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Yuan X, Zhu Z, Huang Z, Yu S, Jin H, Chen B, Yu S, Xue L, Chen M, Zhang J, Wang J, Wu Q, Ding Y. Engineered lytic phage of Bacillus cereus and its application in milk. Int J Food Microbiol 2023; 405:110339. [PMID: 37517118 DOI: 10.1016/j.ijfoodmicro.2023.110339] [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: 04/20/2023] [Revised: 07/09/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023]
Abstract
Phages have been approved for use in the food industry to control bacterial contamination in some countries. However, their broader adoption is hindered by some limitations. For instance, the persistence of infectious phages in the food industry can lead to the emergence of resistant bacteria, which negatively impacts the long-term effectiveness of phages. Additionally, the narrow host range of phages limits their effectiveness against various strains. To address these deficiencies, phage engineering has been proposed as a rational approach for modifying phages. In this study, we developed a simple and efficient engineering method for Bacillus cereus phage, using DK1 as an example, to reduce the number of residual phages and expand its range of hosts. Specifically, we knocked out the appendage gene, which codes for the receptor-binding protein, to produce phage progeny with structural defects in their appendages, resulting in the loss of infectivity after host elimination. Furthermore, we used plasmid-mediated means to express different appendage proteins during phage preparation, which allowed altering the host spectrum of the engineered phages without gene insertion. In practical applications, our engineered phages effectively reduced the number of B. cereus in milk and prevented the amplification of active progeny. Our strategy transformed phages from active viruses into more controllable antibacterial agents, making them safer and more efficient for the prevention and control of B. cereus. Moreover, we believe this strategy will help drive the use of engineered phages in the food industry.
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Affiliation(s)
- Xiaoming Yuan
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China; Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zhenjun Zhu
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Zhichao Huang
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China; Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shan Yu
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China; Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Hui Jin
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China; Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Bo Chen
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China; Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shubo Yu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Liang Xue
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Moutong Chen
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jumei Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Qingping Wu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yu Ding
- Department of Food Science & Engineering, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China.
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Torres-Boncompte J, Catalá-Gregori P, Garcia-Llorens J, Soriano JM, Sevilla-Navarro S. Simultaneous Salmonella and bacteriophage isolation on Modified Semisolid Rappaport Vassiliadis media. Poult Sci 2023; 102:102960. [PMID: 37579648 PMCID: PMC10429287 DOI: 10.1016/j.psj.2023.102960] [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: 04/30/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/16/2023] Open
Abstract
Salmonella represents a food safety concern worldwide. Despite the application of National Control Programs (NCP) against Salmonella, regulated by the European Union, every year the European Food Safety Authority reports new cases. On the look for new alternatives to antibiotics, bacteriophages, or phages, rise as a promising alternative to treat multidrug resistance infections. Although they are known to be ubiquitous in the environment, their high specificity to host cells hinders their isolation and usage for phage therapy. The ISO 6579-1:2017 is performed as a reference method in the NCP and uses an unspecific media to enrich the sample the same way most phage isolation protocols do. Later, the protocol uses a more selective media to isolate the Salmonella, Modified Semisolid Rappaport Vassiliadis (MSRV). This paper aims to find out whether, due to the similarity between phage isolation protocols and the ISO 6579-1:2017, this last one could be used as a protocol to also isolate phages against the same bacterium that is being simultaneously isolated. To do so, 2 experiments were performed to assess phage isolation from MSRV media in in-vivo conditions. The results from experiments 1 and 2 proved that the MSRV media was usable for simultaneous phage and pathogen isolation through a single procedure. Additionally, there is a correlation between the antigenic formulae from the bacteria and the phage's host range, seeming to be effective against bacteria with similar antigenic formulae.
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Affiliation(s)
- Jan Torres-Boncompte
- Food & Health Lab, Institute of Materials Science, University of Valencia, Valencia, 46980, Spain; Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, 12539, Spain
| | - Pablo Catalá-Gregori
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, 12539, Spain; Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Instituto de Ciencias Biomédicas, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, 46113, Spain
| | - Josep Garcia-Llorens
- Food & Health Lab, Institute of Materials Science, University of Valencia, Valencia, 46980, Spain; Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, 12539, Spain
| | - José M Soriano
- Food & Health Lab, Institute of Materials Science, University of Valencia, Valencia, 46980, Spain; Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, University of Valencia-Health Research Institute La Fe, Valencia, 46026, Spain
| | - Sandra Sevilla-Navarro
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), Castellón, 12539, Spain; Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Instituto de Ciencias Biomédicas, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, 46113, Spain.
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Nale JY, Chan B, Nnadi NE, Cheng JKJ, Matts S, Nezam-Abadi N, Turkington CJR, Charreton LM, Bola H, Nazir R, Hoza AS, Wamala SP, Ibanda I, Maina AN, Apopo AA, Msoffe VT, Moremi N, Moore GW, Asiimwe I, Namatovu A, Mutumba P, Kamya D, Nabunje R, Nakabugo I, Kazwala RR, Kangethe E, Negash AA, Watelo AK, Bukamba N, Muhindo G, Lubowa NM, Jillani N, Nyachieo A, Nasinyama G, Nakavuma J, Millard A, Nagel TE, Clokie MRJ. Novel Escherichia coli-Infecting Bacteriophages Isolated from Uganda That Target Human Clinical Isolates. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:141-149. [PMID: 37841386 PMCID: PMC10574529 DOI: 10.1089/phage.2023.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Background The antimicrobial resistance catastrophe is a growing global health threat and predicted to be worse in developing countries. Phages for Global Health (PGH) is training scientists in these regions to isolate relevant therapeutic phages for pathogenic bacteria within their locality, and thus contributing to making phage technology universally available. Materials and Methods During the inaugural PGH workshop in East Africa, samples from Ugandan municipal sewage facilities were collected and two novel Escherichia coli lytic phages were isolated and characterized. Results The phages, UP19 (capsid diameter ∼100 nm, contractile tail ∼120/20 nm) and UP30 (capsid diameter ∼70 nm, noncontractile tail of ∼170/20 nm), lysed ∼82% and ∼36% of the 11 clinical isolates examined, respectively. The genomes of UP19 (171.402 kb, 282 CDS) and UP30 (49.834 kb, 75 CDS) closely match the genera Dhakavirus and Tunavirus, respectively. Conclusion The phages isolated have therapeutic potential for further development against E. coli infections.
