increasing. The industrial use of these bacterial viruses requires the production of large amounts of suitable strictly lytic phages, particularly for food and agricultural applications. This work describes a new approach for phage production. Phages H387 (Siphoviridae) and A511 (Myoviridae) were propagated separately using Listeria ivanovii host cells immobilised in alginate beads. The same batch of alginate beads could be used for four successive and efficient phage productions. This technique enables the production of large volumes of high-titer phage lysates in continuous or semi-continuous (fed-batch) cultures.
Collapse
Affiliation(s)
- Brigitte Roy
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V OA6, Canada.
- Département des Sciences des Aliments, Faculté des Sciences de L'agriculture et de L'alimentation, Université Laval, Québec, QC G1V OA6, Canada.
- Félix d'Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V OA6, Canada.
| | - Cécile Philippe
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V OA6, Canada.
- Félix d'Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V OA6, Canada.
| | - Martin J Loessner
- ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse, 7CH-8092 Zürich, Switzerland.
| | - Jacques Goulet
- Département des Sciences des Aliments, Faculté des Sciences de L'agriculture et de L'alimentation, Université Laval, Québec, QC G1V OA6, Canada.
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC G1V OA6, Canada.
- Félix d'Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V OA6, Canada.
| |
Collapse
|
32
|
Buttimer C, Born Y, Lucid A, Loessner MJ, Fieseler L, Coffey A. Erwinia amylovora phage vB_EamM_Y3 represents another lineage of hairy Myoviridae. Res Microbiol 2018; 169:505-514. [PMID: 29777834 DOI: 10.1016/j.resmic.2018.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/23/2018] [Indexed: 10/16/2022]
Abstract
To date, a small number of jumbo myoviruses have been reported to possess atypical whisker-like structures along the surface of their contractile tails. Erwinia amylovora phage vB_EamM_Y3 is another example. It possesses a genome of 261,365 kbp with 333 predicted ORFs. Using a combination of BLASTP, Interproscan and HHpred, about 21% of its putative proteins could be assigned functions involved in nucleotide metabolism, DNA replication, virion structure and cell wall degradation. The phage was found to have a signal-arrest-release (SAR) endolysin (Y3_301) possessing a soluble lytic transglycosylase domain. Like other SAR endolysins, inducible expression of Y3_301 caused Escherichia coli lysis, which is dependent on the presence of an N-terminal signal sequence. Phylogenetic analysis showed that its closest relatives are other jumbo phages including Pseudomonas aeruginosa phage PaBG and P. putida phage Lu11, sharing 105 and 87 homologous proteins respectively. Like these phages, Y3 also shares a distant relationship to Ralstonia solanacearum phage ΦRSL1 (sharing 55 homologous proteins). As these phages are unrelated to the Rak2-like group of hairy phages, Y3 along with Lu11 represent a second lineage of hairy myoviruses.
Collapse
Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland.
| | - Yannick Born
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland; Agroscope, Research Division Plant Protection, Wädenswil, Switzerland.
| | - Alan Lucid
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Martin J Loessner
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland.
| | - Lars Fieseler
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland.
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland; APC Microbiome Institute, University College, Cork, Ireland.
| |
Collapse
|
33
|
Ghosh K, Senevirathne A, Kang HS, Hyun WB, Kim JE, Kim KP. Complete Nucleotide Sequence Analysis of a Novel Bacillus subtilis-Infecting Bacteriophage BSP10 and Its Effect on Poly-Gamma-Glutamic Acid Degradation. Viruses 2018; 10:E240. [PMID: 29734701 PMCID: PMC5977233 DOI: 10.3390/v10050240] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 01/21/2023] Open
Abstract
While the harmful effects of lactic acid bacterial bacteriophages in the dairy industry are well-established, the importance of Bacillus subtilis-infecting bacteriophages on soybean fermentation is poorly-studied. In this study, we isolated a B. subtilis-infecting bacteriophage BSP10 from Meju (a brick of dried fermented soybean) and further characterized it. This Myoviridae family bacteriophage exhibited a narrow host range against B. subtilis strains (17/52, 32.7%). The genome of bacteriophage BSP10 is 153,767 bp long with 236 open reading frames and 5 tRNAs. Comparative genomics (using dot plot, progressiveMauve alignment, heat-plot, and BLASTN) and phylogenetic analysis strongly suggest its incorporation as a new species in the Nit1virus genus. Furthermore, bacteriophage BSP10 was efficient in the growth inhibition of B. subtilis ATCC 15245 in liquid culture and in Cheonggukjang (a soybean fermented food) fermentation. Artificial contamination of as low as 10² PFU/g of bacteriophage BSP10 during Cheonggukjang fermentation significantly reduced bacterial numbers by up to 112 fold in comparison to the control (no bacteriophage). Moreover, for the first time, we experimentally proved that B. subtilis-infecting bacteriophage greatly enhanced poly-γ-glutamic acid degradation during soybean fermentation, which is likely to negatively affect the functionalities of Cheonggukjang.
