Yesterday was my last day after an exciting four years in @acdarby.bsky.social's lab at Liverpool.

The lab photo below was taken in Birmingham, where I’ll soon be working!

Excited to join @wvschaik.bsky.social, @pathogenomenick.bsky.social, @halllab.bsky.social to work on Public Health Genomics.

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.

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...