Microbiological Phrases for the short of memory

So despite years of trying to learn tables of resistance profiles and antibiotic mechanisms (and trying to teach them this way) I’ve written down the way I’ve managed to remember something about antibiotic – little pearls of wisdom that microbiologists/seniors have trotted out at opportune times at the bedside/wardround, which, when uttered, earn a small nod of acknowledgement.  eg. “Hmm… should we add in metronidazole?” “Well, co-amoxiclav has decent anaerobic cover, but metronidazole will get into any abscess better”.  Funny, as mostly I’m a diagrams sort of person

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ECCMID Day 4 Roundup – Genomics and Microbiomes are here for clinical care

**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.

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Highlights from ECCMID2015 Day 1 – WGS, stewardship and MDROs

**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.**

Day 1 take home messages were

1) Whole genome sequencing is not just a research technique, it works, and is being used by a few groups who are pushing the field forward rapidly to revolutionise the study of transmission, and patient care. I may be biased coming from the Crook/Peto Group, but based on what was shown today, I think the case is very strong indeed.

2) To properly understand transmission requires understanding of phylogeny. To do phylogeny well requires rooting the tree with a proper range of samples, not just your local isolates. I’m going to quote Edward Feil because the quote was awesome (see later post)  on the need for a shared central repository or database of isolates “You may say I’m a Dreamer, but I’m not the only one”.

3) Widespread multidrug resistance is not future, it’s now, and it’s progressing rapidly, year on year the figures are looking drastically worse. I remember ECCMID 2013 and the realisation that ESBLS were endemic in many parts of the world being shocking to me. It feels very much like the same conversations are being had about Carbapenem-Resistant Enterobacteriaceae that were being had about ESBLs 2 years ago.

In depth session descriptions:

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