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Cano I, Blaker E, Hartnell D, Farbos A, Moore KA, Cobb A, Santos EM, van Aerle R. Transcriptomic Responses to Koi Herpesvirus in Isolated Blood Leukocytes from Infected Common Carp. Viruses 2024; 16:380. [PMID: 38543746 PMCID: PMC10974277 DOI: 10.3390/v16030380] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/08/2024] [Accepted: 02/23/2024] [Indexed: 04/01/2024] Open
Abstract
Koi herpesvirus (KHV, CyHV-3) causes severe economic losses in carp farms. Its eradication is challenging due to the establishment of latency in blood leukocytes and other tissues. To understand the molecular mechanisms leading to KHV infection in leukocytes, common carp were bath-exposed to KHV at 17 °C. After confirming the presence of viral transcripts in blood leukocytes at ten days post infection, RNA-Seq was performed on peripheral blood leukocytes on the Illumina NovaSeq. KHV infection triggered a robust immune response mediated by pattern recognition receptors, mainly toll-like receptors (tlr2, tlr5, tlr7, and tlr13), urokinase plasminogen activator surface receptor-like, galectin proteins, and lipid mediators such as leukotriene B4 receptor 1. Enriched pathways showed increased mitochondria oxidative phosphorylation and the activation of signalling pathways such as mitogen-activated protein kinases (MAPKs) and vascular endothelial growth factor (VEGF). KHV-infected leukocytes showed low production of reactive oxygen species (ROS) and glutathione metabolism, high iron export and phagocytosis activity, and low autophagy. Macrophage polarization was deduced from the up-regulation of genes such as arginase non-hepatic 1-like, macrophage mannose receptor-1, crem, il-10, and il-13 receptors, while markers for cytotoxic T cells were observed to be down-regulated. Further work is required to characterise these leukocyte subsets and the molecular events leading to KHV latency in blood leukocytes.
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Affiliation(s)
- Irene Cano
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX2 4TH, UK;
| | - Ellen Blaker
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
| | - David Hartnell
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
| | - Audrey Farbos
- Biosciences, Faculty of Life and Health Sciences, University of Exeter, Exeter EX2 4TH, UK; (A.F.); (K.A.M.)
| | - Karen A. Moore
- Biosciences, Faculty of Life and Health Sciences, University of Exeter, Exeter EX2 4TH, UK; (A.F.); (K.A.M.)
| | - Adele Cobb
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
| | - Eduarda M. Santos
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX2 4TH, UK;
- Biosciences, Faculty of Life and Health Sciences, University of Exeter, Exeter EX2 4TH, UK; (A.F.); (K.A.M.)
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX2 4TH, UK;
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Fletcher J, Manley R, Fitch C, Bugert C, Moore K, Farbos A, Michelsen M, Alathari S, Senior N, Mills A, Whitehead N, Soothill J, Michell S, Temperton B. The Citizen Phage Library: Rapid Isolation of Phages for the Treatment of Antibiotic Resistant Infections in the UK. Microorganisms 2024; 12:253. [PMID: 38399657 PMCID: PMC10893117 DOI: 10.3390/microorganisms12020253] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Antimicrobial resistance poses one of the greatest threats to global health and there is an urgent need for new therapeutic options. Phages are viruses that infect and kill bacteria and phage therapy could provide a valuable tool for the treatment of multidrug-resistant infections. In this study, water samples collected by citizen scientists as part of the Citizen Phage Library (CPL) project, and wastewater samples from the Environment Agency yielded phages with activity against clinical strains Klebsiella pneumoniae BPRG1484 and Enterobacter cloacae BPRG1482. A total of 169 and 163 phages were found for K. pneumoniae and E. cloacae, respectively, within four days of receiving the strains. A third strain (Escherichia coli BPRG1486) demonstrated cross-reactivity with 42 E. coli phages already held in the CPL collection. Seed lots were prepared for four K. pneumoniae phages and a cocktail combining these phages was found to reduce melanisation in a Galleria mellonella infection model. The resources and protocols utilised by the Citizen Phage Library enabled the rapid isolation and characterisation of phages targeted against multiple strains. In the future, within a clearly defined regulatory framework, phage therapy could be made available on a named-patient basis within the UK.
