Richard Goodman

Genomic comparison of highly related pairs of E. coli and K. pneumoniae isolated from faeces and blood of the same neonatal patients hospitalized with fever in Dar es Salaam, Tanzania Blood stream infections (BSIs) are a major cause of hospitalisation and death for children under the age of five in sub-Saharan Africa with members of the Gram-negative bacteria Enterobacterales such ...

Pleased to share our new preprint! We used comparative genomics to determine the relatedness of E. coli and K. pneumoniae isolates from faeces and blood of the same children. We wanted to know if the bloodstream infection started in the gut; are the strains the same?

Our latest preprint is out describing amr.watch - a platform for monitoring AMR trends from global genomics data: www.biorxiv.org/content/10.1... (1/6)

Freshwater snail faecal metagenomes reveal environmental reservoirs of antimicrobial resistance genes across two continents The transfer of antimicrobial resistance genes (ARGs) from environmental microbes to pathogens is a critical but underexplored One Health driver of antimicrobial resistance (AMR). Here, we evaluate fr...

Pleased to share our new preprint... We took a look into freshwater snail faecal metagenomes in four countries and found environmental #AMR reservoirs

@lstmnews.bsky.social @gcagatgcaatg.bsky.social @russstothard.bsky.social

www.biorxiv.org/content/10.1...

Volume 2 of the #AMR Starter Pack is here!
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Follow these amazing people along with those in Vol. 1
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And don't forget to pin the Antimicrobial Resistance feed to get all the AMR posts in one place
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Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)

🚨 New preprint!! How can antibiotic-resistant bacteria increase in abundance in the human gut microbiome, even without antibiotics? 🧐 We show that strain-specific ecological interactions are key to understanding resistance dynamics in microbial communities. 🧵👇 1/5
www.biorxiv.org/content/10.1...

For more information check out the paper.

This was a great team effort led by Fabrice Graf from LSTM and it's great to see it finally published!

Together this shows:

(i) that antibiotic susceptibility can re-emerge after an antibiotic stops being used

(ii) that genetic context should be included in AMR databases

(iii) that chloramphenicol could be reintroduced in certain contexts (e.g critically ill with ESBL-E)

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We then used co-occurrence analysis on a larger dataset of short-read E. coli and K. pneumoniae genomes (n=772) which showed that the catB3∆443–633 (i.e. catB4 in figure) and catB3 genes nearly always co-occurred with aac(6')-Ib-cr, blaOXA-1 and the ESBL gene blaCTX-M-15.

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Another IS element, IS5, was found to insert into the promoter region of catA1, again knocking out its function. This shows how it is important to consider the gene environment along with the gene presence or absence in AMR gene detection and surveillance.

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This truncated catB3 gene (catB3∆443–633) appears as catB4 in some AMR gene databases, even though it doesn't confer phenotypic resistance this results in false positives and genotype-phenotype mismatches.

3/7

Using functional studies and genomics, we found that IS elements were part of the molecular mechanisms driving the rise in chloramphenicol susceptibility. IS26 was found to truncate the chloramphenicol resistance gene catB3, knocking out its function.

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Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase-producing Enterobacterales - Nature Communications In this work, authors probe the molecular mechanism of re-emerging CHL susceptibility in Malawian Enterobacterales isolates, where they identify a stable truncation of resistance genes by insertion se...

As my first post on bsky post, I thought I'd share a recent paper of ours published in
@naturecomms.bsky.social
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Here we use various techniques to determine the molecular mechanisms for an observed rise in chloramphenicol susceptibility at the same time as an increase in ESBL resistance.