Collapse
Affiliation(s)
- Kuntal Ghosh
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Amal Senevirathne
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Hai Seong Kang
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Woo Bin Hyun
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Ji Eun Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, Korea.
| |
Collapse
|
34
|
Ahmadi H, Radford D, Kropinski AM, Lim LT, Balamurugan S. Thermal-Stability and Reconstitution Ability of Listeria Phages P100 and A511. Front Microbiol 2017; 8:2375. [PMID: 29259585 PMCID: PMC5723416 DOI: 10.3389/fmicb.2017.02375] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
The study evaluated the thermal-stability of Listeria phages P100 and A511 at temperatures simulating the preparation of ready-to-eat meats. The phage infectivity after heating to 71°C and holding for a minimum of 30 s, before eventually cooling to 4°C were examined. Higher temperatures of 75, 80, and 85°C were also tested to evaluate their effect on phages thermal-stability. This study found that despite minor differences in the amino acid sequences of their structural proteins, the two phages responded differently to high temperatures. P100 activity declined at least 10 log (PFU mL-1) with exposure to 71°C (30 s) and falling below the limit of detection (1 log PFU mL-1) while, A511 dropped from 108 to 105 PFU mL-1. Cooling resulted in partial reconstitution of P100 phage particles to 103 PFU mL-1. Exposure to 75°C (30 s) abolished A511 activity (8 log PFU mL-1) and both phages showed reconstitution during cooling phase after exposure to 75°C. P100 exhibited reconstitution after treatment at 80°C (30 s), conversely A511 showed no reconstitution activity. Heating P100 to 85°C abolished the reconstitution potential. Substantial differences were found in thermal-stability and reconstitution of the examined phages showing A511 to be more thermo-stable than P100, while P100 exhibited reconstitution during cooling after treatment at 80°C which was absent in A511. The differences in predicted melting temperatures of structural proteins of P100 and A511 were consistent with the observed differences in thermal stability and morphological changes observed with transmission electron microscopy.
Collapse
Affiliation(s)
- Hanie Ahmadi
- Department of Food Science, University of Guelph, Guelph, ON, Canada
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Devon Radford
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Andrew M. Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Loong-Tak Lim
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | | |
Collapse
|
35
|
Leskinen K, Tuomala H, Wicklund A, Horsma-Heikkinen J, Kuusela P, Skurnik M, Kiljunen S. Characterization of vB_SauM-fRuSau02, a Twort-Like Bacteriophage Isolated from a Therapeutic Phage Cocktail. Viruses 2017; 9:v9090258. [PMID: 28906479 PMCID: PMC5618024 DOI: 10.3390/v9090258] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/29/2017] [Accepted: 09/11/2017] [Indexed: 01/09/2023] Open
Abstract
Staphylococcus aureus is a commensal and pathogenic bacterium that causes infections in humans and animals. It is a major cause of nosocomial infections worldwide. Due to increasing prevalence of multidrug resistance, alternative methods to eradicate the pathogen are necessary. In this respect, polyvalent staphylococcal myoviruses have been demonstrated to be excellent candidates for phage therapy. Here we present the characterization of the bacteriophage vB_SauM-fRuSau02 (fRuSau02) that was isolated from a commercial Staphylococcus bacteriophage cocktail produced by Microgen (Moscow, Russia). The genomic analysis revealed that fRuSau02 is very closely related to the phage MSA6, and possesses a large genome (148,464 bp), with typical modular organization and a low G+C (30.22%) content. It can therefore be classified as a new virus among the genus Twortlikevirus. The genome contains 236 predicted genes, 4 of which were interrupted by insertion sequences. Altogether, 78 different structural and virion-associated proteins were identified from purified phage particles by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The host range of fRuSau02 was tested with 135 strains, including 51 and 54 Staphylococcus aureus isolates from humans and pigs, respectively, and 30 coagulase-negative Staphylococcus strains of human origin. All clinical S. aureus strains were at least moderately sensitive to the phage, while only 39% of the pig strains were infected. Also, some strains of Staphylococcus intermedius, Staphylococcus lugdunensis, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus saprophyticus and Staphylococcus pseudointer were sensitive. We conclude that fRuSau02, a phage therapy agent in Russia, can serve as an alternative to antibiotic therapy against S. aureus.