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Affiliation(s)
- Julie Fletcher
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Robyn Manley
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christian Fitch
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Christina Bugert
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Karen Moore
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Audrey Farbos
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Michelle Michelsen
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Shayma Alathari
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Nicola Senior
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Alice Mills
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - Natalie Whitehead
- Exeter Science Centre, Kaleider Studios, 45 Preston Street, Exeter EX1 1DF, UK
| | - James Soothill
- Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Trust, Great Ormond Street, London WC1N 3JH, UK
| | - Stephen Michell
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
| | - Ben Temperton
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK (B.T.)
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Toffoli M, Chohan H, Mullin S, Jesuthasan A, Yalkic S, Koletsi S, Menozzi E, Rahall S, Limbachiya N, Loefflad N, Higgins A, Bestwick J, Lucas-Del-Pozo S, Fierli F, Farbos A, Mezabrovschi R, Lee-Yin C, Schrag A, Moreno-Martinez D, Hughes D, Noyce A, Colclough K, Jeffries AR, Proukakis C, Schapira AHV. Phenotypic effect of GBA1 variants in individuals with and without Parkinson's disease: The RAPSODI study. Neurobiol Dis 2023; 188:106343. [PMID: 37926171 DOI: 10.1016/j.nbd.2023.106343] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/08/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Variants in the GBA1 gene cause the lysosomal storage disorder Gaucher disease (GD). They are also risk factors for Parkinson's disease (PD), and modify the expression of the PD phenotype. The penetrance of GBA1 variants in PD is incomplete, and the ability to determine who among GBA1 variant carriers are at higher risk of developing PD, would represent an advantage for prognostic and trial design purposes. OBJECTIVES To compare the motor and non-motor phenotype of GBA1 carriers and non-carriers. METHODS We present the cross-sectional results of the baseline assessment from the RAPSODI study, an online assessment tool for PD patients and GBA1 variant carriers. The assessment includes clinically validated questionnaires, a tap-test, the University of Pennsyllvania Smell Identification Test and cognitive tests. Additional, homogeneous data from the PREDICT-PD cohort were included. RESULTS A total of 379 participants completed all parts of the RAPSODI assessment (89 GBA1-negative controls, 169 GBA1-negative PD, 47 GBA1-positive PD, 47 non-affected GBA1 carriers, 27 GD). Eighty-six participants were recruited through PREDICT-PD (43 non-affected GBA1 carriers and 43 GBA1-negative controls). GBA1-positive PD patients showed worse performance in visual cognitive tasks and olfaction compared to GBA1-negative PD patients. No differences were detected between non-affected GBA1 carriers carriers and GBA1-negative controls. No phenotypic differences were observed between any of the non-PD groups. CONCLUSIONS Our results support previous evidence that GBA1-positive PD has a specific phenotype with more severe non-motor symptoms. However, we did not reproduce previous findings of more frequent prodromal PD signs in non-affected GBA1 carriers.
