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Matthew J Shepherd

@matthewjshepherd.bsky.social
1K followers 838 following 61 posts

Bicentenary Fellow @manchester.ac.uk within @mermanchester.bsky.social - Understanding opportunistic pathogen evolution - AMR, pathogenesis, niche transitions 🧫🧬 Former Fellow @wiko-berlin.bsky.social

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Reposted by Matthew J Shepherd
Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 17h
Thanks @mermanchester.bsky.social for hosting me,such a great day of science, thanks @bexlowrypalms.bsky.social @matthewjshepherd.bsky.social for the invitation,great to catch up @whelanfj.bsky.social @alanmcn1.bsky.social @drrebeccajhall.bsky.social @mbottery.bsky.social @brockhurstlab.bsky.social
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Fiona J Whelan @whelanfj.bsky.social · 05/08/2026
A huge thank you from the Whelan lab for an excellent #MEEHubs26 conference! Amazing talks, chats, & intl networking! We’re so thankful to have a chance to showcase our work with posters from @ambercutcliffe.bsky.social @fionapoulter.bsky.social @rebeccawallis.bsky.social Michelle Hardman… [1/2]
Amber presenting her poster on Drosophila bacterial infections with Pseudomonas and Streptococcus species. Becky in action explaining her poster on culture enriched metagenomics in the cystic fibrosis lung. Fiona with her poster on comparative genomics of epidemic Pseudomonas aeruginosa strains. Michelle with her poster on high-throughput microbe-microbe competition in the context of cystic fibrosis.
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Will Smith @willpjsmith.bsky.social · 04/08/2026
#Manchester #MEEhubs26 Day 2 is on! Fantastic talks from @olimeacock.bsky.social @melissalawson.bsky.social @evokait.bsky.social on microbial community interactions with keynote by @dundee.ac.uk's Prof. Sarah Coulthurst 🦠↔️🦠
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Wissenschaftskolleg zu Berlin @wiko-berlin.bsky.social · 09/07/2026
CFA: Apply by November 1st! Wiko Early Career Call for fellowships 2027/2028 in the #NaturalSciences and #LifeSciences. Gain time to think during a 3–5 month #fellowship at the Wissenschaftskolleg zu Berlin – Institute for Advanced Study: www.wiko-berlin.de/en/becoming-...
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Matthew J Shepherd @matthewjshepherd.bsky.social · 23/06/2026
Thank you! Generally there was only one apparent origin. A few patients where different patterns of resistance mutations come and go, which might represent independent origins, but hard to be that certain about it. Also a few where there is a change between two different resistant sequence types.
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Wissenschaftskolleg zu Berlin @wiko-berlin.bsky.social · 16/06/2026
Colloquium June 16: Fellow @matthewjshepherd.bsky.social, "Endless forms most virulent – understanding “opportunistic” bacterial infections as evolutionary processes" www.wiko-berlin.de/en/fellows/a... www.wiko-berlin.de/en/wikothequ...
wiko-berlin.de
Wissenschaftskolleg zu Berlin: Shepherd, Matthew
Matthew Shepherd,
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MERMan Research Group (University of Manchester) @mermanchester.bsky.social · 15/06/2026
Last week we kicked off the ecology & evolution seminar series with a fantastic talk by @taylorlabgroup.bsky.social 🧬 A great start to a diverse series of talks organised by @bexlowrypalms.bsky.social & @matthewjshepherd.bsky.social Come and join us for the next one on 25th June!
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Michael Brockhurst @brockhurstlab.bsky.social · 01/05/2026
Why does antibiotic resistance evolution vary between patients? Come to @officialuom.bsky.social @mermanchester.bsky.social to help us find out! 2.5 year @wellcometrust.bsky.social postdoc position in experimental evolution Closing 15 May. Apply here: www.jobs.manchester.ac.uk/Job/JobDetai...
jobs.manchester.ac.uk
Research Associate in Microbial Evolution:Oxford Road
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Ellinor Alseth @ellinoralseth.bsky.social · 28/04/2026
After two lovely weeks at Wiko Berlin with @matthewjshepherd.bsky.social, it's back to spring in the Arctic ❄️
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Alex Wild @alexwild.bsky.social · 24/04/2026
It is so very telling that, after a decade of hollering about FREE SPEECH and DIVERSITY OF THOUGHT, when Republicans got power in Texas Universities they straight up fired people, purged departments, threw away books, and wrote rules prohibiting even talking about particular topics.