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Affiliation(s)
- Janet Yakubu Nale
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Centre for Epidemiology and Planetary Health, School of Veterinary Medicine, Scotland's Rural College, Inverness, Scotland, United Kingdom
| | - Benjamin Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Nnaemeka Emmanuel Nnadi
- Department of Microbiology, Faculty of Natural and Applied Sciences, Plateau State University, Bokkos, Nigeria
| | - Jeffrey Kwok Jone Cheng
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Susan Matts
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Neda Nezam-Abadi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Christopher Jason Richard Turkington
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Lucie Manon Charreton
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Sciences et Humanités, École Supérieur de Biologie, Biochimie, Lyon, France
| | - Harroop Bola
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Imperial College School of Medicine, London, United Kingdom
| | - Ramez Nazir
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Yale-Waterbury Internal Medicine, Waterbury, Connecticut, USA
| | - Abubakar Shaaban Hoza
- Department of Veterinary Microbiology, Parasitology & Biotechnology, College of Veterinary Medicine & Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Samuel Posian Wamala
- Department of Biotechnical and Diagnostic Science, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Ivan Ibanda
- Department of Pharmacology and Therapeutics, School of Medicine and Surgery, King Ceasor University, Kampala, Uganda
| | - Alice Nyambura Maina
- Department of Biology, University of Nairobi, Nairobi, Kenya
- Department of Food Science and Technology, Technical University of Kenya, Nairobi, Kenya
| | | | - Venance Theophil Msoffe
- Department of Biological Sciences, Mkwawa University College of Education, The Constituent College of University of Dar es Salaam, Iringa, Tanzania
| | - Nyambura Moremi
- Department of Research, National Public Health Laboratory, Dar es Salaam, Tanzania
| | - Grace Wanjiru Moore
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Ismail Asiimwe
- Department of Biomolecular Resources and Biolab Sciences, School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Alice Namatovu
- Department of Biomolecular Resources and Biolab Sciences, School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Paul Mutumba
- Department of Biomolecular Resources and Biolab Sciences, School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Deus Kamya
- Department of Biomolecular Resources and Biolab Sciences, School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Ritah Nabunje
- Department of Biomolecular Resources and Biolab Sciences, School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Immaculate Nakabugo
- Department of Biomolecular Resources and Biolab Sciences, School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Rudovick Ruben Kazwala
- Department of Veterinary Medicine & Public Health, College of Veterinary Medicine & Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Erastus Kangethe
- Department of Public Health, Pharmacology and Toxicology, University of Nairobi, Nairobi, Kenya
| | - Abel Abera Negash
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Microbiology, Immunology and Parasitology, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Nelson Bukamba
- Mountain Gorilla Veterinary Project Inc, Department of Wildlife and Aquatic Resources Management, College of Veterinary Medicine, Makerere University Kampala, Uganda
| | | | - Nathan Musisi Lubowa
- Department of Biotechnical and Diagnostic Science, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Ngalla Jillani
- Phage Biology Laboratory, Institute of Primate Research, Karen Nairobi, Kenya
| | - Atunga Nyachieo
- Phage Biology Laboratory, Institute of Primate Research, Karen Nairobi, Kenya
| | - George Nasinyama
- Department of Public Health Kampala International University, Kampala, Uganda
- School of Sciences, Health Sciences, Technology, and Engineering, Unicaf University, Kampala, Uganda
| | - Jesca Nakavuma
- Department of Biomolecular Resources and Biolab Sciences, School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Zaki BM, Mohamed AA, Dawoud A, Essam K, Hammouda ZK, Abdelsattar AS, El-Shibiny A. Isolation, screening and characterization of phage. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:13-60. [PMID: 37739553 DOI: 10.1016/bs.pmbts.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Bacterial resistance threatens public health due to a lack of novel antibacterial classes since the 21st century. Bacteriophages, the most ubiquitous microorganism on Earth and natural predators of bacteria, have the potential to save the world from the post-antibiotic era. Therefore, phage isolation and characterization are in high demand to find suitable phages for therapeutic and bacterial control applications. The chapter presents brief guidance supported by recommendations on the isolation of phages, and initial screening of phage antimicrobial efficacy, in addition to, conducting comprehensive characterization addressing morphological, biological, genomic, and taxonomic features.
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Affiliation(s)
- Bishoy Maher Zaki
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Amira A Mohamed
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Kareem Essam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Zainab K Hammouda
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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McMahon TC, Kingombe CB, Mathews A, Seyer K, Wong A, Blais BW, Carrillo CD. Microbial Antagonism in Food-Enrichment Culture: Inhibition of Shiga Toxin-Producing Escherichia coli and Shigella Species. Front Microbiol 2022; 13:880043. [PMID: 35814680 PMCID: PMC9259949 DOI: 10.3389/fmicb.2022.880043] [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: 02/20/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial pathogens, such as Shiga toxin-producing Escherichia coli (STEC) and Shigella spp., are important causes of foodborne illness internationally. Recovery of these organisms from foods is critical for food safety investigations to support attribution of illnesses to specific food commodities; however, isolation of bacterial cultures can be challenging. Methods for the isolation of STEC and Shigella spp. from foods typically require enrichment to amplify target organisms to detectable levels. Yet, during enrichment, target organisms can be outcompeted by other bacteria in food matrices due to faster growth rates, or through production of antimicrobial agents such as bacteriocins or bacteriophages. The purpose of this study was to evaluate the occurrence of Shigella and STEC inhibitors produced by food microbiota. The production of antimicrobial compounds in cell-free extracts from 200 bacterial strains and 332 food-enrichment broths was assessed. Cell-free extracts produced by 23 (11.5%) of the strains tested inhibited growth of at least one of the five Shigella and seven STEC indicator strains used in this study. Of the 332 enrichment broths tested, cell-free extracts from 25 (7.5%) samples inhibited growth of at least one of the indicator strains tested. Inhibition was most commonly associated with E. coli recovered from meat products. Most of the inhibiting compounds were determined to be proteinaceous (34 of the 48 positive samples, 71%; including 17 strains, 17 foods) based on inactivation by proteolytic enzymes, indicating presence of bacteriocins. The cell-free extracts from 13 samples (27%, eight strains, five foods) were determined to contain bacteriophages based on the observation of plaques in diluted extracts and/or resistance to proteolytic enzymes. These results indicate that the production of inhibitors by food microbiota may be an important challenge for the recovery of foodborne pathogens, particularly for Shigella sonnei. The performance of enrichment media for recovery of Shigella and STEC could be improved by mitigating the impact of inhibitors produced by food microbiota during the enrichment process.
