Clement Tsui PhD 🇭🇰 🇨🇦

Top: FK506-resistant strains isolated from the Mucor circinelloides complex. Phenotypic analysis of FK506-resistant isolates in Mucor janssenii CBS185.68 (PS1), Mucor bainieri CBS293.63 (PS3), and Mucor atramentarius CBS202.28 (PS6). WT, wild-type; M, mendelian mutant; E, epimutant. Bottom: Schematic overview of epigenetic silencing contributing to antifungal resistance in Mucor species. fkbA expression enables FKBP12 production and FK506 sensitivity (yeast-like morphology). Epigenetic silencing of fkbA via RNAi and/or heterochromatin leads to FK506 resistance and hyphal growth. Generated with BioRender.com.

#Antifungal resistance is a global threat, but epigenetic mechanisms drive rapid, reversible adaptation in fungi. This study shows that #RNAi or #heterochromatin driven #epimutations transiently silence the gene fkbA to confer FK506 #tacrolimus resistance in #Mucor @plosbiology.org 🧪 plos.io/4qdttWc

Hi everyone!
The talk I had the chance to give with @fnucleosome.bsky.social last October is now out on Youtube!
If you like evolution, 3D genomics, biodiversity and/or fungi, I think you might like it! 🧬🧪🍄
The submission of this paper has never been that close!

www.youtube.com/watch?v=Plez...

A permanent position as a research scientist is opened in our team! We look for a plant physiologist with expertise in plant / microorganism interactions to identify plant susceptibility factors to fungal disease. Please forward!

Forward genetics reveals microsporidian drug targets and recombination-based resistance https://www.biorxiv.org/content/10.64898/2026.01.30.702766v1

The Amt2 Gene is Key for Cryptococcus neoformans Transmigration Across The Blood-Brain Barrier and Closely Linked to Its Capsule Formation https://www.biorxiv.org/content/10.64898/2026.01.30.702728v1

Plasmid mutation rates scale with copy number | PNAS Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...

New paper out in PNAS!!! 🎉

Do more plasmid copies mean faster evolution?

🧵 Dive into the story

www.pnas.org/doi/10.1073/...

Genomic and physiological signatures of adaptation in pathogenic fungi - Nature Communications Emerging fungal pathogens have detrimental impacts on crops, animals, and humans, however little is known about their transition to a pathogenic lifestyle. This study demonstrates that the transition ...

What enables a fungus to invade a mammal host? @marco-guerreiro.bsky.social unravels signatures of translation adaptation among pathogenic and non-pathogenic species of Trichosporonales. See more: www.nature.com/articles/s41...

A Beginner's Guide to Structural Variants in Eco‐Evolutionary Population Genomics Whole-genome sequencing (WGS) has greatly expanded researchers' ability to study structural variants (SVs), that is, the variation in the presence, number, orientation or position of a DNA sequence. ...

Some science for some sanity:

A Beginner's Guide to Structural Variants in Eco-Evolutionary Population Genomics

onlinelibrary.wiley.com/doi/10.1111/...

Confidence-based prediction of antibiotic resistance at the patient level | mBio Improved diagnostic tools are vital for maintaining efficient treatment of antibiotic-resistant bacteria and for reducing antibiotic overconsumption. In our research, we introduce a new deep learning-...

Confidence-based prediction of antibiotic resistance at the patient level | mBio journals.asm.org/doi/10.1128/...

Carbapenem resistant Klebsiella pneumoniae isolates at a tertiary hospital in Cape Town, South Africa, are dominated by specific local clones rather than previously described international lineages Author summary Carbapenem resistant K. pneumoniae (CRKP) have emerged as a cause of hospital and community acquired infections, posing a significant threat to public health, and have hence been listed...

Checkout this article I found at PLOS: dx.plos.org/10.1371/jour...

Current Epidemiology and Infection Characteristics of Non-Aspergillus Mold Infections: A Multicenter Study in Australia and New Zealand We report 421 non-Aspergillus mold infections from Australasia from 2016 to 2023 and observe an increase in cases caused by dematiaceous molds with a decre

Current Epidemiology and Infection Characteristics of Non-Aspergillus Mold Infections: A Multicenter Study in Australia and New Zealand url: academic.oup.com/cid/article-...

Biofilms: from the cradle of life to life support npj Biofilms and Microbiomes - Biofilms: from the cradle of life to life support

We have just published “Biofilms: from the cradle of life to life support” in @natureportfolio.nature.com #Biofilms & #Microbiomes. It highlights how #bioinformatics and #microbiology come together to study biological systems & food-associated biofilms. Stellar multidisciplinary team! rdcu.be/e0esg

Very good outlines. #genomics #ecology #genetics #education journals.asm.org/doi/epub/10....

New research article

Emerging terbinafine-resistant #Trichophyton indotineae between 2018 and 2023: a multinational genomic epidemiology study

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #MycoSky #AMR #OpenAccess #OA

In this review in Fungal Ecology, Håvard Kauserud (@drhyfe.bsky.social) argues that while the ITS region is by far the best DNA (meta)barcoding marker for fungi, we should not use it naively or simplistically doi.org/10.1016/j.fu...

