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Sánchez C, Garde S, Landete JM, Calzada J, Baker DJ, Evans R, Narbad A, Mayer MJ, Ávila M. Identification, activity and delivery of new LysFA67 endolysin to target cheese spoilage Clostridium tyrobutyricum. Food Microbiol 2024; 117:104401. [PMID: 37919009 DOI: 10.1016/j.fm.2023.104401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 11/04/2023]
Abstract
Bacteriophages and their endolysins are potential biocontrol agents for the anaerobic spoilage organism Clostridium tyrobutyricum, which causes cheese late blowing defect. This study sequenced and compared the genomes of eight bacteriophages from Spanish dairy farms that were active against C. tyrobutyricum, to identify novel species and phage proteins. Phages vB_CtyS-FA67 and vB_CtyS-FA70 shared >94% intergenomic similarity to each other but neither phage had significant similarity to ΦCTP1, the unique C. tyrobutyricum phage sequenced to date. Taxonomic analysis indicated that both phages belong to the class Caudoviricetes and are related to dsDNA viruses with long non-contractile tails. vB_CtyS-FA67 had no other close relatives and encoded a novel endolysin, LysFA67, predicted to belong to the glycoside hydrolase GH24 family. LysFA67 lysed 93% of C. tyrobutyricum cells after 4 min in turbidity reduction assays, retaining lytic activity at pHs 4.2-8.1 and at 30-45 °C. The endolysin remained stable after 30 d storage at 4, 12 and 25 °C, while its activity decreased at -20 °C. LysFA67 lysed several clostridia species, while common dairy bacteria were not affected. Lactococcus lactis INIA 437, used as a cheese starter, was engineered to deliver LysFA67 and red fluorescent LysFA67-mCherry to dairy products. We demonstrated that these engineered strains were able to maintain lytic activity and fluorescence without affecting their technological properties in milk.
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Affiliation(s)
- Carmen Sánchez
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain
| | - Sonia Garde
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain.
| | - José María Landete
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain
| | - Javier Calzada
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain
| | - Dave J Baker
- Science Operations, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Rhiannon Evans
- Science Operations, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Arjan Narbad
- Food, Microbiome and Health Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK
| | - Melinda J Mayer
- Food, Microbiome and Health Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK.
| | - Marta Ávila
- Departamento de Tecnología de Alimentos, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Carretera de La Coruña km 7, 28040, Madrid, Spain.
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Phothichaisri W, Phetruen T, Chankhamhaengdecha S, Janvilisri T, Ounjai P, Fagan RP, Chanarat S. Unraveling Physical Interactions of Clostridioides difficile with Phage and Phage-Derived Proteins Using In Vitro and Whole-Cell Assays. Methods Mol Biol 2024; 2738:245-262. [PMID: 37966604 DOI: 10.1007/978-1-0716-3549-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Physical interactions between bacteria and phages provide valuable insights into the mechanisms of phage infection and may provide information on the use of phages as a therapeutic approach. In this study, we employed a combination of in vitro and whole-cell assays to examine the interactions between Clostridioides difficile and phages and phage-derived proteins. These techniques can also be adapted for studying the physical interactions between other bacterial species and their associated phages.
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Affiliation(s)
- Wichuda Phothichaisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Laboratory of Molecular Cell Biology, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Robert P Fagan
- School of Biosciences, Florey Institute, University of Sheffield, Sheffield, UK
| | - Sittinan Chanarat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
- Laboratory of Molecular Cell Biology, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.
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E S, Gummadi SN. Advances in the applications of Bacteriophages and phage products against food-contaminating bacteria. Crit Rev Microbiol 2023:1-26. [PMID: 37861086 DOI: 10.1080/1040841x.2023.2271098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/17/2023] [Indexed: 10/21/2023]
Abstract
Food-contaminating bacteria pose a threat to food safety and the economy by causing foodborne illnesses and spoilage. Bacteriophages, a group of viruses that infect only bacteria, have the potential to control bacteria throughout the "farm-to-fork continuum". Phage application offers several advantages, including targeted action against specific bacterial strains and minimal impact on the natural microflora of food. This review covers multiple aspects of bacteriophages applications in the food industry, including their use as biocontrol and biopreservation agents to fight over 20 different genera of food-contaminating bacteria, reduce cross-contamination and the risk of foodborne diseases, and also to prolong shelf life and preserve freshness. The review also highlights the benefits of using bacteriophages in bioprocesses to selectively inhibit undesirable bacteria, such as substrate competitors and toxin producers, which is particularly valuable in complex microbial bioprocesses where physical or chemical methods become inadequate. Furthermore, the review briefly discusses other uses of bacteriophages in the food industry, such as sanitizing food processing environments and detecting specific bacteria in food products. The review also explores strategies to enhance the effectiveness of phages, such as employing multi-phage cocktails, encapsulated phages, phage products, and synergistic hurdle approaches by combining them with antimicrobials.
