Preprint arrived just in time, and link to GitHub also!

@yekwah.bsky.social launches FlexIt: the S. flexneri genotyping scheme at @shigellameeting.bsky.social 🎉

here we go … #Shigella2026

And that’s a wrap for #AMR2026 The best one yet, and no worm holes open by bringing to Paul Turners together across continents! @paulturnerlab.bsky.social

... and please be sure to particularly consider the 10 policy-led high priority research questions in Theme 3 so we can deliver the research we need to tackle AMR! 6/n

Check out the paper to see how your genomics activities can contribute to delivering the UK AMR NAP themes … 5/n

The Action Plan is comprised of nine outcomes over four themes and while it mentions UK strengths in genomics and the potential of the technology, it doesn’t explicitly map out where it should be put to use 3/n

Okay, it's the start of the academic year and there have been further funny (and some frustrating) mix ups ... just a gentle reminder that there are two of us - try to make sure you have the right one ...

Are you hungry for some Shigella news? Why not come to the 1st International Shigella meeting www.shigella2026.conferences-pasteur.org/home 20-24 April 2026 Paris

Output != Productivity, which is a measure of efficiency, and the first Figure in this paper seems to suggest that women actually produce more papers per year than men (albeit from a disadvantaged starting point, x-axis is years in research). Graphical abstract also seems misleading on this.

Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!

The honour is real ...

My parents brought the last of my effects over from Oz including my first ever scientific poster (and the only piece of high school work I kept) … maybe I was destined to end up in @geneticscam.bsky.social

So, welcome to your new genomic understanding of S. Panama and please go ahead and check out the data yourselves on the associated ‪@microreact.bsky.social‬ page! microreact.org/project/span... 9/n

As a final analysis we compared the predicted invasiveness of S. Panama with other broad and narrow host range serovars and found it was comparable to other major causes of iNTS (thanks to @nwheeler443.bsky.social‬ for the ML classifier to do so) 8/n

Temporal analysis revealed that the four major clades all emerged in the late 1800s, coincident with European efforts to build the Panama canal (‘Panama Fever’ by ‪@matthewparker70.bsky.social‬ is recommended reading for those with an interest in the history here) 7/n

We also found multidrug resistance cassettes; fluoroquinolone resistance (bumping S. Panama onto the WHO AMR priority pathogens list); and a single extensively drug-resistant isolate 6/n

Although antimicrobial resistance (AMR) levels were low overall (14% of isolates), resistant isolates were predominately found in Clade 2 (European-associated) and Clade 4 (associated with Oceania and Asia) 5/n

Population structure analyses revealed the presence of four major Clades that had significant geographic associations 4/n

To better characterise S. Panama we sequenced a global collection of isolates (n=731) from public health surveillance datasets from @ukhsa.bsky.social‬ @thedohertyinst.bsky.social‬, historical collections from ‪@pasteur.fr‬ and publicly available data (n=105) from 1931 to 2019 3/n

S. Panama causes major disease concerns, including high rates of iNTS in French Guiana, large outbreaks in European pork, AMR in Asia, and outbreaks in American soldiers from where the first (extant) isolate from 1931 came from (More in our 2019 review: 10.1128/IAI.00273-19) 2/n

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

This held true even after adjusting for database size and discovery in Pseudomonas with defence and anti-defence systems having a higher proportion of theoretical pairs involved in significant associations or disassociations across the dataset 7/n

After this we collapsed the accessory genome categories to get a feel for which elements were driving the ongoing accessory genome dynamics of Pseudomonas and found that defence systems contributed the highest number of associations across accessory genome element categories 6/n

We then expanded this analysis to interactions among DSes and other accessory genome elements including anti-defences, phage, ICEs, plasmids, and AMR, and found convincing evidence of dissociations of multiple DSes with mobilizable blaOXA genes 5/n

We explored whether these DS interactions arose from genomic co-localisation (as DSes can aggregate in defence islands) and found that associating DSes were only found on the same contig in <1% of cases and often less frequently than DS pairs that were found to dissociate 4/n

Owing to evidence of mechanistic synergy or antagonism between different defence systems from lab studies, we leveraged nature’s experiment here to pull out defence system interactions that were independent of evolutionary relationships (using @whelanfj.bsky.social coinfinder) 3/n

As part of the @multidefence.bsky.social consortium, we worked with a globally curated dataset of >4,000 P. aeruginosa (from 10.1126/science.adi0908) to reveal differences in the number and composition of defence systems between isolates from (and not from) cystic fibrosis cases 2/n

We found the strains came formed an early branch in the Globally disseminated Lineage 3 of S. sonnei but didn’t find any additional/obvious pathogen changes responsible for success 5/n

Although we know drug resistance has played a key role in driving outbreaks since the 2010s, we don’t know why shigellosis re-emerged in the first place early in the 21st Century? 3/n