iiinova — where your digital self keeps evolving

Reposted by Dr Blanca Perez-Sepulveda

Jay Hinton @jayhinton.bsky.social · 30/10/2025

Proud to be part of this incredible multidisciplinary team uncovering why some people are NOT infected by Salmonella. This new Wellcome Trust @wellcometrust.bsky.social funding will allow us to uncover why some people naturally resist infection and colonisation by Salmonella Typhimurium.

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Dr Blanca Perez-Sepulveda @blancaps.bsky.social · 28/10/2025

A true honour to be working alongside very talented colleagues!!

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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · 27/07/2025

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!

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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · 27/07/2025

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

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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · 27/07/2025

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

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Kate Baker @ksbakes.bsky.social · 27/07/2025

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

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Kate Baker @ksbakes.bsky.social · 27/07/2025

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

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Kate Baker @ksbakes.bsky.social · 27/07/2025

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

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Kate Baker @ksbakes.bsky.social · 27/07/2025

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

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Kate Baker @ksbakes.bsky.social · 27/07/2025

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

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Reposted by Dr Blanca Perez-Sepulveda

Kate Baker @ksbakes.bsky.social · 27/07/2025

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

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Kate Baker @ksbakes.bsky.social · 27/07/2025

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

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Dr Blanca Perez-Sepulveda @blancaps.bsky.social · 01/08/2025

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

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Dr Blanca Perez-Sepulveda @blancaps.bsky.social · 20/05/2025

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

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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...

news.liverpool.ac.uk

Advanced genomics study improves detection of hard-to-find diarrhoeal infections - University of Liverpool News

Advanced genomics study improves detection of hard-to-find diarrhoeal infections

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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.

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Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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!)

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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...

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Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

🔬 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.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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.

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 20/05/2025

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...

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Reposted by Dr Blanca Perez-Sepulveda

Emma Waters @emmabeansworth.bsky.social · 11/04/2025

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 🧑🏻‍🔬🧑🏼‍🔬🧑🏽‍🔬🧑🏾‍🔬🧑🏿‍🔬👨‍🔬👩‍🔬

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Jessica Blair @jessicamablair.bsky.social · 15/04/2025

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 🤩

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Reposted by Dr Blanca Perez-Sepulveda

Ed Cunningham-Oakes @edcoakes.bsky.social · 11/04/2025

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).

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Dr Blanca Perez-Sepulveda @blancaps.bsky.social · 11/04/2025

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!

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Reposted by Dr Blanca Perez-Sepulveda

Microbiology Society @microbiologysociety.org · 08/01/2025

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

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Reposted by Dr Blanca Perez-Sepulveda

Contamination Club @contamclub.bsky.social · 21/11/2024

First 20 sock orders get a free 3D Noodlococcus pin badge!!

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Reposted by Dr Blanca Perez-Sepulveda

Contamination Club @contamclub.bsky.social · 21/11/2024

And we’ve got a surprise this year… You’ve heard of Noodlococcus, now meet NoodloSOCKus 🧦🦠🍜 We’ve loved designing these high-quality crew socks. ContamSocks are now available at ⤵️ www.contam.club ⬅️ 🧫

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Reposted by Dr Blanca Perez-Sepulveda

Contamination Club @contamclub.bsky.social · 21/11/2024

‼️🚨🗓️ CONTAMCALENDAR 2025 🗓️🚨‼️ The ContamCalendar is back for another year! It’s a great one and we hope you’ll love it 🗓️🦠🧫🍄 Get yours here ➡️ www.contam.club ⬅️

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