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Affiliation(s)
- Suja E
- Applied and Industrial Microbiology Laboratory (AIM Lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Sathyanarayana N Gummadi
- Applied and Industrial Microbiology Laboratory (AIM Lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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Khan FM, Chen JH, Zhang R, Liu B. A comprehensive review of the applications of bacteriophage-derived endolysins for foodborne bacterial pathogens and food safety: recent advances, challenges, and future perspective. Front Microbiol 2023; 14:1259210. [PMID: 37869651 PMCID: PMC10588457 DOI: 10.3389/fmicb.2023.1259210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
Foodborne diseases are caused by food contaminated by pathogenic bacteria such as Escherichia coli, Salmonella, Staphylococcus aureus, Listeria monocytogenes, Campylobacter, and Clostridium, a critical threat to human health. As a novel antibacterial agent against foodborne pathogens, endolysins are peptidoglycan hydrolases encoded by bacteriophages that lyse bacterial cells by targeting their cell wall, notably in Gram-positive bacteria due to their naturally exposed peptidoglycan layer. These lytic enzymes have gained scientists' interest in recent years due to their selectivity, mode of action, engineering potential, and lack of resistance mechanisms. The use of endolysins for food safety has undergone significant improvements, which are summarized and discussed in this review. Endolysins can remove bacterial biofilms of foodborne pathogens and their cell wall-binding domain can be employed as a tool for quick detection of foodborne pathogens. We explained the applications of endolysin for eliminating pathogenic bacteria in livestock and various food matrices, as well as the limitations and challenges in use as a dietary supplement. We also highlight the novel techniques of the development of engineering endolysin for targeting Gram-negative bacterial pathogens. In conclusion, endolysin is safe and effective against foodborne pathogens and has no adverse effect on human cells and beneficial microbiota. As a result, endolysin could be employed as a functional bio-preservative agent to improve food stability and safety and maintain the natural taste of food quality.
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Affiliation(s)
- Fazal Mehmood Khan
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Jie-Hua Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Bin Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
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Nazir A, Xu X, Liu Y, Chen Y. Phage Endolysins: Advances in the World of Food Safety. Cells 2023; 12:2169. [PMID: 37681901 PMCID: PMC10486871 DOI: 10.3390/cells12172169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/19/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023] Open
Abstract
As antimicrobial resistance continues to escalate, the exploration of alternative approaches to safeguard food safety becomes more crucial than ever. Phage endolysins are enzymes derived from phages that possess the ability to break down bacterial cell walls. They have emerged as promising antibacterial agents suitable for integration into food processing systems. Their application as food preservatives can effectively regulate pathogens, thus contributing to an overall improvement in food safety. This review summarizes the latest techniques considering endolysins' potential for food safety. These techniques include native and engineered endolysins for controlling bacterial contamination at different points within the food production chain. However, we find that characterizing endolysins through in vitro methods proves to be time consuming and resource intensive. Alternatively, the emergence of advanced high-throughput sequencing technology necessitates the creation of a robust computational framework to efficiently characterize recently identified endolysins, paving the way for future research. Machine learning encompasses potent tools capable of analyzing intricate datasets and pattern recognition. This study briefly reviewed the use of these industry 4.0 technologies for advancing the research in food industry. We aimed to provide current status of endolysins in food industry and new insights by implementing these industry 4.0 strategies revolutionizes endolysin development. It will enhance food safety, customization, efficiency, transparency, and collaboration while reducing regulatory hurdles and ensuring timely product availability.