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Affiliation(s)
- Marco Toffoli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Harneek Chohan
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, UK
| | - Stephen Mullin
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | | | - Selen Yalkic
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Sofia Koletsi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Elisa Menozzi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Soraya Rahall
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Naomi Limbachiya
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Nadine Loefflad
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Abigail Higgins
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Jonathan Bestwick
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, UK
| | - Sara Lucas-Del-Pozo
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Federico Fierli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Audrey Farbos
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Roxana Mezabrovschi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Chiao Lee-Yin
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Anette Schrag
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - David Moreno-Martinez
- Lysosomal Storage Disorders Unit, Royal Free Hospital NHS Foundation Trust and University College London, London, UK
| | - Derralynn Hughes
- Lysosomal Storage Disorders Unit, Royal Free Hospital NHS Foundation Trust and University College London, London, UK
| | - Alastair Noyce
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, UK
| | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - Aaron R Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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Millard RS, Bickley LK, Bateman KS, Verbruggen B, Farbos A, Lange A, Moore KA, Stentiford GD, Tyler CR, van Aerle R, Santos EM. Resistance to white spot syndrome virus in the European shore crab is associated with suppressed virion trafficking and heightened immune responses. Front Immunol 2022; 13:1057421. [PMID: 36636327 PMCID: PMC9831657 DOI: 10.3389/fimmu.2022.1057421] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/01/2022] [Indexed: 12/28/2022] Open
Abstract
Introduction All decapod crustaceans are considered potentially susceptible to White Spot Syndrome Virus (WSSV) infection, but the degree of White Spot Disease (WSD) susceptibility varies widely between species. The European shore crab Carcinus maenas can be infected with the virus for long periods of time without signs of disease. Given the high mortality rate of susceptible species, the differential susceptibility of these resistant hosts offers an opportunity to investigate mechanisms of disease resistance. Methods Here, the temporal transcriptional responses (mRNA and miRNA) of C. maenas following WSSV injection were analysed and compared to a previously published dataset for the highly WSSV susceptible Penaeus vannamei to identify key genes, processes and pathways contributing to increased WSD resistance. Results We show that, in contrast to P. vannamei, the transcriptional response during the first 2 days following WSSV injection in C. maenas is limited. During the later time points (7 days onwards), two groups of crabs were identified, a recalcitrant group where no replication of the virus occurred, and a group where significant viral replication occurred, with the transcriptional profiles of the latter group resembling those of WSSV-susceptible species. We identify key differences in the molecular responses of these groups to WSSV injection. Discussion We propose that increased WSD resistance in C. maenas may result from impaired WSSV endocytosis due to the inhibition of internal vesicle budding by dynamin-1, and a delay in movement to the nucleus caused by the downregulation of cytoskeletal transcripts required for WSSV cytoskeleton docking, during early stages of the infection. This response allows resistant hosts greater time to fine-tune immune responses associated with miRNA expression, apoptosis and the melanisation cascade to defend against, and clear, invading WSSV. These findings suggest that the initial stages of infection are key to resistance to WSSV in the crab and highlight possible pathways that could be targeted in farmed crustacean to enhance resistance to WSD.
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Affiliation(s)
- Rebecca S. Millard
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,*Correspondence: Rebecca S. Millard, ; Eduarda M. Santos,
| | - Lisa K. Bickley
- Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Kelly S. Bateman
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Bas Verbruggen
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Audrey Farbos
- University of Exeter Sequencing Facility, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Anke Lange
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Karen A. Moore
- University of Exeter Sequencing Facility, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Grant D. Stentiford
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Charles R. Tyler
- Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Eduarda M. Santos
- Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom,*Correspondence: Rebecca S. Millard, ; Eduarda M. Santos,
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5
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Millard RS, Bickley LK, Bateman KS, Farbos A, Minardi D, Moore K, Ross SH, Stentiford GD, Tyler CR, van Aerle R, Santos EM. Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp. Viruses 2021; 13:v13061140. [PMID: 34199268 PMCID: PMC8231841 DOI: 10.3390/v13061140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/01/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
White Spot Disease (WSD) presents a major barrier to penaeid shrimp production. Mechanisms underlying White Spot Syndrome Virus (WSSV) susceptibility in penaeids are poorly understood due to limited information related to early infection. We investigated mRNA and miRNA transcription in Penaeus vannamei over 36 h following infection. Over this time course, 6192 transcripts and 27 miRNAs were differentially expressed—with limited differential expression from 3–12 h post injection (hpi) and a more significant transcriptional response associated with the onset of disease symptoms (24 hpi). During early infection, regulated processes included cytoskeletal remodelling and alterations in phagocytic activity that may assist WSSV entry and translocation, novel miRNA-induced metabolic shifts, and the downregulation of ATP-dependent proton transporter subunits that may impair cellular recycling. During later infection, uncoupling of the electron transport chain may drive cellular dysfunction and lead to high mortalities in infected penaeids. We propose that post-transcriptional silencing of the immune priming gene Dscam (downregulated following infections) by a novel shrimp miRNA (Pva-pmiR-78; upregulated) as a potential mechanism preventing future recognition of WSSV that may be suppressed in surviving shrimp. Our findings improve our understanding of WSD pathogenesis in P. vannamei and provide potential avenues for future development of prophylactics and treatments.
