Prophage host interactions: pulling back the curtains on Pseudomonas puppet masters

Lead Research Organisation: University of Salford
Department Name: Sch of Science,Engineering & Environment

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

LES prophages are known to impact the fitness of their lysogen, but lacking any obvious genes to mediate fitness, their importance remains unexplored. We propose to unpick the LES prophages contribution to bacterial fitness and reveal the underappreciated level of control that prophages have over bacterial host functions. Using strategies proven to work in for shigatoxigenic prophages in E. coli, we will first maximise the stability of the prophages during lysogen culture as well as optimise prophage induction conditions. We will use the induction conditions to purify the virions and then use LC-MS/MS to actually identify the prophage genes encoding the structural proteins of the phages. We have produced a comprehensive set of isogenic PAO1 lysogens and designed 36 library conditions from which we will extract total RNA, using 9 strains grown in 2 different media that highlight prophage-mediated phenotypic changes of the host under conditions where the prophages are most stable and under prophage inducing conditions. We will use RNAseq to identify differential gene expression (mRNA and small RNA) as well as identify transcription start sites. The identification of differentially expressed (DE) genes and prophage genes that are expressed from a stable prophage will enable us to build phenotypic assays and prophage gene constructs to test the function of prophage effectors to control the DE profiles of the Pseudomonas host. Having identified prophage effectors of host DE profiles we will then test a variety of strains using Nanostring's nCounter platform to investigate the global nature of our work. These approaches are needed as most phage genomes are comprised of at least 75% "dark matter" (hypothetical or ORFs of unknown function). Understanding the increased fitness of LES will enable better understanding of its biology and will pull back the curtain over mechanisms used by prophages to alter their bacterial hosts.

Planned Impact

Understanding the role of prophages in controlling their bacterial hosts will aid our understanding of bacterial gene regulatory networks, prophage impacts on bacterial hosts and our ability to assign function to genes that simply can not be characterised, currently.
1. SCIENTIFIC COMMUNITY: (microbiologists, phage biologists, genomics researchers). By empirical comparison of isogenic strains that differ only in prophage carriage our data will generate a clearer understanding of how prophage contribute to bacterial fitness. This information will aid bacteriologists in better understanding how bacteria respond to different stresses. Prokaryotic genomes are being sequenced and annotated at an increasing rate, but phage annotation is lagging behind (most genes cannot be annotated), which represents a critical gap in our knowledge - especially around potential genetic targets for intervention. A lack of functional annotation obfuscates study and comparison in microbiological, epidemiological or evolutionary studies. The project described here will begin to provide meaningful functional data, which will inform future experimental approaches, leading to new understanding and breakthroughs in academic and applied microbial research.
2. PUBLIC SECTOR: including clinical and agricultural stakeholders (eg CF Foundation Trust, NHS, WHO, DEFRA, OIE , AHDB). Our research is of direct relevance to key questions about how to treat bacterial diseases in agriculture and healthcare, and will therefore potentially improve farming productivity and wealth as well as the health and welfare of managed animals and humans. On a wider scale, elucidation of P. aeruginosa-phage interactions enables similar studies across a range of other bacteria. Whilst some Pseudomonas species are responsible for infections of economically important crops, cattle or humans, other species have industrial or environmental relevance, forming disruptive biofilms in pipelines or applied as bioremediation agents. A better understanding of phage relationships with these organisms could have wide economic impact on industrial processes and environmental management. Phage therapy approaches using phages informed by our data could have a direct and financially tractable approach for tackling antibiotic resistance.
3. PRIVATE SECTOR: pharmaceutical and biotechnology companies. Considering the catastrophic threat of AMR, our research could inform the development of desperately needed therapeutic strategies based upon new knowledge of gene regulation and environmental response, benefitting the pharmaceutical industry and new public-private partnerships that have formed to address this need (eg Novartis, Vertex Pharmaceuticals, GSK, Phizer, AMR Centre). Our data and methods will also be of great interest to phage therapy companies and will springboard the wider elucidation of function for so many poorly annotated phage genes (eg Adaptive Phage Therapeutics). Such elucidation could reveal novel aspects of phage biology for exploitation to develop revolutionary biotechnologies e.g. the history of CRISPR gene (eg Bayer, Blue Rock Therapeutics). Patients: eg those with Cystic fibrosis, particularly those with drug-resistant P. aeruginosa will benefit from new treatments that could be developed in response to our new understanding of prophage-regulated P. aeruginosa phenotypes. In the longer term, our data will inspire similar research to identify further therapeutic targets, benefiting patients suffering from other bacterial infections.
4. GENERAL PUBLIC AND MEDIA: (eg science festival goers, those with an interest in infection and societal impact of microorganisms). Antibiotic resistance is a global, catastrophic threat, and stories about bacteriophages, conceptually and as therapeutic tools, are increasingly on the public and media radar. Engagement offers the chance to educate and inspire interest in phages, infections, novel treatments and STEM subjects in general.

Publications

10 25 50
 
Title Creative Bacteriophage Animations 
Description A series of short animations created by Digital Media and Animation Undergraduate Students at The University of Salford - Inspired and guided by Microbial Puppet Masters Researchers 
Type Of Art Film/Video/Animation 
Year Produced 2022 
Impact The animations were developed through a series of workshops with the creative students. It helped them to refine their skills in multidisciplinary collaboration and teamwork and blurring the boundaries between science and art. The animations were showcased at Lightwaves art festival and viruses of microbes scientific conference. The animations were well received as delightful, entertaining and served to inspire people and lead them to want to find out more. Full animation videos exist but they are summarised in a sizzle reel (url below) 
URL https://drive.google.com/file/d/1YavoQmWMIyIX0DPsEpLVZv-rYx8vrzFn/view?usp=drivesdk
 
Title MicroCosmic 
Description In collaboration with artist, Paul Miller, we created an immersive Sci-Art Installation led by Paul's artistic interpretation of our work on bacteriophages. The immersive installation used video, sound and sculpture to take visitors on a sensory journey surrounded by the flux of our internal and external realities. The exhibit featured a giant sculpture of a phage (1.5 m diameter). Cosmic-themed projections and interactive sound were mapped onto the sculpture and the surrounding walls to create an immersive experience that was unique to each visitor as sound was progressive and reactive to movement. The installation played on themes of size and the human obsession with our own bodies and the vastness of the Universe. This had dualities with the fact that phages are the most abundant and tiny organisms on the planet, yet if you line them up, they would stretch for 200 million light years. Though invisible, they have an enormous influence on life on earth. Description from the artist: From the microscopic to the infinite vastness of the universe; inspired by pioneering scientific research, this immersive installation of video, sound and sculpture will take us on a sensual journey as we are surrounded by the flux of our internal and external realities. Where is the beginning and where is the end? From a human point of view, our own mind and body are the centre of our universe. Continuous exploration of our biology is revealing more about how we function as discreet organic beings, whilst hosting multitudes of others. We are entwined in an intricate network of data to be deciphered. Discovered just over 100 years ago, bacteriophages (phages) are viruses that infect bacteria. They are the most abundant and diverse organisms on Earth, found in both the natural environment and the human body. Their actions underlie the fundamental biology of our planet. Phages have been in a perpetual evolutionary dance with their bacterial hosts for millions of years. With an appearance evocative of a classic sci-fi alien, the phage, this otherworldly creature, is entering and exploring the inner universe of our bodies. New technologies enable us to discern its influence upon our delicate ecosystem. Just the word virus fills us with apprehension, as does the term alien, bringing forth countless fearful visions of the unknown. But with new research tools and deeper investigation, a more positive outlook is emerging. What does each new insight about ourselves and the universe tell us about existence? What would it mean if finally we knew it all? This installation is inspired by phage research between the Universities of Salford and Liverpool. We have worked together to develop a suite of activities to engage public thinking about the impact of phages on human health. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2022 
Impact Showcased as the flagship piece for Salford Universities contribution to Lightwaves - organised by Quays Culture as part of Light Up the North. The event was hosted at Media City, Salford, UK Dec 4th - Dec 10th. Our exhibit was visited by 2000 members of the public and enabled rich engagement. https://lightupthenorth.com/lightwaves/microcosmic/ 
URL https://www.whoispaulmiller.co.uk/projects#/microcosmic/
 
Description 1. 108 RNA Seq libraries have been generated (this means that all genes expressed and controlled by the bacterial viruses harboured by the host bacterium can now be identified and measured).
2. It was identified that prophage 5 is indeed active and produces phage particles (no susceptible host has yet been found).
3. Re-annotation of all 5 prophage genomes from the Liverpool epidemic strain of Pseudomonas aeruginosa has been completed. Many genes previously uncharaterised now have predicted function.
4. qPPCR assays have been developed for the classfication of viral gene expression profiles (markers of infection state and activity).
5. We  have identified the distinct morphology of phage 4, identifying it as a phage with a long broad flexible tail.
6. All bacterial genomes and integrated prophage combinations have been fully sequenced to confirm their genetic relatedness and our ability to compare them to one another.
Exploitation Route This project will inform others about the impact of previously ignored prophages on the bacterial host's biology.
Sectors Agriculture

Food and Drink

Digital/Communication/Information Technologies (including Software)

Education

Environment

Healthcare

Leisure Activities

including Sports

Recreation and Tourism

Government

Democracy and Justice

Pharmaceuticals and Medical Biotechnology

 
Description Our findings and ideas have backed several National outreach events that have introduced the concepts of bacteriophage to the public.  These uses have included therapeutic and non therapeutic impacts of bacteriophages in a manner that has attracted interest and broadcast from the BBC, the Royal Society and Microbiology Society.  These outputs also include online movie clips from the Royal Society and the Microbiology Society.  We were even involved in informing the Science, Technology and Communications Parliamentary Committee on how the government can improve the effectiveness of phage-related therapies and research in the UK. We also linked up in consultation with the Cystic Fibrosis Trust to enhance their ability to communicate about the risks of Pseudomonas infections and in managing patient expectations about what is possible with phage therapy. This was done through the imaginative production of 3-D virtual worlds and interactive models that help explain in a visual manner what phage are and how they interact with bacteria. We have gone on to develop more accessible pedagogical tools for engagement with a wider range of stakeholders.
First Year Of Impact 2022
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Healthcare,Government, Democracy and Justice,Manufacturing, including Industrial Biotechology,Culture, Heritage, Museums and Collections,Pharmaceuticals and Medical Biotechnology
Impact Types Cultural

Societal

Policy & public services

 
Description Part of the UKRI KTN Phage Innovation Hub
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
URL https://vimeo.com/showcase/10585785
 
Description Response to Government Inquiry on Bacteriophages as Antimicrobial Therapeutics
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
URL https://committees.parliament.uk/work/7045/the-antimicrobial-potential-of-bacteriophages/publication...
 