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Affiliation(s)
- Tanis C. McMahon
- Research and Development, Ottawa Laboratory (Carling), Ontario Laboratory Network, Canadian Food Inspection Agency, Ottawa, ON, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | | | - Amit Mathews
- Microbiology, Greater Toronto Area Laboratory, Ontario Laboratory Network, Canadian Food Inspection Agency, Toronto, ON, Canada
| | - Karine Seyer
- Microbiology (Food), St-Hyacinthe Laboratory, Eastern Laboratories Network, Canadian Food Inspection Agency, St-Hyacinthe, QC, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Burton W. Blais
- Research and Development, Ottawa Laboratory (Carling), Ontario Laboratory Network, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Catherine D. Carrillo
- Research and Development, Ottawa Laboratory (Carling), Ontario Laboratory Network, Canadian Food Inspection Agency, Ottawa, ON, Canada
- *Correspondence: Catherine D. Carrillo,
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Abdelsattar AS, Dawoud A, Makky S, Nofal R, Aziz RK, El-Shibiny A. Bacteriophages: from isolation to application. Curr Pharm Biotechnol 2021; 23:337-360. [PMID: 33902418 DOI: 10.2174/1389201022666210426092002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/29/2021] [Accepted: 03/11/2021] [Indexed: 11/22/2022]
Abstract
Bacteriophages are considered as a potential alternative to fight pathogenic bacteria during the antibiotic resistance era. With their high specificity, they are being widely used in various applications: medicine, food industry, agriculture, animal farms, biotechnology, diagnosis, etc. Many techniques have been designed by different researchers for phage isolation, purification, and amplification, each of which has strengths and weaknesses. However, all aim at having a reasonably pure phage sample that can be further characterized. Phages can be characterized based on their physiological, morphological or inactivation tests. Microscopy, in particular, has opened a wide gate not only for visualizing phage morphological structure, but also for monitoring biochemistry and behavior. Meanwhile, computational analysis of phage genomes provides more details about phage history, lifestyle, and potential for toxigenic or lysogenic conversion, which translate to safety in biocontrol and phage therapy applications. This review summarizes phage application pipelines at different levels and addresses specific restrictions and knowledge gaps in the field. Recently developed computational approaches, which are used in phage genome analysis, are critically assessed. We hope that this assessment provides researchers with useful insights for selection of suitable approaches for Phage-related research aims and applications.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Rana Nofal
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy St, Cairo. Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
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Hamilton A, Harper SJ, Critzer F. Optimization of a Method for the Concentration of Genetic Material in Bacterial and Fungal Communities on Fresh Apple Peel Surfaces. Microorganisms 2020; 8:microorganisms8101480. [PMID: 32993184 PMCID: PMC7601045 DOI: 10.3390/microorganisms8101480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022] Open
Abstract
Apples are the most consumed fruit in the United States and have recently been shown to exhibit some vulnerability to contamination across the supply chain. It is unclear what role a fruit microbiome analysis may serve in future food safety programs interested in understanding changes in the product and the processing environment. Ultimately, sample integrity is key if any of these approaches are to be employed; low microbial loads on apple surfaces, the inability to sample the entire surface, and inefficiency of removal may act as barriers to achieving high-quality DNA. As such, the objective of this study was to identify a reproducible method to concentrate and quantify bacterial and fungal DNA from fresh apple surfaces. Five methods were evaluated: two variations of wash solutions for bath sonication, wash filtration, epidermis excision, and surface swabbing. Epidermis excision returned the highest mean DNA quantities, followed by the sonicated washes and wash filtration. Surface swabbing was consistently below the limit of detection. Based on the quantity of host DNA contamination in surface excision, the sonicated wash solution containing a surfactant presents the greatest opportunity for consistent, high-yielding DNA recovery from the entire apple surface.
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Affiliation(s)
- Alexis Hamilton
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
- Correspondence: ; Tel.:+1-509-786-9209
| | - Scott J. Harper
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA;
| | - Faith Critzer
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
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Abstract
Numerous bacteriophages-viruses of bacteria, also known as phages-have been described for hundreds of bacterial species. The Gram-negative Shigella species are close relatives of Escherichia coli, yet relatively few previously described phages appear to exclusively infect this genus. Recent efforts to isolate Shigella phages have indicated these viruses are surprisingly abundant in the environment and have distinct genomic and structural properties. In addition, at least one model system used for experimental evolution studies has revealed a unique mechanism for developing faster infection cycles. Differences between these bacteriophages and other well-described model systems may mirror differences between their hosts' ecology and defense mechanisms. In this review, we discuss the history of Shigella phages and recent developments in their isolation and characterization and the structural information available for three model systems, Sf6, Sf14, and HRP29; we also provide an overview of potential selective pressures guiding both Shigella phage and host evolution.
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Affiliation(s)
- Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Sarah M Doore
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan 48824, USA;
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Yee MO, Deutzmann J, Spormann A, Rotaru AE. Cultivating electroactive microbes-from field to bench. NANOTECHNOLOGY 2020; 31:174003. [PMID: 31931483 DOI: 10.1088/1361-6528/ab6ab5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Electromicrobiology is an emerging field investigating and exploiting the interaction of microorganisms with insoluble electron donors or acceptors. Some of the most recently categorized electroactive microorganisms became of interest to sustainable bioengineering practices. However, laboratories worldwide typically maintain electroactive microorganisms on soluble substrates, which often leads to a decrease or loss of the ability to effectively exchange electrons with solid electrode surfaces. In order to develop future sustainable technologies, we cannot rely solely on existing lab-isolates. Therefore, we must develop isolation strategies for environmental strains with electroactive properties superior to strains in culture collections. In this article, we provide an overview of the studies that isolated or enriched electroactive microorganisms from the environment using an anode as the sole electron acceptor (electricity-generating microorganisms) or a cathode as the sole electron donor (electricity-consuming microorganisms). Next, we recommend a selective strategy for the isolation of electroactive microorganisms. Furthermore, we provide a practical guide for setting up electrochemical reactors and highlight crucial electrochemical techniques to determine electroactivity and the mode of electron transfer in novel organisms.
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Affiliation(s)
- Mon Oo Yee
- Nordcee, Department of Biology, University of Southern Denmark, Odense, DK-5230, Denmark
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Fister S, Mester P, Witte AK, Sommer J, Schoder D, Rossmanith P. Part of the problem or the solution? Indiscriminate use of bacteriophages in the food industry can reduce their potential and impair growth-based detection methods. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.02.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Sommer J, Trautner C, Witte AK, Fister S, Schoder D, Rossmanith P, Mester PJ. Don't Shut the Stable Door after the Phage Has Bolted-The Importance of Bacteriophage Inactivation in Food Environments. Viruses 2019; 11:E468. [PMID: 31121941 PMCID: PMC6563225 DOI: 10.3390/v11050468] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/05/2019] [Accepted: 05/17/2019] [Indexed: 12/11/2022] Open
Abstract
In recent years, a new potential measure against foodborne pathogenic bacteria was rediscovered-bacteriophages. However, despite all their advantages, in connection to their widespread application in the food industry, negative consequences such as an uncontrolled phage spread as well as a development of phage resistant bacteria can occur. These problems are mostly a result of long-term persistence of phages in the food production environment. As this topic has been neglected so far, this article reviews the current knowledge regarding the effectiveness of disinfectant strategies for phage inactivation and removal. For this purpose, the main commercial phage products, as well as their application fields are first discussed in terms of applicable inactivation strategies and legal regulations. Secondly, an overview of the effectiveness of disinfectants for bacteriophage inactivation in general and commercial phages in particular is given. Finally, this review outlines a possible strategy for users of commercial phage products in order to improve the effectiveness of phage inactivation and removal after application.
