**Standard disclaimer: these are my notes taken during the sessions, as accurate as I can make them, please let me know if any inaccuracies. I’m putting them here as others have said they found them useful. However worth re-checking anything before you re-quote it. If this continues to be useful, I’ll continue. If it’s clear i’m not reaching the standards of accuracy I’m aiming for, I’ll review future posting plans.**
Final day at ECCMID! There was a very high quality Microbiome session, with two outstanding talks from the speakers, as overviews on the applications of microbiome research – highly recommended viewing and links below.
The massive highlight of the genomics session for me was a presentation by one of our collaborators – Phelim Bradley presenting the work done in the Iqbal group and Mykrobe – a tool that uses WGS data to predict antibiotic resistance. I’ll be right up and admit I work with these chaps, and I don’t want to appear biased, but I can only say that the first time I saw this working a few weeks ago I went Oh My GOD…
As fundamentally a clinician taking a ride in the fun world of genomics, this is the first time I’ve seen something involving genomic analysis I can see myself using on the ward. The user interface looked straight out of Apple & something I could teach my granny (/my senior much-respected Consultant population) how to use. And validated on over 1000 Staph. aureus samples, with major and very major error rates <1% compared with culture phenotype. TB and Gram-neg versions also developed. For any clinician agnostic about whether WGS is ready for direct use in patient treatment, the link for the 10 min presentation available at ECCMID live : here ( -worth a look even if you just skip to the demo!)
Updated: for a view of the granny-friendly Apple-esque look – slides up at slideshare:
(ok maybe not granny, unless she’s a Microbiologically-literate elder, but given I’ve spent the last year in a field where people tell you they’ve written a really user-friendly genomic analysis interface which is super easy to use with just basic python scripting – I’m very grateful to any bioinformaticians who consider the intended end-user of their product… )
A very good question from the audience – given cost of sequencing and current times taken to extract DNA/analyse – how can it be used to treat patients (and what benefits over current clinical workflow). Agree – for that reason, I think at the present moment in time for routine diagnostics, in Staph. aureus it certainly would be hard to justify. But given TB takes weeks/months to phenotype, and the cost of sequencing is going down (and nanopore is looking increasingly promising…) incredibly exciting times.
Previous sessions posited that the use of WGS in day-to-day clinical practice was probably a few years away, and also suggested a key challenge is presenting WGS analysis in a way that can be used by non-specialists. The Mykrobe presentation suggested that perhaps we’re really much closer than previously thought…
Rest of the summaries below.