Collapse
Affiliation(s)
- Katarzyna Leskinen
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki 00290, Finland.
| | - Henni Tuomala
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki 00290, Finland.
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland.
| | - Anu Wicklund
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki 00290, Finland.
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland.
| | - Jenni Horsma-Heikkinen
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki 00290, Finland.
| | - Pentti Kuusela
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland.
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki 00290, Finland.
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland.
| | - Saija Kiljunen
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki, Helsinki 00290, Finland.
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland.
| |
Collapse
|
36
|
Radford D, Guild B, Strange P, Ahmed R, Lim LT, Balamurugan S. Characterization of antimicrobial properties of Salmonella phage Felix O1 and Listeria phage A511 embedded in xanthan coatings on Poly(lactic acid) films. Food Microbiol 2017; 66:117-128. [DOI: 10.1016/j.fm.2017.04.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 11/27/2022]
|
37
|
Akhtar M, Viazis S, Christensen K, Kraemer P, Diez-Gonzalez F. Isolation, characterization and evaluation of virulent bacteriophages against Listeria monocytogenes. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.12.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
38
|
Lee S, Kim MG, Lee HS, Heo S, Kwon M, Kim G. Isolation and Characterization of Listeria phages for Control of Growth of Listeria monocytogenes in Milk. Korean J Food Sci Anim Resour 2017; 37:320-328. [PMID: 28515656 PMCID: PMC5434219 DOI: 10.5851/kosfa.2017.37.2.320] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 11/16/2022] Open
Abstract
In this study, two Listeria bacteriophages, LMP1 and LMP7, were isolated from chicken feces as a means of biocontrol of L. monocytogenes. Both bacteriophages had a lytic effect on L. monocytogenes ATCC 7644, 15313, 19114, and 19115. Phages LMP1 and LMP7 were able to inhibit the growth of L. monocytogenes ATCC 7644 and 19114 in tryptic soy broth at 10°C and 30°C. Nevertheless, LMP1 was more effective than LMP7 at inhibiting L. monocytogenes ATCC 19114. On the contrary, LMP7 was more effective than LMP1 at inhibiting L. monocytogenes ATCC 7644. The morphology of LMP1 and LMP7 resembled that of members of the Siphoviridae family. The growth of L. monocytogenes ATCC 7644 was inhibited by both LMP1 and LMP7 in milk; however, the growth of L. monocytogenes ATCC 19114 was only inhibited by LMP1 at 30°C. The lytic activity of bacteriophages was also evaluated at 4°C in milk in order to investigate the potential use of these phages in refrigerated products. In conclusion, these two bacteriophages exhibit different host specificities and characteristics, suggesting that they can be used as a component of a phage cocktail to control L. monocytogenes in the food industry.