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Affiliation(s)
- Julia Sommer
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department for Farm Animal and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Christoph Trautner
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department for Farm Animal and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Anna Kristina Witte
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department for Farm Animal and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
- HTK Hygiene Technologie Kompetenzzentrum GmbH, Buger Str. 80, 96049 Bamberg, Germany.
| | - Susanne Fister
- Former member of Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Milk Technology and Food Science, Department for Farm Animal and Public Veterinary Health, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria.
| | - Dagmar Schoder
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animal and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Peter Rossmanith
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department for Farm Animal and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animal and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Patrick-Julian Mester
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department for Farm Animal and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
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12
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Hahn MW, Koll U, Schmidt J. Isolation and Cultivation of Bacteria. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2019. [DOI: 10.1007/978-3-030-16775-2_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Slabu I, Galman JL, Lloyd RC, Turner NJ. Discovery, Engineering, and Synthetic Application of Transaminase Biocatalysts. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02686] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Iustina Slabu
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - James L. Galman
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Richard C. Lloyd
- Dr.
Reddy’s Laboratories, Chirotech Technology Centre, CB4 0PE Cambridge, United Kingdom
| | - Nicholas J. Turner
- School
of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN Manchester, United Kingdom
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14
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Philippe C, Jaomanjaka F, Claisse O, Laforgue R, Maupeu J, Petrel M, Le Marrec C. A survey of oenophages during wine making reveals a novel group with unusual genomic characteristics. Int J Food Microbiol 2017. [PMID: 28651079 DOI: 10.1016/j.ijfoodmicro.2017.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Oenophages have so far been mostly isolated from red wines under malolactic fermentation (MLF), and correspond to temperate or ex-temperate phages of Oenococcus oeni. Their genomes are clustered into 4 integrase gene sequence groups, which are also related to the chromosomal integration site. Our aims were to survey the occurrence of oenophages in a broader and more diverse collection of samples than those previously explored. Active phages were isolated from 33 out of 166 samples, which mostly originated from must and MLF. Seventy one phage lysates were produced and 30% were assigned to a novel group with unusual genomic characteristics, called unk. All unk members produced similar RAPD and DNA restriction patterns, were negative by PCR for the signature sequences previously identified in the integrase and endolysin genes of oenophages, and lacked any BamHI restriction site in their genome. The data support that development of additional and novel signature genes for assessing oenophage diversity is now required.
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Affiliation(s)
- Cécile Philippe
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France
| | - Fety Jaomanjaka
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; Institut Polytechnique de Bordeaux, ISVV, EA 4577 Oenologie, F-33140 Villenave d'Ornon, France
| | - Olivier Claisse
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; INRA, ISVV, USC 1366 Oenologie, F-33882 Villenave d'Ornon, France
| | - Rémi Laforgue
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; MICROFLORA, ISVV, EA 4577 Oenologie, F-33140 Villenave d'Ornon, France
| | - Julie Maupeu
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; MICROFLORA, ISVV, EA 4577 Oenologie, F-33140 Villenave d'Ornon, France
| | - Melina Petrel
- Univ. Bordeaux, Bordeaux Imaging Center, UMS 3420 CNRS-US4 INSERM, Bordeaux, France
| | - Claire Le Marrec
- Univ. Bordeaux, ISVV, EA 4577, Unité de recherche Oenologie, F-33882 Villenave d'Ornon, France; Institut Polytechnique de Bordeaux, ISVV, EA 4577 Oenologie, F-33140 Villenave d'Ornon, France.
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15
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Abstract
Bacteriophages, viruses that infect bacteria, have re-emerged as powerful regulators of bacterial populations in natural ecosystems. Phages invade the human body, just as they do other natural environments, to such an extent that they are the most numerous group in the human virome. This was only revealed in recent metagenomic studies, despite the fact that the presence of phages in the human body was reported decades ago. The influence of the presence of phages in humans has yet to be evaluated; but as in marine environments, a clear role in the regulation of bacterial populations could be envisaged, that might have an impact on human health. Moreover, phages are excellent vehicles of genetic transfer, and they contribute to the evolution of bacterial cells in the human body by spreading and acquiring DNA horizontally. The abundance of phages in the human body does not pass unnoticed and the immune system reacts to them, although it is not clear to what extent. Finally, the presence of phages in human samples, which most of the time is not considered, can influence and bias microbiological and molecular results; and, in view of the evidences, some studies suggest that more attention needs to be paid to their interference.
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Affiliation(s)
- Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d’Investigació Biomèdica Sant PauBarcelona, Spain
| | - Maite Muniesa
- Department of Microbiology, University of BarcelonaBarcelona, Spain
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16
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Calero-Cáceres W, Méndez J, Martín-Díaz J, Muniesa M. The occurrence of antibiotic resistance genes in a Mediterranean river and their persistence in the riverbed sediment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 223:384-394. [PMID: 28126386 DOI: 10.1016/j.envpol.2017.01.035] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/13/2017] [Accepted: 01/15/2017] [Indexed: 05/25/2023]
Abstract
The spread of antibiotic resistance genes (ARGs) in the environment is a serious concern. Bacterial ARGs can spread via different mobile genetic elements as phage particles, which thereby emerge as novel vectors for environmental dissemination. To assess how climate events, such as heavy rains or water scarcity, could affect the spread of ARGs, it is necessary to know their prevalence and abundance in aquatic environments as well as the potential reservoirs from which they could become mobile. This study evaluates the occurrence of ARGs in the water and sediment of a Mediterranean river. Six clinically relevant ARGs (blaTEM, blaCTX-M, qnrA, qnrS, mecA and sul1) were quantified by qPCR in the bacterial and phage fractions of 69 water and 70 sediment samples from the River Llobregat (NE Spain), collected during both dry and rainy periods. blaTEM and sul1 were the most prevalent and abundant ARGs; the others were more variable. Significant seasonal differences in ARG prevalences and abundances were observed. Since ARGs were detected in the sediment, the persistence of the most abundant ARGs naturally occurring in that sediment (blaTEM and sul1) was evaluated under three conditions. No ARG inactivation occurred in fresh sediment over 14 days; while the ARGs declined by less than 2 log10 units over 35 days in semi-dry and dry sediment. The occurrence of ARGs in water and sediment is influenced by seasonal conditions and they can be mobilized by bacteria and phage particles. In sediment, ARGs persist for long periods and hence sediment can be a natural reservoir of ARGs, from where they can spread and cause the emergence of new resistant strains.
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Affiliation(s)
- William Calero-Cáceres
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Javier Méndez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Julia Martín-Díaz
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain.
