Nicole Lerminiaux

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!

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...

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...

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…

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

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...

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

💾 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...

Releases · tseemann/shovill ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill

💾 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.

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

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)

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...

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

Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010–2021 | Antimicrobial Agents and Chemotherapy Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Gram-negative bacteria. Following the use of carbapenems in clinical practice, the emer...

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

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...

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/...

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...

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!
3/3

An example of the clinician-friendly output report we are designing can be found here: lerminin.github.io/abphm_2025_p...
2/3

Pitch for ABPHM25 poster

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/

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/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...