Collapse
Affiliation(s)
- Sunhee Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Min Gon Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Hee Soo Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Sunhak Heo
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Mirae Kwon
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - GeunBae Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| |
Collapse
|
39
|
Buttimer C, McAuliffe O, Ross RP, Hill C, O’Mahony J, Coffey A. Bacteriophages and Bacterial Plant Diseases. Front Microbiol 2017; 8:34. [PMID: 28163700 PMCID: PMC5247434 DOI: 10.3389/fmicb.2017.00034] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/06/2017] [Indexed: 12/23/2022] Open
Abstract
Losses in crop yields due to disease need to be reduced in order to meet increasing global food demands associated with growth in the human population. There is a well-recognized need to develop new environmentally friendly control strategies to combat bacterial crop disease. Current control measures involving the use of traditional chemicals or antibiotics are losing their efficacy due to the natural development of bacterial resistance to these agents. In addition, there is an increasing awareness that their use is environmentally unfriendly. Bacteriophages, the viruses of bacteria, have received increased research interest in recent years as a realistic environmentally friendly means of controlling bacterial diseases. Their use presents a viable control measure for a number of destructive bacterial crop diseases, with some phage-based products already becoming available on the market. Phage biocontrol possesses advantages over chemical controls in that tailor-made phage cocktails can be adapted to target specific disease-causing bacteria. Unlike chemical control measures, phage mixtures can be easily adapted for bacterial resistance which may develop over time. In this review, we will examine the progress and challenges for phage-based disease biocontrol in food crops.
Collapse
Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of TechnologyCork, Ireland
| | | | - R. P. Ross
- Alimentary Pharmabiotic Centre, University CollegeCork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre, University CollegeCork, Ireland
| | - Jim O’Mahony
- Department of Biological Sciences, Cork Institute of TechnologyCork, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of TechnologyCork, Ireland
| |
Collapse
|
40
|
Radford DR, Ahmadi H, Leon-Velarde CG, Balamurugan S. Propagation method for persistent high yield of diverse Listeria phages on permissive hosts at refrigeration temperatures. Res Microbiol 2016; 167:685-691. [DOI: 10.1016/j.resmic.2016.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 05/27/2016] [Accepted: 05/30/2016] [Indexed: 11/15/2022]
|
41
|
Ozaki T, Abe N, Kimura K, Suzuki A, Kaneko J. Genomic analysis of Bacillus subtilis lytic bacteriophage ϕNIT1 capable of obstructing natto fermentation carrying genes for the capsule-lytic soluble enzymes poly-γ-glutamate hydrolase and levanase. Biosci Biotechnol Biochem 2016; 81:135-146. [PMID: 27885938 DOI: 10.1080/09168451.2016.1232153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacillus subtilis strains including the fermented soybean (natto) starter produce capsular polymers consisting of poly-γ-glutamate and levan. Capsular polymers may protect the cells from phage infection. However, bacteriophage ϕNIT1 carries a γ-PGA hydrolase gene (pghP) that help it to counteract the host cell's protection strategy. ϕNIT had a linear double stranded DNA genome of 155,631-bp with a terminal redundancy of 5,103-bp, containing a gene encoding an active levan hydrolase. These capsule-lytic enzyme genes were located in the possible foreign gene cluster regions between central core and terminal redundant regions, and were expressed at the late phase of the phage lytic cycle. All tested natto origin Spounavirinae phages carried both genes for capsule degrading enzymes similar to ϕNIT1. A comparative genomic analysis revealed the diversity among ϕNIT1 and Bacillus phages carrying pghP-like and levan-hydrolase genes, and provides novel understanding on the acquisition mechanism of these enzymatic genes.
Collapse
Affiliation(s)
- Tatsuro Ozaki
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Naoki Abe
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Keitarou Kimura
- b Laboratory of Applied Microbiology , Food Research Institute-National Agriculture and Food Research Organization (NFRI-NARO) , Tsukuba , Japan
| | - Atsuto Suzuki
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Jun Kaneko
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| |
Collapse
|
42
|
Bardina C, Colom J, Spricigo DA, Otero J, Sánchez-Osuna M, Cortés P, Llagostera M. Genomics of Three New Bacteriophages Useful in the Biocontrol of Salmonella. Front Microbiol 2016; 7:545. [PMID: 27148229 PMCID: PMC4837284 DOI: 10.3389/fmicb.2016.00545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/04/2016] [Indexed: 02/06/2023] Open
Abstract
Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs); 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats (DTR) of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic analysis of large terminase subunits confirms their packaging strategies and grouping to the different phage genus type. All these studies are necessary for the development and the use of an efficient cocktail with commercial applications in bacteriophage therapy against Salmonella.