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17
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Conrad CC, Stanford K, McAllister TA, Thomas J, Reuter T. Competition during enrichment of pathogenicEscherichia colimay result in culture bias. Facets (Ott) 2017. [DOI: 10.1139/facets-2016-0007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Deadly outbreaks and illnesses due to Shiga toxin-producing Escherichia coli (STEC) occur worldwide; however, the cultivation methods required for adequate monitoring and traceback investigations are inefficient at best. Detection of STEC relies heavily on enrichment; yet no standard media or protocols exist. Furthermore, whether enrichment may bias detection of multiple STEC serogroups from complex samples is unknown. Thus, 14 STEC strains of serogroups O157 and the top six non-O157s (O26, O45, O103, O111, O121, and O145) were enriched in pairs for 6–78 h in broth and evaluated by quantitative polymerase chain reaction (qPCR). Here we show that a conventional 6-h enrichment protocol did not result in intra-species culture bias for the isolates tested. However, subsequent enrichments often produced biased cultures, with differences in the qPCR gene copy number ≥2 log10apparent in 12%, 38%, and 52% of competitions after 30, 54, and 78 h of consecutive enrichments, respectively. Some strains were able to prevail and (or) out-compete the opponent strain in 100% of competitions. Our results suggest that culture bias should be considered and (or) evaluated further due to the potential implications during routine pathogen screening and outbreak investigations.
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Affiliation(s)
- Cheyenne C. Conrad
- University of Lethbridge, Biological Sciences Department, Lethbridge, AB T1K 3M4, Canada
- Alberta Agriculture and Forestry, Lethbridge Research Centre, Lethbridge, AB T1J 4V6, Canada
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB T1J 4B1, Canada
| | - Kim Stanford
- Alberta Agriculture and Forestry, Lethbridge Research Centre, Lethbridge, AB T1J 4V6, Canada
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB T1J 4B1, Canada
| | - James Thomas
- University of Lethbridge, Biological Sciences Department, Lethbridge, AB T1K 3M4, Canada
| | - Tim Reuter
- Alberta Agriculture and Forestry, Lethbridge Research Centre, Lethbridge, AB T1J 4V6, Canada
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18
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Brown-Jaque M, Muniesa M, Navarro F. Bacteriophages in clinical samples can interfere with microbiological diagnostic tools. Sci Rep 2016; 6:33000. [PMID: 27609086 PMCID: PMC5016790 DOI: 10.1038/srep33000] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/18/2016] [Indexed: 01/15/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria, and they are found everywhere their bacterial hosts are present, including the human body. To explore the presence of phages in clinical samples, we assessed 65 clinical samples (blood, ascitic fluid, urine, cerebrospinal fluid, and serum). Infectious tailed phages were detected in >45% of ascitic fluid and urine samples. Three examples of phage interference with bacterial isolation were observed. Phages prevented the confluent bacterial growth required for an antibiogram assay when the inoculum was taken from an agar plate containing lysis plaques, but not when taken from a single colony in a phage-free area. In addition, bacteria were isolated directly from ascitic fluid, but not after liquid enrichment culture of the same samples, since phage propagation lysed the bacteria. Lastly, Gram-negative bacilli observed in a urine sample did not grow on agar plates due to the high densities of infectious phages in the sample.
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Affiliation(s)
- Maryury Brown-Jaque
- Department of Microbiology, University of Barcelona, Diagonal 645, Annex, Floor 0, 08028 Barcelona, Spain
| | - Maite Muniesa
- Department of Microbiology, University of Barcelona, Diagonal 645, Annex, Floor 0, 08028 Barcelona, Spain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain
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19
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Screening for Urease-Producing Bacteria from Limestone Caves of Sarawak. BORNEO JOURNAL OF RESOURCE SCIENCE AND TECHNOLOGY 2016. [DOI: 10.33736/bjrst.213.2016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Urease is a key enzyme in the chemical reaction of microorganism and has been found to be associated withcalcification, which is essential in microbially induced calcite precipitation (MICP) process. Three bacterialisolates (designated as LPB19, TSB31 and TSB12) were among twenty-eight bacteria that were isolated fromsamples collected from Sarawak limestone caves using the enrichment culture technique. Isolates LPB19, TSB31and TSB12 were selected based on their quick urease production when compared to other isolates. Phenotypiccharacteristics indicate all three bacterial strains are gram-positive, rod-shaped, motile, catalase and oxidasepositive. Urease activity of the bacterial isolates were measured through changes in conductivity in the absence ofcalcium ions. The bacterial isolates (LPB19, TSB12 and TSB31) showed urease activity of 16.14, 12.45 and 11.41mM urea hydrolysed/min respectively. The current work suggested that these isolates serves as constitutiveproducers of urease, potentially useful in inducing calcite precipitates.
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20
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Calero-Cáceres W, Muniesa M. Persistence of naturally occurring antibiotic resistance genes in the bacteria and bacteriophage fractions of wastewater. WATER RESEARCH 2016; 95:11-8. [PMID: 26978717 DOI: 10.1016/j.watres.2016.03.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/22/2016] [Accepted: 03/01/2016] [Indexed: 05/04/2023]
Abstract
The emergence and prevalence of antibiotic resistance genes (ARGs) in the environment is a serious global health concern. ARGs from bacteria can be mobilized by mobile genetic elements, and recent studies indicate that phages and phage-derived particles, among others, could play a role in the spread of ARGs through the environment. ARGs are abundant in the bacterial and bacteriophage fractions of water bodies and for successful transfer of the ARGs, their persistence in these environments is crucial. In this study, three ARGs (blaTEM, blaCTX-M and sul1) that naturally occur in the bacterial and phage fractions of raw wastewater were used to evaluate the persistence of ARGs at different temperatures (4 °C, 22 °C and 37 °C) and pH values (3, 7 and 9), as well as after various disinfection treatments (thermal treatment, chlorination and UV) and natural inactivation in a mesocosm. Gene copies (GC) were quantified by qPCR; then the logarithmic reduction and significance of the differences between their numbers were evaluated. The ARGs persisted for a long time with minimal reductions after all the treatments. In general, they showed greater persistence in the bacteriophage fraction than in the bacterial fraction. Comparisons showed that the ARGs persisted under conditions that reduced culturable Escherichia coli and infectious coliphages below the limit of detection. The prevalence of ARGs, particularly in the bacteriophage fraction, poses the threat of the spread of ARGs and their incorporation into a new bacterial background that could lead to the emergence of new resistant clones.
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Affiliation(s)
- William Calero-Cáceres
- Department of Microbiology, University of Barcelona, Diagonal 643. Annex. Floor 0, E-08028 Barcelona, Spain
| | - Maite Muniesa
- Department of Microbiology, University of Barcelona, Diagonal 643. Annex. Floor 0, E-08028 Barcelona, Spain.