Title 110 RNA seq libraries from PAO1 and LES phage lysogen strains of PAO1 
Description We have had 110 RNA libaries created and sequeced to enable DE analysis to identify bacterial gene expression profiles that are altered by prophage. These will become publicly avialabe wtih the submission of our first manuscript detailing our data, observations and conclusions. 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? No  
Impact We have demonstrated, though not yet published, that LES prophage carriage impacts bacterial host cell gene expression. We have also demonstrated gene expression control between phages. Our libraries also wre designed to identify small regulatory RNAs and all transcription starts sties within the bacterial host and prophages. 
 
Title 9 ultra high quality genome sequences 
Description In order to faciliate the mapping of 144 RNA seq libraries we are defining the genomes of our single, double, triple and wild type lysogen. This will be important to define the strandedness and transcription start sites. 
Type Of Material Biological samples 
Year Produced 2021 
Provided To Others? No  
Impact This is necessary for the interpretation of our coming datasets. It will be made public and shared when we have mapped our RNAseq data to it. 
 
Title Bioinformatic pipeline for virus annotation 
Description The number of newly available viral genomes and metagenomes has increased exponentially since the development of high throughput sequencing platforms and genome analysis tools. Bioinformatic annotation pipelines are largely based on open reading frame (ORF) calling software, which identifies genes independently of the sequence taxonomical background. Although ORF-calling programs provide a rapid genome annotation, they can misidentify ORFs and start codons; errors that might be perpetuated and propagated over time. This study evaluated the performance of multiple ORF-calling programs for viral genome annotation against the complete RefSeq viral database. Programs outputs varied when considering the viral nucleic acid type versus the viral host. According to the number of ORFs, Prodigal and Metaprodigal were the most accurate programs for DNA viruses, while FragGeneScan and Prodigal generated the most accurate outputs for RNA viruses. Similarly, Prodigal outperformed the benchmark for viruses infecting prokaryotes, and GLIMMER and GeneMarkS produced the most accurate annotations for viruses infecting eukaryotes. When the coordinates of the ORFs were considered, Prodigal scored high for all scenarios except for RNA viruses, where GeneMarkS generated the most reliable results. Overall, the quality of the coordinates predicted for RNA viruses was poorer than for DNA viruses, suggesting the need for improved ORF-calling programs to deal with RNA viruses. Moreover, none of the ORF-calling programs reached 90% accuracy for annotation of DNA viruses. Any automatic annotation can still be improved by manual curation, especially when the presence of ORFs is validated with wet-lab experiments. However, our evaluation of the current ORF-calling programs is expected to be useful for the improvement of viral genome annotation pipelines and highlights the need for more expression data to improve the rigor of reference genomes. 
Type Of Material Technology assay or reagent 
Year Produced 2022 
Provided To Others? Yes  
Impact Invited to give a talk on the tool at a leading European bioinformatics conference 
URL https://github.com/EGTortuero/Benchmarking_ORF_calling_programs_in_viral_genomes
 
Title Newly created Lysogens 
Description Following detailed analysis of ultra high quality sequence data of our PAO1 lysogens (single, double, triple), we identified a small number of mutations, deletions and a duplicate prophage integration that could resut in potential artefacts, masking or suggesting false effects of LES prophage carriage. Thus we systematically created fresh lysogens, re-sequences and re-annotated all. The sequences have been annotated using improved orf-calling tools and manual curation and we are in the process of submitting them to ENA. 
Type Of Material Biological samples 
Year Produced 2022 
Provided To Others? No  
Impact The new genome sequences have resolved these issues and will be important to define the strandedness and transcription start sites of important phage genes to better identiy thier function in transcriptomics experiments. 
 
Title double lysogen Pseudomonas carrying LES prophages 2 and 3 
Description This is a double lysogen of LES prophages 2 and 3 carryied by the type strain PAO1. This strain was found to be unstable, and needed to be remade. Now that we are aware of its instability, we know what colonial phenotypes to be wary of. 
Type Of Material Cell line 
Year Produced 2021 
Provided To Others? Yes  
Impact necessary as a control and test strain for this study. 
 
Title Input files from the ORF annotation programs (zip file) - Comparative analysis of gene prediction tools for viral genome annotation 
Description The file "Inputfiles_from_ORF_annotation_programs.zip" contains all output files for the different ORF calling programs tested (i.e. AUGUSTUS with the three different models (Human, S. aureus and E. coli), FragGeneScan, GeneMarkS, Glimmer, MGA, MetaProdigal, PHANOTATE, Prodigal). These files were used as the first input file to count the number of true positives (TP), false positives (FP) and false negatives (FN) via "coordinateschecker.py". It is important to highlight the type file in the script before running it, as not all programs offer the same output type. These files should be decompressed before using it in any of these scripts. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact this has not been made as of yet. 
URL https://figshare.com/articles/dataset/Input_files_from_the_ORF_annotation_programs_zip_file_-_Compar...
 
Title Viral genomes from GenBank (reference) - Comparative analysis of gene prediction tools for viral genome annotation 
Description The file "viral.genomic.gbk.tar.gz" contains all the RefSeq viral database information in GenBank format, used as the gold standard for the comparisons. In such a way, it should be run as is when using the script "genecounter.py" to count the number of genes, while it is the second (mandatory) input file for the counting of true positives (TP), false positives (FP) and false negatives (FN) via "coordinateschecker.py". In any case, it could also be used for other evaluation purposes. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact This work has featured at several bioinformatics courses run at Evergreen, a meeting in Costa Rica and in Spain. 
URL https://figshare.com/articles/dataset/Viral_genomes_from_GenBank_reference_-_Comparative_analysis_of...
 
Description Collaboration with Dr. Jo Fothergill 
Organisation University of Liverpool
Country United Kingdom 
Sector Academic/University 
PI Contribution Dr. Jo Fothergill has a long term interest in the phages of the LESB58 strain of Pseudomonas aeruginosa. We are characterising these phages in respect to annotation with emperical evidence, gene expression profiles and mutant analyses in ways that were previsouly not possible for her to do. These data provide her with a much clearer picture about what traits these phages birng to Pseudomonas in the cystic fibrosis lung.
Collaborator Contribution Dr. Fothergill has a complete transposon library of the PAO1 strain that will enable us to to test key phenotypes identified from our RNASeq data. She also attends weekly lab meetings and provides useful insight. As part of her research activities focused on phage therapy, she has joined us as a co-investigator in our public engagement activities (Enter the phage) to be showcased at The Royal Society Summer Science Exhibition. Importantly, Dr Fothergill links us up more closely with major stakeholders: The Cystic Fibrosis Trust, who have a strong interest in the public menssages that our Virtual Reality Lungs and working 3D printed interactive models will convey, particilarly for the Cystic fibrosis community invested in the idea of phage therapy, but wanting to know more about different potential outcomes. This collaboration will greatly enhance the visibility and impact of our work with different audiences.
Impact Working with Jo Fothergill, University of Salford and Paul Miller we have successfully bid to be one of 21 exhibitors at this year's (2022) Royal Society's Summer Science Exhibition.
Start Year 2021
 
Description Collabration with Joe Bondy-Demony Group (UCSF) via Prophage Deletion Mutants 
Organisation University of California, San Francisco
Country United States 
Sector Academic/University 
PI Contribution Correspondence with UCSF team members and receipt of mutant strains
Collaborator Contribution Postdoc from the group joined our online lab meeting to discuss their work and creation of mutants and how they might benefit our research. Provision of 5 mutant strains: wt LESB58 that we used, LESB58?prophage-2, LESB58?prophage-5, LESB58?prophage-2,5, and LESB58?phzM
Impact Strains have been received and stored in our - 80oC freezers
Start Year 2021
 
Description We have established a collaboration with Rob Lavigne's group in Leuven (Belgium) 
Organisation University of Leuven
Country Belgium 
Sector Academic/University 
PI Contribution We have been searching for susceptible hosts to support LES phage infection. This has lead to the Leuven group providing us with strains from their large, but unique collection of Pseudomonas phage hosts, due to their long term work in this area.
Collaborator Contribution We have been able to access strains from them that are not available anywhere else prior to publication of the characteristics of these strains.
Impact This is in the early stages and so have not yet confirmed produced outputs from this.
Start Year 2023
 
Description 24th Biennial Evergreen International Phage Meeting 2021 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Do temperate bacteriophages work together as puppet masters of their bacterial hosts? (Role of temperate bacteriophages in their bacterial hosts.)
Year(s) Of Engagement Activity 2021
URL https://sites.evergreen.edu/phagelab/2021-evergreen-meeting/
 
Description A deep dive in to scientific research on bacteriophages 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact This blog post summarises public engagement with our new immersive sci art rinstallation - MicroCosmic showcased at Lightwaves Festival 2022, Media City, Quays Culture.
Visitors later approached us to ask if we would take part in Bradford Science Festival.
Year(s) Of Engagement Activity 2022
URL https://blogs.salford.ac.uk/research/2022/12/08/microcosmic-gave-the-public-a-deep-dive-into-science...
 
