Prophage-host interactions: lifting the curtain on Pseudomonas’ puppet masters

Dr Chloe James shares her phage research in an interview with Prathyusha Vishwanthan

Dr Chloe James in conversation with Prathyusha Vishwanthan

Humans have been aware of bacteriophages as major players in the microbial world for over 100 years. Their most widely recognized feature is their ability to infect and kill specific bacteria, but they are also known to provide some beneficial characteristics to their bacterial host. Apart from a few famous examples, this aspect of phage biology has been largely neglected and the temperate phage-bacteria relationships are not fully understood. Dr Chloe James, a senior lecturer in Medical Microbiology at the University of Salford, has been very curious about this dynamic and has been working on this for a while.

Recently, Dr  James  started a new project funded by the BBSRC, which aims to observe how bacteriophages affect the behaviour of their bacterial host. It  will focus on a notorious opportunistic bacterium, Pseudomonas aeruginosa, a common cause of respiratory infection in cystic fibrosis patients.

Prathyusha Viswanathan interviews Dr Chloe James about her unique and interesting project:

It is quite a different yet interesting topic. How did it all start?

A few years back, I worked on a project examining cases of cystic fibrosis patients who were chronically infected with the Liverpool Epidemic Strain of Pseudomonas aeruginosa. The team had previously found this stain to cause much more severe disease than other strains and to spread from patient to patient, which seemed very unusual.

After sequencing the genome, they found several never-seen-before co-existing prophages. This is where I came in. I regularly monitored phage and bacteria in the patient’s sputum samples for over 2 years. The most notable finding was that these phages were always active and present in abundance. But we could not find any association between the phages and patient condition or antibiotic treatment.

So, this got me extremely curious, like wow, even though the phages are actively killing their bacterial host, the bacteria are still keeping hold of them which means that they must be helping the bacteria in some manner and this point made me determined to find out what they are actually doing. So, I worked with colleagues [Dr. Ian Goodhead and Dr. Heather Allison] to design a project that would better understand how the phages and bacteria affect eachother’s biology, the hypothesis being that temperate bacteriophages do so much more than what we know and at the moment. I think that they pull all kinds of strings and regulate bacterial behavior in different ways.

The BBSRC awarded us funding for 2 postdoctoral researchers to work full time on the project, but we also have some linked projects that are being explored by research students at Salford and Liverpool University.

What achievements have you made so far?

Some key findings of our work are that for one, each of the LES phages seems to be affecting the fitness of the P. aeruginosa host differently and depending on environmental conditions; secondly, together, these temperate phages seem to facilitate rapid evolution of their bacterial host contributing to their adaptation to the CF lung environment; lastly, we think that phages may have an important role in the competitiveness of the LES in CF lungs by acting as anti-competitor weapons (killing other P. aeruginosa strains). But this new project will delve much deeper into the mechanisms of interaction between these intriguing microbial partners. We have published a lot of this work.

These are two complex creatures; you may have noticed many  interactions – have any been particularly unexpected or peculiar?

Yes, that’s true. We are uncovering all kinds of interesting nuggets to follow up on. So far, the most striking discovery is the evidence that the phages are interacting with each-other. This means that the bacteria behave differently depending on which phage they are infected with, and in cases when multiple prophages co-exist together, we observe a completely different behavior. Of course, we also suspect that the bacteria is affecting the biology of the phages. Seeing how the phage infection progresses differently in other P. aeruginosa host strains has helped me direct my thinking in more broader dimensions.

What have been the most recent outputs from the project?

Grace Plahe, a Salford MRes student, presented her work on how LES phages affect bacterial growth and virulence at three different conferences last year. One of her abstracts has been published, and some of her preliminary data helped us to secure the bigger project funding we have now. Since then, two postdoc researchers have been employed on the project, and they will present their preliminary findings on phage-phage interactions and phage genome annotation at the next Microbiology Society annual conference.

What are the upcoming stages of research?

So, our latest funding is to run for 3 years and there are plenty of upcoming tasks on our list. Firstly, our aim is to thoroughly profile the infection cycles of each phage under a range of environmental conditions, and monitor changes in the expression of genes that reports the key stages of the process. We will then conduct a huge transcriptomics experiment which will map global gene expression of bacteria with and without their phage partners. This will show which phages  are regulating which bacterial genes and vice-versa.

