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Lilly Cummins

@lillycummins.bsky.social

940 followers 370 following 52 posts

she/her | Postdoc in Sheppard Lab @ University of Oxford | bacterial evolutionary genomics, pangenomes, AMR | I believe in equality

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Reposted by Lilly Cummins

Erik Bakkeren @erikbakkeren.bsky.social · 1d

Note it in your calendars! Aug 3-5, 2026. Excited to bring back MEEHubs to a hub near you (Switzerland, USA, Canada, Mexico, UK, Ukraine, or virtual only)‼️

MEEhubs @meehubs.bsky.social · 1d

We’re back! ✨ The next #MeeHubs26 is coming with 7 hubs across the globe and incredible lineups at each. Can’t wait to share more soon! meehubs.org

Reposted by Lilly Cummins

Alan McNally @alanmcn1.bsky.social · 1d

After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research

microbiologysociety.org/news/society...

<i>Microbial Genomics </i> Deputy Editor-in-Chief: Call for Expressions of interest

microbiologysociety.org

Lilly Cummins @lillycummins.bsky.social · 1d

Great science-filled afternoon at @microbiologysociety.org HQ watching finalists present at the Early Career Microbiologist of the Year Finals! All the speakers gave fantastic talks on a wide variety of subjects 🦠🧫🔬

Photograph taken from within a seated audience showing a screen with ‘EARLY CAREER MICROBIOLOGIST OF THE YEAR TALK FINAL’

Reposted by Lilly Cummins

Microbiology Society @microbiologysociety.org · 8d

Applications for Outreach and Engagement grant are closing tomorrow at 23.59 BST. Members can apply for up to £1000 to support relevant science outreach or public engagement initiatives. Check your eligibility and apply now: microb.io/OutreachandE....

Outreach and Engagement Grant

Eligible members can apply for up to £1000 to support relevant science outreach or public engagement initiatives that engage new audiences in the art and science in any aspect of microbiology.…

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · 13d

Our fantastic @sheppardlab.bsky.social DPhil student Madison Goforth gives us a global overview of Campylobacter source attribution and the spread of AMR 🌎💊🌎 #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · 14d

Are antibiotics a dead parrot? 🦜Prof Aidan Taylor kicks off the ‘From farm to fork’ session discussing Campylobacter AMR and vaccine development 🧫💉 #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · 14d

Another speaker sponsored by @microbiologysociety.org , Prof Sitara Ajjampur talks about age and exposure to infected poultry in backyard chicken flocks as determinants of Campylobacter infections in children in rural south India 🐓🇮🇳 #CampyUK2025 @ineosoxford.bsky.social @biology.ox.ac.uk

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · 14d

@sheppardlab.bsky.social collaborator Francesca Schiaffino, sponsored by @microbiologysociety.org explains patterns in persistent Campylobacter infections in LMICs, using data from Peru to investigate complex long-term carriage 🐓🇵🇪 #CampyUK2025 @ineosoxford.bsky.social @biology.ox.ac.uk

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · 14d

Fascinating talk from keynote speaker Dr Christine Szymanski about how Campylobacter jejuni has evolved to colonise and survive the breastfed infant gut #CampyUK2025 @ineosoxford.bsky.social @biology.ox.ac.uk

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · 14d

Our very own @sheppardlab.bsky.social DPhil candidate Amy Douglas representing the @ukhsa.bsky.social giving us some Campy stats 🤩🤩🤩 #CampyUK2025 @ineosoxford.bsky.social @biology.ox.ac.uk

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · 14d

And we’re off! Excited for a day full of all things Campy. The Sheppard lab @sheppardlab.bsky.social welcomes everyone to CampyUK, the first conference in the new Life and Mind Building @ox.ac.uk

Lilly Cummins @lillycummins.bsky.social · 16d

Congrats Tabea! Very well deserved 🥳

Lilly Cummins @lillycummins.bsky.social · 19d

‘We identified clone-specific metabolic capabilities… that may contribute to the ecological success and dissemination of most prevalent ExPEC clones’

bioRxiv Genomics @biorxiv-genomic.bsky.social · 23d

Identification of specific metabolic capacities associated with major extraintestinal pathogenic Escherichia coli lineages https://www.biorxiv.org/content/10.1101/2025.09.14.675865v1

Lilly Cummins @lillycummins.bsky.social · 21d

Yes! Jack and Lauren both gave excellent talks, you should be a very proud supervisor!