Description Activities and discussion with degree applicants during applicant visit day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Microbiology activity during applicant visit day at The University of Salford: Activities designed to demonstrate the breadth and depth of microbiology research, highlighting the importance of understanding host-microbe interactions in both health and disease and distinguishing different types of bacteria and viruses. Activities included bioselfies (drawing artworks with visitors own skin microbiota as live paint on agar plates), Gram's-stained slides of bacteria and Giant 3D models of virues, including bacteriophges. Roughly 40 visitors took part in the event, including yr12 and 13 pupils and their families. Several visitors enjoyed sharing their knowledge of microorganisms and one pupil said that they were inspired by bacteriophages for the topic of theri next school assignment.
Year(s) Of Engagement Activity 2022
 
Description Animal and Plant Health Agency at New Scientist Live 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The Animal and Plant Health Agency (APHA), contacted us through The Microbiology Society to ask if they could borrow our 3D printed bacteria models to help them with their display about Biosecurity. Our models would represent bacterial pathogens that colonise livestock (Shigatoxigenic Escherichia coli) and pose a threat to human health through production of a bacteriophage derived toxin. We were able to share our models and organise two local student volunteers from our wider network (one at oxford Uni and one at UCL). This was for the big Public Engagement event organised by New Scientist in London ExCel attended by 23,045 visitors.
Feedback on numbers from the New Scientist Live team are as follows:
It was fantastic to be back at ExCeL London meeting such engaged visitors, learning from our inspirational speakers, and of course, enjoying the fabulous exhibits! We also streamed all our stages and show floor content over the weekend to a further 1,702 international viewers, and this number will grow as more people access the on-demand recordings. We will share more information next month as we are currently surveying our visitors for more insights.

APHA evaluation, using the pledge jars, highlighted that people had learnt about the importance of biosecurity to protect animals and plants in the UK from disease and that they would pledge to do at least one of the pledges listed, with washing your boots or reporting dead wild birds slightly higher. It was great working with you all and thank you so much for helping us represent the giant E.coli microbe at the show! There might be future opportunities to link up so please let us know if we can help at any future events you do.
APHA published a blog on New Scientist Live today: https://aphascience.blo...new-scientist-live-2023
Social media posts:
https://twitter.com/APH...tus/1722902844309897489
https://www.facebook.co...p;set=a.582442270581994
https://www.linkedin.co...ity:7128668764778180608
Year(s) Of Engagement Activity 2023
URL https://live.newscientist.com/whats-on
 
Description Breaking the Mould - Salford University Summer School for sixth form students from Widening Participation areas 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Delivery of a microbial puppet masters workshop during a 3 day residential summer school in partnership with Greater Manchester Higher. The summer school was designed to give prospective students a flavour of bio-science degree courses at University. The aim was to inspire those who might not feel confident that university is for them.
We delivered a 1 h interactive session where pupils trialed our virtual reality lung and interacted with our giant microbial models to understand more about what phages are and h they affect bacterial communities.
Evaluations reported that some students who were not previously considering university, were now after the summer school.
Year(s) Of Engagement Activity 2022
URL https://gmhigher.ac.uk/wp-content/uploads/2022/03/Y12_flyers-2022-Breaking-the-mould.pdf
 
Description Community Science Project 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact The Community Science Project aims to bring research to communities in Merseyside, giving people the opportunity to engage with research that could impact their lives, and shape how is communicated to them in the future. The team work with young people from Widening Participation schools, and pair them with researchers from the Faculty of Health and Life Sciences at The University of Liverpool. Through a series of workshops, researchers share their work with the young people and work with them to develop a hands-on activity that explores this research. The resulting activity will communicates key research in a way that is accessible to the wider community. These activities will then be run by the young people and the researchers at future community science fairs.
One of our wider team Dr Libby Duignan works on a related phage project under the guidance of our collaborator Jo Fothergill. Dr Duignan has been involved in several of our public engagement activities and is now ready to develop and deliver her own. She used our Giant interactive phage and bacteria models to develop an engaging workshop with young people from across Liverpool.
Year(s) Of Engagement Activity 2023
 
Description Conference poster abstract: Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Poster presentation to take place at the Microbiology Society Annual Conference in April 2021
Year(s) Of Engagement Activity 2021
URL https://microbiologysociety.org/event/full-events-listing/annual-conference-online-2021.html
 
Description Determining prophage genome integration under single and co-infection: the case of Pseudomonas aeruginosa LES prophages in P. aeruginosa PAO1 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact González-Tortuero E, Krishnamurthi R, Goodhead IB, Allison HE, James CE. Determining prophage genome integration under single and co-infection: the case of Pseudomonas aeruginosa LES prophages in P. aeruginosa PAO1. Annual Conference Microbiology Society 2022; 2022 April 4-7, Belfast, Northern Ireland, United Kingdom. (Poster Presentation)
Year(s) Of Engagement Activity 2022
URL https://microbiologysociety.org/event/annual-conference/annual-conference-2022.html
 
Description Discussion about viruses with young people at New Scientist Live Schools Day at Manchester Central 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact C. James was booked for an interactive slot on the "engage stage" for a discussion with organisers and school pupils visiting the NewScientistLive event at Manchester Central 14th March 2022. Giant 3D printed models of different types of viruses were used as tools to help engage converation about how viruses infect cells, their specificity, immunity, vaccination and the effects of mutation. Large enveloped virses, like SARS-CoV-2 were compared to bacteriopahges. Parallells were drawn between spike proteins and tail fibres, specificity and mutation. The use of phages as therapy was contrasted with other phages that can increase bacterial virulence and antibiotic resistance. This highlighted the importance of our research aiming to better understand how different phages affect bacterial biology. Roughly 50 students from a range of local schools attended the discussion, which sparked questions about disease transmission and treatment.
Year(s) Of Engagement Activity 2022
URL https://live.newscientist.com/welcome
 
Description Do temperate bacteriophages work together as puppet masters of their bacterial hosts? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation to take place in at Micro Soc Meeting in April
Year(s) Of Engagement Activity 2021
URL https://microbiologysociety.org/event/full-events-listing/annual-conference-online-2021.html
 
Description Evaluation of gene-calling programs for viral genome annotation. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact González-Tortuero E. Evaluation of gene-calling programs for viral genome annotation. International Virus Bioinformatics Meeting 2022; 2022 Mar 23 - 25, Online. (Oral presentation)
Year(s) Of Engagement Activity 2022
URL https://evbc.uni-jena.de/events/vibiom2022/
 
Description Expert response to government report on inquiry into bacteriophages as antimicrobials through The Science Media Centre 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact JANUARY 3, 2024
Chloe James contributed to "Expert reaction to Science, Innovation and Technology Committee report on the antimicrobial potential of bacteriophages" published by the Science Media Centre for info to be picked up by press. There was a particular focus on the use of national lab beeing re-purposed for phage research.
Article title: Scientists react to the 2023-2024 SIT committee report on the antimicrobial potential of bacteriophages.
Example articles that used CJs quote:
https://www.chemistryworld.com/news/science-committee-calls-for-national-lab-being-sold-on-rightmove-to-get-new-lease-of-life/4018746.article
https://news7f.com/science-committee-calls-for-national-lab-being-sold-on-rightmove-to-get-new-lease-of-life-news/
Year(s) Of Engagement Activity 2024
URL https://www.sciencemediacentre.org/expert-reaction-to-science-innovation-and-technology-committee-re...
 
Description GM Microbiomes Network 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact ~50 academics from Manchester, Salford and Manchester Metropolitan University met to share our common research goals in microbiomes research and plan activities as a group - including training, public engagement and acquiring funding for collaborations. CJ represented Salford, summarising our broad microbiomes research and highlighting the role of phages - this opened up several new potential collaborations in research and engagement across the group. A smaller group of 6 of us, representing each institution met as a follow up to plan training and seminar events across GM in the coming year.
Year(s) Of Engagement Activity 2024
 
Description Get Curious 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Activity for the Get Curious series of events run by the Science and Industry Museum, Manchester.
700 visitors attended the 1 day event that was developed as a follow on from our Microbial Puppet Masters Event created for the Royal Society Summer Science Exhibition. We showcased new interactive models and paper crafts as well as virtual reality and student animations to engage with people about phage and how they work. This sparked lots of conversations about viruses good and bad as well as antibiotic resistance and phage therapy as well as careers in science and the latest technologies. Two of our delivery team wrote a blog post about the event for the Microbiology Society blog pages linked to the Knocking out AMR project.
Year(s) Of Engagement Activity 2023
URL https://www.salford.ac.uk/news/microbial-puppet-masters-on-show
 
Description Go Beyond: Event for women in STEM 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Panel discussion as part of a one day Go Beyond event for International womens' day. Practical tips on getting your next position
Year(s) Of Engagement Activity 2023
URL https://www.salford.ac.uk/news/go-beyond-mentoring-initiative-for-future-women-in-stem
 
Description Go Beyond: Event for women in STEM 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Panel discussion as part of a one day Go Beyond event for International womens' day. Practical tips on getting your next position
Year(s) Of Engagement Activity 2023
URL https://www.salford.ac.uk/news/go-beyond-mentoring-initiative-for-future-women-in-stem
 
Description Hosted main event for a "Meet the Scientists Day" at the Victoria Gallery and Museum, University of Liverpool 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact This day is a full day event hosted by the University at its Victoria Gallery and Museum. We wre given the entire first floor of the building to use to present our bespoke virtual lung/biofilm/phage infection story designed for the general publish as well as cystic fibrosis patients and their families. We also had lots of hands on activities to demonstrate how bacterial cells are infected by phages and what the various coutcomes can be. This presentation was a chance for us to show people the impact and understanding we are generating about phags from the BBSRC funding.
Year(s) Of Engagement Activity 2024
 
Description Importance of public engagement for the dissemination of research information. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact This activity was scheduled for Post docs and PHD students.
Year(s) Of Engagement Activity 2022
 
Description Interview on BBC Health Check podcast for The World Service and BBC Sounds 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Pre-arranged interview with BBC presenter Claudia Hammond for BBC Health Check Podcast - aired on the BBC World Service and available on their BBC Sounds website.
Podcast Released On: 07 Jul 2022 Available for over a year
Blurb: Claudia Hammond is at the Royal Society Summer Science Exhibition in London looking at the latest medical research. Claudia speaks to ..... senior lecturer, Chloe James on the super powers of bacteriophages and how they work as puppet masters.
8 min clip [min 1:39 - 9:12] aired on 5 different live broadcasts in UK, Australasia, Americas, Africa, Europe and Middle East and Internet, as well as available to listen or download permanently from BBC Sounds website.
Year(s) Of Engagement Activity 2023
URL https://www.bbc.co.uk/sounds/play/w3ct32wl
 
Description Interview with The Microbiology Society about our research showcase at The Royal Society Summer Science Exhibition (YouTube) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Microbiology Society produced this video interview about our work as part of their mission to champion the work of their members. It was broadcast on YouTube to inform people about what we are doing and to invite people to come and talk to us about our work at the event that week. 941 views and 12 likes.
Year(s) Of Engagement Activity 2022
URL https://www.youtube.com/watch?v=GtCsqq8J-yE
 
Description Interview with Undergraduate Biomed Sci Student for the University of Salford Bioscientist Magazine: Prophage host interactions: pulling back the curtains on Pseudomonas puppet masters 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Undergraduate students on The University of Salford, Biomedical Science Society have recently launched their student-led magazine "The Bioscientist". Chloe James was interviewed by one of the students this week about her research, in particular the BBSRC funded project for an article in the next issue to be released at Easter. The magazine is read by staff and students on related courses, but has also been favorably reviewed by the Institute of Biomedical Science (IBMS) on their website.
Year(s) Of Engagement Activity 2021
URL https://www.ibms.org/resources/news/ibms-e-students-inspired-by-biomedical-scientist-magazine/
 
Description Invited Talk and Oxford Bacteriophages 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Professor Heather Allison
Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK

Prophages, what are they doing in that genome?