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Natalie Bennett @nataliegreenpeer.bsky.social · 14/04/2026
The risks of antimicrobial resistance have been increasing, while harmful biocides have continued to be used where they are not needed. The government must act now to reduce these risks and safeguard our future. #AMR #MicroBio26
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MERMan Research Group (University of Manchester) @mermanchester.bsky.social · 08/04/2026
Last week's seminar featured excellent talks from @fionapoulter.bsky.social on understanding the evolution of epidemic Pseudomonas aeruginosa and Holly Richardson on why heterogeneity matters: predicting antibiotic resistance in cystic fibrosis. Thanks to @microbesng.bsky.social for the nice snacks!
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Jenna Norton @jenna-m-norton.bsky.social · 07/04/2026
1) Being apolitical is a myth. (Hyde seems to agree.) We all approach the world with our beliefs & biases. Pretending scientists are superhuman is silly & even dangerous. Thankfully, the scientific process is set up to mitigate such biases through transparency & open debate.
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Rebecca Lowry Palmer @bexlowrypalms.bsky.social · 31/03/2026
📢 Excited to be offering a Plant Health vacation studentship this summer on plant disease biocontrol and predatory bacteria! Supervised by me at Manchester Uni! @manchester.ac.uk If interested—or know someone who might be—please share and apply! my.rsb.org.uk/services.php... 28th April deadline 🌿🍅🦠
my.rsb.org.uk
myRSB: Me and the RSB
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Cornish Skipper #FBPE #RejoinEU 🇪🇺🔶🌹💚💙 @cornishskipper.wsocial.eu · 27/03/2026
“Australians can now live & work freely in the EU for 4 years and vice versa That means they now have 𝒎𝒐𝒓𝒆 EU rights than British people. Free movement offered millions of us fantastic opportunities but Brexiteers slammed that door shut, most shamefully on their own children”
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Joseph Guhlin @josephguhlin.bsky.social · 24/03/2026
Coconuts
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Shu-Sin Chng @figlegend.bsky.social · 23/03/2026
Here is it! Super new science from us on horizontal gene transfer & bact defense systems! Liyana OW YONG discovered the first-of-its-kind defense factor AbjA that triggers 'abortive conjugation' as a defense mechanism, by targeting the T4SS! How neat?! #MicroSky 1/7 www.biorxiv.org/content/10.6...
biorxiv.org
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Will Smith @willpjsmith.bsky.social · 20/03/2026
Here’s the latest preprint from my work on evolved resistance to Type VI Secretion system (T6SS) weaponry, funded by a @wellcometrust.bsky.social Sir Henry Wellcome Fellowship. So happy to see this out! www.biorxiv.org/content/10.6...
biorxiv.org
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Willem van Schaik @wvschaik.bsky.social · 20/03/2026
Really excited that this paper has come out in @lancetmicrobe.bsky.social, collaboration led by @alanmcn1.bsky.social and Nina van Sorge (@amsterdamumc.bsky.social) Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021 www.thelancet.com/journals/lan...
thelancet.com
Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis
Our data show the vital need for ongoing genomic surveillance of microbial pathogen populations to guide appropriate intervention strategies. Additionally, genomic insights of a pathogen population fr...
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Zamin Iqbal @zaminiqbal.bsky.social · 20/03/2026
Madness. A bacterium with a 10kb genome, lost replication initiation, translation.., relies on symbiotic host. www.nature.com/articles/s41...
nature.com
Convergent extreme reductive evolution in ancient planthopper symbioses - Nature Communications
Symbiotic bacteria can have exceedingly small genomes. This study finds that ancient bacterial symbionts of planthoppers have repeatedly evolved the smallest known genomes, losing most biosynthetic fu...
