This was great team science and many thanks are also due to @danielleingle.bsky.social @ellarodwell.bsky.social @charlotteechong.bsky.social @malakades.bsky.social, @jayhinton.bsky.social and @neilhall.bsky.social of Salmonella10k, @mariechattaway.bsky.social Ben Howden, Deb Williamson and more!

Massive thanks to the phenomenal co-first authors @1caiseypulford and @blancaps.bsky.social‬ and especially to one of my favourite scientists to work with, co-corresponding author and fellow history fanatic @weill_xavier 10/n

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

Finally out!! It was a long time in the making, I hope you enjoy it!! #salmonella #iNTS #AMR

Great work led by the talented @edcoakes.bsky.social!!

Our paper is out!! Take a look at this comprehensive 🧵 by @edcoakes.bsky.social, one of the most talented and persistent scientists I work with

12/12 📰 For more background and wider context, check out the @liverpooluni.bsky.social press release covering this study’s impact on understanding and diagnosing infectious intestinal diseases: news.liverpool.ac.uk/2025/05/20/a...

11/12 🙏 A big thank you to all my amazing collaborators who made this work possible @blancaps.bsky.social @jayhinton.bsky.social @acdarby.bsky.social (PI) and many of the INTEGRATE consortium not on BlueSky. Thank you to @nihr.bsky.social for funding via the second HPRU-GI @livuni-ives.bsky.social.

9/12 📊 RNA/DNA ratios differed significantly between positive and negative cases, helping distinguish true infection from bystander carriage and providing a molecular readout of microbial activity.

8/12 📦 Critically, RNA in stool remained stable enough for pathogen detection without preservatives (and after self-sample and surviving the mail service!), providing evidence for the routine potential of metatranscriptomics in clinical settings (with some work!)

7/12 🧫 For the first time, we captured a comprehensive snapshot of Salmonella gene expression from a human stool sample. These data reveal how bacteria survive and adapt after leaving the gut. Explore via Hinton Lab’s interactive browser: jb.hintonlab.com/index.html?d...

6/12 🦠➡️🧬 Metatranscriptomics also detected Cryptosporidium via its RNA virus, CSpV1, previously reported in diarrhoeic animals (doi.org/10.1186/s135...). Cryptosporidium was undetectable in metagenomic data, suggesting RNA sequencing can sensitively detect it when DNA methods fall short.

5/12 🦠 Metatranscriptomics captured active Adenovirus F infections via broad transcriptome coverage (in a couple of samples, near complete!), despite it being a DNA virus, highlighting its use in profiling ongoing viral activity during diarrhoeal illness.

4/12 🧪 Metatranscriptomics showed superior sensitivity, with strong correlation to conventional diagnostics for 6/15 pathogens and to Luminex for 8/14. 🧬 Metagenomics performed well for some targets but showed lower overall concordance.

🔬 3/12 As a part of the INTEGRATE study, we sequenced stool from 1,067 patients using both metagenomics and metatranscriptomics. We identified pathogens in these data and benchmarked against routine diagnostics and Luminex xTAG GPP, a multiplex test for key bacterial, viral, and parasitic pathogens.

2/12 💩 Diarrhoea affects ~18 million annually in the UK, yet traditional diagnostics often miss causes, especially hard-to-culture or emerging pathogens. Our work shows how next-generation sequencing can transform the detection and understanding of GI infections.

1/12 🎉 We're excited to announce our Genome Medicine paper benchmarking 1000+ metagenomes (DNA) and metatranscriptomes (RNA) from infectious intestinal disease patients against pathogen diagnostics. The full dataset is public to accelerate pathogen discovery & surveillance: doi.org/10.1186/s130...

Absolutely love this new publication by my colleagues @blancaps.bsky.social & @emmabeansworth.bsky.social We need to foster an inclusive research culture with diverse representation to tackle global issues now and in future. www.nature.com/articles/s44...

And a huge thanks to @jessicamablair.bsky.social for inviting me to write this piece. We knew how important & timely such a piece was but little did we know that it would be even more important now more than ever. Let’s us all keep pushing for a more inclusive scientific community 🧑🏻‍🔬🧑🏼‍🔬🧑🏽‍🔬🧑🏾‍🔬🧑🏿‍🔬👨‍🔬👩‍🔬

Really delighted to see this out in npj antimicrobials and resistance! @emmabeansworth.bsky.social @blancaps.bsky.social & @edcoakes.bsky.social have done a fantastic job with this 🤩

Delighted to have to have contributed to this alongside excellent scientists! @emmabeansworth.bsky.social @blancaps.bsky.social. As a scientific community, it’s currently more important than ever to continue advocating for EDI. Please read our thoughts in the context of AMR (link in quoted post).

What an honour it has been to co-write this piece with the super talented @emmabeansworth.bsky.social and @edcoakes.bsky.social! Thanks Emma for the invitation to reflect on an imperative topic, I hope this will start many important conversations!

It’s official: The Microbiology Society is on Bluesky!

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