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Affiliation(s)
- Rebecca S. Millard
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Correspondence: (R.S.M.); (E.M.S.); Tel.: +44-(0)-1392-724607 (E.M.S.)
| | - Lisa K. Bickley
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
| | - Kelly S. Bateman
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Audrey Farbos
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK; (A.F.); (K.M.)
| | - Diana Minardi
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Karen Moore
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK; (A.F.); (K.M.)
| | - Stuart H. Ross
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Grant D. Stentiford
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Charles R. Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
| | - Ronny van Aerle
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Eduarda M. Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Correspondence: (R.S.M.); (E.M.S.); Tel.: +44-(0)-1392-724607 (E.M.S.)
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6
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Cano I, Santos EM, Moore K, Farbos A, van Aerle R. Evidence of Transcriptional Shutoff by Pathogenic Viral Haemorrhagic Septicaemia Virus in Rainbow Trout. Viruses 2021; 13:v13061129. [PMID: 34208332 PMCID: PMC8231187 DOI: 10.3390/v13061129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
The basis of pathogenicity of viral haemorrhagic septicaemia virus (VHSV) was analysed in the transcriptome of a rainbow trout cell line inoculated with pathogenic and non-pathogenic VHSV isolates. Although both VHSV isolates showed similar viral replication patterns, the number of differentially expressed genes was 42-fold higher in cells inoculated with the non-pathogenic VHSV at 3 h post inoculation (hpi). Infection with the non-pathogenic isolate resulted in Gene Ontologies (GO) enrichment of terms such as immune response, cytokine-mediated signalling pathway, regulation of translational initiation, unfolded protein binding, and protein folding, and induced an over-representation of the p53, PPAR, and TGF-β signalling pathways. Inoculation with the pathogenic isolate resulted in the GO enrichment of terms related to lipid metabolism and the salmonella infection KEGG pathway involved in the rearrangement of the cytoskeleton. Antiviral response was evident at 12hpi in cells infected with the pathogenic isolate. Overall, the data showed a delay in the response of genes involved in immune responses and viral sensing in cells inoculated with the pathogenic isolate and suggest transcriptional shutoff and immune avoidance as a critical mechanism of pathogenicity in VHSV. These pathways offer opportunities to further understand and manage VHSV pathogenicity in rainbow trout.
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Affiliation(s)
- Irene Cano
- International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Barrack Road, The Nothe, Weymouth DT4 8UB, Dorset, UK;
- Correspondence:
| | - Eduarda M. Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, Devon, UK;
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, Devon, UK
| | - Karen Moore
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, Devon, UK; (K.M.); (A.F.)
| | - Audrey Farbos
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, Devon, UK; (K.M.); (A.F.)