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Affiliation(s)
- Amina Nazir
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (A.N.); (X.X.); (Y.L.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Xiaohui Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (A.N.); (X.X.); (Y.L.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (A.N.); (X.X.); (Y.L.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Yibao Chen
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (A.N.); (X.X.); (Y.L.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
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Choi D, Kong M. LysGR1, a novel thermostable endolysin from Geobacillus stearothermophilus bacteriophage GR1. Front Microbiol 2023; 14:1178748. [PMID: 37275144 PMCID: PMC10237291 DOI: 10.3389/fmicb.2023.1178748] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Geobacillus stearothermophilus is a highly thermophilic, spore-forming Gram-positive bacterium that causes flat sour spoilage in low-acid canned foods. To address this problem, we isolated G. stearothermophilus-infecting phage GR1 from the soil and characterized its endolysin LysGR1. Phage GR1 belongs to the Siphoviridae family and possesses a genome of 79,387 DNA bps with 108 putative open reading frames. GR1 demonstrated a very low degree of homology to previously reported phages, indicating that it is novel. The endolysin of GR1 (LysGR1) contains an N-terminal amidase domain as an enzymatically active domain (EAD) and two C-terminal LysM domains as a cell wall binding domain (CBD). Although GR1 is specific to certain strains of G. stearothermophilus, LysGR1 showed a much broader lytic range, killing all the tested strains of G. stearothermophilus and several foodborne pathogens, such as Clostridium perfringens, Listeria monocytogenes, and Escherichia coli O157:H7. LysGR1_EAD, alone, also exhibits lytic activity against a wide range of bacteria, including Bacillus cereus, which is not terminated by a full-length endolysin. Both LysGR1 and its EAD effectively remove the G. stearothermophilus biofilms and are highly thermostable, retaining about 70% of their lytic activity after a 15-min incubation at 70°C. Considering the high thermal stability, broad lytic activity, and biofilm reduction efficacy of LysGR1 and its EAD, we hypothesize that these enzymes could act as promising biocontrol agents against G. stearothermophilus and as foodborne pathogens.
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Munir MT, Mtimet N, Guillier L, Meurens F, Fravalo P, Federighi M, Kooh P. Physical Treatments to Control Clostridium botulinum Hazards in Food. Foods 2023; 12:foods12081580. [PMID: 37107375 PMCID: PMC10137509 DOI: 10.3390/foods12081580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Clostridium botulinum produces Botulinum neurotoxins (BoNTs), causing a rare but potentially deadly type of food poisoning called foodborne botulism. This review aims to provide information on the bacterium, spores, toxins, and botulisms, and describe the use of physical treatments (e.g., heating, pressure, irradiation, and other emerging technologies) to control this biological hazard in food. As the spores of this bacterium can resist various harsh environmental conditions, such as high temperatures, the thermal inactivation of 12-log of C. botulinum type A spores remains the standard for the commercial sterilization of food products. However, recent advancements in non-thermal physical treatments present an alternative to thermal sterilization with some limitations. Low- (<2 kGy) and medium (3-5 kGy)-dose ionizing irradiations are effective for a log reduction of vegetative cells and spores, respectively; however, very high doses (>10 kGy) are required to inactivate BoNTs. High-pressure processing (HPP), even at 1.5 GPa, does not inactivate the spores and requires heat combination to achieve its goal. Other emerging technologies have also shown some promise against vegetative cells and spores; however, their application to C. botulinum is very limited. Various factors related to bacteria (e.g., vegetative stage, growth conditions, injury status, type of bacteria, etc.) food matrix (e.g., compositions, state, pH, temperature, aw, etc.), and the method (e.g., power, energy, frequency, distance from the source to target, etc.) influence the efficacy of these treatments against C. botulinum. Moreover, the mode of action of different physical technologies is different, which provides an opportunity to combine different physical treatment methods in order to achieve additive and/or synergistic effects. This review is intended to guide the decision-makers, researchers, and educators in using physical treatments to control C. botulinum hazards.