We will also perform experiments by exposing the bacteria to both favourable as well as challenging conditions, so that this will help us to identify why the bacteria is keeping hold of so many elements that could so easily kill it and most importantly, we will also construct a series of mutants and perform functional assays to confirm our theories about how these phage puppet masters are pulling the strings.

it seems that your findings have a wide scope in research and  could help thought processes in other fields, leading to new  technologies; yet temperate phage research is rare and has not yet been given much importance. What do you have to say about this?

Very true, I agree. This aspect of phage research has not been given much attention. Most of the research is concentrated on the destructive nature of bacteriophages towards specific bacteria for developing antibacterial treatments. There is a lot of renewed excitement in that area at the moment, with real potential to improve treatment of infections caused by antibiotic resistant bacteria. Whilst the beneficial effects of prophages on bacteria have not been ignored, the scale of this has been grossly underestimated. There is so much more left undiscovered. There are relatively few published findings on the regulatory properties of temperate phages and yet there is a huge amount of genome evidence to show us that ~60% of the sequenced bacterial strains carry prophages in their genomes, and even more  tantalisingly, over 70% of most prophage genes are of unknown function. We know they are present everywhere, and that bacteria are keeping hold of them even though they can present a considerable cost, but we don’t know what they are doing!

I am sure there are many exciting crossroads for this type of research, and you were absolutely correct, this type of research would also help other research fields to understand the pathology of disease better and could inform completely novel approaches to patient treatment and management. In fact, CRISPR systems were actually invented by bacteria, in order to protect them against bacteriophage attack! So, studying phage-bacteria interactions can indeed trigger revolutionary new fields of research and I hope that some of our findings will lead to new thinking in all kinds of areas that I haven’t even considered.

For the Love of Global Health: Ongoing University of Salford Microbiology Research in Uganda

Professor Richard Birtles shares with us about ongoing University of Salford Research taking place in Uganda.

By Prof. Richard Birtles 

In late 2015 I got an email from Louise Ackers, a Professor in the Health School, asking if there were any microbiologists at Salford University. I told her, yes, there were a few, including me and my colleague Dr Chloe James. Looking back, this was yet another moment of serendipity that changed my life – another “bit of luck out of the blue” that serves to remind me that just when you think life is getting predictable, there’s always a surprise just around the corner. Louise was looking for some help with a project she was planning in Uganda focused on educating hospital staff to improve antimicrobial stewardship.  

Six months later, Chloe and I were in Fort Portal, the biggest town in western Uganda, washing our hands like fury in front of groups of doctors and nurses to illustrate a good way of controlling transmission of Staphylococcus aureus infections. By this point we had learnt a lot about the appalling impact of infection (particularly sepsis) on maternal mortality in Uganda and we wanted to try and do something to help.  

We arranged for the regional hospital to collect Saureus clinical isolates for us and, with the help of a new PhD student, we set about characterising these to see how they were related to one another and the extent of their resistance to antibiotics – hoping to get a better understanding of where mothers pick up infection from and how best to treat  infections. This work involved sequencing bacterial genomes and, with the help of my colleague Dr Ian Goodhead, we were able to do this in collaboration with microbiologists at Makerere University in Kampala as a way of transferring expertise in genomic techniques that are well-established in the UK to Uganda.  

Staff at Fort Portal Regional Referral Hospital use VR developed by Chloe and others at Salford University to learn about antimicrobial stewardship. 

We used our free time in Fort Portal to explore some other avenues – I’m interested in tick-borne infections of livestock, so we had a day-trip to nearby farms to pull ticks off cows (later tested by an MSc student) and Chloe had us collecting chicken poo as part of a project on the epidemiology of the food-borne zoonotic pathogen Campylobacter jejuni.  

Chloe’s PhD student, Paz, collecting faecal samples from Ugandan chickens to screen for Campylobacter jejuni and other zoonotic pathogens. 