Collapse
Affiliation(s)
| | | | | | | | | | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Molecular Microbiology, Universitat Autònoma de BarcelonaBarcelona, Spain
| | | |
Collapse
|
43
|
Hsieh SE, Tseng YH, Lo HH, Chen ST, Wu CN. Genomic analysis of Staphylococcus phage Stau2 isolated from medical specimen. Virus Genes 2015; 52:107-16. [PMID: 26706853 DOI: 10.1007/s11262-015-1276-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/10/2015] [Indexed: 11/30/2022]
Abstract
Stau2 is a lytic myophage of Staphylococcus aureus isolated from medical specimen. Exhibiting a broad host range against S. aureus clinical isolates, Stau2 is potentially useful for topical phage therapy or as an additive in food preservation. In this study, Stau2 was firstly revealed to possess a circularly permuted linear genome of 133,798 bp, with low G + C content, containing 146 open reading frames, but encoding no tRNA. The genome is organized into several modules containing genes for packaging, structural proteins, replication/transcription and host-cell-lysis, with the structural proteins and DNA polymerase modules being organized similarly to that in Twort-like phages of Staphylococcus. With the encoded DNA replication genes, Stau2 can possibly use its own system for replication. In addition, analysis in silico found several introns in seven genes, including those involved in DNA metabolism, packaging, and structure, while one of them (helicase gene) is experimentally confirmed to undergo splicing. Furthermore, phylogenetic analysis suggested Stau2 to be most closely related to Staphylococcus phages SA11 and Remus, members of Twort-like phages. The results of sodium dodecyl sulfate polyacrylamide gel electrophoresis showed 14 structural proteins of Stau2 and N-terminal sequencing identified three of them. Importantly, this phage does not encode any proteins which are known or suspected to be involved in toxicity, pathogenicity, or antibiotic resistance. Therefore, further investigations of feasible therapeutic application of Stau2 are needed.
Collapse
Affiliation(s)
- Sue-Er Hsieh
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 406, Taiwan
| | - Yi-Hsiung Tseng
- Department of Microbiology, Tzu Chi University, Hualien, 970, Taiwan
| | - Hsueh-Hsia Lo
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 406, Taiwan
| | - Shui-Tu Chen
- Pediatrics Department, Nantou Hospital, Department of Health, Nantou, 540, Taiwan
| | - Cheng-Nan Wu
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 406, Taiwan.
| |
Collapse
|
44
|
Stambach NR, Carr SA, Cox CR, Voorhees KJ. Rapid Detection of Listeria by Bacteriophage Amplification and SERS-Lateral Flow Immunochromatography. Viruses 2015; 7:6631-41. [PMID: 26694448 PMCID: PMC4690885 DOI: 10.3390/v7122962] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/02/2015] [Accepted: 12/10/2015] [Indexed: 11/16/2022] Open
Abstract
A rapid Listeria detection method was developed utilizing A511 bacteriophage amplification combined with surface-enhanced Raman spectroscopy (SERS) and lateral flow immunochromatography (LFI). Anti-A511 antibodies were covalently linked to SERS nanoparticles and printed onto nitrocellulose membranes. Antibody-conjugated SERS nanoparticles were used as quantifiable reporters. In the presence of A511, phage-SERS nanoparticle complexes were arrested and concentrated as a visible test line, which was interrogated quantitatively by Raman spectroscopy. An increase in SERS intensity correlated to an increase in captured phage-reporter complexes. SERS limit of detection was 6 × 10(6) pfu·mL(-1), offering detection below that obtainable by the naked eye (LOD 6 × 10(7) pfu·mL(-1)). Phage amplification experiments were carried out at a multiplicity of infection (MOI) of 0.1 with 4 different starting phage concentrations monitored over time using SERS-LFI and validated by spot titer assay. Detection of L. monocytogenes concentrations of 1 × 10(7) colony forming units (cfu)·mL(-1), 5 × 10(6) cfu·mL(-1), 5 × 10(5) cfu·mL(-1) and 5 × 10(4) cfu·mL(-1) was achieved in 2, 2, 6, and 8 h, respectively. Similar experiments were conducted at a constant starting phage concentration (5 × 10(5) pfu·mL(-1)) with MOIs of 1, 2.5, and 5 and were detected in 2, 4, and 5 h, respectively.