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/03/2026
Very much looking forward to visiting and meeting those working @mpiib-berlin.mpg.de next week, and the chance to speak about my postdoc work on within-patient AMR evolution, thanks to @keyfm.bsky.social and @mfenk.bsky.social for the kind invitation.
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Anne Applebaum @anneapplebaum.wsocial.eu · 18/03/2026
Trump does not think strategically, historically, geographically, or even rationally. He does not connect actions he takes on one day to events that occur weeks later. Allied leaders know that if they help him in the Gulf, he won't be grateful, or even remember www.theatlantic.com/ideas/2026/0...
theatlantic.com
Everyone but Trump Understands What He’s Done
Allied leaders know that any positive gesture they make will count for nothing.
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Eduardo Rocha @epcrocha.bsky.social · 17/03/2026
Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky
ecoevorxiv.org
From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
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Alf Soler-Bistué 🦠🔬🧫 @alfmicrobe.bsky.social · 17/03/2026
Just published! at @narjournal.bsky.social . A new example of how gene order in bacterial genomes impacts cell physiology. Inthis episode we messed up with RNA polymerase genes! academic.oup.com/nar/article/...
academic.oup.com
Evolutionary constraints on RNA polymerase gene positioning in the genome of fast-growing bacteria
Abstract. How gene order along chromosomes affects cellular homeostasis and genome evolution remains poorly understood. Bacterial chromosomes are organized
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Fiona J Whelan @whelanfj.bsky.social · 13/03/2026
📣 The Whelan lab is hiring a bioinformatics postdoc 📣 Together with @fabricejpierre.bsky.social, we are offering a 1-year bioinformatic PDRA position in comparative genomics of Pseudomonas aeruginosa. To find out more please visit whelanlab.co.uk/contact/. Applications close 3 April 2026!
jobs.manchester.ac.uk
Research Associate in Microbial Genomics:Manchester
This postdoctoral research position is part of a Cystic Fibrosis Canada Early Career Investigator Award funded for 3-years led by Dr. Fabrice Jean-Pierre and Dr. Fiona Whelan. The aim of this project is to identify the genetic changes that arise in the Pseudomonas aeruginosa genome following perturbations – such as antibiotic treatment – in an in vitro system. The PDRA will use a large dataset of P. aeruginosa genomes and experimental metadata to predict key mutationsto the organism.
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Daria Van Tyne @dariavantyne.bsky.social · 17/03/2026
Study 2: Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium www.medrxiv.org/content/10.6...
medrxiv.org
Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium
Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in h...
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Daria Van Tyne @dariavantyne.bsky.social · 17/03/2026
Study #1: Within-patient evolution of Pseudomonas aeruginosa populations during antimicrobial treatment journals.asm.org/doi/10.1128/...
journals.asm.org
Within-patient evolution of Pseudomonas aeruginosa populations during antimicrobial treatment | mSphere
Pseudomonas aeruginosa infections are notoriously difficult to treat and are associated with high rates of morbidity and mortality. While the genetic basis of resistance in P. aeruginosa is well docum...
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Ellinor Alseth @ellinoralseth.bsky.social · 16/03/2026
Excited to say that I'll be visiting @matthewjshepherd.bsky.social at Wiko Berlin from the 8th-22nd of April, so if anyone is in or around the Berlin area around then and want to chat—let me know! 🦠
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Alberto HCA @albertohca.bsky.social · 10/03/2026
Excited to share our latest work! 📝 We measured the fitness effect of 136 AMR genes and found that many are neutral or even beneficial without selection. 🤯🧬 Oxygen availability can flip their fitness and our stochastic model indicates that oxygen fluctuations help maintain them. Learn more 👇🏼
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David Cleary @bacterioskeptic.bsky.social · 09/03/2026
Today is the start of the 5th Analysing Microbial Genomic Data course at @unibirmingham.bsky.social #AMGDMar26 - in the last three years we’ve trained nearly 80 attendees from six countries and multiple UK universities
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Neil Lewis @neil-lewis.bsky.social · 05/03/2026
FT comments section this morning - saying what everyone else is thinking, right?