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Barrack Road, The Nothe, Weymouth DT4 8UB, Dorset, UK;
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, Devon, UK
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7
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Hamilton PB, Lockyer AE, Uren Webster TM, Studholme DJ, Paris JR, Baynes A, Nicol E, Dawson DA, Moore K, Farbos A, Jobling S, Stevens JR, Tyler CR. Investigation into Adaptation in Genes Associated with Response to Estrogenic Pollution in Populations of Roach ( Rutilus rutilus) Living in English Rivers. Environ Sci Technol 2020; 54:15935-15945. [PMID: 33227200 DOI: 10.1021/acs.est.0c00957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Exposure of male fish to estrogenic substances from wastewater treatment works (WwTWs) results in feminization and reduced reproductive fitness. Nevertheless, self-sustaining populations of roach (Rutilus rutilus) inhabit river stretches polluted with estrogenic WwTW effluents. In this study, we examine whether such roach populations have evolved adaptations to tolerate estrogenic pollution by comparing frequency differences in single-nucleotide polymorphisms (SNPs) between populations sampled from rivers receiving either high- or low-level WwTW discharges. SNPs within 36 "candidate" genes, selected for their involvement in estrogenic responses, and 120 SNPs in reference genes were genotyped in 465 roaches. There was no evidence for selection in highly estrogen-dependent candidate genes, including those for the estrogen receptors, aromatases, and vitellogenins. The androgen receptor (ar) and cytochrome P450 1A genes were associated with large shifts in allele frequencies between catchments and in individual populations, but there is no clear link to estrogen pollution. Selection at ar in the effluent-dominated River Lee may have resulted from historical contamination with endocrine-disrupting pesticides. Critically, although our results suggest population-specific selection including at genes related to endocrine disruption, there was no strong evidence that the selection resulted from exposure to estrogen pollution.
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Affiliation(s)
- Patrick B Hamilton
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
- College of Medicine and Health, University of Exeter, St Luke's Campus, Heavitree Road, Exeter EX1 2LU, U.K
| | - Anne E Lockyer
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex UB8 3PH, U.K
| | - Tamsyn M Uren Webster
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
- Biosciences, College of Science, Swansea University, Swansea SA2 8PP, U.K
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Josephine R Paris
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Alice Baynes
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex UB8 3PH, U.K
| | - Elizabeth Nicol
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex UB8 3PH, U.K
| | - Deborah A Dawson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, U.K
| | - Karen Moore
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Audrey Farbos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Susan Jobling
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex UB8 3PH, U.K
| | - Jamie R Stevens
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
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Yemataw Z, Muzemil S, Ambachew D, Tripathi L, Tesfaye K, Chala A, Farbos A, O’Neill P, Moore K, Grant M, Studholme DJ. Genome sequence data from 17 accessions of Ensete ventricosum, a staple food crop for millions in Ethiopia. Data Brief 2018; 18:285-293. [PMID: 29896517 PMCID: PMC5996239 DOI: 10.1016/j.dib.2018.03.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 11/17/2022] Open
Abstract
We present raw sequence reads and genome assemblies derived from 17 accessions of the Ethiopian orphan crop plant enset (Ensete ventricosum (Welw.) Cheesman) using the Illumina HiSeq and MiSeq platforms. Also presented is a catalogue of single-nucleotide polymorphisms inferred from the sequence data at an average density of approximately one per kilobase of genomic DNA.