This talk focussed on much of the work done over the past few BBSRC grants.
Year(s) Of Engagement Activity 2023
URL http://lpmhealthcare.com/phages-2023/speakers-agenda/
 
Description Invited talk at University of Oxford annual Phages conference 2020 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The talk described our preliminary data that lead to the award of this grant and introduced our planned programme of work. The talk sparked questions from interested researchers and fruitful discussions that could lead to future collaborations. After the conference, we were contacted by one delegate who was keen to join a network of prophage researchers with us. We have made contact with one meeting since then and will build on this to further develop the network.
Year(s) Of Engagement Activity 2020
URL http://lpmhealthcare.com/phages-2020-virtual/
 
Description Invited talk for International Virus Bioinformatics Meeting (March 2022_Online) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Following submission of manuscript on virus annotation as a preprint, this talk was invited: González-Tortuero E (2022) Evaluation of gene-calling programs for viral genome annotation. International Virus Bioinformatics Meeting 2022. Online, 23 - 25 March.

Title: Evaluation of gene-calling programs for viral genome annotation.
Enrique González-Tortuero1,*, Revathy Krishnamurthi2, Heather E. Allison2, Ian B. Goodhead1, Chloë E. James1
1 School of Science, Engineering and Environment (SEE), University of Salford, M5 4WT. United Kingdom
2 Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, L69 7ZB. United Kingdom
*Corresponding author: e.gonzaleztortuero@salford.ac.uk

Abstract
The number of newly available viral genomes and metagenomes has increased exponentially due to the development of high throughput sequencing platforms and genome analysis tools. Genome annotation pipelines are mainly based on gene-calling software, which identifies genes independently of the sequence taxonomical background. Although gene-calling programs provide a rapid genome annotation, they can misidentify genes and start codons, perpetuating errors over time. This study evaluated the performance of multiple gene-calling programs for viral genome annotation against the complete RefSeq viral database. Prodigal and FragGeneScan were the most accurate programs for DNA and RNA viruses, respectively, according to the number of coding genes. When the coordinates of the coding genes were considered, Prodigal scored high for DNA viruses, while GeneMarkS generated the most reliable results for RNA viruses. Overall, the quality of the coordinates predicted for RNA viruses was poorer than for DNA viruses, suggesting the need for improved gene-calling programs to deal with RNA viruses. Moreover, none of the gene-calling programs reached 90% accuracy for annotation of DNA viruses. Manual curation should improve any automatic annotation, especially when the presence of genes is validated with wet-lab experiments. Our evaluation of the current gene-calling programs is expected to be helpful for the improvement of viral genome annotation pipelines and highlights the need for more expression data to improve the rigor of reference genomes.
Year(s) Of Engagement Activity 2022
URL https://evbc.uni-jena.de/events/vibiom2022/
 
Description Invited talk for the Early Career Section of Oxford Bacteriophages 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Revathy Krishnamurthi
Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK

Prophage mediated rewiring of gene expression landscapes in Pseudomonas aeruginosa

Presentation of our first RNA seq outputs from the project
Year(s) Of Engagement Activity 2023
URL http://lpmhealthcare.com/phages-2023/speakers-agenda/
 
Description Invited talk: Presentation of public outreach to the Oxford Bacteriophages Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Public engagement Talk:
Professor Chloe James
School of Science Engineering and Environment, University of Salford, Manchester, UK

Microbial Puppet Masters: immersive SciArt installations and activities to inspire wider public conversations about bacteriophages
Year(s) Of Engagement Activity 2023
URL http://lpmhealthcare.com/phages-2023/speakers-agenda/
 
Description Invitied talk at University of Oxford's Annual Phages Conference 2020 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The talk sparked interest in the idea that silaent prophage might contribute more to their bacterial host phenotype then previously thought.
Year(s) Of Engagement Activity 2020
URL http://lpmhealthcare.com/phages-2020-virtual/
 
Description Knocking out AMR - Workshop on therapeutics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Chloe James took part in a workshop organised by The Microbiology Society - Knocking out AMR project. A group of 20 experts in AMR from across academic, industrial and clinical sectors of the UK and Ireland were invited to the one day systems mapping event to discuss "therapeutics" as one of 3 arms of the project (diagnostics and surveillance are the others). In her role as member of the oversight group, CJ chaired one of the groups and will submit a report in April. The outcomes will be used to shape the activities of the project that will influence national and international collaborative research strategies and policy. Bacteriophages featured as the major alternative therapeutic, and we discussed challenges and how they might be overcome, including how a better understanding of unknown phage gene functions can help.
Year(s) Of Engagement Activity 2024
URL https://microbiologysociety.org/our-work/knocking-out-antimicrobial-resistance.html
 
Description Level-Up Human Popular Science Podcast 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Invited as a panelist on the popular science podcast series "Level-Up Human". Scientists are invited onto the show to make pitches for how they would improve the human body. My pitch was to have better command over our internal armies of bacteriophages. On the show I described what bacteriophages are and plugged our project, recently funded by BBSRC. The podcast organisers' feedback was that it was a great show, and the transcript was published as a follow up to the episode on their website.
Year(s) Of Engagement Activity 2020
URL https://play.acast.com/s/leveluphuman/s2e10-self-scratchingbacks
 
Description Magazine Article for Microbiology Today - Extended Reality: New Frontiers of Microbiology Teaching 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact C. James invited to contribute to May 2022 edition of Microbiology Today (The Microbiology Society quarterly magazine). The circulation of Microbiology Today is not restricted to 7000+ members of the Microbiology Society as it is also used to promote the understanding of microbiology to a wider public, including opinion formers, policymakers and teachers.
The article is an opinion piece about the changing landscape of microbiology in higher education and describes our latest developments towards a virtual reality lung to enhance understanding of phage-bacteria interactions in the context of cystic fibrosis. The article has been submitted and accepted, with a release date of May 2022. This no impact can yet be recorded.
Year(s) Of Engagement Activity 2022
URL https://microbiologysociety.org/members-outreach-resources/microbiology-today.html
 
Description MicroCosmic: An Immersive SciArt Installation to Inspire Conversations with Young People About Bacteriophages as Microbial Puppet Masters 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was a talk on the impact of the public outreach work for the work done on this grant. The talk also featured information on how our models were developed and how it was received.
Year(s) Of Engagement Activity 2023
URL https://microbiologysociety.org/event/society-events-and-meetings/annual-conference-2023.html?keywor...
 
Description Microbe_Talk. Microbiology Society Podcast on AMR and Phages 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Microbiology Society invited Chloe James to record a Podcast Interview with them as part of the Knocking out AMR project, for which Chloe is on the oversight committee. In the interview, we discuss the challenge of AMR and some different ways of tackling it through surveillance, diagnostics and novel therapeutics. There is a particular focus on our work on phages as potential solutions. We also talk about the importance of creativity and art and public engagement in tackling the global problem of AMR.

The recording was promoted n twitter and linked in and is available to listen on the society website. The society has 5000 members but also engages with clinicians, industry and government.
Year(s) Of Engagement Activity 2023
URL https://microbiologysociety.org/news-press/podcast-microbe-talk.html
 
