The Bakery

Lab News

Catch up on some of our latest stories.

It’s been a really busy year for the Bakery and we’ve had some updates to the dream team!

Dr. Becky Bengtsson has moved on to a new job in industry (see alumni page) after finalising her awesome work on the GEMS Shigella, recently published in Nature Microbiology

In the meantime, the multitalented Dr. Charlotte Chong has joined the team on an EPSRC funded collaborative wet lab project to validate mathematical models of antimicrobial resistance emergence. In addition to her awesome lab skills, Charlotte has several ongoing bioinformatic projects including being our chief nanopore data expert.

We’re also really lucky to have Dr. Nicola Love join the team half-time as part of the Health Protection Research Unit in Gastrointestinal Diseases. Nicola is looking into the epidemiology of travel-associated diarrhoeal disease in the UK.

Welcome to our new team members and best of luck in your next steps Becky JB the first!

The whole lab attended the Microbiology Society’s annual conference and we were grateful to the organisers for giving us the opportunity to share our ongoing work. Becky Bengtsson’s and Malaka’s main projects were both accepted for oral presentations and Becky Bennett’s, George’s, and Lewis’s work were shared as poster presentations.

If you have access to the catch-up platform and want to see our stuff you’ll find the group’s work in the following sessions, or keep you eyes on the website/our twitter feed for the papers:

Becky Bengtsson presented Informing shigellosis prevention and control through pathogen genomics in Public Health Microbiology

Malaka De Silva presented A tale of two plasmids: contributions of plasmid-associated phenotypes to epidemiological success in Shigella in the Secret Life of Mobile Genetic Elements

George Stenhouse presented Genomic epidemiology of Shigella in South Africa in Public Health Microbiology

Becky Bennett presented Utilisation of historical isolates to identify key genetic drivers in the long-term success of Shigella as pathogens in the Genetics and Genomics Forum

Lewis Mason presented Genomic epidemiology of the first London outbreak of antimicrobial resistant sexually transmitted shigellosis in Public Health Microbiology

Congratulations to all the team members on their efforts at the conference and particularly to Lewis Mason who won the Most Promising Poster Prize sponsored by the Journal of Medical Microbiology!

We had a great time at the conference and were grateful to have the opportunity to hear about all the cool stuff everyone is doing, to network with our sceintific colleagues, and discuss our work. Thank you Microbiology Society!

We are superexcited to have our first lab funded and led primary analysis papers out (on Shigella of course!)

Becky Bengtsson led supercool analyses looking at the changes in the accessory genome and structural variation that occurred over the course of persistent infections among men who have sex with men and contrasted these with incidences of reinfection. We saw the acquisition of antimicrobial resistance determinants and specific functional signatures for those regions that varied. We also generated a high quality reference genome and biobanked isolate of the clinically important serotype S. flexneri 3a.

George Stenhouse led the first study characterising Shigella from Malawi by whole genome sequencing. We found that the isolates were perdominately S. flexneri and S. boydii of diverse serotypes and also found plasmid mediated quinolone resistance on a plasmid shared internationally among diverse Shigella serotypes and geographic locations. We’re really excited to have started our collaborations with Liverpool-MLW and to have been the home for George’s first first-author paper!

Although we haven’t had a chance to get together and celebrate properly yet, both lead authors have received their now-traditional Bakery publication mugs!

Check out the papers now published in mBio and Microbial genomics

We were recently awarded a BBSRC project grant to study Convergent evolution of Enterobacteriaceae in epidemiological networks with high antimicrobial use and are super excited to be working with our long-term collaborators at PHE and the University of Edinburgh Claire Jenkins and Tim Dallman, as well as with Sam Sheppard at the University of Bath, and Jamie Hall down the corridor at the University of Liverpool.

We will use signatures of convergent evolution among MSM-associated shigellosis outbreaks as a marker for adaptation to transmission among high antimicrobial use environments combining genomic epidemiology, bacterial GWAS, what we have coined ‘bulk phenotyping of epidemiological replicates’, and experimental evolution to characterise and validate, as well as determine the relative contribution of genetic changes that contribute to the evolution of antimicrobial resistance.

Congratulations are due to the whole team of investigators on this award and a special thanks goes to Malaka De Silva, who will transition from PDRA to researcher Co-investigator on this project. Malaka is normally based in the wet-lab so when COVID hit, he got sent home and I got sent on secondment. I asked him if he wanted to spend his time at home co-writing a grant I had been working on and he jumped at the opporunity with his typical enthusiasm.

The hard work certainly paid off, and we’re all really excited about getting stuck into this work in the summer!

