Nicole Lerminiaux
@nic-ler.bsky.social
Computational Biologist @ National Microbiology Laboratory, Public Health Agency of Canada | working on microbes, AMR, plasmids, genomics 🦠🧬
Polypolish v0.7.1 is out! github.com/rrwick/Polyp... Main new feature is better handling of read name suffixes, which makes it easier to use Polypolish with aligners other than BWA-MEM. I've been using it with minibwa, which seems pretty great: github.com/lh3/minibwa
GitHub - rrwick/Polypolish: a short-read polishing tool for long-read assemblies
a short-read polishing tool for long-read assemblies - rrwick/Polypolish
github.com
🚨 New preprint with @annadewar.bsky.social 🚨 Do plasmids “ameliorate” towards their hosts? Maybe… We show that the classic plasmid-host GC correlation is confounded by population structure, and argue that plasmid mobility shapes the opportunity for host-associated compositional evolution.
Mobility shapes plasmid GC content evolution
Plasmids are frequently AT-rich relative to their bacterial hosts. Despite this tendency towards lower GC content, plasmid and host chromosome GC content are positively correlated across diverse collections of plasmid-host pairs. However, the evolutionary processes underlying this pattern remain unclear. The classic model of amelioration predicts that horizontally acquired DNA gradually converges on host nucleotide composition. However, because plasmids can repeatedly transfer between bacterial hosts, the opportunity for such host-associated evolution may depend on their transmission dynamics. Using 50,936 plasmid-host pairs from a public sequence database, we found that the apparent global correlation between plasmid and host chromosome GC content was largely driven by differences between bacterial species rather than within species. We therefore accounted for plasmid and host population structure when testing how plasmid mobility shaped host-associated compositional evolution. We compared two contrasting regimes: a population of 3,682 Enterobacterales plasmids distributed across diverse host backgrounds, and six long-term host-associated plasmids from a Rhizobium leguminosarum lineage with INSeq-determined gene essentiality data. In the Enterobacterales population, GC content variation was overwhelmingly explained by plasmid lineage rather than host phylogeny, and conjugative plasmids showed greater similarity to their host chromosomes than mobilisable or non-mobilisable plasmids. In the Rhizobium leguminosarum plasmids, synonymous-site composition was more similar to the host chromosome among genes required across multiple host life stages. Together, these results support a model in which plasmid mobility influences the opportunity for host-associated evolutionary processes to alter nucleotide composition. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 319534/Z/24/Z St. John's College, University of Oxford, UK
doi.org
New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)
Benchmark update: Ilesta, Autocycler-fast and new versions
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...
Dorado v2.0.0: no more sup?
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...
biorxiv.org
My first foray into linear plasmids in a new-to-me bug (VRE) - they are pretty neat! 🧵1/n
medRxivpreprint@medrxivpreprint.bsky.social · 3mo agoLinear plasmid prevalence and linezolid resistance gene carriage in vancomycin-resistant Enterococcus in Canada from 2009-2024 https://www.medrxiv.org/content/10.64898/2026.05.08.26352429v1
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
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...
Novel transposon Tn8026 acts as a global driver of transmissible linezolid resistance in Enterococcus via a linear plasmid
Linezolid is a critical last-resort antimicrobial for multidrug-resistant Enterococcus faecium , particularly against vancomycin-resistant lineages where therapeutic options are severely limited. Whil...
medrxiv.org
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!
biorxiv.org
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...
A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome
Plasmids play a pivotal role in the horizontal gene transfer (HGT) of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (Kp...
microbiologyresearch.org
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...
biorxiv.org
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...
Convergence and global molecular epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus: a population genomic analysis
Klebsiella pneumoniae is an important pathogen of humans and animals. In the past five years, increasing reports of convergent strains that carry both…
sciencedirect.com
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... 🧵1/4
Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing
The gold standard for bloodstream infection (BSI) diagnostics involves culturing positive blood cultures (BC) using phenotypic methods for organism identification and antimicrobial resistance (AMR) te...
biorxiv.org
💾 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...
Release Heading into the sunset · tseemann/prokka
The future This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
💾 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...
Releases · tseemann/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill
github.com
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.
Dorottya Nagy@dotnagy.bsky.social · 10mo agoPleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1... Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!
Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)
Autocycler: long-read consensus assembly for bacterial genomes
AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l
doi.org
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...
Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling
Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...
biorxiv.org
Check out our ChroQueTas tool (github.com/nmquijada/Ch...) and get ready to screen AMR in your fungal genomes by using FungAMR info!
GitHub - nmquijada/ChroQueTas: A user-friendly tool to screen antimicrobial resistance in fungal genomes
A user-friendly tool to screen antimicrobial resistance in fungal genomes - nmquijada/ChroQueTas
github.com
Nature Microbiology@natmicrobiol.nature.com · 12mo ago#Resource An online, manually curated, and continually updating database of fungal antimicrobial resistance mutations that provides a starting point for further research in fungal AMR @christianlandry.bsky.social @camillebed17.bsky.social @nmquijada.bsky.social #MicroSky 🦠🍄💉 rdcu.be/eAUZm
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
Plasmid genomic epidemiology of bla NDM carbapenemase-producing Enterobacterales in Canada from 2010 to 2023
Carbapenems are broad-spectrum antibiotics that are losing effectiveness against infections caused by multidrug-resistant Enterobacterales that have acquired carbapenemase genes. The New Delhi metallo...
microbiologyresearch.org
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...
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...
Global emergence and transmission dynamics of carbapenemase-producing Citrobacter freundii sequence type 22 high-risk international clone: a retrospective, genomic, epidemiological study
Our study provides evidence to suggest that Citrobacter species are emerging carriers of carbapenem-resistance genes. These findings provide insight into the population structure of CPC species and hi...
thelancet.com
Enjoying #APBHM25 - lots of super talks and excited to try out all the new tools! I'm virtually presenting poster # 115 on our lab & bioinf workflow to rapidly identify bacteria & fungi organisms and AMR determinants from positive blood cultures, check it out here: github.com/lerminin/abp... 1/3
Happy to see this out - please try my code and break it! Also come see me at #ABPHM25 in the showcase today, where I’m presenting AMRGen, an R package for combining and exploring AMR geno pheno data. It was used to help make many of these rules interpretamr.github.io/AMRgen/
Kat Holt@katholt.bsky.social · last yr.Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight) interpretamr.github.io/AMRrules
www.biorxiv.org/content/10.1... Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use) github.com/rrwick/Autoc...
Autocycler: long-read consensus assembly for bacterial genomes
Motivation: Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using ...
biorxiv.org
🦠🧬🖥️ New Bakta DB v6.0 released! After a year, it was time for a Bakta database update - and it's a huge one: - IPS: 330.9M - PSC: 135.3M - PSCC: 37M doi.org/10.5281/zeno... 👇 1/6
Bakta database
This data repository contains the mandatory DB for Bakta. It is available in two versions: the default (db.tar.gz or) and a lightweight alternative (db-light.tar.gz). Bakta is a tool for the rapid & s...
doi.org
A work that started 10y ago with a simple experiment with a curious result. Great to see it finally published. Massive effort by @nic-ler.bsky.social and Andrew Cameron! Happy to have contributed to this!
Jay Hinton@jayhinton.bsky.social · last yr.Really exciting work: The Salmonella Colicin Col1b cannot only KILL a competing E. coli population, but also AMPLIFY metabolic contributions of susceptible bacteria by liberating β-gal… From @nic-ler.bsky.social. @kroegerlab.bsky.social, Andrew Cameron and others ‼️ academic.oup.com/ismej/advanc...