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Andre Cornman @ancornman1.bsky.social · 03/03/2026
Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required. We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵
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Lilly Cummins @lillycummins.bsky.social · 02/03/2026
I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts! rdcu.be/e6pHY
rdcu.be
Epistasis and co-adaptation in bacterial genome evolution
Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...
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Alan McNally @alanmcn1.bsky.social · 23/02/2026
Make no mistake this is a concerted and organised attempt to completely undermine science and expert opinion. This is Covid denialism on steroids and it’s on all of academia to see this for what it is and push back as strongly as possible
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Will Ratcliff @wcratcliff.bsky.social · 03/02/2026
New paper out! Here's a puzzle: phototrophy, the ability to use light for energy, is one of life's great innovations. It evolved early and transformed the biosphere. But it evolved 2x. Why not just once, why not more? Our work suggests the answer is priority effects. www.nature.com/articles/s44...
nature.com
Priority effects inhibit the repeated evolution of phototrophy - npj Complexity
npj Complexity - Priority effects inhibit the repeated evolution of phototrophy
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Carl T. Bergstrom @carlbergstrom.com · 22/02/2026
This trip through Aotearoa New Zealand has provided one illustration after another about the value of heroic conservation efforts.
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Siobhán O'Brien @siderophile.bsky.social · 18/02/2026
MENI is back! Join us in Dublin this August 2026 for our 3rd Meeting for Microbial Evolution in Ireland. We are delighted to have @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @jpjhall.bsky.social and @tweethinking.bsky.social join us as keynote speakers this year. miniurl.com/MENI
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Adam Mulkern @mulkern.bsky.social · 21/02/2026
Cancer therapies exploit DNA repair defects to kill tumours. We asked whether the same logic could constrain antibiotic resistance evolution... www.biorxiv.org/content/10.6...
biorxiv.org
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Matthew J Shepherd @matthewjshepherd.bsky.social · 21/02/2026
Thank you!!!
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
It has been a pleasure to work on this huge study with @brockhurstlab.bsky.social, Niamh Harrington, @taoranfu.bsky.social, @jofoth.bsky.social, @scottishwormboy.bsky.social, Claudia Igler, Dylan Childs, Kenny Cagney, Anastasia Kotarra and Beth Grimsey (21/21)
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
Additionally, we identify fitness costs that shaped treatment-driven resistance dynamics in some patients, that could be leveraged to improve treatment, but that fitness costs posed little barrier to long-term persistence of resistance in other patients (20/21)
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
Together, our study outlines multiple ways AMR diagnosis and treatments could be improved by integrating knowledge of evolutionary processes - Detecting pre-existing resistance is highly important, and could predict how long treatment is likely to be successful for (19/21)
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
Our findings highlight that even for patients with the same infection type, and treatment with the same antimicrobial, there are multiple, varied and complex ecological and evolutionary mechanisms by which resistance can emerge (18/21)
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
This suggests an ecological alteration between distinct subpopulations, and that maintenance of this diversity within the infection may explain resistance oscillations. (17/21)
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
So why is costly resistance accompanied by cyclical dynamics in oscillatory trajectories, but not in monotonic ones? We found that higher genetic distances between pairs of samples with different treatment phases, versus the same phases, for oscillatory trajectories only (16/21)
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
Monotonic trajectories were significantly associated with spontaneous mutations, and despite frequently being accompanied by fitness costs there was low negative selection during off phases - evidence that costly resistance mutations can persist in vivo, even when treatment was withdrawn (15/21)
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
Average changes in resistance allele frequency matched the phenotypic dynamics we observed. In particular, for oscillatory trajectories, there was strong positive selection on resistance alleles during on phases, and strong negative selection during off phases (14/21)
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
We then tested whether the different trajectories we had observed corresponded to different underlying allele frequency dynamics for resistance-associated loci. We found these were predictive of trajectory in 77% of patients. (13/21)
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Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026
The dominance of pre-existing resistance was additionally concerning, as it accelerated time taken for infections to become majority-resistant - with most of these cases gaining breakpoint resistance by day 14 of the year-long trial. (12/21)
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