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21
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Cortés P, Spricigo DA, Bardina C, Llagostera M. Remarkable diversity of Salmonella bacteriophages in swine and poultry. FEMS Microbiol Lett 2014; 362:1-7. [DOI: 10.1093/femsle/fnu034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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22
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Improving detection of Shiga toxin-producing Escherichia coli by molecular methods by reducing the interference of free Shiga toxin-encoding bacteriophages. Appl Environ Microbiol 2014; 81:415-21. [PMID: 25362055 DOI: 10.1128/aem.02941-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Detection of Shiga toxin-producing Escherichia coli (STEC) by culture methods is advisable to identify the pathogen, but recovery of the strain responsible for the disease is not always possible. The use of DNA-based methods (PCR, quantitative PCR [qPCR], or genomics) targeting virulence genes offers fast and robust alternatives. However, detection of stx is not always indicative of STEC because stx can be located in the genome of temperate phages found in the samples as free particles; this could explain the numerous reports of positive stx detection without successful STEC isolation. An approach based on filtration through low-protein-binding membranes and additional washing steps was applied to reduce free Stx phages without reducing detection of STEC bacteria. River water, food, and stool samples were spiked with suspensions of phage 933W and, as a STEC surrogate, a lysogen harboring a recombinant Stx phage in which stx was replaced by gfp. Bacteria were tested either by culture or by qPCR for gfp while phages were tested using qPCR targeting stx in phage DNA. The procedure reduces phage particles by 3.3 log10 units without affecting the recovery of the STEC population (culturable or assessed by qPCR). The method is applicable regardless of phage and bacteria densities and is useful in different matrices (liquid or solid). This approach eliminates or considerably reduces the interference of Stx phages in the detection of STEC by molecular methods. The reduction of possible interference would increase the efficiency and reliability of genomics for STEC detection when the method is applied routinely in diagnosis and food analysis.
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23
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Engel P, Stepanauskas R, Moran NA. Hidden diversity in honey bee gut symbionts detected by single-cell genomics. PLoS Genet 2014; 10:e1004596. [PMID: 25210772 PMCID: PMC4161309 DOI: 10.1371/journal.pgen.1004596] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/02/2014] [Indexed: 12/29/2022] Open
Abstract
Microbial communities in animal guts are composed of diverse, specialized bacterial species, but little is known about how gut bacteria diversify to produce genetically and ecologically distinct entities. The gut microbiota of the honey bee, Apis mellifera, presents a useful model, because it consists of a small number of characteristic bacterial species, each showing signs of diversification. Here, we used single-cell genomics to study the variation within two species of the bee gut microbiota: Gilliamella apicola and Snodgrassella alvi. For both species, our analyses revealed extensive variation in intraspecific divergence of protein-coding genes but uniformly high levels of 16S rRNA similarity. In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. Furthermore, gene repertoires differ markedly among strains in both species, implying distinct metabolic capabilities. Our results show that, despite minimal divergence at 16S rRNA genes, in situ diversification occurs within gut communities and generates bacterial lineages with distinct ecological niches. Therefore, important dimensions of microbial diversity are not evident from analyses of 16S rRNA, and single cell genomics has potential to elucidate processes of bacterial diversification. Gut microbial communities are often complex, consisting of bacteria from divergent phyla as well as multiple strains of each of the constituent species. But because the composition of these communities is typically assessed using 16S rRNA analyses, little is known about genomic changes associated with in situ diversification of bacterial lineages in animal guts. We undertook a single-cell genomic approach to investigate the diversification within two species of the gut microbiota of honey bees. Each species exhibited a surprisingly high level of genomic variation, despite uniformity in the 16S rRNA sequences. Our data indicate that genetically and ecologically distinct lineages can evolve in the gut of the same host species in the presence of frequent recombination at 16S rRNA genes. These findings parallel observations from mammals, suggesting that in situ diversification of a few bacterial lineages is a common pattern in the evolution of gut communities.
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Affiliation(s)
- Philipp Engel
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Nancy A. Moran
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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24
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Martínez-Castillo A, Muniesa M. Implications of free Shiga toxin-converting bacteriophages occurring outside bacteria for the evolution and the detection of Shiga toxin-producing Escherichia coli. Front Cell Infect Microbiol 2014; 4:46. [PMID: 24795866 PMCID: PMC3997033 DOI: 10.3389/fcimb.2014.00046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 03/27/2014] [Indexed: 11/13/2022] Open
Abstract
In this review we highlight recent work that has increased our understanding of the distribution of Shiga toxin-converting phages that can be detected as free phage particles, independently of Shiga toxin-producing bacteria (STEC). Stx phages are a quite diverse group of temperate phages that can be found in their prophage state inserted within the STEC chromosome, but can also be found as phages released from the cell after activation of their lytic cycle. They have been detected in extraintestinal environments such as water polluted with feces from humans or animals, food samples or even in stool samples of healthy individuals. The high persistence of phages to several inactivation conditions makes them suitable candidates for the successful mobilization of stx genes, possibly resulting in the genes reaching a new bacterial genomic background by means of transduction, where ultimately they may be expressed, leading to Stx production. Besides the obvious fact that Stx phages circulating between bacteria can be, and probably are, involved in the emergence of new STEC strains, we review here other possible ways in which free Stx phages could interfere with the detection of STEC in a given sample by current laboratory methods and how to avoid such interference.
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Affiliation(s)
| | - Maite Muniesa
- Department of Microbiology, Faculty of Biology, University of BarcelonaBarcelona, Spain
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25
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Johnson RP, Holtslander B, Mazzocco A, Roche S, Thomas JL, Pollari F, Pintar KDM. Detection and prevalence of verotoxin-producing Escherichia coli O157 and non-O157 serotypes in a Canadian watershed. Appl Environ Microbiol 2014; 80:2166-75. [PMID: 24487525 PMCID: PMC3993149 DOI: 10.1128/aem.03391-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 01/17/2014] [Indexed: 11/20/2022] Open
Abstract
Verotoxin-producing Escherichia coli (VTEC) strains are the cause of food-borne and waterborne illnesses around the world. Traditionally, surveillance of the human population as well as the environment has focused on the detection of E. coli O157:H7. Recently, increasing recognition of non-O157 VTEC strains as human pathogens and the German O104:H4 food-borne outbreak have illustrated the importance of considering the broader group of VTEC organisms from a public health perspective. This study presents the results of a comparison of three methods for the detection of VTEC in surface water, highlighting the efficacy of a direct VT immunoblotting method without broth enrichment for detection and isolation of O157 and non-O157 VTEC strains. The direct immunoblot method eliminates the need for an enrichment step or the use of immunomagnetic separation. This method was developed after 4 years of detecting low frequencies (1%) of E. coli O157:H7 in surface water in a Canadian watershed, situated within one of the FoodNet Canada integrated surveillance sites. By the direct immunoblot method, VTEC prevalence estimates ranged from 11 to 35% for this watershed, and E. coli O157:H7 prevalence increased to 4% (due to improved method sensitivity). This direct testing method provides an efficient means to enhance our understanding of the prevalence and types of VTEC in the environment. This study employed a rapid evidence assessment (REA) approach to frame the watershed findings with watershed E. coli O157:H7 prevalences reported in the literature since 1990 and the knowledge gap with respect to VTEC detection in surface waters.
