Nicole Lerminiaux
@nic-ler.bsky.social
Computational Biologist @ National Microbiology Laboratory, Public Health Agency of Canada | working on microbes, AMR, plasmids, genomics 🦠🧬
Reposted by Nicole Lerminiaux
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...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 14, 2026 at 10:14 AM
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...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Reposted by Nicole Lerminiaux
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…
www.sciencedirect.com
January 7, 2026 at 2:13 PM
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...
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
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...
www.biorxiv.org
December 16, 2025 at 3:38 PM
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
www.biorxiv.org/content/10.6...
🧵1/4
Reposted by Nicole Lerminiaux
💾 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...
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
December 15, 2025 at 9:09 PM
💾 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...
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...
Reposted by Nicole Lerminiaux
💾 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...
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
December 13, 2025 at 9:15 PM
💾 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...
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...
Reposted by Nicole Lerminiaux
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.
September 29, 2025 at 6:57 AM
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.
Reposted by Nicole Lerminiaux
Reposted by Nicole Lerminiaux
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...
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...
www.biorxiv.org
September 7, 2025 at 2:56 PM
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...
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...
Reposted by Nicole Lerminiaux
Check out our ChroQueTas tool (github.com/nmquijada/Ch...) and get ready to screen AMR in your fungal genomes by using FungAMR info!
August 18, 2025 at 8:03 PM
Check out our ChroQueTas tool (github.com/nmquijada/Ch...) and get ready to screen AMR in your fungal genomes by using FungAMR info!
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
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...
www.microbiologyresearch.org
August 6, 2025 at 1:21 PM
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
1/8
Reposted by Nicole Lerminiaux
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...
www.medrxiv.org/content/10.1...
July 30, 2025 at 2:11 AM
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...
www.medrxiv.org/content/10.1...
Reposted by Nicole Lerminiaux
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/...
July 23, 2025 at 7:35 AM
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/...
Reposted by Nicole Lerminiaux
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...
#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...
www.thelancet.com
July 21, 2025 at 7:57 AM
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...
#IDSky #ClinMicro #AMR #MedSky
@lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
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
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
May 22, 2025 at 2:47 PM
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
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
Reposted by Nicole Lerminiaux
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/
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
May 22, 2025 at 11:57 AM
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/
Reposted by Nicole Lerminiaux
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, 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 ...
www.biorxiv.org
May 16, 2025 at 12:22 AM
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, 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...
Reposted by Nicole Lerminiaux
🦠🧬🖥️ 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
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
March 6, 2025 at 8:59 AM
🦠🧬🖥️ 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
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
Reposted by Nicole Lerminiaux
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!
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...
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...
Lysis of Escherichia coli by colicin Ib contributes to bacterial cross-feeding by releasing active β-galactosidase
Abstract. The diffusible toxin ColIb produced by Salmonella enterica serovar Typhimurium SL1344 is a potent inhibitor of Escherichia coli growth. To identi
academic.oup.com
February 24, 2025 at 11:21 AM
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!