Description Microbial Puppet Masters at Lightwaves 2022 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Following on from the success of our exhibit at The Royal Society Summer Science Exhibition, we secured a slot to exhibit our work as part of Lightwaves 2022 - an art festival at Media City UK, Salford.
The event invites visitors to explore a trail of dramatic light art installations that animate and transform the urban waterside environment around Salford Quays and MediaCity each winter. Most artworks were displayed from Thursday 1st to Sunday 4th December, but our installation was one of two that remained on show until 9th December. Visitors of all ages came to enjoy illuminated works from established as well as emerging artists, local and national, bringing a variety of different pieces; thought-provoking, surprising and playful.
Lightwaves Festival is part of the Quays Culture Programme, a partnership initiative with a mission to animate public spaces, bringing extraordinary art into the heart of the community for everyone to experience free of charge.
Our exhibit centred around our new immersive artwork "MicroCosmic" created by artist Paul Miller (see creative art entry). The art played with scale, video, light and sound and explored concepts of the vast unknown and the human obsession with their bodies. Phages, though unfathomably tiny are the most abundant and diverse organisms on the planet. Looking like aliens from outer space, they have untold impact on our planet, including inside the body. The installation conveys the feeling of being in vivo and provides a unique experience to each visitor through moveent reactive video and sound projected onto a giant ichsahederal
phage sculpture (1.3 m diameter). Outside the enclosed, cave-like art installation, our exhibit also included our Giant interactive models of bacteria and phage that demonstrate the scientific concepts we are investigating. Since the event was delivered in the run up to Christmas, we also ran a phage-making workshop, entitled Faberge phage. Visitors were invited to join us at our large crafting tables to cut out, fold and make their own ichosahederal Christmas tree decoration. The iconic shape is not only the shape of the phages we work with, but also has meaning for architects and mathematicians. Once the basic shape was folded and stuck, visitors had the opportunity to decorate their creations with sparkles, sequins and gemstones and either hand them on our exhibit trees, or take them to put pride of place on their Christmas tree at home. The activity promoted rich conversation about phages, viruses, bacterial infections, cystic fibrosis, sci art and careers in science, art and communication.
The exhibit was also accompanied by phage-inspired animations displayed on giant screens - created by digital media and animation students at The University of Salford.
>2000 visitors came to our exhibit alone.
Visitors thoroughly enjoyed the exhibit. They were interested and intrigued to know more. Many learned a lot about phage that they had never heard of before. They were excited at the prospect of phages as novel therapeutics and intrigued by the research and how to become a scientific researcher with a creative side.
Visitor Feedback:
"We all thoroughly enjoyed the Lightwaves Festival especially the indoor Microcosmic event. Left feeling chilled. Thanks"
"Really liked the interaction and projections together! And being able to control them."
"Fun activities and engaging poster"
"Peaceful until you touch the orb"
"Tranquil"
"Wonderful and ward"
"Very Calming"
"Amazing"
"Thanks, this was very inspirational"
"Great, entertaining and educational, Many Thanks"
"The evening was really enjoyable. The children really enjoyed the lights display. My son 2, and my mother in law 82, also loved it. Fun for all the family"
"Oh my, it was amazing, Simon was really helpful"
"What an amazing experience to have available for free. Light in the dark months is always a perker! Good for the soul. Many Thanks"
"Tamsin, Jake and Lyn were fantastic! Thank you so much for all your help. You deserve a raise!"
"A fantastic light show with warmth at the end of the 13 stop trail. Highly recommended"
"Lovely display, entertaining and educational. Well worth a visit"
"Magical"
"brilliant"
"Absolutely wonderful"
"Interactive"
"Gorgeous, really satisfying interaction. Beautiful sound design."
"Enjoyed the interaction with the different bits"
"Thank you! Beautiful space and good explanations by Team! "
"Great interactivity for the children. Good displays. Very instructive"
"Very nice"
"A fantastic inspiring lights evening. I loved seeing how many young people + kids were interacting with the art works! Thanks"
"Had amazing time, thanks for your help to show better"
"Fantastic experience in the University as part of Lightwaves. Exhibit was amazing & my boys thoroughly enjoyed building their phages. Thank you for the very helpful & informative helpers!"
"Very atmospheric. Soothing. Relaxing. Strange in a good way. Shadow puppets. Hmmm."
"Really interesting combining art and science. So nice to be invited into part of the University. Warm too!"
"It made me calm" James, age 7
"Amazing sensory experience"
"Really enjoyed this installation. So tranquil. Loved controlling the shapes and patterns."
"It was like being inside a volcano" Alex, age 7
"Chloe was amazing. Thanks for being so good with the kids!"
"The Microcosmic show really touched with my spiritual and religious side of Islam. Islam teaches us that we can not see tiny particles and atoms with the naked eye. We can not see god. We can experience him and feel through experience. There is a creator"
"Very cleverly designed to show the naked eye"
"I liked the shiny lights and the fire. The bird on fire was awesome. I didn't know what a phoenix was before tonight. The space themed lights were cool. Space must be peaceful as there is no sound" Liam age 5 ½
Year(s) Of Engagement Activity 2022
URL https://lightupthenorth.com/lightwaves/
 
Description Microbiology Society Annual Meeting 2021 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster Presentation: Do temperate bacteriophages work together as puppet masters of their bacterial hosts. Pseudomonas aeruginosa is one of the major causes of morbidity in cystic fibrosis (CF) patients.
The Liverpool Epidemic Strain (LES) is associated with more severe disease and is transmissible between hosts. Comparative genomics revealed that the LES genome had obtained five new genomic islands and five novel prophages. Previous studies detected abundant free LES phages in CF patient sputum and isolated three active LES phages from LES cultures. These phages were found to confer fitness advantages to LES, but the specific mechanisms are not known. Our study aims at understanding the molecular mechanisms by which these prophages impact the biology of the P. aeruginosa host.
We used a well-characterised laboratory strain of P. aeruginosa (PAO1) that is susceptible to lysogenic infection by three LES phages. This enabled the construction of lysogen variants harbouring three LES prophages (specifically ?2, ?3 and ?4) in all possible combinations, creating single, double and triple lysogens. Our preliminary comparison of growth characteristics revealed direct phage-specific effects and interactions between the prophages. Transcriptome studies of these lysogens under varying conditions will help to identify the specific interactions, which will be confirmed through mutant construction and phenotypic analyses.
IMPORTANCE: Our study shows that LES phages increase the fitness of their host through specific interactions. Further investigation in clinically relevant conditions could identify unique targets for tackling recalcitrant P. aeruginosa infections.
Year(s) Of Engagement Activity 2021
URL https://microbiologysociety.org/event/full-events-listing/annual-conference-online-2021.html?keyword...
 
Description Morson Maker Space: Medical Microbiology Research Case Study at The University of Salford 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Printed and online pamphlet advertising the skills, creativity and collaborative working practices of the Morson Maker Space at The University of Salford.
The pamphlet describes a case study featuring our work and how we collaborated as a creative team to create interactive models of giant microbes to convey threshold concepts of our work on phages.
This has inspired others to approach the maker space for new projects and may need to commercial production of our modes for use by educators.
file:///C:/Users/els262/AppData/Local/Microsoft/Windows/INetCache/Content.Outlook/90VE3CA7/Makerspace%20Case%20Studies%20Microbial.pdf
Year(s) Of Engagement Activity 2022
 
Description Museum After Hours 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Invited by Science and Industry Museum to showcase our work at their Museum After Hours event linked to their lager installation - Operation Ouch. Sold out: 700 tickets
CJ joined the artist (Paul Miller) in a discussion about the work and the collaboration. Accompanied by our usual microbial puppet masters activities.
We secured half price tickets for all SEE staff and students and the school subsidised this further so we could offer 25 free places to students. In addition we invited several stakeholders.
Year(s) Of Engagement Activity 2023
URL https://www.scienceandi...s-on/museum-after-hours
 
Description Offered talk at M62Microbe Seminar Series 2021 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact The M62Microbe group includes a range of researchers from acaedmic institutions that are located along the M62 motorway (Liverpool, Manchester, MMU, Salford, Sheffield, York, Lancaster..). The group shares a specific interest in microbial ecology and evolution. Each institution takes turns to offer an update on their research. The University of Salford contribution from our group was presented by González-Tortuero E (2021) Understanding the role of Pseudomonas aeruginosa LES prophages. M62Microbe Seminar. Online, 6 May.
Year(s) Of Engagement Activity 2021
 
Description Online News article from The University of Salford: Giant models of bacteria and viruses for Royal Society Summer Science Exhibition 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Reporting our development of activities for engaging with the public about phages
Year(s) Of Engagement Activity 2022
URL https://www.salford.ac.uk/news/salford-microbiology-researchers-create-giant-models-royal-society-su...
 
Description Oral Presentation2 at 11th Oxford Bacteriophage Conference (PHAGES 2021). Online 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Offered Oral Presentation at 11th International Oxford Bacteriophage Conference (PHAGES 2021). Online, 7 - 8 September.
Title: Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages
Authors: Enrique González-Tortuero1, Revathy Krishnamurthi2, Joanne L. Fothergill2, Ian B. Goodhead1, Heather E. Allison2 and Chloe E. James1
1School of Science, Engineering and Environment, University of Salford, Cockcroft Building, Salford M5 4NT, UK
2Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Crown St, Liverpool L69 7ZB, UK

Pseudomonas aeruginosa is an important opportunistic pathogen, causing nosocomial infections. The Liverpool Epidemic Strain (LES), a major cause of mortality and morbidity in cystic fibrosis patients, harbours five prophages associated with increased fitness and survival in models of infection. However, ~76.5% of the LES prophage genes are hypothetical proteins. Also, little is known about the LES prophage interactions with the lysogen and other prophages. In this study, we used the VIral Genome Annotation (VIGA) pipeline to re-annotate the LES prophage genomes and improve the prediction of gene function. The RefSeq viral proteins database was used for homology-based gene prediction and the Prokaryotic Virus Orthologous Genes (PVOGs) and Reference Viral DataBase (RVDB) were used for HMM-based protein function prediction. InterProScan 5.47-5.82 and Infernal 1.1.3 (with Rfam 14.3) were applied to enrich the gene function prediction for all genes and ncRNA elements, respectively. The number of putative coding sequences had increased 1.17-1.43 times. Multiple genes related to DNA recombination and host cell lysis were identified in this reannotation. Also, we have identified new ncRNA elements in these prophages, such as tRNAs in prophages 2 and 5 and a putative regulatory ncRNA, related to the plant viral Hammerhead-II ribozyme, in prophage 4. All this new information will be combined with data from future RNAseq experiments to map the expression profiles of each LES prophage under inducing and non-inducing conditions to characterise interactions between the prophages and their lysogen host.
Year(s) Of Engagement Activity 2021
URL http://lpmhealthcare.com/phages-2021/#:~:text=Due%20to%20the%20ongoing%20COVID,5%20years%20of%20thei...
 
Description Oxford Bacteriophage Conference 2021 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Do temperate bacteriophages work together as puppet masters of their bacterial hosts? (Role of temperate bacteriophages in their bacterial hosts.)
Year(s) Of Engagement Activity 2021
URL http://lpmhealthcare.com/phages-2021/
 
Description Participation in PI and PDRA Career Development Programme - Prosper Cohort Pilot Programme 2022 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Prosper Cohort Pilot Programme 2022- Career Development programme conducted by University of Liverpool, University of Manchester and Lancaster University, which is funded by the Research England RED fund.
Year(s) Of Engagement Activity 2021,2022
URL https://www.liverpool.ac.uk/researcher/prosper/postdoc-career-development-pilot/
 
Description Phage Phrenzy 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Two postgraduate researchers from The University of Liverpool were invited to write a blog post for the Microbiology Society webpages about our public engagement activities on phages. This was published as part of the Microbiology Society Knocking out AMR project.
Year(s) Of Engagement Activity 2023
URL https://microbiologysociety.org/blog/phage-phrenzy-science-and-art-collide-at-the-science-and-indust...
 
Description Poster Presentation 2 for Microbiology Society Annual Conference_April 2022 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster Presentation at UK and Irelands largest Microbiology conference - reporting an update of work from last year:
Title: Determining prophage genome integration under single and co-infection: the case of Pseudomonas aeruginosa LES prophages in P. aeruginosa PAO1.