Digital CRISPR-based diagnostics for quantification of Candida auris and resistance mutations - Nature Biomedical Engineering dSHERLOCK is a nucleic acid platform for the quantification of double-stranded DNA targets using CRISPR/Cas and isothermal amplification and is applied to quantify pathogen C. auris in clinical survei...

Rolando, J.C., Thieme, A., Weckman, N.E. et al. Digital CRISPR-based diagnostics for quantification of Candida auris and resistance mutations. Nat. Biomed. Eng (2026). doi.org/10.1038/s415...

nph.onlinelibrary.wiley.com/share/EHWXER...

Pathogen-inspired engineering of plant protease enhances late blight resistance | PNAS www.pnas.org/doi/10.1073/...

Fig. 1 Evolution and potential contributions of alternative splicing (AS) along the speciation continuum.

#TansleyInsight: Evolutionary #genetics of alternative splicing in #plants

@peterinnes1.bsky.social, Nolan Kane & @chriscrsmith.bsky.social
👇

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

#LatestIssue

Tree bark microbes for climate management Microbes living in bark can process the greenhouse gases methane, hydrogen, and carbon monoxide

Tree bark microbes for climate management | Science www.science.org/doi/10.1126/...

Genomic determinants of antibiotic resistance for Helicobacter pylori treatment: a retrospective phenotypic and genotypic observational study Mutations in specific genes are reliable indicators to clarithromycin and levofloxacin resistance in H pylori, making them useful markers for the development of diagnostic assays and molecular monitor...

Genomic determinants of antibiotic resistance for Helicobacter pylori treatment: a retrospective phenotypic and genotypic observational study - The Lancet Microbe www.thelancet.com/journals/lan...

Within-host evolution of Klebsiella spp. from intestinal carriage to bacteremia Gut colonization by the Gram-negative bacillus Klebsiella pneumoniae is a significant risk factor for extra-intestinal infections. However, the mechanisms by which this opportunistic pathogen causes d...

📣 preprint alert!
We sampled #klebsiella isolates from💩 patients when they entered the hospital & 🩸 after development of infection.

🎯 We tracked phenotypic changes & correlate them w genotypic changes.
@klebclub.bsky.social
-in collab with Clermont-Ferrand lab
#microsky
🧵
doi.org/10.64898/202...

Butyrolactol A enhances caspofungin efficacy via flippase inhibition in drug-resistant fungi Chen et al. identify the natural product butyrolactol A as an inhibitor of the phospholipid flippase Apt1-Cdc50, which it locks in a nonfunctional state. By disrupting membrane homeostasis and enhanci...

Butyrolactol A enhances caspofungin efficacy via flippase inhibition in drug-resistant fungi: Cell www.cell.com/cell/fulltex...

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Troubleshooting common errors in assemblies of long-read metagenomes www.nature.com/articles/s41... #jcampubs

Release Next time I'll try to be FASTA · tseemann/any2fasta New features Option -k is keep processing even when some inputs fail option -g to include GBK version suffix option s to strip desc from>id desc in ID lines Support for PDB protein structure forma...

💾 any2fasta 0.8.1 is released!

The FASTA format is now 40 years old (Pearson & Lipman) and any2fasta makes it easy for your scripts and pipelines that accept FASTA to also accept other formats, even if compressed! eg. .gbk.gz

#bioinformatiocs #microbiology #genomcs
github.com/tseemann/any...

Figure 1: The Rothman-Dahly Evidence Pyramid (original version) An equilateral triangle with a small blue section labelled "Thoughtful, well-conducted studies of any design" at the top, with the remaining space colored red and labelled "The other shit"

‪It has a name now 😜

Many thanks to Ken for agreeing to put his good name to my...artwork. The image is in the public domain (CC 0), but citations to the linked documents are warmly welcomed.

✅ zenodo.org/records/1808...

✅ pubmed.ncbi.nlm.nih.gov/24452418/

The changing roles of Escherichia coli - Nature Microbiology Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

The changing roles of Escherichia coli www.nature.com/articles/s41... #jcampubs

On-site microbial community analysis in rivers: integrating autonomous sampling with a portable sequencing workflow Studies focused on bacterial diversity in rivers often face significant limitations. Traditional sampling approaches frequently overlook spatial and temporal variability at the reach scale. Molecular ...

www.biorxiv.org/content/10.6...

Antifungal susceptibility profile of clinically relevant species of the genus Sporothrix: establishment of Epidemiological Cutoff Values (ECVs) according to CLSI broth microdilution methodology https://www.biorxiv.org/content/10.64898/2025.12.19.695392v1

Candida auris skin tropism and antifungal resistance are mediated by carbonic anhydrase Nce103 Nature Microbiology - Candida auris can scavenge carbon dioxide from microenvironments through Nce103 to sustain fitness when colonizing human skin.

#Candida auris skin tropism and antifungal #resistance are mediated by carbonic anhydrase Nce103. Nat Microbiol (2025). rdcu.be/eV1h7