Podcast – EMBARK

Date:June 1, 2020Posted By:johanCategory:EMBARK NEWSTag:Johan Bengtsson-Palme, Outreach, Podcast

UAC AMR Studio Podcast

EMBARK coordinator Johan Bengtsson-Palme joins this month’s AMR Studio Podcast from the Uppsala Antibiotic Center. The interview was recorded in December, but most of it is still highly relevant. The discussion centers on the role of the environment in AMR development and EMBARK will help. The podcast can be found in the normal places, such as iTunes and Spotify.

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A @JPIAMR funded program to improve monitoring of antimicrobial resistance in the environment

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Craig MacLean @CraigMacLean9·

24 Jun

This is a lecture that I gave @CCDD_HSPH a few months ago that gives a good overview of recent work that we have done on evolutionary drivers of AMR in real world pathogen populations - mainly unpublished
https://www.youtube.com/watch?v=-lQt_9awbmg

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Luis Pedro Coelho🌻@luispedrocoelho·

24 Jun

Very few tools/projects seem to be running rgi in the more conservative mode

(even if they think they are—I know I personally was not aware of this nuance until @svetlana_up started digging into it and showed me)

https://github.com/search?q=rgi+main&type=code https://twitter.com/svetlana_up/status/1539997813987221509

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Johan BengtssonPalme @bengtssonpalme·

23 Jun

Many years ago, I learnt about this thing called Future Research Leaders - a type of grant you’d only get if you were a particularly promising young researcher. It’s a strange (but good) feeling to now be named one of them this year. https://twitter.com/strategiskaSSF/status/1539176118929997825

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EMBARK @EMBARK_JPIAMR·

24 Jun

.@svetlana_up @luispedrocoelho
(@BigDataBiology) wrote an important blogpost from their experience on metagenomic annotation of antibiotic resistome:

If you are using RGI for your resistome study, you probably want --exclude_nudge

Svetlana U. Perović@svetlana_up

I love to use RGI @arpcard (&other tools!) for metagenomic annotation but you should be careful w/DEFAULT run

BLASTP is much more sensitive vs DIAMOND & finds these hits that should've never been reported (e-value>1) & RGIdefault promotes them to Strict
👉https://www.big-data-biology.org/blog/2022/06/23/exclude_nudge/

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