Author: Jon Otter (@jonotter)

Using machine learning to super-charge anti-infective drug discovery: the case of Halicin

Jon Otter (@jonotter) Antibiotic resistance , , , ,

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Yes, it’s true. There is more to HCAI & AMR (and this blog) than COVID-19! To prove it, I’m posting on something different today – the use of AI to streamline the anti-infective drug discovery process. Scientists at MIT have used machine learning (aka “deep learning”) to improve the drug discovery process, by predicting antimicrobial activity in molecules that are different from known antibiotics. This process has yielded Halicin, a promising candidate molecule for a broad-spectrum antimicrobial agent – which is, of course, a long way from clinical trials!

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Coronavirunoia

Jon Otter (@jonotter) COVID-19, Uncategorized , , , ,

I guess it was inevitable really – the Coronavirus paranoia (or Coronavirunoia) is setting in!

I called my local GP today to get an appointment for my son…

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Update on 2019-nCoV: part 11 – where will it end?

Jon Otter (@jonotter) coronavirus, Uncategorized , , , , ,

I’m sure we’ve all been following the emerging story of the 2019-nCoV outbreak closely, with the third cases reported in the UK yesterday (pleased to see this is where you’d expect the UK to be based on Marc’s post earlier)! There’s been a small explosion of publications in the peer reviewed literature. I’ve chosen one slightly randomly to discuss today: a short modelling study providing some insight on the likely volume of unreported cases (very much the ice berg and not the tip!) and some sense of where this outbreak will end (it depends on how we respond, globally).

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Update on 2019-nCoV: part 8 – ‘silent’ transmission

Jon Otter (@jonotter) coronavirus , , , ,

One of the key questions that we posed when this virus first emerged was is ‘silent’ transmission (that is transmission to others before symptoms become apparent) possible? And if it’s possible, is it the norm? A short letter published in yesterday’s New England Journal of Medicine answers the first part of that: silent transmission of 2019-nCoV is possible – but just how common is it?

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Update on 2019-nCoV: part 6 (winging its way around the world)?

Jon Otter (@jonotter) coronavirus , , , ,

I am interested, selfishly, in understanding the risk to Europe presented by the novel coronavirus (which now has a “working” name: 2019-nCoV; catchy isn’t it?!). It seems likely that there will be more imported cases, and possibly also some limited cross-transmission in Europe over the coming weeks.

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Novel coronavirus outbreak: an update

Jon Otter (@jonotter) coronavirus , , , , ,

I posted at the beginning of last week about the emergence of the as-yet-formally-unnamed novel coronavirus that has emerged in China. At that stage, it could have been a parochial anomaly in the annals of ID history. What a difference a week makes! Now we are looking at a rapidly emerging international outbreak!

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Can you GES which carbapenemase caused this CPE outbreak?

Jon Otter (@jonotter) CRE , , , , , , ,

An unusual and interesting outbreak of CPE was published recently in Clinical Infectious Diseases. Several key points: don’t rely solely on a PCR detecting the “Big 5” carbapenemases (NDM, KPC, OXA-48, IMP, VIM) – at some point you need to test for phenotypic carbapenemase activity; WGS can really help us in unravelling complex transmission routes; and covert plasmid propagation within and between species is a reality.

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Hello Novel Coronavirus

Jon Otter (@jonotter) coronavirus , , , , ,

As I’m sure you’ve heard (unless you’ve been living under a rock), there’s something going on in China: a Novel Coronavirus has been identified, associated with an outbreak affecting 44 people (one of whom has died and a small number of whom are critically unwell) in Wuhan Providence, China. Here’s what we know so far:

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CPE has landed in East London

Jon Otter (@jonotter) CRE , , , , , , ,

The team at Barts Health, one of the largest NHS hospital groups in the country, has published the findings of a point prevalence screen of all inpatients for carbapenemase-producing organism (CPO) carriage. Overall, 30 (3.1%) of the 977 patient tested were carrying 35 different CPOs (all but one of which were CPE). Risk factors for CPO carriage included hospitalisation abroad, any hospitalisation, and overseas travel (especially to India, Pakistan, and Bangladesh). These findings help us to understand an emerging picture of CPO in the UK.

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The most visited Reflections posts of 2019

Jon Otter (@jonotter) Roundup , , ,

As 2019 draws to a close, I thought it would be fun to share the most visited posts of 2019 on Reflections. And here they are:

Blog post % views of top 10 posts Year published
Do you know your CRO from your CPO from your CRE from your CPE? 11.4 2013
Focusing on the role of nurses in environmental hygiene 11.3 2018
Hand hygiene and the courage to challenge: a personal reflection 11.1 2019
Bad things happen when you don’t do hand hygiene 10.7 2019
We need to win hearts and minds to improve hand hygiene practice 10.7 2019
Dispersal of CPE from contaminated sinks and drains: a refection from Infection Prevention 2019 9.6 2019
CRE can survive on dry surfaces for longer than you may expect 9.3 2014
CPE infection prevention and control guidelines: an update 8.8 2019
An endless one-sided confidence in Pip-tazo? 8.6 2018
Studying bacteriophages: catch-22 8.5 2019

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