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Affiliation(s)
- Muhammad Tanveer Munir
- EnvA, Unit of Hygiene, Quality and Food Safety, 94700 Maisons-Alfort, France
- Anses, Laboratory of Food Safety, 94700 Maisons-Alfort, France
| | - Narjes Mtimet
- EnvA, Unit of Hygiene, Quality and Food Safety, 94700 Maisons-Alfort, France
- Anses, Laboratory of Food Safety, 94700 Maisons-Alfort, France
| | | | - François Meurens
- INRAE, Oniris, BIOEPAR, 44307 Nantes, France
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC J2S 2M2, Canada
| | - Phillipe Fravalo
- Chaire Agroalimentaire du Cnam, Conservatoire des Arts et Métiers, EPN7, 22440 Ploufragan, France
| | - Michel Federighi
- EnvA, Unit of Hygiene, Quality and Food Safety, 94700 Maisons-Alfort, France
- Anses, Laboratory of Food Safety, 94700 Maisons-Alfort, France
| | - Pauline Kooh
- Anses, Unit UERALIM, 94700 Maisons-Alfort, France
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A Broad-Spectrum Phage Endolysin (LysCP28) Able to Remove Biofilms and Inactivate Clostridium perfringens Strains. Foods 2023; 12:foods12020411. [PMID: 36673503 PMCID: PMC9858456 DOI: 10.3390/foods12020411] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Clostridium perfringens is a gram-positive, anaerobic, spore-forming bacterium capable of producing four major toxins which cause disease symptoms and pathogenesis in humans and animals. C. perfringens strains carrying enterotoxins can cause food poisoning in humans and are associated with meat consumption. An endolysin, named LysCP28, is encoded by orf28 from C. perfringens bacteriophage BG3P. This protein has an N-terminal glycosyl-hydrolase domain (lysozyme) and a C-terminal SH3 domain. Purified LysCP28 (38.8 kDa) exhibited a broad spectrum of lytic activity against C. perfringens strains (77 of 96 or 80.21%), including A, B, C, and D types, isolated from different sources. Moreover, LysCP28 (10 μg/mL) showed high antimicrobial activity and was able to lyse 2 × 107 CFU/mL C. perfringens ATCC 13124 and C. perfringens J21 (animal origin) within 2 h. Necessary due to this pathogenic bacterium's ability to form biofilms, LysCP28 (18.7 μg/mL) was successfully evaluated as an antibiofilm agent in both biofilm removal and formation inhibition. Finally, to confirm the efficacy of LysCP28 in a food matrix, duck meat was contaminated with C. perfringens and treated with endolysin (100 µg/mL and 50 µg/mL), which reduced viable bacteria by 3.2 and 3.08 units-log, respectively, in 48 h at 4 °C. Overall, the endolysin LysCP28 could potentially be used as a biopreservative to reduce C. perfringens contamination during food processing.
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Lee W, Matthews A, Moore D. Safety Evaluation of a Novel Algal Feed Additive for Poultry Production. Avian Dis 2022; 66:1-11. [PMID: 36214407 DOI: 10.1637/aviandiseases-d-22-00043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022]
Abstract
Feed additives are critical components for poultry health and the economic viability of antibiotic-free poultry production. The aim of the present study is to evaluate the safety of a novel algal-derived feed additive, a dried biomass powder produced from Chlamydomonas reinhardtii strain crAL082, modified to express an N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) and a lysozyme-type enzyme (EC 3.2.1.17). A 42-day oral toxicity study showed that the crAL082 dried biomass powder was fully tolerated by broiler chicken based on the lack of detrimental effects found in performance, mortality, hematology, blood clinical chemistry, and histopathologic results compared with those of a nontreated control group, resulting in a "No Observed Adverse Effect Level" of 5000 ppm, the highest dose tested. The study demonstrates the first-ever safety result of a C. reinhardtii microalgae dried biomass powder used as a feed additive in broiler chickens. Furthermore, safety is shown for the two additional enzymes expressed within the C. reinhardtii crAL082 strain and ingested by the birds.