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Affiliation(s)
- Zerihun Yemataw
- Southern Agricultural Research Institute, Areka Agricultural Research Center, P.O. Box 79, Areka, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, AddisAbaba, Ethiopia
| | - Sadik Muzemil
- Southern Agricultural Research Institute, Areka Agricultural Research Center, P.O. Box 79, Areka, Ethiopia
| | - Daniel Ambachew
- Southern Agricultural Research Institute, Areka Agricultural Research Center, P.O. Box 79, Areka, Ethiopia
| | - Leena Tripathi
- International Institute of Tropical Agriculture, P.O. Box 30709, Nairobi, Kenya
| | - Kassahun Tesfaye
- Addis Ababa University, Institute of Biotechnology, P.O. Box 1176, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Science and Technology, P.O. Box 32853, Addis Ababa, Ethiopia
| | - Alemayheu Chala
- Hawassa University, Awassa College of Agriculture, P.O. Box 05, Hawassa, Ethiopia
| | - Audrey Farbos
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom
- Exeter Sequencing Service, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Paul O’Neill
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom
- Exeter Sequencing Service, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Karen Moore
- Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom
- Exeter Sequencing Service, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Murray Grant
- Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Castanho IM, Murray TK, Farbos A, Lunnon K, Collier DA, Ahmed Z, Paszkiewicz K, O'Neill MJ, Mill J. [P1–144]: TRANSCRIPTIONAL AND EPIGENOMIC PROFILING IN THE ENTORHINAL CORTEX IN AMYLOID AND TAU MOUSE MODELS OF ALZHEIMER's DISEASE. Alzheimers Dement 2017. [DOI: 10.1016/j.jalz.2017.06.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Alkeskas A, Ogrodzki P, Saad M, Masood N, Rhoma NR, Moore K, Farbos A, Paszkiewicz K, Forsythe S. The molecular characterisation of Escherichia coli K1 isolated from neonatal nasogastric feeding tubes. BMC Infect Dis 2015; 15:449. [PMID: 26497222 PMCID: PMC4620641 DOI: 10.1186/s12879-015-1210-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/13/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The most common cause of Gram-negative bacterial neonatal meningitis is E. coli K1. It has a mortality rate of 10-15 %, and neurological sequelae in 30-50 % of cases. Infections can be attributable to nosocomial sources, however the pre-colonisation of enteral feeding tubes has not been considered as a specific risk factor. METHODS Thirty E. coli strains, which had been isolated in an earlier study, from the residual lumen liquid and biofilms of neonatal nasogastric feeding tubes were genotyped using pulsed-field gel electrophoresis, and 7-loci multilocus sequence typing. Potential pathogenicity and biofilm associated traits were determined using specific PCR probes, genome analysis, and in vitro tissue culture assays. RESULTS The E. coli strains clustered into five pulsotypes, which were genotyped as sequence types (ST) 95, 73, 127, 394 and 2076 (Achman scheme). The extra-intestinal pathogenic E. coli (ExPEC) phylogenetic group B2 ST95 serotype O1:K1:NM strains had been isolated over a 2 week period from 11 neonates who were on different feeding regimes. The E. coli K1 ST95 strains encoded for various virulence traits associated with neonatal meningitis and extracellular matrix formation. These strains attached and invaded intestinal, and both human and rat brain cell lines, and persisted for 48 h in U937 macrophages. E. coli STs 73, 394 and 2076 also persisted in macrophages and invaded Caco-2 and human brain cells, but only ST394 invaded rat brain cells. E. coli ST127 was notable as it did not invade any cell lines. CONCLUSIONS Routes by which E. coli K1 can be disseminated within a neonatal intensive care unit are uncertain, however the colonisation of neonatal enteral feeding tubes may be one reservoir source which could constitute a serious health risk to neonates following ingestion.
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Affiliation(s)
- Aldukali Alkeskas
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Pauline Ogrodzki
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Mohamed Saad
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Naqash Masood
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Nasreddin R Rhoma
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Karen Moore
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, Exeter, EX4 4QD, UK.
| | - Audrey Farbos
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, Exeter, EX4 4QD, UK.
| | - Konrad Paszkiewicz
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, Exeter, EX4 4QD, UK.