Collapse
Affiliation(s)
- Nicholas R Stambach
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - Stephanie A Carr
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - Christopher R Cox
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| | - Kent J Voorhees
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| |
Collapse
|
45
|
Pitaksutheepong C, Abhisingha M, Dumnin J, Visessanguan W. Isolation, detection and inactivation of a Myoviridae bacteriophage infecting Bacillus amyloliquefaciens FB11. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-014-1022-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
|
46
|
Strydom A, Witthuhn CR. Listeria monocytogenes: A Target for Bacteriophage Biocontrol. Compr Rev Food Sci Food Saf 2015. [DOI: 10.1111/1541-4337.12153] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amy Strydom
- Dept. of Microbial, Biochemical and Food Biotechnology; Univ. of the Free State; Private Bag 339 Bloemfontein 9300 South Africa
| | - Corli R. Witthuhn
- Dept. of Microbial, Biochemical and Food Biotechnology; Univ. of the Free State; Private Bag 339 Bloemfontein 9300 South Africa
| |
Collapse
|
47
|
Liu M, Bischoff KM, Gill JJ, Mire-Criscione MD, Berry JD, Young R, Summer EJ. Bacteriophage application restores ethanol fermentation characteristics disrupted by Lactobacillus fermentum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:132. [PMID: 26339290 PMCID: PMC4558781 DOI: 10.1186/s13068-015-0325-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Contamination of corn mash by lactic acid bacteria (LAB) reduces the efficiency of the ethanol fermentation process. The industry relies heavily on antibiotics for contamination control and there is a need to develop alternative methods. The goals of this study were to determine the diversity and abundance of bacteria contaminating commercial ethanol fermentations, and to evaluate the potential of anti-LAB bacteriophages in controlling production losses. RESULTS Bacterial populations in 27 corn mash samples collected from nine different commercial plants were determined by pyrosequencing of 16S rRNA amplicons. The results showed that the most abundant bacteria (>50 % of total population) in 24 of the 27 samples included LAB genera such as Lactobacillus, Streptococcus, Lactococcus, Weissella, Enterococcus, and Pediococcus. Lactobacillus was identified as the most prevalent genus at all fermentation stages in all plants, accounting for between 2.3 and 93.7 % of each population and constituting the major genus (>50 %) in nine samples from five plants and the most abundant genus in five other samples. Lactobacillus species, including L. delbrueckii, L. fermentum, L. mucosae, and L. reuteri were the most well-represented species. Two bacteriophages that target L. fermentum strains from ethanol plants, vB_LfeS_EcoSau and vB_LfeM_EcoInf (EcoSau and EcoInf), were isolated and characterized as a siphophage and a myophage, respectively. Analysis of the 31,703 bp genome of EcoSau revealed its similarity to the P335-like phage group, and the 106,701 bp genome of phage EcoInf was determined to be a novel phage type despite its distant relationship to the SPO1-like phages. Addition of phages EcoSau and EcoInf to L. fermentum-contaminated corn mash fermentation models restored the yields of ethanol and reduced levels of residual glucose, lactic acid, and acetic acid to that comparable to the infection-free control. CONCLUSIONS This study provides detailed insight into the microbiota contaminating commercial ethanol fermentations, and highlights the abundance of LAB, especially L. delbrueckii, L. fermentum, L. mucosae, and L. reuteri, in the process. This study suggests that phages with broad coverage of major LAB species can be applied directly to corn mash for antibiotic-free control of contamination in the ethanol fermentation industry.