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Affiliation(s)
- Weiluo Lee
- Axitan Ltd., Ground Floor Offices, Whittle Way, SG1 2FS, Stevenage, United Kingdom,
| | | | - Daniel Moore
- Colorado Quality Research, Inc., Wellington, CO 80549
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Specific Isolation of Clostridium botulinum Group I Cells by Phage Lysin Cell Wall Binding Domain with the Aid of S-Layer Disruption. Int J Mol Sci 2022; 23:ijms23158391. [PMID: 35955526 PMCID: PMC9368847 DOI: 10.3390/ijms23158391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/05/2023] Open
Abstract
Clostridium botulinum is a notorious pathogen that raises health and food safety concerns by producing the potent botulinum neurotoxin and causing botulism, a potentially fatal neuroparalytic disease in humans and animals. Efficient methods for the identification and isolation of C. botulinum are warranted for laboratory diagnostics of botulism and for food safety risk assessment. The cell wall binding domains (CBD) of phage lysins are recognized by their high specificity and affinity to distinct types of bacteria, which makes them promising for the development of diagnostic tools. We previously identified CBO1751, which is the first antibotulinal phage lysin showing a lytic activity against C. botulinum Group I. In this work, we assessed the host specificity of the CBD of CBO1751 and tested its feasibility as a probe for the specific isolation of C. botulinum Group I strains. We show that the CBO1751 CBD specifically binds to C. botulinum Group I sensu lato (including C. sporogenes) strains. We also demonstrate that some C. botulinum Group I strains possess an S-layer, the disruption of which by an acid glycine treatment is required for efficient binding of the CBO1751 CBD to the cells of these strains. We further developed CBO1751 CBD-based methods using flow cytometry and magnetic separation to specifically isolate viable cells of C. botulinum Group I. These methods present potential for applications in diagnostics and risk assessment in order to control the botulism hazard.
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Cruz KCP, Enekegho LO, Stuart DT. Bioengineered Probiotics: Synthetic Biology Can Provide Live Cell Therapeutics for the Treatment of Foodborne Diseases. Front Bioeng Biotechnol 2022; 10:890479. [PMID: 35656199 PMCID: PMC9152101 DOI: 10.3389/fbioe.2022.890479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/29/2022] [Indexed: 11/15/2022] Open
Abstract
The rising prevalence of antibiotic resistant microbial pathogens presents an ominous health and economic challenge to modern society. The discovery and large-scale development of antibiotic drugs in previous decades was transformational, providing cheap, effective treatment for what would previously have been a lethal infection. As microbial strains resistant to many or even all antibiotic drug treatments have evolved, there is an urgent need for new drugs or antimicrobial treatments to control these pathogens. The ability to sequence and mine the genomes of an increasing number of microbial strains from previously unexplored environments has the potential to identify new natural product antibiotic biosynthesis pathways. This coupled with the power of synthetic biology to generate new production chassis, biosensors and “weaponized” live cell therapeutics may provide new means to combat the rapidly evolving threat of drug resistant microbial pathogens. This review focuses on the application of synthetic biology to construct probiotic strains that have been endowed with functionalities allowing them to identify, compete with and in some cases kill microbial pathogens as well as stimulate host immunity. Weaponized probiotics may have the greatest potential for use against pathogens that infect the gastrointestinal tract: Vibrio cholerae, Staphylococcus aureus, Clostridium perfringens and Clostridioides difficile. The potential benefits of engineered probiotics are highlighted along with the challenges that must still be met before these intriguing and exciting new therapeutic tools can be widely deployed.
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Filik K, Szermer-Olearnik B, Oleksy S, Brykała J, Brzozowska E. Bacteriophage Tail Proteins as a Tool for Bacterial Pathogen Recognition—A Literature Review. Antibiotics (Basel) 2022; 11:antibiotics11050555. [PMID: 35625199 PMCID: PMC9137617 DOI: 10.3390/antibiotics11050555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/23/2022] Open
Abstract
In recent years, a number of bacterial detection methods have been developed to replace time-consuming culture methods. One interesting approach is to mobilize the ability of phage tail proteins to recognize and bind to bacterial hosts. In this paper, the authors provide an overview of the current methodologies in which phage proteins play major roles in detecting pathogenic bacteria. Authors focus on proteins capable of recognizing highly pathogenic strains, such as Acinetobacter baumannii, Campylobacter spp., Yersinia pestis, Pseudomonas aeruginosa, Listeria monocytogenes, Staphylococcus aureus, Enterococcus spp., Salmonella spp., and Shigella. These pathogens may be diagnosed by capture-based detection methods involving the use of phage protein-coated nanoparticles, ELISA (enzyme-linked immunosorbent assay)-based methods, or biosensors. The reviewed studies show that phage proteins are becoming an important diagnostic tool due to the discovery of new phages and the increasing knowledge of understanding the specificity and functions of phage tail proteins.