| | - Stephen Forsythe
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
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11
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Masood N, Moore K, Farbos A, Paszkiewicz K, Dickins B, McNally A, Forsythe S. Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit. BMC Genomics 2015; 16:750. [PMID: 26438044 PMCID: PMC4594962 DOI: 10.1186/s12864-015-1961-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/29/2015] [Indexed: 11/25/2022] Open
Abstract
Background Cronobacter sakazakii is a member of the genus Cronobacter that has frequently been isolated from powdered infant formula (PIF) and linked with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. The Cronobacter MLST scheme has reported over 400 sequence types and 42 clonal complexes; however C. sakazakii clonal complex 4 (CC4) has been linked strongly with neonatal infections, especially meningitis. There have been a number of reported Cronobacter outbreaks over the last three decades. The largest outbreak of C. sakazakii was in a neonatal intensive care unit (NICU) in France (1994) that lasted over 3 months and claimed the lives of three neonates. The present study used whole genome sequencing data of 26 isolates obtained from this outbreak to reveal their relatedness. This study is first of its kind to use whole genome sequencing data to analyse a Cronobacter outbreak. Methods Whole genome sequencing data was generated for 26 C. sakazakii isolates on the Illumina MiSeq platform. The whole genome phylogeny was determined using Mugsy and RaxML. SNP calls were determined using SMALT and SAMtools, and filtered using VCFtools. Results The whole genome phylogeny suggested 3 distant clusters of C. sakazakii isolates were associated with the outbreak. SNP typing and phylogeny indicate the source of the C. sakazakii could have been from extrinsic contamination of reconstituted infant formula from the NICU environment and personnel. This pool of strains would have contributed to the prolonged duration of the outbreak, which was up to 3 months. Furthermore 3 neonates were co-infected with C. sakazakii from two different genotype clusters. Conclusion The genomic investigation revealed the outbreak consisted of an heterogeneous population of C. sakazakii isolates. The source of the outbreak was not identified, but probably was due to environmental and personnel reservoirs resulting in extrinsic contamination of the neonatal feeds. It also indicated that C. sakazakii isolates from different genotype clusters have the ability to co-infect neonates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1961-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naqash Masood
- Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Karen Moore
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, EX4 4QD, Exeter, UK
| | - Audrey Farbos
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, EX4 4QD, Exeter, UK
| | - Konrad Paszkiewicz
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, EX4 4QD, Exeter, UK
| | - Ben Dickins
- Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Alan McNally
- Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Stephen Forsythe
- Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
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Laver T, Harrison J, O'Neill PA, Moore K, Farbos A, Paszkiewicz K, Studholme DJ. Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol Detect Quantif 2015; 3:1-8. [PMID: 26753127 PMCID: PMC4691839 DOI: 10.1016/j.bdq.2015.02.001] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/05/2015] [Accepted: 02/18/2015] [Indexed: 01/15/2023]
Abstract
The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G + C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2 kb and 1 kb respectively, while the longest single read was 98 kb. The whole length of a 5 kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data.
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Affiliation(s)
- T Laver
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - J Harrison
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - P A O'Neill
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; Wellcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, Stocker Road, University of Exeter, Exeter EX4 4QD, UK
| | - K Moore
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; Wellcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, Stocker Road, University of Exeter, Exeter EX4 4QD, UK
| | - A Farbos
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; Wellcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, Stocker Road, University of Exeter, Exeter EX4 4QD, UK
| | - K Paszkiewicz
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; Wellcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, Stocker Road, University of Exeter, Exeter EX4 4QD, UK
| | - D J Studholme
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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Abstract
In the world of high-throughput sequencing there are numerous challenges to effective data quality control. There are no single quality metrics which are appropriate in all conditions. Here we detail the different open source software used at the Exeter Sequencing Service to provide generic quality control information, as well as more specific metrics for genomic and transcriptomic libraries run on Illumina platforms.
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Affiliation(s)
- Konrad H Paszkiewicz
- Exeter Sequencing Service, Biosciences, College of Life and Environmental Science, University of Exeter Exeter, UK
| | - Audrey Farbos
- Exeter Sequencing Service, Biosciences, College of Life and Environmental Science, University of Exeter Exeter, UK
| | - Paul O'Neill
- Exeter Sequencing Service, Biosciences, College of Life and Environmental Science, University of Exeter Exeter, UK
| | - Karen Moore
- Exeter Sequencing Service, Biosciences, College of Life and Environmental Science, University of Exeter Exeter, UK
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