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Affiliation(s)
- R. P. Johnson
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - B. Holtslander
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - A. Mazzocco
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - S. Roche
- Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - J. L. Thomas
- Ontario Ministry of the Environment, Etobicoke, Ontario, Canada
| | - F. Pollari
- FoodNet Canada, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - K. D. M. Pintar
- FoodNet Canada, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
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Ottesen AR, Gonzalez A, Bell R, Arce C, Rideout S, Allard M, Evans P, Strain E, Musser S, Knight R, Brown E, Pettengill JB. Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere. PLoS One 2013; 8:e73079. [PMID: 24039862 PMCID: PMC3767688 DOI: 10.1371/journal.pone.0073079] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/16/2013] [Indexed: 11/19/2022] Open
Abstract
The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite indication by all media, that samples were culture negative for Salmonella. Our results substantiate the nascent utility of metagenomic methods to improve both biological and bioinformatic pathogen detection methods.
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Affiliation(s)
- Andrea R. Ottesen
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America
| | - Antonio Gonzalez
- Biofrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
- Biofrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Rebecca Bell
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America
| | - Caroline Arce
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America
| | - Steven Rideout
- Virginia Tech, Virginia Agricultural Experiment Station, Painter, Virginia, United States of America
| | - Marc Allard
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America
| | - Peter Evans
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America
| | - Errol Strain
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America
| | - Steven Musser
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America
- Howard Hughes Medical Institute, Boulder, Colorado, United States of America
| | - Eric Brown
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America
| | - James B. Pettengill
- Molecular Methods and Subtyping Branch, Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America
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27
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van den Bogert B, Erkus O, Boekhorst J, de Goffau M, Smid EJ, Zoetendal EG, Kleerebezem M. Diversity of human small intestinal Streptococcus and Veillonella populations. FEMS Microbiol Ecol 2013; 85:376-88. [PMID: 23614882 DOI: 10.1111/1574-6941.12127] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/15/2013] [Accepted: 03/25/2013] [Indexed: 01/08/2023] Open
Abstract
Molecular and cultivation approaches were employed to study the phylogenetic richness and temporal dynamics of Streptococcus and Veillonella populations in the small intestine. Microbial profiling of human small intestinal samples collected from four ileostomy subjects at four time points displayed abundant populations of Streptococcus spp. most affiliated with S. salivarius, S. thermophilus, and S. parasanguinis, as well as Veillonella spp. affiliated with V. atypica, V. parvula, V. dispar, and V. rogosae. Relative abundances varied per subject and time of sampling. Streptococcus and Veillonella isolates were cultured using selective media from ileostoma effluent samples collected at two time points from a single subject. The richness of the Streptococcus and Veillonella isolates was assessed at species and strain level by 16S rRNA gene sequencing and genetic fingerprinting, respectively. A total of 160 Streptococcus and 37 Veillonella isolates were obtained. Genetic fingerprinting differentiated seven Streptococcus lineages from ileostoma effluent, illustrating the strain richness within this ecosystem. The Veillonella isolates were represented by a single phylotype. Our study demonstrated that the small intestinal Streptococcus populations displayed considerable changes over time at the genetic lineage level because only representative strains of a single Streptococcus lineage could be cultivated from ileostoma effluent at both time points.
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29
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Pettengill JB, McAvoy E, White JR, Allard M, Brown E, Ottesen A. Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection. BMC Res Notes 2012; 5:378. [PMID: 22839680 PMCID: PMC3441234 DOI: 10.1186/1756-0500-5-378] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 07/10/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Enriching environmental samples to increase the probability of detection has been standard practice throughout the history of microbiology. However, by its very nature, the process of enrichment creates a biased sample that may have unintended consequences for surveillance or resolving a pathogenic outbreak. With the advent of next-generation sequencing and metagenomic approaches, the possibility now exists to quantify enrichment bias at an unprecedented taxonomic breadth. FINDINGS We investigated differences in taxonomic profiles of three enriched and unenriched tomato phyllosphere samples taken from three different tomato fields (n = 18). 16S rRNA gene meteganomes were created for each of the 18 samples using 454/Roche's pyrosequencing platform, resulting in a total of 165,259 sequences. Significantly different taxonomic profiles and abundances at a number of taxonomic levels were observed between the two treatments. Although as many as 28 putative Salmonella sequences were detected in enriched samples, there was no significant difference in the abundance of Salmonella between enriched and unenriched treatments. CONCLUSIONS Our results illustrate that the process of enriching greatly alters the taxonomic profile of an environmental sample beyond that of the target organism. We also found evidence suggesting that enrichment may not increase the probability of detecting a target. In conclusion, our results further emphasize the need to develop metagenomics as a validated culture independent method for pathogen detection.
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Affiliation(s)
- James B Pettengill
- FDA Center for Food Safety and Applied Nutrition, Division of Microbiology, Molecular Methods and Subtyping, College Park, MD 20740, USA
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Colomer-Lluch M, Jofre J, Muniesa M. Antibiotic resistance genes in the bacteriophage DNA fraction of environmental samples. PLoS One 2011; 6:e17549. [PMID: 21390233 PMCID: PMC3048399 DOI: 10.1371/journal.pone.0017549] [Citation(s) in RCA: 219] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 02/07/2011] [Indexed: 02/07/2023] Open
Abstract
Antibiotic resistance is an increasing global problem resulting from the pressure of antibiotic usage, greater mobility of the population, and industrialization. Many antibiotic resistance genes are believed to have originated in microorganisms in the environment, and to have been transferred to other bacteria through mobile genetic elements. Among others, β-lactam antibiotics show clinical efficacy and low toxicity, and they are thus widely used as antimicrobials. Resistance to β-lactam antibiotics is conferred by β-lactamase genes and penicillin-binding proteins, which are chromosomal- or plasmid-encoded, although there is little information available on the contribution of other mobile genetic elements, such as phages. This study is focused on three genes that confer resistance to β-lactam antibiotics, namely two β-lactamase genes (blaTEM and blaCTX-M9) and one encoding a penicillin-binding protein (mecA) in bacteriophage DNA isolated from environmental water samples. The three genes were quantified in the DNA isolated from bacteriophages collected from 30 urban sewage and river water samples, using quantitative PCR amplification. All three genes were detected in the DNA of phages from all the samples tested, in some cases reaching 104 gene copies (GC) of blaTEM or 102 GC of blaCTX-M and mecA. These values are consistent with the amount of fecal pollution in the sample, except for mecA, which showed a higher number of copies in river water samples than in urban sewage. The bla genes from phage DNA were transferred by electroporation to sensitive host bacteria, which became resistant to ampicillin. blaTEM and blaCTX were detected in the DNA of the resistant clones after transfection. This study indicates that phages are reservoirs of resistance genes in the environment.