Caisey successfully defends her PhD thesis ‘The genomic epidemiology of nontyphoidal Salmonella serovars and their association with invasive disease during enjoyable discussions with her examiners Mal Horsborough and Alison Mather. As if that wasn’t enough, within the same month, she also had her thesis work accepted for publication in Nature Microbiology and landed her dream job at Public Health England!

We are so happy for Caisey in her success and were mutually delighted to find that we may still have the opportunity to collaborate in her new role!

During March to August 2020, I was seconded 80% as an external advisor to the Government Office for Science team that convenes the Scientific Advisory Group for Emergencies. It was an absolute honour to work alongside this team and contribute to the pandemic response in this way, and an eye-opening experience into the machinations of science advice and policy.

I was also so, so proud of my amazing team who continued their work in my absence and essentially just cracked on despite the limited supervision I was able to provide during this time, and the challenges the pandemic posed. Thanks team.

Kate and Becky travelled to Public Health England to present Becky’s early results analysing Shigella from the Murray Collection.

As part of a centenary celebration of the National Collection of Type Cultures, Kate presented a talk called ‘Standing on the shoulders of giants: Professors Murray and a century of dysentery’ which covered a brief history of the role of dysentery in forming the NCTC, the Murray collection of Enterobacteriaceae and Becky’s early results from new analyses of the collection.

It was a wonderful day celebrating the legacy and achievements of the collection in the last 100 year as well as some great perspectives on the future of the collection. A personal highlight was meeting both Rita Legros and Vicki Hughes who were instrumental in bringing the Murray collection to UK and the early work with the collection. I had no idea they would be there and was a little star struck truth be told. For me it really captured the essence of the day – passing on these important resources through the generations - Becky and I hope to do justice to the legacy they have passed on through the work of the NCTC.

Becky Bengtsson and Kate travelled to Washington DC to present Becky’s early results from analysis of Shigella from the Global Enteric Multicentre Study at the American Society for Tropical Medicine and Hygiene’s annual meeting.

Becky presented her findings relevant to population structure, antimicrobial resistance and predicted vaccine efficacy based on the genomic analysis of isolates from the study. They were really well received with loads of interest at her poster and great questions from the attendees.

It was a great conference all round and we then enjoyed a thoroughly engaging visit with our key collaborator Associate Professor Sharon Tennant (who was awarded the Bailey K. Ashford Medal for distinguished work in tropical medicine at the conference - Congratulations Sharon!) at the Centre for Vaccine Development at the University of Maryland, Baltimore.

Awesome work Becky and thanks for hosting us Sharon!

Becky Bennett is away from the lab completing a Professional Internship for PhD students, which runs as part of the BBSRC Doctoral Training Program between Liverpool, Newcastle, and Durham.

Becky is enjoying her placement in the IP commercialisation department of the University of Liverpool, getting involved in a wide range of projects, from deciding whether to file for IP protection to helping individuals apply for funding to spin out their IP into a start up to contacting companies to strike potential licensing deals (basically getting a great overview of the technology transfer and IP world).

She also coincidentally participated in the Environment and Microbiology workshop of Biotech Yes! Her team (Hydroot!) won their heat based on a GM root-associated bacteria that will save water in agriculture (and eventually the planet!) The national final is on the 10th of December at the Royal Society.

We wish Becky and her team mates the best of luck at nationals and look forward to having her back in the lab after Christmas!

And who can blame them? Lovely country, lovely people, lovely science.

Rebecca Bennett, George Stenhouse and Caisey Pulford have all been over to the land of Maple syrup to attend the ‘Taming the BEAST, eh?’ course. We’re all really excited to hear about what they learned when they return.

At the same time, Malaka De Silva returned to the University of Manitoba to defend his thesis (spolier alert: he nailed it) and we look forward to welcoming the newly-minted Doctor back to the Bakery once he’s done celebrating. Congratulations Malaka!

Kate is going to Boston to give a talk at Harvard University’s Microbial Sciences Iniative (hosted by Michael Baym - thanks Michael!) and the Gordon Research Microbial Population Biology conference (Thanks Ben Kerr and Ellie Harrison!). Finds time in airport pub to finally publish website! Thanks to Will Rowe for the help (and pushing!) to get the website up and running!

In other news, George is at an epidemiology training course at the London School of Hygeine and Tropical Medicine and the others are holding the fort back in Liverpool, including the now-officially-Dr(!) Rebecca Bengtsson who graduated from her PhD at the University of Edinburgh this Saturday past - Congratulations Rebecca!