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Pathogen Dynamics Unit @pducambridge.bsky.social · Aug 8

Out this week from @virologyhouldcroft.bsky.social and colleagues 👀

Charlotte Houldcroft @virologyhouldcroft.bsky.social · Aug 8

I'm pleased to share a preprint today, paper 2/3 of a trilogy (you'll have to wait for the Return of the Jedi). In 2021-22, lots of countries saw unprecedented transmission of enteric adenovirus F41 in children. There were lots of hypotheses about what caused this.
www.biorxiv.org/content/10.1...

Viral Diversity Influences T Cell Responses to Enteric Human Adenoviruses F40 and F41

Background Human enteric species F adenoviruses are a leading cause of diarrhoea-associated paediatric morbidity and mortality worldwide. The cellular immune response (antigen-specific cytotoxic T cel...

www.biorxiv.org

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Reposted by Pathogen Dynamics Unit

Kate Baker @ksbakes.bsky.social · Aug 7

I hope all my fellow #shigellaphiles have 20 - 24 April 2026 blocked out in their diaries for @shigellameeting.bsky.social next year in Paris! In the meantime, check out (and join) our starter pack to start community building now 🧫

The Shigella Meeting @shigellameeting.bsky.social · Aug 7

Why not follow our @shigellameeting.bsky.social starterpack of people who are speaking at and attending the conference - please message to be added to the starter pack if you're planning on coming or we haven't found you yet! go.bsky.app/6Vbwhjc

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Pathogen Dynamics Unit @pducambridge.bsky.social · Jul 27

This one has been a long time coming: we delivered this through institutional changes and the team incubated two babies 👶 👶 alongside this phenomenal work dissecting the genomic epidemiology of a globally important Salmonella serovar causing iNTS disease worldwide! 🧬 🧫 💊

Kate Baker @ksbakes.bsky.social · Jul 27

There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n

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Pathogen Dynamics Unit @pducambridge.bsky.social · Jul 26

This week, @emiliefinch.bsky.social and @jandraor.bsky.social from our team delivered a hands-on workshop on infectious disease modelling.
Participants from KAUST were introduced to the fundamentals of transmission dynamics.

Huge thanks to all the participants for their curiosity and engagement.

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Pathogen Dynamics Unit @pducambridge.bsky.social · Jul 6

@ksbakes.bsky.social is representing PDU at the GRC Microbial Population Biology conference this week introducing the AMR through time and space session - check out the work of the other attendees here:

Mike Blazanin @mikeblazanin.bsky.social · Jul 3

Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!

go.bsky.app/GGxRjzC

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Reposted by Pathogen Dynamics Unit

Kate Baker @ksbakes.bsky.social · Jul 4

Smashing time at the @pducambridge.bsky.social retreat this week!

Charlotte Houldcroft @virologyhouldcroft.bsky.social · Jul 4

Ipswich looking glorious in the sun. Brilliant 48h with the @pducambridge.bsky.social solving the pressing questions in infectious diseases, competing in penalty shoot outs and cooking up a storm #PDURetreat

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Charlotte Houldcroft @virologyhouldcroft.bsky.social · Jul 4

Ipswich looking glorious in the sun. Brilliant 48h with the @pducambridge.bsky.social solving the pressing questions in infectious diseases, competing in penalty shoot outs and cooking up a storm #PDURetreat

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Pathogen Dynamics Unit @pducambridge.bsky.social · May 23

Final one before the weekend ... check out this amazing new preprint from @charlotteechong.bsky.social where she uncovers what the dominant forces are shaping accessory genome dynamics in the WHO AMR priority pathogen Pseudomonas aeruginosa 🧫 🛡️💊

Kate Baker @ksbakes.bsky.social · May 23

Defence Systems are so hot right now 🔥 🔥 🔥 so check out our latest preprint to see how DSes contribute to niche adaptation, interact with each other, and drive accessory genome interactions in Pseudomonas aeruginosa 1/n
www.biorxiv.org/content/10.1...

Defence systems drive accessory genome interactions in Pseudomonas aeruginosa

As well as undergoing mutational selection, bacterial genomes are shaped by a complex evolutionary interplay among diverse accessory genome elements (AGEs). In this study we define AGEs as encompassin...

www.biorxiv.org

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Pathogen Dynamics Unit @pducambridge.bsky.social · May 23

Check out the latest from the lab on Sexually Transmissible shigellosis where @lewiscemason.bsky.social and co unpick why this relatively obscure disease re-emerged endemically in the 21st Century 🔬 🧫 🕵️ 🧬

Kate Baker @ksbakes.bsky.social · May 23

Sexually transmissible shigellosis has gone from an obscure cause of sporadic outbreaks to a sustained endemic AMR priority in only two decades! 🧫💊 Check out our latest preprint to understand how this happened 1/11
www.medrxiv.org/content/10.1...

The natural history of the emergence of sexually transmissible shigellosis

Shigellosis is a gastrointestinal illness caused by bacteria belonging to one of four species of Shigella . Sexually transmissible shigellosis was first reported in 1974, but recently there has been a...

www.medrxiv.org

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Department of Genetics, University of Cambridge @geneticscam.bsky.social · Mar 17

It's the 3rd week of Women’s History Month and we want to introduce you to Dr Angkana Huang [Hat], Postdoctoral Research Fellow @pducambridge.bsky.social

Read about her research project and how she is involved in making science more equitable in the Global South ⬇️
www.gen.cam.ac.uk/womens-histo...