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13
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Huang S, Tian Y, Wang Y, García P, Liu B, Lu R, Wu L, Bao H, Pang M, Zhou Y, Wang R, Zhang H. The Broad Host Range Phage vB_CpeS_BG3P Is Able to Inhibit Clostridium perfringens Growth. Viruses 2022; 14:v14040676. [PMID: 35458406 PMCID: PMC9033094 DOI: 10.3390/v14040676] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/10/2022] Open
Abstract
Clostridium perfringens is an important pathogen for both humans and animals, causing human foodborne disease and necrotic enteritis in poultry. In the present study, a C. perfringens-specific phage, vB_CpeS_BG3P (designated as BG3P hereafter), was isolated from chicken farm sewage. Both electron microscopy and phylogenetic analysis suggested that phage BG3P is a novel phage belonging to Siphoviridae family. Phage BG3P exhibited a broad host range against different C. perfringens isolates (90.63% of strains were infected). Sequencing of the complete genome revealed a linear double-stranded DNA (43,528 bp) with 28.65% GC content. After sequence analysis, 73 open reading frames (orfs) were predicted, of which only 13 were annotated with known functions. No tRNA and virulence encoding genes were detected. It should be noted that the protein of orf 15 has 97.92% homology to C. perfringens-specific chloramphenicol resistance protein, which has not been reported for any C. perfringens phage. Phylogenetic analysis of the ssDNA binding protein demonstrated that this phage is closely related to C. perfringens phages phiSM101 and phi3626. In considering future use as an antimicrobial agent, some biological characteristics were observed, such as a good pH (3−11) stability and moderate temperature tolerance (<60 °C). Moreover, bacteriophage BG3P showed a good antimicrobial effect against C. perfringens liquid cultures. Thus, phage treatment with MOI ≥ 100 completely inhibited bacterial growth compared to untreated cultures. Although phage BG3P shows good lytic efficiency and broad host range in vitro, future development and application may need to consider removal of the chloramphenicol-like resistance gene or exploring its lysin for future antibacterial applications.
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Affiliation(s)
- Sisi Huang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Yuan Tian
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yongjuan Wang
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China;
| | - Pilar García
- Dairy Research Institute of Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain;
| | - Banhong Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Rui Lu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Liting Wu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Hongduo Bao
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Maoda Pang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Yan Zhou
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Ran Wang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Hui Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
- Correspondence: ; Tel.: +86-25-84391627; Fax: +86-25-84391617
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Deka D, Annapure US, Shirkole SS, Thorat BN. Bacteriophages: An organic approach to food decontamination. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.16101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Darshana Deka
- Department of Food Engineering and Technology Institute of Chemical Technology Mumbai, ICT – IOC Campus Bhubaneswar India
| | - U. S. Annapure
- Department of Food Engineering and Technology Institute of Chemical Technology Mumbai India
| | - S. S. Shirkole
- Department of Food Engineering and Technology Institute of Chemical Technology Mumbai, ICT – IOC Campus Bhubaneswar India
| | - B. N. Thorat
- Department of Food Engineering and Technology Institute of Chemical Technology Mumbai, ICT – IOC Campus Bhubaneswar India
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15
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Rahman MU, Wang W, Sun Q, Shah JA, Li C, Sun Y, Li Y, Zhang B, Chen W, Wang S. Endolysin, a Promising Solution against Antimicrobial Resistance. Antibiotics (Basel) 2021; 10:1277. [PMID: 34827215 PMCID: PMC8614784 DOI: 10.3390/antibiotics10111277] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global crisis for human public health which threatens the effective prevention and control of ever-increasing infectious diseases. The advent of pandrug-resistant bacteria makes most, if not all, available antibiotics invalid. Meanwhile, the pipeline of novel antibiotics development stagnates, which prompts scientists and pharmacists to develop unconventional antimicrobials. Bacteriophage-derived endolysins are cell wall hydrolases which could hydrolyze the peptidoglycan layer from within and outside of bacterial pathogens. With high specificity, rapid action, high efficiency, and low risk of resistance development, endolysins are believed to be among the best alternative therapeutic agents to treat multidrug resistant (MDR) bacteria. As of now, endolysins have been applied to diverse aspects. In this review, we comprehensively introduce the structures and activities of endolysins and summarize the latest application progress of recombinant endolysins in the fields of medical treatment, pathogen diagnosis, food safety, and agriculture.
