Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added.
💾 github.com/steineggerla...
📄 doi.org/10.64898/2026.03.13.711249
Fish farming cages floating on a calm lake with text about Canadian Federal GRDI and antimicrobial resistance.
Explore Canada’s leadership in antimicrobial resistance (AMR) through a One Health lens! Browse this GRDI-AMR collection from the Canadian Journal of Microbiology for more info and research ▶️ https://ow.ly/TNuN50XXrjS
🇨🇦 Rob Beiko
Until joining @loolibear.bsky.social's lab in July, I embarrassingly hadn't had much experience with plasmids.
So when I started, Leah said "here you go, have a look at this dataset".
What a fun ride this has been.
Preprint out today and thread below
www.medrxiv.org/content/10.6...
New pre-print with @wtmatlock.bsky.social!!!
www.biorxiv.org/content/10.6...
What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!
Fascinating and important study on Klebsiella plasmid diversity
'Plasmids from human, animal and marine [Klebsiella pneumoniae complex] isolates formed shared genetic clusters spanning ecological boundaries'
www.microbiologyresearch.org/content/jour...
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
It has been a long road, but our paper on Klebsiella plasmids is finally out in Lancet Microbe. Thanks to all co authors but especially Marjorie Gibbon and Natacha Couto www.sciencedirect.com/science/arti...
venae also produces a clinician-friendly HTML results report summarizing sequencing quality, organism identity, and AMR determinants. See the example report here:
phac-nml.github.io/venae/tests/...
🧵4/4
Workflow map of the venae pipeline https://github.com/phac-nml/venae
We built venae, a pipeline written in #Nextflow, which removes host reads, assess quality, identifies species, performs assembly, detects #AMR genes, and runs species-specific typing
🧵3/4
github.com/phac-nml/venae
Our turnaround time was around 4 h after blood cultures flagged positive - much faster than conventional methods! We were fortunate to obtain a lot of clinical samples (n=307🩸) which allowed us to design a really robust workflow
🧵2/4
Thrilled to see this preprint finally out! This was an exciting collab and massive effort building a workflow for rapid ID of bacterial & fungal pathogens and #AMR determinants in bloodstream infections using @nanoporetech.com sequencing
www.biorxiv.org/content/10.6...
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💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
💾 Shovill 1.4.1 has been released!
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.
For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...
Check out our ChroQueTas tool (github.com/nmquijada/Ch...) and get ready to screen AMR in your fungal genomes by using FungAMR info!
This makes it incredibly difficult to track NDM plasmids across the country for surveillance purposes! Long-read sequencing is recommended for resolving NDM plasmid structure, cluster membership, and potential transposon-mediated spread in future studies
8/8
Heatmap and genetic structure of NDM plasmids from a single site site
We searched for trends at specific sites and found examples of how a plasmid can be stable and maintain its structure for months, and also how a single event (recombination with a co-resident plasmid) can dramatically change plasmid structure and consequently classification by MOB-suite/pling
7/8
Plasmid map depicting OXA and NDM genes
We found 11.4 % of isolates encoded both NDM and OXA-48 in the same cell. Nine plasmids encoded both NDM and OXA-48-type genes on the same backbone, which haven't been seen much in the lit yet. Five were in Kleb pneumo ST16 on an IncX3 backbone
6/8
Upset plot of plasmid replicons
Most of the NDM plasmids in our dataset were IncF-type (not a popular type in other studies) and had multiple #AMR genes and mobile elements. This made it impossible to predict plasmid clusters for isolates with short-read only data
5/8
We used MOB-suite (github.com/phac-nml/mob...) and pling (github.com/iqbal-lab-or...) to group plasmids, and while we didn’t do a thorough comparison, their trends were the same: many small clusters = lots of diversity
4/8
NDM plasmid diversity is extremely high and plasmid transfer has not played a major role in NDM spread across Canada. This is unlike KPC and OXA-48-type plasmids over the same surveillance period
KPC: journals.asm.org/doi/full/10....
OXA: www.microbiologyresearch.org/content/jour...
3/8
Figure depicting species and genes found in the isolate dataset
We had a big dataset (1032 isolates, 226 complete NDM plasmids) over 14 years of #AMR surveillance data from the Canadian Nosocomial Infection Surveillance Program (CNISP)
2/8
The final installment in our plasmid surveillance trilogy is now out in @microbiologysociety.org #MGen! We examined NDM plasmid distribution across years of Canadian surveillance data, and found NDM plasmids are super diverse www.microbiologyresearch.org/content/jour...
1/8
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...
graphical abstract of the article the extended mobility of plasmids
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
Citrobacter freundii ain't ever been a friend of ours... now becoming even more hostile!
#IDSky #ClinMicro #AMR #MedSky
@lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
And our analysis pipeline venae (Snakemake, Nextflow coming soon) here: github.com/phac-nml/venae
Feel free to reach out with questions/comments!
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