Collapse
Affiliation(s)
- Mei Liu
- />Ecolyse Inc., 11142 Hopes Creek Rd., College Station, TX 77845 USA
| | - Kenneth M. Bischoff
- />Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, IL 61604 USA
| | - Jason J. Gill
- />Center for Phage Technology, 2128 TAMU, Texas A&M University, College Station, TX 77843 USA
- />Department of Animal Science, 2471 TAMU, Texas A&M University, College Station, TX 77843 USA
| | | | - Joel D. Berry
- />Center for Phage Technology, 2128 TAMU, Texas A&M University, College Station, TX 77843 USA
| | - Ry Young
- />Center for Phage Technology, 2128 TAMU, Texas A&M University, College Station, TX 77843 USA
- />Department of Biochemistry and Biophysics, 2128 TAMU, Texas A&M University, College Station, TX 77843 USA
| | | |
Collapse
|
48
|
Comparative genomic and morphological analyses of Listeria phages isolated from farm environments. Appl Environ Microbiol 2015; 80:4616-25. [PMID: 24837381 DOI: 10.1128/aem.00720-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The genus Listeria is ubiquitous in the environment and includes the globally important food-borne pathogen Listeria monocytogenes. While the genomic diversity of Listeria has been well studied, considerably less is known about the genomic and morphological diversity of Listeria bacteriophages. In this study, we sequenced and analyzed the genomes of 14 Listeria phages isolated mostly from New York dairy farm environments as well as one related Enterococcus faecalis phage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. These Listeria phages, based on gene orthology and morphology, together with previously sequenced Listeria phages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large genome (~135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (~66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) of E. faecalis phages, with medium-sized genomes (~56 kb), was identified, which grouped together and shares morphological features with the novel Listeria phage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes.
Collapse
|
49
|
Eugster MR, Morax LS, Hüls VJ, Huwiler SG, Leclercq A, Lecuit M, Loessner MJ. Bacteriophage predation promotes serovar diversification in Listeria monocytogenes. Mol Microbiol 2015; 97:33-46. [PMID: 25825127 DOI: 10.1111/mmi.13009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2015] [Indexed: 11/30/2022]
Abstract
Listeria monocytogenes is a bacterial pathogen classified into distinct serovars (SVs) based on somatic and flagellar antigens. To correlate phenotype with genetic variation, we analyzed the wall teichoic acid (WTA) glycosylation genes of SV 1/2, 3 and 7 strains, which differ in decoration of the ribitol-phosphate backbone with N-acetylglucosamine (GlcNAc) and/or rhamnose. Inactivation of lmo1080 or the dTDP-l-rhamnose biosynthesis genes rmlACBD (lmo1081-1084) resulted in loss of rhamnose, whereas disruption of lmo1079 led to GlcNAc deficiency. We found that all SV 3 and 7 strains actually originate from a SV 1/2 background, as a result of small mutations in WTA rhamnosylation and/or GlcNAcylation genes. Genetic complementation of different SV 3 and 7 isolates using intact alleles fully restored a characteristic SV 1/2 WTA carbohydrate pattern, including antisera reactions and phage adsorption. Intriguingly, phage-resistant L. monocytogenes EGDe (SV 1/2a) isolates featured the same glycosylation gene mutations and were serotyped as SV 3 or 7 respectively. Again, genetic complementation restored both carbohydrate antigens and phage susceptibility. Taken together, our data demonstrate that L. monocytogenes SV 3 and 7 originate from point mutations in glycosylation genes, and we show that phage predation represents a major driving force for serovar diversification and evolution of L. monocytogenes.
Collapse
Affiliation(s)
- Marcel R Eugster
- Institute of Food, Nutrition and Health, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Laurent S Morax
- Institute of Food, Nutrition and Health, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Vanessa J Hüls
- Institute of Food, Nutrition and Health, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Simona G Huwiler
- Institute of Food, Nutrition and Health, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Alexandre Leclercq
- Institut Pasteur, French National Reference Center and WHO Collaborating Center for Listeria, 75015, Paris, France
| | - Marc Lecuit
- Institut Pasteur, French National Reference Center and WHO Collaborating Center for Listeria, 75015, Paris, France
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, CH-8092, Zurich, Switzerland
| |
Collapse
|
50
|
Receptor binding proteins of Listeria monocytogenes bacteriophages A118 and P35 recognize serovar-specific teichoic acids. Virology 2015; 477:110-118. [DOI: 10.1016/j.virol.2014.12.035] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 01/06/2023]
|