Authors:
Enrique González-Tortuero1, Revathy Krishnamurthi2, Ian B Goodhead1, Heather E Allison2, Chloë E James1
1School of Science, Engineering and Environment, University of Salford, Salford, United Kingdom
2Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom

Abstract (250 words as maximum)
Pseudomonas aeruginosa is an important opportunistic pathogen, causing nosocomial infections. The Liverpool Epidemic Strain (LES) is a major cause of mortality and morbidity in cystic fibrosis patients and harbours five prophages associated with increased fitness and survival in models of infection. However, little is known about how the co-habiting LES prophages influence the success of their bacterial host or how they interact with each-other. Our study aims to better characterise LES prophage gene function and identify the molecular mechanisms by which they impact the biology of the P. aeruginosa host. We re-annotated the genomes of three LES prophages (?2, ?3 and ?4) following lysogenic infection of the well-characterised P. aeruginosa strain PAO1 to create single, double and triple lysogen variants harbouring all combinations of prophages. Manual curation revealed putative functions of previously unidentified ORFs. We also determined the integration sites of each LES prophage when carried alone or in combination with others in the model host PAO1 genome. While prophage ?4 tended to target the host genome in random coordinates due to the transposase activity, both prophages ?2 and ?3 integrated in specific regions of the host genome. Interestingly, the integration regions of both prophages ?2 and ?3 are very close when they co-infect together the host, leading to chromosomal rearrangements and the loss of a ribosomal gene cluster in P. aeruginosa. These data are crucial for unveiling the vast dark matter of temperate phages and enhancing our understanding how bacterial and prophage genomes co-evolve.
Year(s) Of Engagement Activity 2022
URL https://microbiologysociety.org/event/annual-conference/annual-conference-2022.html
 
Description Poster Presentation 2 for Microbiology Society Annual Conference_online May 2021 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presented at the UK and Ireland's largest Microbiology Conference:
Title: Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages.

Authors:
Enrique González-Tortuero1, Revathy Krishnamurthi2, Ian B Goodhead1, Heather E Allison2, Chloe E James1
1School of Science, Engineering and Environment, University of Salford, Salford, United Kingdom
2Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom

Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen, causing nosocomial infections. The Liverpool Epidemic Strain (LES), a major cause of mortality and morbidity in cystic fibrosis patients, harbours five prophages associated with increased fitness and survival in models of infection. However, ~76.5% of the LES prophage genes are hypothetical proteins. Also, little is known about the LES prophage interactions with the lysogen and other prophages. In this study, we used the VIral Genome Annotation (VIGA) pipeline to re-annotate the LES prophage genomes and improve the prediction of gene function. The RefSeq viral proteins database was used for homology-based gene prediction and the Prokaryotic Virus Orthologous Genes (PVOGs) and Reference Viral DataBase (RVDB) were used for HMM-based protein function prediction. InterProScan 5.47-5.82 and Infernal 1.1.3 (with Rfam 14.3) were applied to enrich the gene function prediction for all genes and ncRNA elements, respectively. The number of putative coding sequences had increased 1.17-1.43 times. Multiple genes related to DNA recombination and host cell lysis were identified in this reannotation. Also, we have identified new ncRNA elements in these prophages, such as tRNAs in prophages 2 and 5 and a putative regulatory ncRNA, misidentified as the plant viral Hammerhead-II ribozyme, in prophage 4. All this new information will be combined with data from future RNAseq experiments to map the expression profiles of each LES prophage under inducing and non-inducing conditions to characterise interactions between the prophages and their lysogen host.
Year(s) Of Engagement Activity 2021
URL https://microbiologysociety.org/event/full-events-listing/annual-conference-online-2021.html
 
Description Poster Presentation 3 for Microbiology Society Annual Conference (2022): How do temperate bacteriophages affect the fitness of Pseudomonas aeruginosa? An update 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact An update on this work presented at The Microbiology Society Annual Conference April 2022: How do temperate bacteriophages affect the fitness of Pseudomonas aeruginosa?
Grace Plahe?, Heather E. Alison?, Ian Goodhead? and Chloe James?

Abstract
The Liverpool Epidemic Strain (LES) of Pseudomonas aeruginosa is a key opportunistic pathogen and a major cause of morbidity and mortality in cystic fibrosis (CF) patients. It carries distinctive prophages within its genome, which provide fitness advantages that have not been well characterised.
This project explores the dynamics between P. aeruginosa PAO1 and 3 LES phage using different models of infection and treatment regimens.

{{This poster includes latest data using the G. mellonella infection model to detemine the effect of prophage carriage on virulence}}
Year(s) Of Engagement Activity 2022
URL https://microbiologysociety.org/event/annual-conference/annual-conference-2022.html
 
Description Poster Presentation at Oxford Bacteriophage 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact LES Phage 5: length, encapsidation, amplification, and relationship with other Pseudomonas phages

Reem A Talat1,2, Enrique González-Tortuero 3,4, Revathy Krishnamurthi1, Jo L Fothergill1, Chloe E. James3, Heather E Allison1

1Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, L69 7ZB, UK

2College of Environment sciences and Technology, University of Mosul, Iraq

3School of Science, Engineering and Environment (SEE), University of Salford, M5 4WT, UK

4European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany

aeruginosa LES is an opportunistic pathogen that is transmissible between CF patients. LES is also capable of infecting the lungs of non-CF patients and superinfecting patients with other P. aeruginosa strains. Within the P. aeruginosa LES genome lie 20 genomic islands, including the presence of five active prophages and cryptic, prophage-like element. LES f5 is a temperate and active Pseudomonas prophage that plays an essential role in host's competitiveness. Seventy-six ORFs are predicted in LES Pseudomonas phage 5 genome. Following careful re-annotation, only 20 ORFs lack a functional prediction (Hypothetical protein). We proved that the total length of LES phage 5 genome is 50,235 bp, and the attL and attR regions were located at 2,690,327 - 2,690,341 and 2,740,547 - 2,740,561 in the P. aeruginosa LESB58 genome, respectively. It was proved that LES phage 5 is a complete, inducible phage because it encapsidates its DNA. There are 4 additional LES prophages in LESB58. They LESB58 prophages 2,3 and 4 all share some degree of homology with LES phage 5. Moreover, LES phage 2,3,4 and 5 have significant spontaneous induction rates in the log and stationery growth phases of their lysogens. Differences between the replication outcomes of all LES phages were detected, Work is ongoing to identify a P. aeruginosa host that will support LES phage 5 infection for further characterisation.
Year(s) Of Engagement Activity 2023
URL http://lpmhealthcare.com/phages-2023/speakers-agenda/
 
Description Poster Presentation for Microbiology Conference: How do temperate bacteriophages affect the fitness of Pseudomonas aeruginosa? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Poster abstract accepted for presentation at The Microbiology Society annual conference 2021
Year(s) Of Engagement Activity 2021
URL https://microbiologysociety.org/event/full-events-listing/annual-conference-online-2021.html
 
Description Poster Presentation for Microbiology Conference: How do temperate bacteriophages affect the fitness of Pseudomonas aeruginosa? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Poster presentation at the Microbiology Society Annual Conference
Year(s) Of Engagement Activity 2021
URL https://microbiologysociety.org/event/full-events-listing/annual-conference-online-2021.html
 
Description Poster Presentation for Phages 20 Conference: How do temperate bacteriophages affect the fitness of Pseudomonas aeruginosa? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at virtual International Phages conference organised by University of Oxford, online for the 1st time in 2020.
Year(s) Of Engagement Activity 2020
URL http://lpmhealthcare.com/phages-2020/
 
Description Presentation at Oxford Bacteriophage Meeting 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr Enrique González-Tortuero
School of Science, Engineering, and Environment (SEE), University of Salford, Salford, Greater Manchester, UK

After midnight: Pseudomonas aeruginosa and their "Gremlins" the LES prophages.

This was a talk at the meeting
Year(s) Of Engagement Activity 2023
URL http://lpmhealthcare.com/phages-2023/speakers-agenda/
 
Description Project Website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We have launched a website that shares the research and engagement activities of our project team.
Year(s) Of Engagement Activity 2021
URL https://www.liverpool.ac.uk/infection-veterinary-and-ecological-sciences/research/prophage-puppet-ma...
 
Description Pulling Back the Curtain on Microbial Puppet Masters: News Article from The University of Liverpool 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact University of Liverpool Comms team reporting on our engagement with The Royal Society Summer Science Exhibition with quotes from members of the team from The University of Liverpool
Year(s) Of Engagement Activity 2022
URL https://news.liverpool.ac.uk/2022/07/15/pulling-back-the-curtain-on-microbial-puppet-masters/
 
Description Research spotlight of our work from The Cystic Fibrosis Trust 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Patients, carers and/or patient groups
Results and Impact As major stakeholders, the cystic fibrosis trust are interested in our work investigating how phages influence infections of the cystic fibrosis lung. The trust recognise the importance of engaging with the public, and particularly cystic fibrosis patients, to manage expectations about phage therapy as it becomes more prominent in the public eye. The public engagement officers at the trust worked with us to develop an accessible narrative for our exhibit. They also interviewed one of our exhibit team members and collaborator (Jo Fothergill) about our work and the exhibit.
Year(s) Of Engagement Activity 2022
URL https://www.cysticfibrosis.org.uk/news/bacteriophages-learning-more-about-these-microbial-puppet-mas...
 