Fort Portal is also the “home” of a UK/Uganda charity called Knowledge for Change (K4C). K4C has been offering placements for Salford University nursing and midwifery students for several years and we were very keen that they expand their offering to include Biomed and HBID students. It took a while to get things sorted, but the first group of BMS and HBID students went out to Fort Portal with Chloe in June 2018 and had a wonderful, life-changing month-long experience embedded in local microbiology, parasitology and haematology services. Here’s what BMS student Adrian Beck said: “This placement had a very positive impact on my personality. The most important thing I noticed is Ugandans have so little [materially] but are still so happy; I am grateful now that I have roof over my head and my good health!”. 

Our work on S. aureus as a cause of maternal sepsis and other hospital-acquired infections started to yield results (, and Chloe returned to Fort Portal in January 2020 to share these results with hospital and public health staff. She used virtual reality kits to help her deliver messages about antibiotic resistance and how it develops. Through continuing collaboration with Louise Ackers this work also contributed to improved antimicrobial stewardship both locally and nationally. 

An infectious control ( hand hygiene) class at Kibiito Health Centre.  

In late 2017 we were chosen to showcase the work we’d been doing in Fort Portal to a delegation of academics from the University of Gulu who were visiting Salford University. Gulu is in northern Uganda, a region devastated by civil war in the 1990s and 2000s and now accommodating hundreds of thousands of refugees from South Sudan and the Democratic Republic of Congo. The University in Gulu is new and very keen to establish collaborations with Institutions that have strong global health research, thus in January 2018 Chloe, Ian and I made a reciprocal visit to Gulu aiming to develop these collaborations. 

We had an amazing, exhausting trip, which included me addressing prisoners in a remote jail about body lice and the infections they transmit, and encounter with children suffering from the terrible “nodding disease”, the cause of which remains a mystery. Ian and one of his PhD students were able to carry out field work collecting tsetse flies, which transmit sleeping sickness. We established links with scientists working on black flies that transmit river blindness and are now working together exploring the microbiomes of black fly guts and their possible impact on Onchocerca volvulus transmission.  

The one person we didn’t meet in Gulu was Dr Richard Echodu, the Director of Gulu University’s new multifunctional research laboratories, who was away in Kampala. However, in early 2020 yet another moment of serendipity led to our working together on the biggest Salford-Uganda collaboration to date. Richard and I were talking about a grant application to support the black fly microbiome work mentioned above, when I mentioned COVID-19.  Richard spoke passionately about how unprepared Uganda was for the pandemic and we both agreed to look out for funding that might give us the opportunity to contribute the country’s response to the virus. A week or two later, Ian found a call for the UK Government through its Global Challenges Research Fund that seemed to fit the bill. What followed was pandemonium as Ian, Richard and I raced to submit our application (at the same time as converting all our teaching to online and teaching students as befuddled by all the changes as we were), but submit we did, and a month later we got the surprising news that we’d been funded.  

The project started last August and under the management of the magnificent Dr Judy Mwangi (who just completed her PhD at Salford University) with fantastic support from Louise Ackers and many other people, we are now six months in and still standing. Working in two countries during the pandemic has thrown up many barriers but this week our diagnostic laboratory opened for business with the approval of the Ugandan Ministry of Health. We now aim to test at least 25,000 people for SARS-Cov2 infection in the next few months and to compliment this with genome sequencing by the summer.  

Me playing a rather passive role in collecting ticks off local cattle. Doing most of the work is my ex-Phd student Jess and Philip (right), a Regional Veterinary Health Officer. 

We’re particularly interested in the impact the virus is having on refugee communities and how the epidemiology of infections might be shaped by risk factors quite different to those recognised in the UK, such as age and obesity. Most Ugandans are young and not fat, but they are far more likely to be carrying parasites or be malnourished than Salford residents. Hopefully, this time next year, we’ll have some answers and we’ll also have helped Gulu University establish itself on the national stage as a centre of molecular microbiology research excellence because the need for such expertise will not go away with COVID19.                   

So, as far as this story goes, we’re nowhere near the end, but maybe we’re at the end of the beginning. There will undoubtedly be many opportunities for oldies like me, Ian, Chloe and Louise, who have loved global health for many years, but there are also opportunities for those just starting out; those who recognise that the relevance of biomedicine and bioscience extends way beyond the boundaries of Salford, or Manchester, or the north-west, or the UK. There’s a big world out there waiting!  

K4C placements are available (again) from September 2021 and are open to all, regardless of whether you are still a student or not. For more information, check out their website,