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Affiliation(s)
| | - Juan Jofre
- Department of Microbiology, University of Barcelona, Barcelona, Spain
| | - Maite Muniesa
- Department of Microbiology, University of Barcelona, Barcelona, Spain
- * E-mail:
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31
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Specific detection of Salmonella enterica and Escherichia coli strains by using ELISA with bacteriophages as recognition agents. Eur J Clin Microbiol Infect Dis 2011; 30:1067-73. [PMID: 21318732 PMCID: PMC3156329 DOI: 10.1007/s10096-011-1193-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 01/25/2011] [Indexed: 11/05/2022]
Abstract
The use of bacteriophages, instead of antibodies, in the ELISA-based detection of bacterial strains was tested. This procedure appeared to be efficient, and specific strains of Salmonella enterica and Escherichia coli could be detected. The sensitivity of the assay was about 105 bacterial cells/well (106/ml), which is comparable with or outperforms other ELISA tests detecting intact bacterial cells without an enrichment step. The specificity of the assay depends on the kind of bacteriophage used. We conclude that the use of bacteriophages in the detection and identification of bacteria by an ELISA-based method can be an alternative to the use of specific antibodies. The advantages of the use of bacteriophages are their environmental abundance (and, thus, a possibility to isolate various phages with different specificities) and the availability of methods for obtaining large amounts of phage lysates, which are simple, rapid, cheap, and easy.
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Jin YO, Mattes TE. A quantitative PCR assay for aerobic, vinyl chloride- and ethene-assimilating microorganisms in groundwater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:9036-9041. [PMID: 21033659 DOI: 10.1021/es102232m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Vinyl chloride (VC) is a known human carcinogen that is primarily formed in groundwater via incomplete anaerobic dechlorination of chloroethenes. Aerobic, ethene-degrading bacteria (etheneotrophs), which are capable of both fortuitous and growth-linked VC oxidation, could be important in natural attenuation of VC plumes that escape anaerobic treatment. In this work, we developed a quantitative, real-time PCR (qPCR) assay for etheneotrophs in groundwater. We designed and tested degenerate qPCR primers for two functional genes involved in aerobic, growth-coupled VC- and ethene-oxidation (etnC and etnE). Primer specificity to these target genes was tested by comparison to nucleotide sequence databases, PCR analysis of template DNA extracted from isolates and environmental samples, and sequencing of qPCR products obtained from VC-contaminated groundwater. The assay was made quantitative by constructing standard curves (threshold cycle vs log gene copy number) with DNA amplified from Mycobacterium strain JS60, an etheneotrophic isolate. Analysis of groundwater samples from three different VC-contaminated sites revealed that etnC abundance ranged from 1.6 × 10(3) - 1.0 × 10(5) copies/L groundwater while etnE abundance ranged from 4.3 × 10(3) - 6.3 × 10(5) copies/L groundwater. Our data suggest this novel environmental measurement method will be useful for supporting VC bioremediation strategies, assisting in site closure, and conducting microbial ecology studies involving etheneotrophs.
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Affiliation(s)
- Yang Oh Jin
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, Iowa 52242, USA
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Singer RS, Mayer AE, Hanson TE, Isaacson RE. Do microbial interactions and cultivation media decrease the accuracy of Salmonella surveillance systems and outbreak investigations? J Food Prot 2009; 72:707-13. [PMID: 19435216 DOI: 10.4315/0362-028x-72.4.707] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cultivation methods are commonly used in Salmonella surveillance systems and outbreak investigations, and consequently, conclusions about Salmonella evolution and transmission are highly dependent on the performance characteristics of these methods. Past studies have shown that Salmonella serotypes can exhibit different growth characteristics in the same enrichment and selective media. This could lead not only to biased conclusions about the dominant strain present in a sample with mixed Salmonella populations, but also to a low sensitivity for detecting a Salmonella strain in a sample with only a single strain present. The objective of this study was to determine whether cultivation media select preferentially for specific strains of Salmonella in heterogeneous cultures. In this study, four different Salmonella strains (one Salmonella Newport, two Salmonella Typhimurium, and one Salmonella Enteritidis) were competed in a broth-based experiment and a bovine fecal experiment with varied combinations and concentrations of each strain. In all experiments, the strain of Salmonella Newport was the most competitive, regardless of the starting concentration and cultivation protocol. One strain of Salmonella Typhimurium was rarely detected in competition, even when it was the only strain present in bovine feces. Overall, the probability of detecting a specific Salmonella strain had little to do with its starting concentration in the sample. The bias introduced by culture could be dramatically biasing Salmonella surveillance systems and hindering traceback investigations during Salmonella outbreaks. Future studies should focus on the microbiological explanations for this Salmonella interstrain variability, approaches for minimizing the bias, and estimations of the public health significance of this bias.
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Affiliation(s)
- Randall S Singer
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, 300A VSB, 1971 Commonwealth Avenue, University of Minnesota, St. Paul, Minnesota 55108, USA.
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O'Flynn G, Coffey A, Fitzgerald G, Ross RP. Salmonella enterica phage-resistant mutant colonies display an unusual phenotype in the presence of phage Felix 01. Lett Appl Microbiol 2007; 45:581-5. [PMID: 17908223 DOI: 10.1111/j.1472-765x.2007.02242.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To investigate irregular colony morphology formation in Salmonella enterica serovar Typhimurium DPC6046 in the presence of a lytic phage, Felix 01. METHODS AND RESULTS Phage-resistant derivatives of the parent strain DPC6046 were isolated which exhibited an irregular colony morphology. These were subjected to viability studies by using confocal scanning laser microscopy and live/dead BacLight stain to evaluate the cell viability within the colony. The phenomenon was also observed with other S. enterica serotypes tested which were normally sensitive to phage Felix. In the case of strain DPC6046, dead cells were clearly evident at the irregular edges of the phage-resistant colonies in locations where the cell density was lower. This colony morphology was not apparent with two other Salmonella phages tested. CONCLUSIONS These findings support the hypothesis that the unusual morphology is due to reversion to phage sensitivity and consequent cell death within the colony as it forms. SIGNIFICANCE AND IMPACT OF THE STUDY The irregular colony morphology observed is peculiar to phage Felix. The confocal scanning laser microscopy methodology allowed the basis for the irregular morphology to be elucidated.
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Affiliation(s)
- G O'Flynn
- Moorepark Food Research Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
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35
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Guzmán C, Jofre J, Montemayor M, Lucena F. Occurrence and levels of indicators and selected pathogens in different sludges and biosolids. J Appl Microbiol 2007; 103:2420-9. [DOI: 10.1111/j.1365-2672.2007.03487.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Muniesa M, Jofre J. The contribution of induction of temperate phages to the numbers of free somatic coliphages in waters is not significant. FEMS Microbiol Lett 2007; 270:272-6. [PMID: 17343678 DOI: 10.1111/j.1574-6968.2007.00676.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Somatic coliphages have been proposed as indicators of water quality. But several factors have been considered a drawback for their use as indicators. We evaluated the contribution of temperate phages to the numbers of somatic coliphages detected in water by ISO (International Standards Organization) standardised methods. Prophage induction from naturally occurring bacteria was assayed with mitomycin C, ciprofloxacin and UV irradiation. Results indicate that the presence of prophages will not influence the determinations of somatic coliphages in water.
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Affiliation(s)
- Maite Muniesa
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
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