Description Return of the Microbial Puppet Masters 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact This blog reports on our research and how we have been engaging with public audiences about our aims, objectives and findings as well as wider discussions about bacteriophages as therapeutics.
Following the event, we were contacted by the organisers of Bradford Science Festival to ask us to take part
Year(s) Of Engagement Activity 2022
URL https://blogs.salford.ac.uk/research/2022/12/09/return-of-the-microbial-puppet-masters/
 
Description Revisiting LES prophages genomes and determining their integration in P. aeruginosa PAO1 under single and co-infection. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact González-Tortuero E, Krishnamurthi R, Fothergill JL, Goodhead IB, Allison HE, James CE. Revisiting LES prophages genomes and determining their integration in P. aeruginosa PAO1 under single and co-infection. Viruses of Microbes (VoM) 2022; 2022 Jul 18-22, Guimarães, Portugal. Poster Presentation
Year(s) Of Engagement Activity 2022
URL https://fems-microbiology.org/opportunities/viruses-of-microbes-vi-the-latest-conquests/
 
Description Revisiting LES prophages genomes inside P. aeruginosa PAO1 under single and co-infection 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was a poster presented t the annual Microbiology Society Meeting ion Birmingham. This was the abstract:
P312
Revisiting LES prophages genomes inside P. aeruginosa PAO1 under single and
co-infection
Enrique González-Tortuero ORCID iD1, Revathy Krishnamurthi ORCID iD2, Ian Goodhead ORCID iD1, Jo
Fothergill ORCID iD2, Heather Allison ORCID iD2, Chloe James ORCID iD1
1University of Salford, Salford, United Kingdom. 2University of Liverpool, Liverpool, United Kingdom
Abstract
Pseudomonas aeruginosa Liverpool Epidemic Strain (LES) is a significant cause of mortality and
morbidity in cystic fibrosis patients. Their increased fitness and survival in infection models are related
to the presence of five active prophages, which are not well characterized due to the high percentage
(~76.5%) of their hypothetical genes. Additionally, the combined influence of the co-habiting LES
prophages on the success of their bacterial host is not well studied. Here, we created single-, double-
and triple-lysogen variants of the well-characterised P. aeruginosa strain PAO1 after infection of
combinations of the LES prophages ?2, ?3 and ?4. High-quality genomic sequences of the different P.
aeruginosa PAO1 lysogens and the LES prophages ?2, ?3 and ?4 were retrieved. All this information
will be relevant for RNAseq experiments to map the differential expression gene profiles of the LES
prophages and predict the metabolic and physiological changes induced by these phages under inducing
and non-inducing conditions. Moreover, these findings will be key for the role of temperate phages and
for improving our understanding of host-phage coevolution.
Year(s) Of Engagement Activity 2023
URL https://microbiologysociety.org/event/society-events-and-meetings/annual-conference-2023.html?keywor...
 
Description Royal Society Summer Science Exhibition: Enter the Phage 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact We successfully applied for the opportunity to exhibit our research at the Royal Society Summer Science Exhibition (awarded October 2021). We were one of just 21 exhibitors chosen. We have since acquired supporting funding of £42,642 and £6000 (University of Salford Public engagement and Impact Funds) and £2600 (University of Liverpool, impact fund) and applied for an additional £2000 from The Wellcome Trust, public engagement fund.
We are well underway with development of a new 3D virtual reality lung environment in partnership with creative practitioners (shoot shoot) as well as interactive working models of bacteria and phage interactions for the event, which will take place over a week in July 2022 and be supported with digital content online and publicity form both out institutions, Microbiology Society and the Royal Society. Legacy from this event will also promote engagement with The Cystic Fibrosis Trust as well as tools for use at further public engagement and outreach events as well as University open days, both online and in person.
Year(s) Of Engagement Activity 2022
 
Description Royal Society Summer Science Exhibition: Podcast from the red sofa 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact As part of The Royal Society Summer Science Exhibition. The organisers invited exhibitors for 10 minute interviews live on the red sofa for their podcast to publicise the event. Heather Allison and Chloe James were asked to explain what our exhibit - Microbial Puppet Masters: what the work is about, how we demonstrate key concepts and why this work is important.
See minute 30:35 - 41:46 on YouTube video link 5700 views 147 likes.
Year(s) Of Engagement Activity 2022
URL https://www.youtube.com/watch?v=bUrPA3E8ggY
 
Description Talk at Online Phage Research Seminar Platform Hosted by Andrew Millard at The University of Leicester 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Introducing our research project to a PGR audience, this sparked interest in the project and helped to build plans for the prophage research network
Year(s) Of Engagement Activity 2020
URL http://millardlab.org/meeting-phage/
 
Description Talk at VoM-UK : Prophages are "not" silent carriers in their host: Pseudomonas aeruginosa LESB58 as case in point. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Revathy Krishnamurthy, University of Liverpool and Quadram
Institute of Biosciences and Enrique Gonzalez-Tortuero, University of Salford and University of Northumbria
Prophages are "not" silent carriers in their host: Pseudomonas aeruginosa LESB58 as case in point.
Abstract:
The Pseudomonas aeruginosa Liverpool Epidemic Strain (LES) is
associated with severe disease in cystic fibrosis patients and can be
transmitted between patients and their families. The LES genome
harbours five novel prophages, which can be detected as free, infective
phages in the sputum of CF patients. They confer competitive advantages
to their host, but the specific mechanisms are not known. Our study aims
to identify the molecular mechanisms by which the LES prophages impact
the biology of the P. aeruginosa host.
We constructed strains of P. aeruginosa PAO1 carrying infected with all
possible combinations of the LES phages ?2, ?3 and ?4, creating single,
double, and triple lysogens. Through growth profiling experiments, we
identified the conditions in which phage production in a lysogen
population was either minimal or extensive. Further, we optimised the
conditions suitable for transcriptomics sample collection and library
preparation. Finally, we sequenced 108 samples in total to understand the
transcriptomics landscape of these lysogens in both induced and
uninduced (stable lysogeny) conditions.
Preliminary results of our study indicate that these prophages play an
important role in shaping the physiological state of their bacterial host.
Further screening will be done with the recombinant strains to
understand the impact of transcriptional regulators and the genes that
are uncoupled from the phage regulatory network of these prophages
upon their host.
Year(s) Of Engagement Activity 2024
URL https://www.northumbria.ac.uk/about-us/news-events/events/2024/01/viruses-of-microbes-2024/
 
Description Talking Salford Podcast: Women in STEM 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact PODCAST AD: In this special episode to mark Women In STEM Day on Sunday 11 February we bring you two unique stories from one of our leading scientists, Professor Chloe James and one of our STEM graduates Paz Aranega-Bou, who is now working at the UK Health Security Agency.
Chloe talks through her experience as an academic in microbiology, how the experience for a woman in STEM differs in different countries and what more can be done to encourage young women and girls to pursue a career in STEM subjects.
Next, former Erasmus student and PhD graduate Paz chats through her experience of studying from Salford after coming from Spain, the integral work she did during the COVID-19 pandemic and what her advice would be for current microbiology students ahead of entering the industry.
Talking Salford is an official podcast from The University of Salford.
All episodes are available on all podcasting platforms with the video version available to watch on YouTube.
Year(s) Of Engagement Activity 2023
URL https://www.youtube.com/watch?v=fQM9yjf727Y
 
Description The Royal Society Summer Science Exhibition 2022 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The Royal Society Summer Science Exhibition is an annual event in which the Royal Society opens its doors to the public so they can engage with top scientists about their latest research. We were selected as one of just 16 exhibitors from 25 applications. The event attracted 6774 people throughout the week July 5th-10th
Our exhibit was called "Microbial Puppet Masters" and focused on key concepts of our research: Bacteriophages (phages), which are viruses that infect and kill bacteria, but can also form partnerships as prophages, acting like internal puppet masters to change the fundamental biology of their bacterial hosts. Specifically, we focused on the case of cystic fibrosis (CF), a disease familiar to most as it is covered in the school curriculum and has piqued the interest and emotions of many. There has been a recent resurgence in excitement about "Phage therapy" as a potential saviour in treatment bacterial infections of the CF lung. But our research also explores the other side: bacteriophages that can enhance bacterial survival, affording them "super-powers" in the same niche.

Our Exhibit included several different elements:

1. Giant Microbial Games: We teamed up with Morson Makerspace (University of Salford) to address the lack of awareness of bacteriophages in the public arena. Together, we designed a set of visually engaging and tactile working models of bacteria and phages (a million x bigger than the real thing), to demonstrate the different relationships between these microbial partners. Influenced by games such as "Pop-Up Pirate" and "Bukaroo". The models were created using 3D printing, flexible moving parts and spring-loaded internal mechanisms. We produced phage "keys" of different shapes to be fitted into the right "receptor" on the bacterial model to trigger a response. This demonstrated key messages about phage shape, size, diversity and specificity as well as the different ways they affect bacteria.
Elements of theater and competition were added for use of the models at public engagement events. We built a life-sized mock biological safety hood in which visitors were invited to handle the models and compete with each-other to see who could trigger a reaction 1st, who would trigger bacterial death, and who would trigger the superpowers!

2. A virtual reality journey through the microbial communities of chronically infected lungs. We worked with artist Paul Miller and virtual reality creator, Richard England (Reflex Arc) to develop a virtual lung. The user is immersed into the airways of the lung, and magnification is increased to see microbial colonisers within the thick mucus that lines the airways. One of three possible bacteria - phage interactions are witnessed by each user (limited to 5 min per person). The narration for the experience was developed in collaboration with the public engagement officers at the Cystic Fibrosis Trust as key stakeholders. We wanted to ensure our narration was sensitive to the experience of people with cystic fibrosis and in a language that was accessible to a general public audience. A bespoke musical sound track was overlaid with sampling of a track by Professor Craig Winstanley informed by the genome sequence of the Liverpool Epidemic Strain of Pseudomonas aeruginosa (a major cause of morbidity and mortality in cystic fibrosis patients). The soundtrack was further developed with harp, flute and horn sounds to complement the visual events, giving a feeling of breathing.

3. Our data on phage genome annotation was presented as interactive diagrams created by Enrique Gonzalez Tortuero and Reem Almeran on iPads to support conversations with visitors about our research methods and findings.
Publicity Materials: We produced banners, stickers, tattoos and postcards with QR codes linked to an evaluation quiz on our website

Student Experience and Skills Building: We built a 23 person-strong team of student volunteers from both Salford and Liverpool Universities to join us for the whole week in London (all-expenses paid). We held a 2-day training session at MCUK in advance, where all had a chance to meet and learn about the project, each-others work and develop their skills in public engagement. They did a fantastic job delivering the exhibit, talking with the public about phages and their own research. It was an enriching experience for all - enabling cross-fertilisation of ideas between students of the 2 universities and the collaborating artists about art, research, research impact and career progression. Many had never been to London before, and we stayed all together in halls of residence right in the centre by the Science Museum and Royal College of Music, not to mention the exhibit itself in The Royal Society Buildings on the Mall.