Lilly Cummins @lillycummins.bsky.social · 22d

Amazing news Rachel! Very well deserved 👏

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · Aug 29

#CampyUK2025 there are still one or two spaces for late breaking posters - please contact us!

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · Aug 4

📣 Keynote speaker announced #CampyUK2025

Dr Aidan Taylor @uniofreading.bsky.social ‘Taming Campylobacter: From Molecular Insights to Real-World Interventions’

24-25th Sep, register now!

campyuk.web.ox.ac.uk/registration

@biology.ox.ac.uk @ineosoxford.bsky.social @microbiologysociety.org

campyuk.web.ox.ac.uk

Reposted by Lilly Cummins

Greg McCallum @gemccallum.bsky.social · Jul 30

Delighted to have this review out with @jpjhall.bsky.social!

We discuss the risk of transmission of antimicrobial resistance in the hospital sink drain microbiome, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks 🪠🦠

doi.org/10.1038/s442...

The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens - npj Antimicrobials and Resistance

npj Antimicrobials and Resistance - The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens

Reposted by Lilly Cummins

CampyUK2025 @campyuk2025.bsky.social · Jul 31

📣 Keynote speaker announced

Prof David Kelly @sheffielduni.bsky.social will join us at #CampyUK2025 to discuss "Campylobacter and Oxygen: A Double-Edged Sword."

24/25th Sep, register now!

campyuk.web.ox.ac.uk/speakers#col...

@biology.ox.ac.uk @microbiologysociety.org @ineosoxford.bsky.social

campyuk.web.ox.ac.uk

Lilly Cummins @lillycummins.bsky.social · Jul 25

One week extension to submit abstracts and benefit from the early bird discounted registration fee!

CampyUK2025 @campyuk2025.bsky.social · Jul 25

📣 The deadline for abstract submission and early bird registration has been extended to 7th August. Registration fees will increase after this date! Visit campyuk.web.ox.ac.uk/home to secure your place! #microsky @biology.ox.ac.uk @microbiologysociety.org @ineosoxford.bsky.social

campyuk.web.ox.ac.uk

Lilly Cummins @lillycummins.bsky.social · Jul 23

Thanks for the feedback! We’ll definitely correct this for publication ☺️

Lilly Cummins @lillycummins.bsky.social · Jul 23

We hope that GOLD-GWAS will be a useful tool for understanding pathogen evolution more broadly and takes us a step closer to achieving accurate genotype-phenotype mapping 5/5 #microsky

Lilly Cummins @lillycummins.bsky.social · Jul 23

Our biologically informed way of filtering GWAS results allowed us to examine parts of the genome that covary with SCCmec. Interestingly, among the genes that co-varied with SCCmec were those linked to resistance to other antibiotics, highlighting the integrated nature of resistance mechanisms 4/

Lilly Cummins @lillycummins.bsky.social · Jul 23

Rather than asking what genomic elements co-occur with phenotypic resistance (which we know will likely be resistance genes) we adapted the standard GWAS approach by incorporating a genomic ‘masking’ step prior to association mapping that removes resistance genes and their associated LD regions 3/

Diagram explaining how genomic masking filters GWAS results

Lilly Cummins @lillycummins.bsky.social · Jul 23

GOLD-GWAS (Guided Omission of Linkage Disequilibrium - Genome Wide Association Study) detects genomic regions that co-vary with a target gene/region of interest. This is important for discovering what co-evolves with ARGs in the genome to unpick the complicated evolutionary stepping stones of AMR 2/