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Andrews K, Landeryou T, Sicheritz-Pontén T, Nale JY. Diverse Prophage Elements of Salmonella enterica Serovars Show Potential Roles in Bacterial Pathogenicity. Cells 2024; 13:514. [PMID: 38534358 DOI: 10.3390/cells13060514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
Nontyphoidal salmonellosis is an important foodborne and zoonotic infection that causes significant global public health concern. Diverse serovars are multidrug-resistant and encode several virulence indicators; however, little is known on the role prophages play in driving these traits. Here, we extracted prophages from seventy-five Salmonella genomes which represent the fifteen important serovars in the United Kingdom. We analyzed the intact prophages for the presence of virulence genes and established their genomic relationships. We identified 615 prophages from the Salmonella strains, from which 195 prophages are intact, 332 are incomplete, while 88 are questionable. The average prophage carriage was found to be 'extreme' in S. Heidelberg, S. Inverness, and S. Newport (10.2-11.6 prophages/strain), 'high' in S. Infantis, S. Stanley, S. Typhimurium, and S. Virchow (8.2-9.0 prophages/strain), 'moderate' in S. Agona, S. Braenderup, S. Bovismorbificans, S. Choleraesuis, S. Dublin, and S. Java (6.0-7.8 prophages/strain), and 'low' in S. Javiana and S. Enteritidis (5.8 prophages/strain). Cumulatively, 61 virulence genes (1500 gene copies) were detected from representative intact prophages and linked to Salmonella delivery/secretion system (42.62%), adherence (32.7%), magnesium uptake (3.88%), regulation (5%), stress/survival (1.6%), toxins (10%), and antivirulence (1.6%). Diverse clusters were formed among the intact prophages and with bacteriophages of other enterobacteria, suggesting different lineages and associations. Our work provides a strong body of data to support the contributions diverse prophages make to the pathogenicity of Salmonella, including thirteen previously unexplored serovars.
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Affiliation(s)
- Kirstie Andrews
- Centre for Epidemiology and Planetary Health, School of Veterinary Medicine, Scotland's Rural College, Inverness IV2 5NA, UK
| | - Toby Landeryou
- Centre for Epidemiology and Planetary Health, School of Veterinary Medicine, Scotland's Rural College, Inverness IV2 5NA, UK
| | - Thomas Sicheritz-Pontén
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Janet Yakubu Nale
- Centre for Epidemiology and Planetary Health, School of Veterinary Medicine, Scotland's Rural College, Inverness IV2 5NA, UK
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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) 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Thanki AM, Taylor-Joyce G, Dowah A, Nale JY, Malik D, Clokie MRJ. Unravelling the Links between Phage Adsorption and Successful Infection in Clostridium difficile. Viruses 2018; 10:E411. [PMID: 30082660 PMCID: PMC6116197 DOI: 10.3390/v10080411] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/23/2018] [Accepted: 08/05/2018] [Indexed: 01/02/2023] Open
Abstract
Bacteriophage (phage) therapy is a promising alternative to antibiotics for the treatment of bacterial pathogens, including Clostridiumdifficile. However, as for many species, in C. difficile the physical interactions between phages and bacterial cells have not been studied in detail. The initial interaction, known as phage adsorption, is initiated by the reversible attachment of phage tail fibers to bacterial cell surface receptors followed by an irreversible binding step. Therefore binding can dictate which strains are infected by the phage. In this study, we investigated the adsorption rates and irreversible binding of three C. difficile myoviruses: CDHM1, CDHM3 and CDHM6 to ten strains that represent ten prevalent C. difficile ribotypes, regardless of their ability to infect. CDHM1 and CDHM3 phage particles adsorbed by ~75% to some strains that they infected. The infection dynamics for CDHM6 are less clear and ~30% of the phage particles bound to all strains, irrespective of whether a successful infection was established. The data highlighted adsorption is phage-host specific. However, it was consistently observed that irreversible binding had to be above 80% for successful infection, which was also noted for another two C. difficile myoviruses. Furthermore, to understand if there is a relationship between infection, adsorption and phage tail fibers, the putative tail fiber protein sequences of CDHM1, CDHM3 and CDHM6 were compared. The putative tail fiber protein sequence of CDHM1 shares 45% homology at the amino acid level to CDHM3 and CDHM6, which are identical to each other. However, CDHM3 and CDHM6 display differences in adsorption, which highlights that there is no obvious relationship between putative tail fiber sequence and adsorption. The importance of adsorption and binding to successful infection is often overlooked, and this study provides useful insights into host-pathogen interactions within this phage-pathogen system.
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Affiliation(s)
- Anisha Mahendra Thanki
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 7RH, UK.
| | | | - Ahmed Dowah
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 7RH, UK.
| | - Janet Yakubu Nale
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 7RH, UK.
| | - Danish Malik
- Chemical Engineering Department, Loughborough University, Loughborough LE11 3TU, UK.
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