Social Media
Posts were shared on Twitter, Facebook and Instagram to increase market share and were used to measure impact. Twitter: posts were generated before and during the event using the @EngageSalford Twitter handle and the hashtags #MicrobialPuppetMasters and #SummerScience
Twitter analytics:15 tweets (17/06-09/07/22),
- 171 Retweets and 328 likes.
- 54 link clicks
- 44 Mentions
- 16 Comments/Quoted Tweets
- 16,101 video views
- 67,875 tweet impressions
In comparison to the previous 23 days the twitter handle increased its impressions by over 16,000. This suggests that the content of the tweets was able to generate a wider audience than usual. The account also witnessed a following increase of 30, which suggests that the content from the event was valuable and interesting to the viewers, in comparison to the previous two months which had an increase of 5.

Evaluation from Public:
https://forms.office.com/Pages/DesignPageV2.aspx?subpage=design&FormId=QCm1Zbb0vUGDPTAz7Lz24dH0arEXYaBKtOw8noh3aj9UOTA3WFk5WjRZQUtOOUxHMlVXMDdXRTZBSC4u&Token=effd2517a1374c3891f71b397213ce0b
During the event we used a quiz (6 questions) to measure impact and gather feedback:
- 42 responses
- 90% of the participants had learnt something new about phage
- 40% had never heard about phage prior to the event.
- 26% were willing to give contact details for further information.
- Follow-up not yet begun
Evaluation from our delivery team:
We also developed a survey to capture how the delivery team felt the event went, and how experience affected them: verbal feedback - a really enjoyable and enriching experience
https://forms.office.com/r/1qPW0J6t0N

Feedback from Julie Maxton (executive director of The Royal Society) Letter to our VC: "On behalf of the Officers and Council of the Royal Society, I would like to thank you and your team very much indeed for bringing Microbial Puppet Masters to the 2022 Summer Science Exhibition. Visitors thoroughly enjoyed the VR experience to discover how bacteriophages transform bacteria to trigger diseases. Your enthusiasm and that of the rest of your exhibition team was fabulous throughout the week, something many visitors commented on as the highlight of their visit. We were also grateful for your participation in Summer Science Live on Saturday 9 July, where your demonstrations and explanations enthused our online audience. We really do appreciate the hard work involved in planning and delivering your exhibit. We hope you will continue to use the content created for the exhibition to engage the public with your fascinating science in the future. Thank you again for giving the Society your valuable time and expertise".

UoS Press Release
https://www.salford.ac.uk/news/pulling-back-curtain-microbial-puppet-masters

Event Evaluation from The Royal Society: The Summer Science Exhibition aims to:
• Provide an opportunity for the public and school groups to meet and question scientists about the cutting-edge research they are undertaking and demonstrating.
• Inspire and enthuse visitors of all ages about the potential for science through hands-on interaction and participation.
• Use the Royal Society's status as the UK's National Academy of Science to lead by example and champion excellence in public engagement.
• Enable UK scientists to showcase their research and gain public engagement experience in association with the Royal Society.
• Give young people the aspiration to be scientists.
• Reach new audiences with science including families, young professionals and people looking for a great, free day out in London.
• The core Summer Science team and volunteers undertook external training in accessibility and inclusion to deliver a more accessible exhibition.
Highlights
• 93.8% of visitors rated the exhibition 'excellent' or 'good'.
• 74% of teachers said they had gained ideas for new lesson content during their visit.
• 75% of volunteers were 'very likely' to recommend volunteering at the exhibition to a friend or colleague.
• 330,000 views of all digital Summer Science content.
- Total number of visitors: 6,774
- Responses from visitors:
"It was very fun and I would do it again and recommend it to others."
"9/10 Would recommend to anyone interested in science"
The predominant age for this year was visitors under 25 years old, 38%
"Would like to see an adult session so we can have the chance to enjoy interactive activities
better. Kids are taking them all"
"Bring back the weekday evening events for adults, the exhibition had too many children"
"Too many children! Much better to have two events"
"More multimedia support/activities for adults (20-30 yo)"
• 7% of respondents considered themselves to have a disability
• 93.8% of visitors rated the exhibition 'excellent' or 'good'.
• The majority of visitors spent 1 - 3 hours at the exhibition (68%). Only 6% spent less than an hour.
"Excellent afternoon. Everyone explained their work clearly, enthusiastically, and kept me totally
fascinated - brilliant communicators"
"THE EXHIBITION INCREASED MY INTEREST IN SCIENCE"
"THE EXHIBITION GAVE ME THE CHANCE TO DISCUSS RESEARCH WITH SCIENTISTS"
"I LEARNT SOMETHING NEW FROM THE EXHIBITION"
I LEARNT SOMETHING ABOUT SCIENTIFIC CAREERS"
"THE EXHIBITION INCREASED MY UNDERSTANDING OF HOW SCIENCE IMPACTS OUR DAILY LIVES"
"I WOULD RECOMMEND THE EVENT TO OTHERS"
"It is particularly good that you can approach every exhibit with no previous knowledge of that topic and be drawn in so that you move on with some understanding and ever greater curiosity. Thank you for providing a free event. This is an investment in our future"

We also took part in the "Talk Science Careers" activities: Our team provided 3 x 45-minute-long career sessions aimed at students in KS4 (or equivalent). Exhibitors had a 15-minute Q&A with a school group before they moved to the next school group. Over 45 minutes, schools were able to meet representatives from three different exhibits. Q&A, facilitated by a member of Royal Society staff, began with a brief introduction from the exhibitors.
The aim of these sessions was to give school students a sense of what life is like as a researcher and to demonstrate the varied career routes into science.
School visitor profile:
• 766 students and staff visited the exhibition (32 individual schools booked and attended). 27% were fee-paying schools compared to the national average
of 10.9% fee-paying schools (independent). 47.4% of the schools had not been to the Summer Science Exhibition before.
• 45% of all schools came from outside of London, with 13% of those coming from outside the home counties.
Teacher survey:
• 100% of teachers rated their overall Exhibition visit as very good or good.
• 100% confirmed that they had personally gained more scientific knowledge during their visit.
• 74% of teachers said they had gained ideas for new lesson content during their visit.
• 74% agreed or strongly agreed that the students that attended the Talk Science Careers sessions had gained a greater understanding about the skills used in scientific jobs.

Follow-on Activities
- Salford University Summer school "Breaking the Mould" We used the models again at a Bioscience summer school for yr 12 students. Feedback for the whole event was fantastic
- Schools Visit at Liverpool The models were demonstrated by one of our postdoctoral team to young children visiting Liverpool University
- Lightwaves The success of Royal Society Event, enabled us to secure an exhibitor spot at Lightwaves Festival at Media City December 22. An annual festival of light, expecting 400,000 visitors https://lightupthenorth.com/festivals/lightwaves/ This event gave us an opportunity to shine a light on wider Lung research at Salford and in the Northwest.
- The Giant models have also been used in a range of lecture sessions, researcher soap-box slots, schools visits and stakeholder engagement sessions.
Year(s) Of Engagement Activity 2022
URL https://royalsociety.org/science-events-and-lectures/2022/summer-science-exhibition/
 
Description The role of temperate bacteriophages in the polylysogenic Liverpool Epidemic Strain of Pseudomonas aeruginosa PAO1. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster in IVoM 2022- The role of temperate bacteriophages in the polylysogenic Liverpool Epidemic Strain of Pseudomonas aeruginosa PAO1.
Year(s) Of Engagement Activity 2022
URL https://fems-microbiology.org/opportunities/viruses-of-microbes-vi-the-latest-conquests/
 
Description University of Liverpool Christmas Lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact University of Liverpool School of Life Sciences Christmas lecture to which ~500 A level students from around the Merseyside area attended. Talk entitled:The Power of Small Packages
Year(s) Of Engagement Activity 2023
 
Description University of Salford Press Release: Pulling Back the Curtains on Microbial Puppet Masters 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Press release providing advance information to media organisations about our exhibit at The Royal Society Summer Science Exhibitions. The press were granted preview entry to the event to interview researchers about their work of interest to their audiences.
Our press release was picked up by BBC World Service and Daily Telegraph - leading to considerable coverage on Health check podcast.
Year(s) Of Engagement Activity 2022
URL https://www.salford.ac.uk/news/pulling-back-curtain-microbial-puppet-masters
 
Description Using Molecular Biology, Next Generation Sequencing and Bioinformatics to Understand the Contributions of Prophage 5 to the Phenotype of Its Host, Pseudomonas aeruginosa Epidemic Strain LESB58 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Poster presentated at the UoL Faculty of Health and Life Sciences for second year students. Reem A. Talat1,2*, Enrique González-Tortuero 3,4, Revathy Krishnamurthi1, Jo L. Fothergill1, Chloe E. James3, Heather E. Allison1
Year(s) Of Engagement Activity 2023
 
Description Validation of the expression of phage marker genes from the Liverpool Epidemic Strain of Pseudomonas aeruginosa using qRT-PCR 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Revathy Krishnamurthi: Poster in MicroSoc2022 -Validation of the expression of phage marker genes from the Liverpool Epidemic Strain of Pseudomonas aeruginosa using qRT-PCR
Year(s) Of Engagement Activity 2022
URL https://microbiologysociety.org/event/annual-conference/annual-conference-2022.html
 
Description Validation of the expression of phage markere genes from the Liverpool Epidemic Strain of Pseudomonas aeruginosa using qRT-PCR. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Krishnamurthi R, González-Tortuero E, Plahe G, Fothergill JL, Goodhead IB, James CE, Allison HE. Validation of the expression of phage markere genes from the Liverpool Epidemic Strain of Pseudomonas aeruginosa using qRT-PCR. Annual Conference Microbiology Society 2022; 2022 April 4-7, Belfast, Northern Ireland, United Kingdom. (Poster Presentation)
Year(s) Of Engagement Activity 2022
URL https://microbiologysociety.org/event/annual-conference/annual-conference-2022.html
 
Description WP Summer School 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact 2nd running of WP champions outreach event - this time as part of a wider 3 day residential summer school on UoS Peel campus.
Attended by 30 x yer12 students (17-18 year-olds).
Quiz/Survey deployed... very positive feedback about how this inspired students to want to continue with science subjects at HE
Year(s) Of Engagement Activity 2023
 
Description Wonders of microbiology with nearly 300 attendees at the Victoria Gallery and Museum's 'Wizarding School'- October 2022. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact This was an event to get children interested in Science
Year(s) Of Engagement Activity 2022