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Affiliation(s)
- Mujeeb ur Rahman
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Weixiao Wang
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China;
| | - Qingqing Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Junaid Ali Shah
- College of Life Sciences, Jilin University, Changchun 130012, China;
| | - Chao Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Yuanrui Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Bailing Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China;
| | - Wei Chen
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China;
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
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16
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Morzywolek A, Plotka M, Kaczorowska AK, Szadkowska M, Kozlowski LP, Wyrzykowski D, Makowska J, Waters JJ, Swift SM, Donovan DM, Kaczorowski T. Novel Lytic Enzyme of Prophage Origin from Clostridium botulinum E3 Strain Alaska E43 with Bactericidal Activity against Clostridial Cells. Int J Mol Sci 2021; 22:ijms22179536. [PMID: 34502443 PMCID: PMC8430805 DOI: 10.3390/ijms22179536] [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: 05/26/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 01/13/2023] Open
Abstract
Clostridium botulinum is a Gram-positive, anaerobic, spore-forming bacterium capable of producing botulinum toxin and responsible for botulism of humans and animals. Phage-encoded enzymes called endolysins, which can lyse bacteria when exposed externally, have potential as agents to combat bacteria of the genus Clostridium. Bioinformatics analysis revealed in the genomes of several Clostridium species genes encoding putative N-acetylmuramoyl-l-alanine amidases with anti-clostridial potential. One such enzyme, designated as LysB (224-aa), from the prophage of C. botulinum E3 strain Alaska E43 was chosen for further analysis. The recombinant 27,726 Da protein was expressed and purified from E. coli Tuner(DE3) with a yield of 37.5 mg per 1 L of cell culture. Size-exclusion chromatography and analytical ultracentrifugation experiments showed that the protein is dimeric in solution. Bioinformatics analysis and results of site-directed mutagenesis studies imply that five residues, namely H25, Y54, H126, S132, and C134, form the catalytic center of the enzyme. Twelve other residues, namely M13, H43, N47, G48, W49, A50, L73, A75, H76, Q78, N81, and Y182, were predicted to be involved in anchoring the protein to the lipoteichoic acid, a significant component of the Gram-positive bacterial cell wall. The LysB enzyme demonstrated lytic activity against bacteria belonging to the genera Clostridium, Bacillus, Staphylococcus, and Deinococcus, but did not lyse Gram-negative bacteria. Optimal lytic activity of LysB occurred between pH 4.0 and 7.5 in the absence of NaCl. This work presents the first characterization of an endolysin derived from a C. botulinum Group II prophage, which can potentially be used to control this important pathogen.
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Affiliation(s)
- Agnieszka Morzywolek
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland; (A.M.); (M.S.)
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland; (A.M.); (M.S.)
- Correspondence: (M.P.); (T.K.)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland;
| | - Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland; (A.M.); (M.S.)
| | - Lukasz P. Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland;
| | - Dariusz Wyrzykowski
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland; (D.W.); (J.M.)
| | - Joanna Makowska
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland; (D.W.); (J.M.)
| | - Jerel J. Waters
- Animal Biosciences and Biotechnology Laboratory, ARS, NEA, USDA, Beltsville, MD 20705-2350, USA; (J.J.W.); (S.M.S.); (D.M.D.)
| | - Steven M. Swift
- Animal Biosciences and Biotechnology Laboratory, ARS, NEA, USDA, Beltsville, MD 20705-2350, USA; (J.J.W.); (S.M.S.); (D.M.D.)
| | - David M. Donovan
- Animal Biosciences and Biotechnology Laboratory, ARS, NEA, USDA, Beltsville, MD 20705-2350, USA; (J.J.W.); (S.M.S.); (D.M.D.)
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland; (A.M.); (M.S.)
- Correspondence: (M.P.); (T.K.)
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17
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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.
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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.)
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