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Pathogen Dynamics Unit @pducambridge.bsky.social · Mar 6

Check out this amazing new NextFlow GWAS pipeline (based on pyseer) by our very own @rositea.bsky.social, a first year PhD student in the PDU!

Charles Wei @rositea.bsky.social · Mar 2

Tired of fragmented bacterial GWAS workflows? Try BaGPipe (Bacterial GWAS Pipeline)—a fully automated, flexible Nextflow pipeline integrating Pyseer for streamlined association studies. Reproducible. Scalable. Efficient. doi.org/10.1101/2025...
#Nextflow #BacterialGWAS #AMR #Bioinformatics

BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies

Microbial genome-wide association study (GWAS) tools often require manual data processing steps, lack comprehensive workflows, and are limited by scalability issues, thus hindering the exploration of ...

doi.org

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Pathogen Dynamics Unit @pducambridge.bsky.social · Feb 14

A way to use cross sectional serological data to reconstruct the changing circulation patterns of pathogens. All in an R package.

Simon Cauchemez @scauchemez.bsky.social · Feb 11

Serological data provide key insights on pathogen circulation. We introduce a new R package, Rsero, which is a pipeline to store and analyze age-stratified sero data, estimate the history of pathogen circulation and compare different transmission models.
journals.plos.org/ploscompbiol...

RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies

Author summary Antibodies are immune markers of past infections. Seroprevalence studies that characterize the seropositivity status in the population have been used for decades in epidemiological stud...

journals.plos.org

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Pathogen Dynamics Unit @pducambridge.bsky.social · Jan 2

Great way to start the year! A paper in @nature.com by our amazing @noemie presenting a way to use sequences to identify pathogen lineages, quantify their fitness, and identify potentially important genes/snps . Works across bugs, even with minimally and biased set of sequences.

Noémie Lefrancq @noemielefrancq.bsky.social · Jan 2

Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx

We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.

🧵 A thread... 1/n
#IDSky #IDModelling

Learning the fitness dynamics of pathogens from phylogenies - Nature

Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of…

buff.ly

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Pathogen Dynamics Unit @pducambridge.bsky.social · Jan 1

Great way to finish the year! Paper by our @huangat.bsky.social in @pnas.org showing that relying on seroconversions in cohorts will usually lead to horribly biased #dengue incidence estimates whereas models relying on age data from local hospital typically robust.

Angkana T. Huang (HAT) @huangat.bsky.social · Jan 1

No one best way to measure #infection risk in populations.

Cross-sectional sero: weak temporal signal, CXR, waning as we know. Extra care needed for longitudinal #serology as Ab kinetics and assay noise can mess up estimates by a lot. Cases can be powerful!
www.pnas.org/doi/10.1073/pnas.2411768121

Reconciling heterogeneous dengue virus infection risk estimates from different study designs | PNAS

Uncovering rates at which susceptible individuals become infected with a pathogen, i.e., the force of infection (FOI), is essential for assessing t...

eur03.safelinks.protection.outlook.com

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Kate Baker @ksbakes.bsky.social · Dec 19

Certain sublineages of antimicrobial resistant bacteria dominate the surveillance landscape, but what causes them to become resistant? Check out our latest work in Shigella to find out and/or read the thread below www.medrxiv.org/content/10.1101/2024.10.27.24316207v2
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Reposted by Pathogen Dynamics Unit

Malaka De Silva @malakades.bsky.social · Dec 20

Very excited to present our latest work as my first post on Bluesky. Thanks to all co-authors for their valuable contributions! A truly mammoth effort with many different fields of expertise coming together. Looking forward to working with all of you in future as well. #Microsky

Kate Baker @ksbakes.bsky.social · Dec 19

Certain sublineages of antimicrobial resistant bacteria dominate the surveillance landscape, but what causes them to become resistant? Check out our latest work in Shigella to find out and/or read the thread below www.medrxiv.org/content/10.1101/2024.10.27.24316207v2
1/n

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Reposted by Pathogen Dynamics Unit

Kate Baker @ksbakes.bsky.social · Dec 7

Really enjoying having @atjcagan.bsky.social in the @geneticscam.bsky.social who drew this fab piece at our recent research day. Contains some exciting teasers for our next awesome piece of work landing before Christmas! Thanks Alex!

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Pathogen Dynamics Unit @pducambridge.bsky.social · Dec 20

Apologies for the website glitch - it's www.pdu.gen.cam.ac.uk

PDU | PDU

www.pdu.gen.cam.ac.uk

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Reposted by Pathogen Dynamics Unit

Kate Baker @ksbakes.bsky.social · Dec 20

Really excited to launch the new iteration of the Bakery as part of the Pathogen Dynamics Unit, co-led with @hsalje.bsky.social and @virologyhouldcroft.bsky.social Has been awesome working together this last year and really excited for things to come! Please follow and repost.

Pathogen Dynamics Unit @pducambridge.bsky.social · Dec 20

Hello world! After a year in the making, the Pathogen Dynamics Unit is ready to launch! Check out our website (pdu.gen.cam.ac.uk) and follow the team (bsky.app/profile/did:...) to keep up with the latest from our infectious disease supergroup based at @geneticscam.bsky.social

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Pathogen Dynamics Unit @pducambridge.bsky.social · Dec 20

Hello world! After a year in the making, the Pathogen Dynamics Unit is ready to launch! Check out our website (pdu.gen.cam.ac.uk) and follow the team (bsky.app/profile/did:...) to keep up with the latest from our infectious disease supergroup based at @geneticscam.bsky.social

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